From 5fa9ec486cbd52f6f0beb2891020bf28dc2729f0 Mon Sep 17 00:00:00 2001 From: mjaquiery Date: Tue, 22 Nov 2022 10:28:41 +0000 Subject: [PATCH 01/79] update docker config to use override --- docker-compose.dev.yml | 82 - docker-compose.override.yml | 10 + docker-compose.yml | 4 +- docs/DevelopmentGuide.md | 16 +- docs/ProjectStructure.md | 1 - frontend/package-lock.json | 46801 ---------------------------------- frontend/package.json | 32 +- frontend/yarn.lock | 9855 +++---- 8 files changed, 4128 insertions(+), 52673 deletions(-) delete mode 100644 docker-compose.dev.yml create mode 100644 docker-compose.override.yml delete mode 100644 frontend/package-lock.json diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml deleted file mode 100644 index 878591ad..00000000 --- a/docker-compose.dev.yml +++ /dev/null @@ -1,82 +0,0 @@ -version: "2" -services: - app: - image: app - build: - dockerfile: Dockerfile - context: ./backend - depends_on: - - redis - - rabbitmq - - postgres - ports: - - "5001:5000" - volumes: - - ./backend:/usr/app - - "${GALVANALYSER_HARVESTER_TEST_PATH}:/usr/test_data" - - "${GALVANALYSER_HARVESTER_BASE_PATH}:/usr/data" - - "${CELERY_LOG_DIR}:/var/log/celery" - restart: unless-stopped - working_dir: /usr/app - command: ./server.sh - restart: unless-stopped - env_file: - - ./.env - worker: - image: app - command: ./worker.sh - depends_on: - - app - volumes: - - ./backend:/usr/app - - "${GALVANALYSER_HARVESTER_BASE_PATH}:/usr/data" - - "${CELERY_LOG_DIR}:/var/log/celery" - - working_dir: /usr/app - restart: unless-stopped - env_file: - - ./.env - frontend: - image: frontend_dev - build: - dockerfile: Dockerfile_dev - context: ./frontend - depends_on: - - app - ports: - - "3000:3000" - volumes: - - ./frontend:/app - restart: unless-stopped - working_dir: /app - command: yarn start - restart: unless-stopped - env_file: - - ./.env - rabbitmq: - image: "rabbitmq" - ports: - - "5672:5672" - env_file: - - ./.env - restart: unless-stopped - redis: - image: redis:5.0-alpine - restart: always - command: redis-server --requirepass ${REDIS_PASSWORD} - ports: - - "6379:6379" - volumes: - - "${REDIS_DATA_PATH}:/var/lib/redis" - postgres: - image: "postgres" - stop_signal: SIGINT # Fast Shutdown mode - ports: - - "5433:5433" - command: -p 5433 - volumes: - - "${GALVANALYSER_DATA_PATH}:/var/lib/postgresql/data" - env_file: - - ./.env - restart: unless-stopped - diff --git a/docker-compose.override.yml b/docker-compose.override.yml new file mode 100644 index 00000000..de9592e1 --- /dev/null +++ b/docker-compose.override.yml @@ -0,0 +1,10 @@ +version: "2" +services: + frontend: + image: frontend_dev + build: + dockerfile: Dockerfile_dev + context: ./frontend + ports: + - "3000:3000" + command: yarn start diff --git a/docker-compose.yml b/docker-compose.yml index 9d8c2f33..9821d127 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -18,8 +18,7 @@ services: - "${CELERY_LOG_DIR}:/var/log/celery" restart: unless-stopped working_dir: /usr/app - command: ./server.sh - restart: unless-stopped + command: ./server.sh env_file: - ./.env worker: @@ -49,7 +48,6 @@ services: - ./frontend:/app restart: unless-stopped working_dir: /app - restart: unless-stopped env_file: - ./.env rabbitmq: diff --git a/docs/DevelopmentGuide.md b/docs/DevelopmentGuide.md index ac21c9de..c8a15128 100644 --- a/docs/DevelopmentGuide.md +++ b/docs/DevelopmentGuide.md @@ -34,8 +34,22 @@ docker-compose run --rm app python manage.py test ### To run the entire stack for development +Create a `docker-compose.override.yml` file in the root directory next to `docker-compose.yml`. +Put the following in there: + +```yaml +version: "2" +services: + frontend: + image: frontend_dev + build: + dockerfile: Dockerfile_dev + context: ./frontend + +``` + ```bash -sudo docker-compose -f docker-compose.dev.yml up +sudo docker-compose up ``` The main difference from the production `docker-compose.yml` file is that the developer diff --git a/docs/ProjectStructure.md b/docs/ProjectStructure.md index 0151a763..c45e5337 100644 --- a/docs/ProjectStructure.md +++ b/docs/ProjectStructure.md @@ -4,7 +4,6 @@ Below is a tree diagram of the folder structure of this project and a short desc ``` ├── .env -- configuration environment variables for the server ├── docker-compose.yml -- docker-compose file for production -├── docker-compose.dev.yml -- docker-compose file for development ├── backend/ -- The flask backend and harvester code │ ├── Dockerfile -- docker file for production and development │ ├── galvanalyser/ -- Library files for interacting with the database diff --git a/frontend/package-lock.json b/frontend/package-lock.json deleted file mode 100644 index b905149e..00000000 --- a/frontend/package-lock.json +++ /dev/null @@ -1,46801 +0,0 @@ -{ - 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+"@types/eslint-scope@^3.7.3": + version "3.7.4" + resolved "https://registry.yarnpkg.com/@types/eslint-scope/-/eslint-scope-3.7.4.tgz#37fc1223f0786c39627068a12e94d6e6fc61de16" + integrity sha512-9K4zoImiZc3HlIp6AVUDE4CWYx22a+lhSZMYNpbjW04+YF0KWj4pJXnEMjdnFTiQibFFmElcsasJXDbdI/EPhA== + dependencies: + "@types/eslint" "*" + "@types/estree" "*" + +"@types/eslint@*", "@types/eslint@^7.29.0 || ^8.4.1": + version "8.4.10" + resolved "https://registry.yarnpkg.com/@types/eslint/-/eslint-8.4.10.tgz#19731b9685c19ed1552da7052b6f668ed7eb64bb" + integrity sha512-Sl/HOqN8NKPmhWo2VBEPm0nvHnu2LL3v9vKo8MEq0EtbJ4eVzGPl41VNPvn5E1i5poMk4/XD8UriLHpJvEP/Nw== dependencies: "@types/estree" "*" "@types/json-schema" "*" @@ -2045,6 +2259,30 @@ resolved "https://registry.yarnpkg.com/@types/estree/-/estree-0.0.39.tgz#e177e699ee1b8c22d23174caaa7422644389509f" integrity sha512-EYNwp3bU+98cpU4lAWYYL7Zz+2gryWH1qbdDTidVd6hkiR6weksdbMadyXKXNPEkQFhXM+hVO9ZygomHXp+AIw== +"@types/estree@^0.0.51": + version "0.0.51" + 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"@types/body-parser" "*" + "@types/express-serve-static-core" "^4.17.18" + "@types/qs" "*" + "@types/serve-static" "*" + "@types/glob@^7.1.1": version "7.2.0" resolved "https://registry.yarnpkg.com/@types/glob/-/glob-7.2.0.tgz#bc1b5bf3aa92f25bd5dd39f35c57361bdce5b2eb" @@ -2060,10 +2298,24 @@ dependencies: "@types/node" "*" -"@types/html-minifier-terser@^5.0.0": - version "5.1.2" - resolved "https://registry.yarnpkg.com/@types/html-minifier-terser/-/html-minifier-terser-5.1.2.tgz#693b316ad323ea97eed6b38ed1a3cc02b1672b57" - integrity sha512-h4lTMgMJctJybDp8CQrxTUiiYmedihHWkjnF/8Pxseu2S6Nlfcy8kwboQ8yejh456rP2yWoEVm1sS/FVsfM48w== +"@types/hast@^2.0.0": + version "2.3.4" + resolved "https://registry.yarnpkg.com/@types/hast/-/hast-2.3.4.tgz#8aa5ef92c117d20d974a82bdfb6a648b08c0bafc" + integrity sha512-wLEm0QvaoawEDoTRwzTXp4b4jpwiJDvR5KMnFnVodm3scufTlBOWRD6N1OBf9TZMhjlNsSfcO5V+7AF4+Vy+9g== + dependencies: + "@types/unist" "*" + +"@types/html-minifier-terser@^6.0.0": + version "6.1.0" + resolved "https://registry.yarnpkg.com/@types/html-minifier-terser/-/html-minifier-terser-6.1.0.tgz#4fc33a00c1d0c16987b1a20cf92d20614c55ac35" + integrity sha512-oh/6byDPnL1zeNXFrDXFLyZjkr1MsBG667IM792caf1L2UPOOMf65NFzjUH/ltyfwjAGfs1rsX1eftK0jC/KIg== + +"@types/http-proxy@^1.17.8": + version "1.17.9" + resolved "https://registry.yarnpkg.com/@types/http-proxy/-/http-proxy-1.17.9.tgz#7f0e7931343761efde1e2bf48c40f02f3f75705a" + integrity sha512-QsbSjA/fSk7xB+UXlCT3wHBy5ai9wOcNDWwZAtud+jXhwOM3l+EYZh8Lng4+/6n8uar0J7xILzqftJdJ/Wdfkw== + dependencies: + "@types/node" "*" "@types/istanbul-lib-coverage@*", "@types/istanbul-lib-coverage@^2.0.0", "@types/istanbul-lib-coverage@^2.0.1": version "2.0.4" @@ -2092,7 +2344,7 @@ expect "^29.0.0" pretty-format "^29.0.0" -"@types/json-schema@*", "@types/json-schema@^7.0.3", "@types/json-schema@^7.0.5", "@types/json-schema@^7.0.7", "@types/json-schema@^7.0.8": +"@types/json-schema@*", "@types/json-schema@^7.0.4", "@types/json-schema@^7.0.5", "@types/json-schema@^7.0.8", "@types/json-schema@^7.0.9": version "7.0.11" resolved "https://registry.yarnpkg.com/@types/json-schema/-/json-schema-7.0.11.tgz#d421b6c527a3037f7c84433fd2c4229e016863d3" integrity sha512-wOuvG1SN4Us4rez+tylwwwCV1psiNVOkJeM3AUWUNWg/jDQY2+HE/444y5gc+jBmRqASOm2Oeh5c1axHobwRKQ== @@ -2102,6 +2354,18 @@ resolved "https://registry.yarnpkg.com/@types/json5/-/json5-0.0.29.tgz#ee28707ae94e11d2b827bcbe5270bcea7f3e71ee" integrity sha512-dRLjCWHYg4oaA77cxO64oO+7JwCwnIzkZPdrrC71jQmQtlhM556pwKo5bUzqvZndkVbeFLIIi+9TC40JNF5hNQ== +"@types/mdast@^3.0.0": + version "3.0.10" + resolved "https://registry.yarnpkg.com/@types/mdast/-/mdast-3.0.10.tgz#4724244a82a4598884cbbe9bcfd73dff927ee8af" + integrity sha512-W864tg/Osz1+9f4lrGTZpCSO5/z4608eUp19tbozkq2HJK6i3z1kT0H9tlADXuYIb1YYOBByU4Jsqkk75q48qA== + dependencies: + "@types/unist" "*" + +"@types/mime@*": + version "3.0.1" + resolved "https://registry.yarnpkg.com/@types/mime/-/mime-3.0.1.tgz#5f8f2bca0a5863cb69bc0b0acd88c96cb1d4ae10" + integrity sha512-Y4XFY5VJAuw0FgAqPNd6NNoV44jbq9Bz2L7Rh/J6jLTiHBSBJa9fxqQIvkIld4GsoDOcCbvzOUAbLPsSKKg+uA== + "@types/minimatch@*": version "5.1.2" resolved "https://registry.yarnpkg.com/@types/minimatch/-/minimatch-5.1.2.tgz#07508b45797cb81ec3f273011b054cd0755eddca" @@ -2112,22 +2376,17 @@ resolved "https://registry.yarnpkg.com/@types/node/-/node-18.11.9.tgz#02d013de7058cea16d36168ef2fc653464cfbad4" integrity sha512-CRpX21/kGdzjOpFsZSkcrXMGIBWMGNIHXXBVFSH+ggkftxg+XYP20TESbh+zFvFj3EQOl5byk0HTRn1IL6hbqg== -"@types/normalize-package-data@^2.4.0": - version "2.4.1" - resolved "https://registry.yarnpkg.com/@types/normalize-package-data/-/normalize-package-data-2.4.1.tgz#d3357479a0fdfdd5907fe67e17e0a85c906e1301" - integrity sha512-Gj7cI7z+98M282Tqmp2K5EIsoouUEzbBJhQQzDE3jSIRk6r9gsz0oUokqIUR4u1R3dMHo0pDHM7sNOHyhulypw== - "@types/parse-json@^4.0.0": version "4.0.0" resolved "https://registry.yarnpkg.com/@types/parse-json/-/parse-json-4.0.0.tgz#2f8bb441434d163b35fb8ffdccd7138927ffb8c0" integrity sha512-//oorEZjL6sbPcKUaCdIGlIUeH26mgzimjBB77G6XRgnDl/L5wOnpyBGRe/Mmf5CVW3PwEBE1NjiMZ/ssFh4wA== -"@types/prettier@^2.0.0": +"@types/prettier@^2.1.5": version "2.7.1" resolved "https://registry.yarnpkg.com/@types/prettier/-/prettier-2.7.1.tgz#dfd20e2dc35f027cdd6c1908e80a5ddc7499670e" integrity sha512-ri0UmynRRvZiiUJdiz38MmIblKK+oH30MztdBVR95dv/Ubw6neWSb8u1XpRb72L4qsZOhz+L+z9JD40SJmfWow== -"@types/prop-types@*", "@types/prop-types@^15.7.4": +"@types/prop-types@*", "@types/prop-types@^15.7.5": version "15.7.5" resolved "https://registry.yarnpkg.com/@types/prop-types/-/prop-types-15.7.5.tgz#5f19d2b85a98e9558036f6a3cacc8819420f05cf" integrity sha512-JCB8C6SnDoQf0cNycqd/35A7MjcnK+ZTqE7judS6o7utxUCg6imJg3QK2qzHKszlTjcj2cn+NwMB2i96ubpj7w== @@ -2137,6 +2396,16 @@ resolved "https://registry.yarnpkg.com/@types/q/-/q-1.5.5.tgz#75a2a8e7d8ab4b230414505d92335d1dcb53a6df" integrity sha512-L28j2FcJfSZOnL1WBjDYp2vUHCeIFlyYI/53EwD/rKUBQ7MtUUfbQWiyKJGpcnv4/WgrhWsFKrcPstcAt/J0tQ== +"@types/qs@*": + version "6.9.7" + resolved "https://registry.yarnpkg.com/@types/qs/-/qs-6.9.7.tgz#63bb7d067db107cc1e457c303bc25d511febf6cb" + integrity sha512-FGa1F62FT09qcrueBA6qYTrJPVDzah9a+493+o2PCXsesWHIn27G98TsSMs3WPNbZIEj4+VJf6saSFpvD+3Zsw== + +"@types/range-parser@*": + version "1.2.4" + resolved "https://registry.yarnpkg.com/@types/range-parser/-/range-parser-1.2.4.tgz#cd667bcfdd025213aafb7ca5915a932590acdcdc" + integrity sha512-EEhsLsD6UsDM1yFhAvy0Cjr6VwmpMWqFBCb9w07wVugF7w9nfajxLuVmngTIpgS6svCnm6Vaw+MZhoDCKnOfsw== + "@types/react-is@^16.7.1 || ^17.0.0": version "17.0.3" resolved "https://registry.yarnpkg.com/@types/react-is/-/react-is-17.0.3.tgz#2d855ba575f2fc8d17ef9861f084acc4b90a137a" @@ -2144,7 +2413,7 @@ dependencies: "@types/react" "*" -"@types/react-transition-group@^4.2.0": +"@types/react-transition-group@^4.4.5": version "4.4.5" resolved "https://registry.yarnpkg.com/@types/react-transition-group/-/react-transition-group-4.4.5.tgz#aae20dcf773c5aa275d5b9f7cdbca638abc5e416" integrity sha512-juKD/eiSM3/xZYzjuzH6ZwpP+/lejltmiS3QEzV/vmb/Q8+HfDmxu+Baga8UEMGBqV88Nbg4l2hY/K2DkyaLLA== @@ -2160,33 +2429,55 @@ "@types/scheduler" "*" csstype "^3.0.2" -"@types/resolve@0.0.8": - version "0.0.8" - resolved "https://registry.yarnpkg.com/@types/resolve/-/resolve-0.0.8.tgz#f26074d238e02659e323ce1a13d041eee280e194" - integrity sha512-auApPaJf3NPfe18hSoJkp8EbZzer2ISk7o8mCC3M9he/a04+gbMF97NkpD2S8riMGvm4BMRI59/SZQSaLTKpsQ== +"@types/resolve@1.17.1": + version "1.17.1" + resolved "https://registry.yarnpkg.com/@types/resolve/-/resolve-1.17.1.tgz#3afd6ad8967c77e4376c598a82ddd58f46ec45d6" + integrity sha512-yy7HuzQhj0dhGpD8RLXSZWEkLsV9ibvxvi6EiJ3bkqLAO1RGo0WbkWQiwpRlSFymTJRz0d3k5LM3kkx8ArDbLw== dependencies: "@types/node" "*" +"@types/retry@0.12.0": + version "0.12.0" + resolved "https://registry.yarnpkg.com/@types/retry/-/retry-0.12.0.tgz#2b35eccfcee7d38cd72ad99232fbd58bffb3c84d" + integrity sha512-wWKOClTTiizcZhXnPY4wikVAwmdYHp8q6DmC+EJUzAMsycb7HB32Kh9RN4+0gExjmPmZSAQjgURXIGATPegAvA== + "@types/scheduler@*": version "0.16.2" resolved "https://registry.yarnpkg.com/@types/scheduler/-/scheduler-0.16.2.tgz#1a62f89525723dde24ba1b01b092bf5df8ad4d39" integrity sha512-hppQEBDmlwhFAXKJX2KnWLYu5yMfi91yazPb2l+lbJiwW+wdo1gNeRA+3RgNSO39WYX2euey41KEwnqesU2Jew== -"@types/source-list-map@*": - version "0.1.2" - resolved "https://registry.yarnpkg.com/@types/source-list-map/-/source-list-map-0.1.2.tgz#0078836063ffaf17412349bba364087e0ac02ec9" - integrity sha512-K5K+yml8LTo9bWJI/rECfIPrGgxdpeNbj+d53lwN4QjW1MCwlkhUms+gtdzigTeUyBr09+u8BwOIY3MXvHdcsA== +"@types/semver@^7.3.12": + version "7.3.13" + resolved "https://registry.yarnpkg.com/@types/semver/-/semver-7.3.13.tgz#da4bfd73f49bd541d28920ab0e2bf0ee80f71c91" + integrity sha512-21cFJr9z3g5dW8B0CVI9g2O9beqaThGQ6ZFBqHfwhzLDKUxaqTIy3vnfah/UPkfOiF2pLq+tGz+W8RyCskuslw== + +"@types/serve-index@^1.9.1": + version "1.9.1" + resolved "https://registry.yarnpkg.com/@types/serve-index/-/serve-index-1.9.1.tgz#1b5e85370a192c01ec6cec4735cf2917337a6278" + integrity sha512-d/Hs3nWDxNL2xAczmOVZNj92YZCS6RGxfBPjKzuu/XirCgXdpKEb88dYNbrYGint6IVWLNP+yonwVAuRC0T2Dg== + dependencies: + "@types/express" "*" + +"@types/serve-static@*", "@types/serve-static@^1.13.10": + version "1.15.0" + resolved "https://registry.yarnpkg.com/@types/serve-static/-/serve-static-1.15.0.tgz#c7930ff61afb334e121a9da780aac0d9b8f34155" + integrity sha512-z5xyF6uh8CbjAu9760KDKsH2FcDxZ2tFCsA4HIMWE6IkiYMXfVoa+4f9KX+FN0ZLsaMw1WNG2ETLA6N+/YA+cg== + dependencies: + "@types/mime" "*" + "@types/node" "*" + +"@types/sockjs@^0.3.33": + version "0.3.33" + resolved "https://registry.yarnpkg.com/@types/sockjs/-/sockjs-0.3.33.tgz#570d3a0b99ac995360e3136fd6045113b1bd236f" + integrity sha512-f0KEEe05NvUnat+boPTZ0dgaLZ4SfSouXUgv5noUiefG2ajgKjmETo9ZJyuqsl7dfl2aHlLJUiki6B4ZYldiiw== + dependencies: + "@types/node" "*" "@types/stack-utils@^2.0.0": version "2.0.1" resolved "https://registry.yarnpkg.com/@types/stack-utils/-/stack-utils-2.0.1.tgz#20f18294f797f2209b5f65c8e3b5c8e8261d127c" integrity sha512-Hl219/BT5fLAaz6NDkSuhzasy49dwQS/DSdu4MdggFB8zcXv7vflBI3xp7FEmkmdDkBUI2bPUNeMttp2knYdxw== -"@types/tapable@^1", "@types/tapable@^1.0.5": - version "1.0.8" - resolved "https://registry.yarnpkg.com/@types/tapable/-/tapable-1.0.8.tgz#b94a4391c85666c7b73299fd3ad79d4faa435310" - integrity sha512-ipixuVrh2OdNmauvtT51o3d8z12p6LtFW9in7U79der/kwejjdNchQC5UMn5u/KxNoM7VHHOs/l8KS8uHxhODQ== - "@types/testing-library__jest-dom@^5.9.1": version "5.14.5" resolved "https://registry.yarnpkg.com/@types/testing-library__jest-dom/-/testing-library__jest-dom-5.14.5.tgz#d113709c90b3c75fdb127ec338dad7d5f86c974f" @@ -2194,33 +2485,22 @@ dependencies: "@types/jest" "*" -"@types/uglify-js@*": - version "3.17.1" - resolved "https://registry.yarnpkg.com/@types/uglify-js/-/uglify-js-3.17.1.tgz#e0ffcef756476410e5bce2cb01384ed878a195b5" - integrity sha512-GkewRA4i5oXacU/n4MA9+bLgt5/L3F1mKrYvFGm7r2ouLXhRKjuWwo9XHNnbx6WF3vlGW21S3fCvgqxvxXXc5g== - dependencies: - source-map "^0.6.1" +"@types/trusted-types@^2.0.2": + version "2.0.2" + resolved "https://registry.yarnpkg.com/@types/trusted-types/-/trusted-types-2.0.2.tgz#fc25ad9943bcac11cceb8168db4f275e0e72e756" + integrity sha512-F5DIZ36YVLE+PN+Zwws4kJogq47hNgX3Nx6WyDJ3kcplxyke3XIzB8uK5n/Lpm1HBsbGzd6nmGehL8cPekP+Tg== -"@types/webpack-sources@*": - version "3.2.0" - resolved "https://registry.yarnpkg.com/@types/webpack-sources/-/webpack-sources-3.2.0.tgz#16d759ba096c289034b26553d2df1bf45248d38b" - integrity sha512-Ft7YH3lEVRQ6ls8k4Ff1oB4jN6oy/XmU6tQISKdhfh+1mR+viZFphS6WL0IrtDOzvefmJg5a0s7ZQoRXwqTEFg== - dependencies: - "@types/node" "*" - "@types/source-list-map" "*" - source-map "^0.7.3" +"@types/unist@*", "@types/unist@^2.0.0", "@types/unist@^2.0.2": + version "2.0.6" + resolved "https://registry.yarnpkg.com/@types/unist/-/unist-2.0.6.tgz#250a7b16c3b91f672a24552ec64678eeb1d3a08d" + integrity sha512-PBjIUxZHOuj0R15/xuwJYjFi+KZdNFrehocChv4g5hu6aFroHue8m0lBP0POdK2nKzbw0cgV1mws8+V/JAcEkQ== -"@types/webpack@^4.41.8": - version "4.41.33" - resolved "https://registry.yarnpkg.com/@types/webpack/-/webpack-4.41.33.tgz#16164845a5be6a306bcbe554a8e67f9cac215ffc" - integrity sha512-PPajH64Ft2vWevkerISMtnZ8rTs4YmRbs+23c402J0INmxDKCrhZNvwZYtzx96gY2wAtXdrK1BS2fiC8MlLr3g== +"@types/ws@^8.5.1": + version "8.5.3" + resolved "https://registry.yarnpkg.com/@types/ws/-/ws-8.5.3.tgz#7d25a1ffbecd3c4f2d35068d0b283c037003274d" + integrity sha512-6YOoWjruKj1uLf3INHH7D3qTXwFfEsg1kf3c0uDdSBJwfa/llkwIjrAGV7j7mVgGNbzTQ3HiHKKDXl6bJPD97w== dependencies: "@types/node" "*" - "@types/tapable" "^1" - "@types/uglify-js" "*" - "@types/webpack-sources" "*" - anymatch "^3.0.0" - source-map "^0.6.0" "@types/yargs-parser@*": version "21.0.0" @@ -2234,6 +2514,13 @@ dependencies: "@types/yargs-parser" "*" +"@types/yargs@^16.0.0": + version "16.0.4" + resolved "https://registry.yarnpkg.com/@types/yargs/-/yargs-16.0.4.tgz#26aad98dd2c2a38e421086ea9ad42b9e51642977" + integrity 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+anymatch@^3.0.3, anymatch@~3.1.2: + version "3.1.3" + resolved "https://registry.yarnpkg.com/anymatch/-/anymatch-3.1.3.tgz#790c58b19ba1720a84205b57c618d5ad8524973e" + integrity sha512-KMReFUr0B4t+D+OBkjR3KYqvocp2XaSzO55UcB6mgQMd3KbcE+mWTyvVV7D/zsdEbNnV6acZUutkiHQXvTr1Rw== dependencies: normalize-path "^3.0.0" picomatch "^2.0.4" -aproba@^1.1.1: - version "1.2.0" - resolved "https://registry.yarnpkg.com/aproba/-/aproba-1.2.0.tgz#6802e6264efd18c790a1b0d517f0f2627bf2c94a" - integrity sha512-Y9J6ZjXtoYh8RnXVCMOU/ttDmk1aBjunq9vO0ta5x85WDQiQfUF9sIPBITdbiiIVcBo03Hi3jMxigBtsddlXRw== +arg@^5.0.2: + version "5.0.2" + resolved "https://registry.yarnpkg.com/arg/-/arg-5.0.2.tgz#c81433cc427c92c4dcf4865142dbca6f15acd59c" + integrity sha512-PYjyFOLKQ9y57JvQ6QLo8dAgNqswh8M1RMJYdQduT6xbWSgK36P/Z/v+p888pM69jMMfS8Xd8F6I1kQ/I9HUGg== argparse@^1.0.7: version "1.0.10" @@ -2701,6 +2941,11 @@ argparse@^1.0.7: dependencies: sprintf-js "~1.0.2" +argparse@^2.0.1: + version "2.0.1" + resolved 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array.prototype.flat@^1.2.5: version "1.3.1" resolved "https://registry.yarnpkg.com/array.prototype.flat/-/array.prototype.flat-1.3.1.tgz#ffc6576a7ca3efc2f46a143b9d1dda9b4b3cf5e2" @@ -2789,7 +3009,7 @@ array.prototype.flat@^1.2.5: es-abstract "^1.20.4" es-shim-unscopables "^1.0.0" -array.prototype.flatmap@^1.3.0: +array.prototype.flatmap@^1.3.1: version "1.3.1" resolved "https://registry.yarnpkg.com/array.prototype.flatmap/-/array.prototype.flatmap-1.3.1.tgz#1aae7903c2100433cb8261cd4ed310aab5c4a183" integrity sha512-8UGn9O1FDVvMNB0UlLv4voxRMze7+FpHyF5mSMRjWHUMlpoDViniy05870VlxhfgTnLbpuwTzvD76MTtWxB/mQ== @@ -2810,27 +3030,23 @@ array.prototype.reduce@^1.0.5: es-array-method-boxes-properly "^1.0.0" is-string "^1.0.7" -arrify@^2.0.1: - version "2.0.1" - resolved "https://registry.yarnpkg.com/arrify/-/arrify-2.0.1.tgz#c9655e9331e0abcd588d2a7cad7e9956f66701fa" - integrity sha512-3duEwti880xqi4eAMN8AyR4a0ByT90zoYdLlevfrvU43vb0YZwZVfxOgxWrLXXXpyugL0hNZc9G6BiB5B3nUug== 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postcss-normalize-unicode "^5.1.1" + postcss-normalize-url "^5.1.0" + postcss-normalize-whitespace "^5.1.1" + postcss-ordered-values "^5.1.3" + postcss-reduce-initial "^5.1.1" + postcss-reduce-transforms "^5.1.0" + postcss-svgo "^5.1.0" + postcss-unique-selectors "^5.1.1" + +cssnano-utils@^3.1.0: + version "3.1.0" + resolved "https://registry.yarnpkg.com/cssnano-utils/-/cssnano-utils-3.1.0.tgz#95684d08c91511edfc70d2636338ca37ef3a6861" + integrity sha512-JQNR19/YZhz4psLX/rQ9M83e3z2Wf/HdJbryzte4a3NSuafyp9w/I4U+hx5C2S9g41qlstH7DEWnZaaj83OuEA== -cssnano@^4.1.10: - version "4.1.11" - resolved "https://registry.yarnpkg.com/cssnano/-/cssnano-4.1.11.tgz#c7b5f5b81da269cb1fd982cb960c1200910c9a99" - integrity sha512-6gZm2htn7xIPJOHY824ERgj8cNPgPxyCSnkXc4v7YvNW+TdVfzgngHcEhy/8D11kUWRUMbke+tC+AUcUsnMz2g== +cssnano@^5.0.6: + version "5.1.14" + resolved "https://registry.yarnpkg.com/cssnano/-/cssnano-5.1.14.tgz#07b0af6da73641276fe5a6d45757702ebae2eb05" + integrity 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"https://registry.yarnpkg.com/csstype/-/csstype-3.1.1.tgz#841b532c45c758ee546a11d5bd7b7b473c8c30b9" integrity sha512-DJR/VvkAvSZW9bTouZue2sSxDwdTN92uHjqeKVm+0dAqdfNykRzQ95tay8aXMBAAPpUiq4Qcug2L7neoRh2Egw== -cyclist@^1.0.1: - version "1.0.1" - resolved "https://registry.yarnpkg.com/cyclist/-/cyclist-1.0.1.tgz#596e9698fd0c80e12038c2b82d6eb1b35b6224d9" - integrity sha512-NJGVKPS81XejHcLhaLJS7plab0fK3slPh11mESeeDq2W4ZI5kUKK/LRRdVDvjJseojbPB7ZwjnyOybg3Igea/A== - d3-array@2, d3-array@^2.3.0: version "2.12.1" resolved "https://registry.yarnpkg.com/d3-array/-/d3-array-2.12.1.tgz#e20b41aafcdffdf5d50928004ececf815a465e81" @@ -4313,11 +4091,6 @@ d3-format@^1.4.4: resolved "https://registry.yarnpkg.com/d3-format/-/d3-format-1.4.5.tgz#374f2ba1320e3717eb74a9356c67daee17a7edb4" integrity sha512-J0piedu6Z8iB6TbIGfZgDzfXxUFN3qQRMofy2oPdXzQibYGqPB/9iMcxr/TGalU+2RsyDO+U4f33id8tbnSRMQ== -d3-hierarchy@^1.1.8: - version "1.1.9" - resolved 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"https://registry.yarnpkg.com/d3-time-format/-/d3-time-format-2.3.0.tgz#107bdc028667788a8924ba040faf1fbccd5a7850" - integrity sha512-guv6b2H37s2Uq/GefleCDtbe0XZAuy7Wa49VGkPVPMfLL9qObgBST3lEHJBMUp8S7NdLQAGIvr2KXk8Hc98iKQ== - dependencies: - d3-time "1" - -d3-time@1, d3-time@^1.0.11: - version "1.1.0" - resolved "https://registry.yarnpkg.com/d3-time/-/d3-time-1.1.0.tgz#b1e19d307dae9c900b7e5b25ffc5dcc249a8a0f1" - integrity sha512-Xh0isrZ5rPYYdqhAVk8VLnMEidhz5aP7htAADH6MfzgmmicPkTo8LhkLxci61/lCB7n7UmE3bN0leRt+qvkLxA== - "d3-time@1 - 2", d3-time@^2.1.1: version "2.1.1" resolved "https://registry.yarnpkg.com/d3-time/-/d3-time-2.1.1.tgz#e9d8a8a88691f4548e68ca085e5ff956724a6682" @@ -4382,13 +4143,10 @@ d3-time@1, d3-time@^1.0.11: dependencies: d3-array "2" -d@1, d@^1.0.1: - version "1.0.1" - resolved "https://registry.yarnpkg.com/d/-/d-1.0.1.tgz#8698095372d58dbee346ffd0c7093f99f8f9eb5a" - integrity sha512-m62ShEObQ39CfralilEQRjH6oAMtNCV1xJyEx5LpRYUVN+EviphDgUc/F3hnYbADmkiNs67Y+3ylmlG7Lnu+FA== - dependencies: - es5-ext "^0.10.50" - type "^1.0.1" +d3-time@^1.0.11: + version "1.1.0" + resolved "https://registry.yarnpkg.com/d3-time/-/d3-time-1.1.0.tgz#b1e19d307dae9c900b7e5b25ffc5dcc249a8a0f1" + integrity sha512-Xh0isrZ5rPYYdqhAVk8VLnMEidhz5aP7htAADH6MfzgmmicPkTo8LhkLxci61/lCB7n7UmE3bN0leRt+qvkLxA== damerau-levenshtein@^1.0.8: version "1.0.8" @@ -4404,14 +4162,14 @@ data-urls@^2.0.0: whatwg-mimetype "^2.3.0" whatwg-url "^8.0.0" -debug@2.6.9, debug@^2.2.0, debug@^2.3.3, debug@^2.6.0, debug@^2.6.9: +debug@2.6.9, debug@^2.6.0, debug@^2.6.9: version "2.6.9" resolved "https://registry.yarnpkg.com/debug/-/debug-2.6.9.tgz#5d128515df134ff327e90a4c93f4e077a536341f" integrity sha512-bC7ElrdJaJnPbAP+1EotYvqZsb3ecl5wi6Bfi6BJTUcNowp6cvspg0jXznRTKDjm/E7AdgFBVeAPVMNcKGsHMA== dependencies: ms "2.0.0" -debug@4, debug@^4.0.1, debug@^4.1.0, debug@^4.1.1, debug@^4.3.1: +debug@4, debug@^4.0.0, debug@^4.1.0, debug@^4.1.1, debug@^4.3.2, debug@^4.3.4: version "4.3.4" resolved 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sha512-hjf+xovcEn31w/EUYdTXQh/8smFL/dzYjohQGEIgjyNavaJfBY2p5F527Bo1VPATxv0VYTUC2bOcXvqFwk78Og== - dedent@^0.7.0: version "0.7.0" resolved "https://registry.yarnpkg.com/dedent/-/dedent-0.7.0.tgz#2495ddbaf6eb874abb0e1be9df22d2e5a544326c" integrity sha512-Q6fKUPqnAHAyhiUgFU7BUzLiv0kd8saH9al7tnu5Q/okj6dnupxyTgFIBjVzJATdfIAm9NAsvXNzjaKa+bxVyA== -deep-equal@^1.0.1: - version "1.1.1" - resolved "https://registry.yarnpkg.com/deep-equal/-/deep-equal-1.1.1.tgz#b5c98c942ceffaf7cb051e24e1434a25a2e6076a" - integrity sha512-yd9c5AdiqVcR+JjcwUQb9DkhJc8ngNr0MahEBGvDiJw8puWab2yZlh+nkasOnZP+EGTAP6rRp2JzJhJZzvNF8g== - dependencies: - is-arguments "^1.0.4" - is-date-object "^1.0.1" - is-regex "^1.0.4" - object-is "^1.0.1" - object-keys "^1.1.1" - regexp.prototype.flags "^1.2.0" - deep-equal@^2.0.5: version "2.1.0" resolved "https://registry.yarnpkg.com/deep-equal/-/deep-equal-2.1.0.tgz#5ba60402cf44ab92c2c07f3f3312c3d857a0e1dd" @@ -4488,15 +4224,26 @@ deepmerge@^4.2.2: resolved 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reusify "^1.0.4" -fault@^1.0.2: +fault@^1.0.0: version "1.0.4" resolved "https://registry.yarnpkg.com/fault/-/fault-1.0.4.tgz#eafcfc0a6d214fc94601e170df29954a4f842f13" integrity sha512-CJ0HCB5tL5fYTEA7ToAq5+kTwd++Borf1/bifxd9iT70QcXr4MRrO3Llf8Ifs70q+SJcGHFtnIE/Nw6giCtECA== dependencies: format "^0.2.0" -faye-websocket@^0.11.3, faye-websocket@^0.11.4: +faye-websocket@^0.11.3: version "0.11.4" resolved "https://registry.yarnpkg.com/faye-websocket/-/faye-websocket-0.11.4.tgz#7f0d9275cfdd86a1c963dc8b65fcc451edcbb1da" integrity sha512-CzbClwlXAuiRQAlUyfqPgvPoNKTckTPGfwZV4ZdAhVcP2lh9KUxJg2b5GkE7XbjKQ3YJnQ9z6D9ntLAlB+tP8g== @@ -5505,11 +5112,6 @@ fb-watchman@^2.0.0: dependencies: bser "2.1.1" -figgy-pudding@^3.5.1: - version "3.5.2" - resolved "https://registry.yarnpkg.com/figgy-pudding/-/figgy-pudding-3.5.2.tgz#b4eee8148abb01dcf1d1ac34367d59e12fa61d6e" - integrity sha512-0btnI/H8f2pavGMN8w40mlSKOfTK2SVJmBfBeVIj3kNw0swwgzyRq0d5TJVOwodFmtvpPeWPN/MCcfuWF0Ezbw== - file-entry-cache@^6.0.1: 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find-up@^4.0.0, find-up@^4.1.0: +find-root@^1.1.0: + version "1.1.0" + resolved "https://registry.yarnpkg.com/find-root/-/find-root-1.1.0.tgz#abcfc8ba76f708c42a97b3d685b7e9450bfb9ce4" + integrity sha512-NKfW6bec6GfKc0SGx1e07QZY9PE99u0Bft/0rzSD5k3sO/vwkVUpDUKVm5Gpp5Ue3YfShPFTX2070tDs5kB9Ng== + +find-up@^3.0.0: + version "3.0.0" + resolved "https://registry.yarnpkg.com/find-up/-/find-up-3.0.0.tgz#49169f1d7993430646da61ecc5ae355c21c97b73" + integrity sha512-1yD6RmLI1XBfxugvORwlck6f75tYL+iR0jqwsOrOxMZyGYqUuDhJ0l4AXdO1iX/FTs9cBAMEk1gWSEx1kSbylg== + dependencies: + locate-path "^3.0.0" + +find-up@^4.0.0, find-up@^4.1.0: version "4.1.0" resolved "https://registry.yarnpkg.com/find-up/-/find-up-4.1.0.tgz#97afe7d6cdc0bc5928584b7c8d7b16e8a9aa5d19" integrity sha512-PpOwAdQ/YlXQ2vj8a3h8IipDuYRi3wceVQQGYWxNINccq40Anw7BlsEXCMbt1Zt+OLA6Fq9suIpIWD0OsnISlw== @@ -5591,12 +5188,21 @@ find-up@4.1.0, find-up@^4.0.0, find-up@^4.1.0: locate-path "^5.0.0" path-exists "^4.0.0" -find-up@^3.0.0: - version "3.0.0" 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minimalistic-crypto-utils "^1.0.1" +highlight.js@^10.4.1, highlight.js@~10.7.0: + version "10.7.3" + resolved "https://registry.yarnpkg.com/highlight.js/-/highlight.js-10.7.3.tgz#697272e3991356e40c3cac566a74eef681756531" + integrity sha512-tzcUFauisWKNHaRkN4Wjl/ZA07gENAjFl3J/c480dprkGTg5EQstgaNFqBfUqCq54kZRIEcreTsAgF/m2quD7A== -hoist-non-react-statics@^3.1.0, hoist-non-react-statics@^3.3.2: +hoist-non-react-statics@^3.3.1: version "3.3.2" resolved "https://registry.yarnpkg.com/hoist-non-react-statics/-/hoist-non-react-statics-3.3.2.tgz#ece0acaf71d62c2969c2ec59feff42a4b1a85b45" integrity sha512-/gGivxi8JPKWNm/W0jSmzcMPpfpPLc3dY/6GxhX2hQ9iGj3aDfklV4ET7NjKpSinLpJ5vafa9iiGIEZg10SfBw== @@ -6126,11 +5609,6 @@ hoopy@^0.1.4: resolved "https://registry.yarnpkg.com/hoopy/-/hoopy-0.1.4.tgz#609207d661100033a9a9402ad3dea677381c1b1d" integrity sha512-HRcs+2mr52W0K+x8RzcLzuPPmVIKMSv97RGHy0Ea9y/mpcaK+xTrjICA04KAHi4GRzxliNqNJEFYWHghy3rSfQ== -hosted-git-info@^2.1.4: - version "2.8.9" - resolved 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is-decimal "^1.0.0" -is-arguments@^1.0.4, is-arguments@^1.1.0, is-arguments@^1.1.1: +is-arguments@^1.1.0, is-arguments@^1.1.1: version "1.1.1" resolved "https://registry.yarnpkg.com/is-arguments/-/is-arguments-1.1.1.tgz#15b3f88fda01f2a97fec84ca761a560f123efa9b" integrity sha512-8Q7EARjzEnKpt/PCD7e1cgUS0a6X8u5tdSiMqXhojOdoV9TsMsiO+9VLC5vAmO8N7/GmXn7yjR8qnA6bVAEzfA== @@ -6515,11 +5893,6 @@ is-arrayish@^0.2.1: resolved "https://registry.yarnpkg.com/is-arrayish/-/is-arrayish-0.2.1.tgz#77c99840527aa8ecb1a8ba697b80645a7a926a9d" integrity sha512-zz06S8t0ozoDXMG+ube26zeCTNXcKIPJZJi8hBrF4idCLms4CG9QtK7qBl1boi5ODzFpjswb5JPmHCbMpjaYzg== -is-arrayish@^0.3.1: - version "0.3.2" - resolved "https://registry.yarnpkg.com/is-arrayish/-/is-arrayish-0.3.2.tgz#4574a2ae56f7ab206896fb431eaeed066fdf8f03" - integrity sha512-eVRqCvVlZbuw3GrM63ovNSNAeA1K16kaR/LRY/92w0zxQ5/1YzwblUX652i4Xs9RwAGjW9d9y6X88t8OaAJfWQ== - is-bigint@^1.0.1: version "1.0.4" resolved 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resolved "https://registry.yarnpkg.com/json-parse-even-better-errors/-/json-parse-even-better-errors-2.3.1.tgz#7c47805a94319928e05777405dc12e1f7a4ee02d" integrity sha512-xyFwyhro/JEof6Ghe2iz2NcXoj2sloNsWr/XsERDK/oiPCfaNhl5ONfp+jQdAZRQQ0IJWNzH9zIZF7li91kh2w== @@ -7543,6 +6850,11 @@ json-schema-traverse@^1.0.0: resolved "https://registry.yarnpkg.com/json-schema-traverse/-/json-schema-traverse-1.0.0.tgz#ae7bcb3656ab77a73ba5c49bf654f38e6b6860e2" integrity sha512-NM8/P9n3XjXhIZn1lLhkFaACTOURQXjWhV4BA/RnOv8xvgqtqpAX9IO4mRQxSx1Rlo4tqzeqb0sOlruaOy3dug== +json-schema@^0.4.0: + version "0.4.0" + resolved "https://registry.yarnpkg.com/json-schema/-/json-schema-0.4.0.tgz#f7de4cf6efab838ebaeb3236474cbba5a1930ab5" + integrity sha512-es94M3nTIfsEPisRafak+HDLfHXnKBhV3vU5eqPcS3flIWqcxJWgXHXiey3YrpaNsanY5ei1VoYEbOzijuq9BA== + json-stable-stringify-without-jsonify@^1.0.1: version "1.0.1" resolved 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@@ jsonfile@^6.0.1: optionalDependencies: graceful-fs "^4.1.6" -jss-plugin-camel-case@^10.5.1: +jsonpointer@^5.0.0: + version "5.0.1" + resolved "https://registry.yarnpkg.com/jsonpointer/-/jsonpointer-5.0.1.tgz#2110e0af0900fd37467b5907ecd13a7884a1b559" + integrity sha512-p/nXbhSEcu3pZRdkW1OfJhpsVtW1gd4Wa1fnQc9YLiTfAjn0312eMKimbdIQzuZl9aa9xUGaRlP9T/CJE/ditQ== + +jss-plugin-camel-case@^10.9.0: version "10.9.2" resolved "https://registry.yarnpkg.com/jss-plugin-camel-case/-/jss-plugin-camel-case-10.9.2.tgz#76dddfa32f9e62d17daa4e3504991fd0933b89e1" integrity sha512-wgBPlL3WS0WDJ1lPJcgjux/SHnDuu7opmgQKSraKs4z8dCCyYMx9IDPFKBXQ8Q5dVYij1FFV0WdxyhuOOAXuTg== @@ -7585,58 +6895,50 @@ jss-plugin-camel-case@^10.5.1: hyphenate-style-name "^1.0.3" jss "10.9.2" -jss-plugin-default-unit@^10.5.1: +jss-plugin-compose@^10.9.0: version "10.9.2" - resolved "https://registry.yarnpkg.com/jss-plugin-default-unit/-/jss-plugin-default-unit-10.9.2.tgz#3e7f4a1506b18d8fe231554fd982439feb2a9c53" - integrity 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postcss@^7.0.6: +postcss@^7.0.35: version "7.0.39" resolved "https://registry.yarnpkg.com/postcss/-/postcss-7.0.39.tgz#9624375d965630e2e1f2c02a935c82a59cb48309" integrity sha512-yioayjNbHn6z1/Bywyb2Y4s3yvDAeXGOyxqD+LnVOinq6Mdmd++SW2wUNVzavyyHxd6+DxzWGIuosg6P1Rj8uA== @@ -9591,7 +8370,7 @@ postcss@^7, postcss@^7.0.0, postcss@^7.0.1, postcss@^7.0.14, postcss@^7.0.17, po picocolors "^0.2.1" source-map "^0.6.1" -postcss@^8.1.0: +postcss@^8.3.5, postcss@^8.4.18, postcss@^8.4.4: version "8.4.19" resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.19.tgz#61178e2add236b17351897c8bcc0b4c8ecab56fc" integrity sha512-h+pbPsyhlYj6N2ozBmHhHrs9DzGmbaarbLvWipMRO7RLS+v4onj26MPFXA5OBYFxyqYhUJK456SwDcY9H2/zsA== @@ -9610,25 +8389,20 @@ prelude-ls@~1.1.2: resolved "https://registry.yarnpkg.com/prelude-ls/-/prelude-ls-1.1.2.tgz#21932a549f5e52ffd9a827f570e04be62a97da54" integrity sha512-ESF23V4SKG6lVSGZgYNpbsiaAkdab6ZgOxe52p7+Kid3W3u3bxR4Vfd/o21dmN7jSt0IwgZ4v5MUd26FEtXE9w== -prepend-http@^1.0.0: - 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char-regex "^1.0.2" strip-ansi "^6.0.0" +string-length@^5.0.1: + version "5.0.1" + resolved "https://registry.yarnpkg.com/string-length/-/string-length-5.0.1.tgz#3d647f497b6e8e8d41e422f7e0b23bc536c8381e" + integrity sha512-9Ep08KAMUn0OadnVaBuRdE2l615CQ508kr0XMadjClfYpdCyvrbFp6Taebo8yyxokQ4viUd/xPPUA4FGgUa0ow== + dependencies: + char-regex "^2.0.0" + strip-ansi "^7.0.1" + string-natural-compare@^3.0.1: version "3.0.1" resolved "https://registry.yarnpkg.com/string-natural-compare/-/string-natural-compare-3.0.1.tgz#7a42d58474454963759e8e8b7ae63d71c1e7fdf4" integrity sha512-n3sPwynL1nwKi3WJ6AIsClwBMa0zTi54fn2oLU6ndfTSIO05xaznjSf15PcBZU6FNWbmN5Q6cxT4V5hGvB4taw== -string-width@^3.0.0, string-width@^3.1.0: - version "3.1.0" - resolved "https://registry.yarnpkg.com/string-width/-/string-width-3.1.0.tgz#22767be21b62af1081574306f69ac51b62203961" - integrity sha512-vafcv6KjVZKSgz06oM/H6GDBrAtz8vdhQakGjFIvNrHA6y3HCF1CInLy+QLq8dTJPQ1b+KDUqDFctkdRW44e1w== - dependencies: - emoji-regex "^7.0.1" - is-fullwidth-code-point "^2.0.0" - strip-ansi "^5.1.0" - -string-width@^4.1.0, string-width@^4.2.0, string-width@^4.2.3: +string-width@^4.1.0, string-width@^4.2.0: version "4.2.3" resolved "https://registry.yarnpkg.com/string-width/-/string-width-4.2.3.tgz#269c7117d27b05ad2e536830a8ec895ef9c6d010" integrity sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g== @@ -11137,7 +9602,7 @@ string-width@^4.1.0, string-width@^4.2.0, string-width@^4.2.3: is-fullwidth-code-point "^3.0.0" strip-ansi "^6.0.1" -string.prototype.matchall@^4.0.7: +string.prototype.matchall@^4.0.6, string.prototype.matchall@^4.0.8: version "4.0.8" resolved "https://registry.yarnpkg.com/string.prototype.matchall/-/string.prototype.matchall-4.0.8.tgz#3bf85722021816dcd1bf38bb714915887ca79fd3" integrity sha512-6zOCOcJ+RJAQshcTvXPHoxoQGONa3e/Lqx90wUA+wEzX78sg5Bo+1tQo4N0pohS0erG9qtCqJDjNCQBjeWVxyg== @@ -11169,7 +9634,7 @@ string.prototype.trimstart@^1.0.5: define-properties "^1.1.4" es-abstract "^1.20.4" -string_decoder@^1.0.0, string_decoder@^1.1.1: +string_decoder@^1.1.1: version "1.3.0" resolved "https://registry.yarnpkg.com/string_decoder/-/string_decoder-1.3.0.tgz#42f114594a46cf1a8e30b0a84f56c78c3edac21e" integrity sha512-hkRX8U1WjJFd8LsDJ2yQ/wWWxaopEsABU1XfkM8A+j0+85JAGppt16cr1Whg6KIbb4okU6Mql6BOj+uup/wKeA== @@ -11183,7 +9648,7 @@ string_decoder@~1.1.1: dependencies: safe-buffer "~5.1.0" -stringify-object@^3.3.0: +stringify-object@^3.2.0, stringify-object@^3.3.0: version "3.3.0" resolved "https://registry.yarnpkg.com/stringify-object/-/stringify-object-3.3.0.tgz#703065aefca19300d3ce88af4f5b3956d7556629" integrity sha512-rHqiFh1elqCQ9WPLIC8I0Q/g/wj5J1eMkyoiD6eoQApWHP0FtlK7rqnhmabL5VUY9JQCcqwwvlOaSuutekgyrw== @@ -11192,27 +9657,6 @@ stringify-object@^3.3.0: is-obj "^1.0.1" is-regexp "^1.0.0" -strip-ansi@6.0.0: - version "6.0.0" - resolved "https://registry.yarnpkg.com/strip-ansi/-/strip-ansi-6.0.0.tgz#0b1571dd7669ccd4f3e06e14ef1eed26225ae532" - integrity 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strip-ansi@^6.0.1: dependencies: ansi-regex "^5.0.1" +strip-ansi@^7.0.1: + version "7.0.1" + resolved "https://registry.yarnpkg.com/strip-ansi/-/strip-ansi-7.0.1.tgz#61740a08ce36b61e50e65653f07060d000975fb2" + integrity sha512-cXNxvT8dFNRVfhVME3JAe98mkXDYN2O1l7jmcwMnOslDeESg1rF/OZMtK0nRAhiari1unG5cD4jG3rapUAkLbw== + dependencies: + ansi-regex "^6.0.1" + strip-bom@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/strip-bom/-/strip-bom-3.0.0.tgz#2334c18e9c759f7bdd56fdef7e9ae3d588e68ed3" @@ -11230,24 +9681,21 @@ strip-bom@^4.0.0: resolved "https://registry.yarnpkg.com/strip-bom/-/strip-bom-4.0.0.tgz#9c3505c1db45bcedca3d9cf7a16f5c5aa3901878" integrity sha512-3xurFv5tEgii33Zi8Jtp55wEIILR9eh34FAW00PZf+JnSsTmV/ioewSgQl97JHvgjoRGwPShsWm+IdrxB35d0w== -strip-comments@^1.0.2: - version "1.0.2" - resolved "https://registry.yarnpkg.com/strip-comments/-/strip-comments-1.0.2.tgz#82b9c45e7f05873bee53f37168af930aa368679d" - integrity 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-to-regex-range@^2.1.0: - version "2.1.1" - resolved "https://registry.yarnpkg.com/to-regex-range/-/to-regex-range-2.1.1.tgz#7c80c17b9dfebe599e27367e0d4dd5590141db38" - integrity sha512-ZZWNfCjUokXXDGXFpZehJIkZqq91BcULFq/Pi7M5i4JnxXdhMKAK682z8bCW3o8Hj1wuuzoKcW3DfVzaP6VuNg== - dependencies: - is-number "^3.0.0" - repeat-string "^1.6.1" - to-regex-range@^5.0.1: version "5.0.1" resolved "https://registry.yarnpkg.com/to-regex-range/-/to-regex-range-5.0.1.tgz#1648c44aae7c8d988a326018ed72f5b4dd0392e4" @@ -11542,16 +9946,6 @@ to-regex-range@^5.0.1: dependencies: is-number "^7.0.0" -to-regex@^3.0.1, to-regex@^3.0.2: - version "3.0.2" - resolved "https://registry.yarnpkg.com/to-regex/-/to-regex-3.0.2.tgz#13cfdd9b336552f30b51f33a8ae1b42a7a7599ce" - integrity sha512-FWtleNAtZ/Ki2qtqej2CXTOayOH9bHDQF+Q48VpWyDXjbYxA4Yz8iDB31zXOBUlOHHKidDbqGVrTUvQMPmBGBw== - dependencies: - define-property "^2.0.2" - extend-shallow "^3.0.2" - regex-not "^1.0.2" - safe-regex "^1.1.0" - toidentifier@1.0.1: version "1.0.1" resolved "https://registry.yarnpkg.com/toidentifier/-/toidentifier-1.0.1.tgz#3be34321a88a820ed1bd80dfaa33e479fbb8dd35" @@ -11567,6 +9961,13 @@ tough-cookie@^4.0.0: universalify "^0.2.0" url-parse "^1.5.3" +tr46@^1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/tr46/-/tr46-1.0.1.tgz#a8b13fd6bfd2489519674ccde55ba3693b706d09" + integrity sha512-dTpowEjclQ7Kgx5SdBkqRzVhERQXov8/l9Ft9dVM9fmg0W0KQSVaXX9T4i6twCPNtYiZM53lpSSUAwJbFPOHxA== + dependencies: + punycode "^2.1.0" + tr46@^2.1.0: version "2.1.0" resolved "https://registry.yarnpkg.com/tr46/-/tr46-2.1.0.tgz#fa87aa81ca5d5941da8cbf1f9b749dc969a4e240" @@ -11574,16 +9975,16 @@ tr46@^2.1.0: dependencies: punycode "^2.1.1" +trough@^1.0.0: + version "1.0.5" + resolved "https://registry.yarnpkg.com/trough/-/trough-1.0.5.tgz#b8b639cefad7d0bb2abd37d433ff8293efa5f406" + integrity sha512-rvuRbTarPXmMb79SmzEp8aqXNKcK+y0XaB298IXueQ8I2PsrATcPBCSPyK/dDNa2iWOhKlfNnOjdAOTBU/nkFA== + tryer@^1.0.1: version "1.0.1" resolved 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type-check@~0.3.2: dependencies: prelude-ls "~1.1.2" -type-detect@4.0.8: +type-detect@4.0.8, type-detect@^4.0.8: version "4.0.8" resolved "https://registry.yarnpkg.com/type-detect/-/type-detect-4.0.8.tgz#7646fb5f18871cfbb7749e69bd39a6388eb7450c" integrity sha512-0fr/mIH1dlO+x7TlcMy+bIDqKPsw/70tVyeHW787goQjhmqaZe10uwLujubK9q9Lg6Fiho1KUKDYz0Z7k7g5/g== +type-fest@^0.16.0: + version "0.16.0" + resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-0.16.0.tgz#3240b891a78b0deae910dbeb86553e552a148860" + integrity sha512-eaBzG6MxNzEn9kiwvtre90cXaNLkmadMWa1zQMs3XORCXNbsH/OewwbxC5ia9dCxIxnTAsSxXJaa/p5y8DlvJg== + type-fest@^0.20.2: version "0.20.2" resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-0.20.2.tgz#1bf207f4b28f91583666cb5fbd327887301cd5f4" @@ -11645,21 +10046,6 @@ type-fest@^0.21.3: resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-0.21.3.tgz#d260a24b0198436e133fa26a524a6d65fa3b2e37" integrity 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"https://registry.yarnpkg.com/type-is/-/type-is-1.6.18.tgz#4e552cd05df09467dcbc4ef739de89f2cf37c131" @@ -11668,16 +10054,6 @@ type-is@~1.6.18: media-typer "0.3.0" mime-types "~2.1.24" -type@^1.0.1: - version "1.2.0" - resolved "https://registry.yarnpkg.com/type/-/type-1.2.0.tgz#848dd7698dafa3e54a6c479e759c4bc3f18847a0" - integrity sha512-+5nt5AAniqsCnu2cEQQdpzCAh33kVx8n0VoFidKpB1dVVLAN/F+bgVOqOJqOnEnrhp222clB5p3vUlD+1QAnfg== - -type@^2.7.2: - version "2.7.2" - resolved "https://registry.yarnpkg.com/type/-/type-2.7.2.tgz#2376a15a3a28b1efa0f5350dcf72d24df6ef98d0" - integrity sha512-dzlvlNlt6AXU7EBSfpAscydQ7gXB+pPGsPnfJnZpiNJBDj7IaJzQlBZYGdEi4R9HmPdBv2XmWJ6YUtoTa7lmCw== - typedarray-to-buffer@^3.1.5: version "3.1.5" resolved "https://registry.yarnpkg.com/typedarray-to-buffer/-/typedarray-to-buffer-3.1.5.tgz#a97ee7a9ff42691b9f783ff1bc5112fe3fca9080" @@ -11685,11 +10061,6 @@ typedarray-to-buffer@^3.1.5: dependencies: is-typedarray "^1.0.0" -typedarray@^0.0.6: - version "0.0.6" - resolved 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"https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-20.2.9.tgz#2eb7dc3b0289718fc295f362753845c41a0c94ee" + integrity sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w== -yargs@^13.3.2: - version "13.3.2" - resolved "https://registry.yarnpkg.com/yargs/-/yargs-13.3.2.tgz#ad7ffefec1aa59565ac915f82dccb38a9c31a2dd" - integrity sha512-AX3Zw5iPruN5ie6xGRIDgqkT+ZhnRlZMLMHAs8tg7nRruy2Nb+i5o9bwghAogtM08q1dpr2LVoS8KSTMYpWXUw== +yargs@^16.2.0: + version "16.2.0" + resolved "https://registry.yarnpkg.com/yargs/-/yargs-16.2.0.tgz#1c82bf0f6b6a66eafce7ef30e376f49a12477f66" + integrity sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw== dependencies: - cliui "^5.0.0" - find-up "^3.0.0" - get-caller-file "^2.0.1" - require-directory "^2.1.1" - require-main-filename "^2.0.0" - set-blocking "^2.0.0" - string-width "^3.0.0" - which-module "^2.0.0" - y18n "^4.0.0" - yargs-parser "^13.1.2" - -yargs@^15.4.1: - version 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"https://registry.yarnpkg.com/zwitch/-/zwitch-1.0.5.tgz#d11d7381ffed16b742f6af7b3f223d5cd9fe9920" + integrity sha512-V50KMwwzqJV0NpZIZFwfOD5/lyny3WlSzRiXgA0G7VUnRlqttta1L6UQIHzd6EuBY/cHGfwTIck7w1yH6Q5zUw== From 46a4ba7f422289e17639edb53fa52118ad0d0c02 Mon Sep 17 00:00:00 2001 From: mjaquiery Date: Wed, 23 Nov 2022 12:09:37 +0000 Subject: [PATCH 02/79] update react and dependencies --- frontend/index.html | 43 ++++ frontend/package.json | 4 + frontend/src/App.js | 350 ++----------------------------- frontend/src/App.test.js | 2 + frontend/src/Cells.js | 32 +-- frontend/src/Core.js | 329 +++++++++++++++++++++++++++++ frontend/src/DatasetDetail.js | 20 +- frontend/src/Datasets.js | 25 ++- frontend/src/Equipment.js | 32 +-- frontend/src/Files.js | 18 +- frontend/src/FormComponents.js | 18 +- frontend/src/GetDatasetMatlab.js | 2 +- frontend/src/GetDatasetPython.js | 2 +- frontend/src/HarvesterDetail.js | 40 ++-- frontend/src/Harvesters.js | 34 +-- frontend/src/Login.js | 20 +- frontend/src/index.js | 9 +- frontend/yarn.lock | 112 +++++++++- 18 files changed, 620 insertions(+), 472 deletions(-) create mode 100644 frontend/index.html create mode 100644 frontend/src/Core.js diff --git a/frontend/index.html b/frontend/index.html new file mode 100644 index 00000000..5da4d64f --- /dev/null +++ b/frontend/index.html @@ -0,0 +1,43 @@ + + + + + + + + + + + + + Galvanalyser + + + +
+ + + diff --git a/frontend/package.json b/frontend/package.json index 634963e2..96f0566a 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -6,7 +6,11 @@ "dependencies": { "@emotion/react": "^11.10.5", "@emotion/styled": "^11.10.5", + "@mui/icons-material": "^5.10.15", + "@mui/lab": "^5.0.0-alpha.109", "@mui/material": "^5.10.15", + "@mui/styles": "^5.10.15", + "@mui/x-data-grid": "^5.17.12", "@nivo/core": "^0.80.0", "@nivo/line": "^0.80.0", "@testing-library/jest-dom": "^5.11.4", diff --git a/frontend/src/App.js b/frontend/src/App.js index 686e4a5e..9f441526 100644 --- a/frontend/src/App.js +++ b/frontend/src/App.js @@ -1,345 +1,21 @@ -import React, {useEffect} from "react"; -import { - Switch, - Route, - Redirect, - Link, - useHistory, - useLocation, - matchPath, -} from "react-router-dom"; -import Login from "./Login" -import Harvesters from "./Harvesters" -import DatasetDetail from "./DatasetDetail" -import Cells from "./Cells" -import SpeedIcon from '@material-ui/icons/Speed'; -import Equipment from "./Equipment" -import Datasets from "./Datasets" -import TableChartIcon from '@material-ui/icons/TableChart'; -import Dialog from '@material-ui/core/Dialog'; -import DialogActions from '@material-ui/core/DialogActions'; -import DialogContent from '@material-ui/core/DialogContent'; -import DialogContentText from '@material-ui/core/DialogContentText'; -import DialogTitle from '@material-ui/core/DialogTitle'; -import BatteryUnknownIcon from '@material-ui/icons/BatteryUnknown'; -import BackupIcon from '@material-ui/icons/Backup'; -import {loggedIn, logout, getToken, getUser, isAdmin} from "./Api" -import { makeStyles } from '@material-ui/core/styles'; -import CssBaseline from '@material-ui/core/CssBaseline'; - -import clsx from 'clsx'; -import Drawer from '@material-ui/core/Drawer'; -import AppBar from '@material-ui/core/AppBar'; -import Toolbar from '@material-ui/core/Toolbar'; -import List from '@material-ui/core/List'; -import Typography from '@material-ui/core/Typography'; -import Divider from '@material-ui/core/Divider'; -import IconButton from '@material-ui/core/IconButton'; -import Button from '@material-ui/core/Button'; -import MenuIcon from '@material-ui/icons/Menu'; -import ChevronLeftIcon from '@material-ui/icons/ChevronLeft'; - -import ListItem from '@material-ui/core/ListItem'; -import ListItemIcon from '@material-ui/core/ListItemIcon'; -import ListItemText from '@material-ui/core/ListItemText'; -import { ReactComponent as GalvanalyserLogo } from './Galvanalyser-logo.svg'; - -const PrivateRoute = ({ component: Component, ...rest }) => { - const logged = loggedIn(); - - return ( - logged - ? - : - )} /> -} - -const drawerWidth = 240; - -const useStyles = makeStyles((theme) => ({ - root: { - display: 'flex', - }, - toolbar: { - paddingRight: 24, // keep right padding when drawer closed - }, - toolbarIcon: { - display: 'flex', - alignItems: 'center', - justifyContent: 'flex-end', - padding: '0 8px', - ...theme.mixins.toolbar, - }, - appBar: { - zIndex: theme.zIndex.drawer + 1, - transition: theme.transitions.create(['width', 'margin'], { - easing: theme.transitions.easing.sharp, - duration: theme.transitions.duration.leavingScreen, - }), - }, - appBarShift: { - marginLeft: drawerWidth, - width: `calc(100% - ${drawerWidth}px)`, - transition: theme.transitions.create(['width', 'margin'], { - easing: theme.transitions.easing.sharp, - duration: theme.transitions.duration.enteringScreen, - }), - }, - galvanalyserLogo: { - height: '40px' - }, - menuButton: { - marginRight: 36, - }, - menuButtonHidden: { - display: 'none', - }, - title: { - marginLeft: 16, - flexGrow: 1, - }, - drawerPaper: { - position: 'relative', - whiteSpace: 'nowrap', - width: drawerWidth, - transition: theme.transitions.create('width', { - easing: theme.transitions.easing.sharp, - duration: theme.transitions.duration.enteringScreen, - }), - }, - drawerPaperClose: { - overflowX: 'hidden', - transition: theme.transitions.create('width', { - easing: theme.transitions.easing.sharp, - duration: theme.transitions.duration.leavingScreen, - }), - width: theme.spacing(7), - [theme.breakpoints.up('sm')]: { - width: theme.spacing(9), - }, - }, - appBarSpacer: theme.mixins.toolbar, - content: { - flexGrow: 1, - height: '100vh', - overflow: 'auto', - }, - container: { - paddingTop: theme.spacing(4), - paddingBottom: theme.spacing(4), - }, - paper: { - padding: theme.spacing(2), - display: 'flex', - overflow: 'auto', - flexDirection: 'column', - }, - fixedHeight: { - height: 240, - }, -})); +/* +* Theme wrapper for the app. Body in Core.js +*/ +import React from "react"; +import { createTheme, StyledEngineProvider } from '@mui/material/styles'; +import { ThemeProvider } from "@mui/styles"; +import Core from "./Core.js" +const theme = createTheme(); export default function App() { - const { pathname } = useLocation(); - const classes = useStyles(); - const [user, setUser] = React.useState(null); - - useEffect(() => { - getUser().then(setUser) - }, []); - - const handleLogin = () => { - getUser().then(setUser) - } - - const userIsAdmin = isAdmin() - - let userDisplayName = '' - if (user) { - userDisplayName = userIsAdmin ? - user.username + " (Admin)" : - user.username - } - - const datasetsPath = "/" - const isDatasetPath = matchPath(pathname, - {path: datasetsPath, exact:true} - ) - const harvestersPath = "/harvesters" - const isHarvestersPath = matchPath(pathname, - {path: harvestersPath, exact:true} - ) - const cellsPath = "/cells" - const isCellsPath = matchPath(pathname, - {path: cellsPath, exact:true} - ) - const equipmentPath = "/equipment" - const isEquipmentPath = matchPath(pathname, - {path: equipmentPath, exact:true} - ) - console.log('paths:', isDatasetPath, isHarvestersPath) - - - const [open, setOpen] = React.useState(false); - const handleDrawerOpen = () => { - setOpen(true); - }; - const handleDrawerClose = () => { - setOpen(false); - }; - - const [tokenOpen, setTokenOpen] = React.useState(false); - const [token, setToken] = React.useState(); - - const handleTokenOpen = () => { - getToken().then(response => response.json()).then(data => { - setToken(data.access_token) - setTokenOpen(true); - }); - }; - - const handleTokenClose = () => { - setTokenOpen(false); - }; - - const tokenGenerator = ( - - - - - {"API Token"} - - - - {token} - - - - - - - - ) - - const mainListItems = ( -
- - - - - - - - - - - - - - - - - - - - - - - - - - -
- ); - - let history = useHistory(); - - const logged_in = ( -
- - - - - - - - - - - - {tokenGenerator} - - - - -
- - - -
- - {mainListItems} - -
-
- {/* A looks through its children s and - renders the first one that matches the current URL. */} - - - - - - - -
-
- ); - - return ( - - - - - - {logged_in} - - + + + + + ); } diff --git a/frontend/src/App.test.js b/frontend/src/App.test.js index 1f03afee..89bdec4f 100644 --- a/frontend/src/App.test.js +++ b/frontend/src/App.test.js @@ -1,6 +1,8 @@ import { render, screen } from '@testing-library/react'; import App from './App'; +globalThis.IS_REACT_ACT_ENVIRONMENT = true; + test('renders learn react link', () => { render(); const linkElement = screen.getByText(/learn react/i); diff --git a/frontend/src/Cells.js b/frontend/src/Cells.js index bb795180..8f96570d 100644 --- a/frontend/src/Cells.js +++ b/frontend/src/Cells.js @@ -1,20 +1,20 @@ import React, { useEffect, useState } from 'react'; -import Typography from '@material-ui/core/Typography'; -import TextField from '@material-ui/core/TextField'; -import { makeStyles } from '@material-ui/core/styles'; -import Table from '@material-ui/core/Table'; -import TableBody from '@material-ui/core/TableBody'; -import Paper from '@material-ui/core/Paper'; -import Tooltip from '@material-ui/core/Tooltip'; -import AddIcon from '@material-ui/icons/Add'; -import IconButton from '@material-ui/core/IconButton'; -import TableCell from '@material-ui/core/TableCell'; -import Container from '@material-ui/core/Container'; -import SaveIcon from '@material-ui/icons/Save'; -import TableContainer from '@material-ui/core/TableContainer'; -import TableHead from '@material-ui/core/TableHead'; -import DeleteIcon from '@material-ui/icons/Delete'; -import TableRow from '@material-ui/core/TableRow'; +import Typography from '@mui/material/Typography'; +import TextField from '@mui/material/TextField'; +import { makeStyles } from '@mui/styles' +import Table from '@mui/material/Table'; +import TableBody from '@mui/material/TableBody'; +import Paper from '@mui/material/Paper'; +import Tooltip from '@mui/material/Tooltip'; +import AddIcon from '@mui/icons-material/Add'; +import IconButton from '@mui/material/IconButton'; +import TableCell from '@mui/material/TableCell'; +import Container from '@mui/material/Container'; +import SaveIcon from '@mui/icons-material/Save'; +import TableContainer from '@mui/material/TableContainer'; +import TableHead from '@mui/material/TableHead'; +import DeleteIcon from '@mui/icons-material/Delete'; +import TableRow from '@mui/material/TableRow'; import { cells, add_cell, update_cell, delete_cell diff --git a/frontend/src/Core.js b/frontend/src/Core.js new file mode 100644 index 00000000..200f856a --- /dev/null +++ b/frontend/src/Core.js @@ -0,0 +1,329 @@ +import React, {useEffect} from "react"; +import { + Routes, + Route, + Outlet, + Navigate, + Link, + useNavigate, + useLocation, + matchPath, +} from "react-router-dom"; +import Login from "./Login" +import Harvesters from "./Harvesters" +import DatasetDetail from "./DatasetDetail" +import Cells from "./Cells" +import SpeedIcon from '@mui/icons-material/Speed'; +import Equipment from "./Equipment" +import Datasets from "./Datasets" +import TableChartIcon from '@mui/icons-material/TableChart'; +import Dialog from '@mui/material/Dialog'; +import DialogActions from '@mui/material/DialogActions'; +import DialogContent from '@mui/material/DialogContent'; +import DialogContentText from '@mui/material/DialogContentText'; +import DialogTitle from '@mui/material/DialogTitle'; +import BatteryUnknownIcon from '@mui/icons-material/BatteryUnknown'; +import BackupIcon from '@mui/icons-material/Backup'; +import {loggedIn, logout, getToken, getUser, isAdmin} from "./Api" +import { makeStyles} from "@mui/styles"; +import CssBaseline from '@mui/material/CssBaseline'; + +import clsx from 'clsx'; +import Drawer from '@mui/material/Drawer'; +import AppBar from '@mui/material/AppBar'; +import Toolbar from '@mui/material/Toolbar'; +import List from '@mui/material/List'; +import Typography from '@mui/material/Typography'; +import Divider from '@mui/material/Divider'; +import IconButton from '@mui/material/IconButton'; +import Button from '@mui/material/Button'; +import MenuIcon from '@mui/icons-material/Menu'; +import ChevronLeftIcon from '@mui/icons-material/ChevronLeft'; + +import ListItem from '@mui/material/ListItem'; +import ListItemIcon from '@mui/material/ListItemIcon'; +import ListItemText from '@mui/material/ListItemText'; +import { ReactComponent as GalvanalyserLogo } from './Galvanalyser-logo.svg'; + +const PrivateRoute = (component) => { + const logged = loggedIn(); + + return logged? component : ; +} + +const drawerWidth = 240; + +const useStyles = makeStyles((theme) => ({ + root: { + display: 'flex', + }, + toolbar: { + paddingRight: 24, // keep right padding when drawer closed + }, + toolbarIcon: { + display: 'flex', + alignItems: 'center', + justifyContent: 'flex-end', + padding: '0 8px', + ...theme.mixins.toolbar, + }, + appBar: { + zIndex: theme.zIndex.drawer + 1, + transition: theme.transitions.create(['width', 'margin'], { + easing: theme.transitions.easing.sharp, + duration: theme.transitions.duration.leavingScreen, + }), + }, + appBarShift: { + marginLeft: drawerWidth, + width: `calc(100% - ${drawerWidth}px)`, + transition: theme.transitions.create(['width', 'margin'], { + easing: theme.transitions.easing.sharp, + duration: theme.transitions.duration.enteringScreen, + }), + }, + galvanalyserLogo: { + height: '40px' + }, + menuButton: { + marginRight: 36, + }, + menuButtonHidden: { + display: 'none', + }, + title: { + marginLeft: 16, + flexGrow: 1, + }, + drawerPaper: { + position: 'relative', + whiteSpace: 'nowrap', + width: drawerWidth, + transition: theme.transitions.create('width', { + easing: theme.transitions.easing.sharp, + duration: theme.transitions.duration.enteringScreen, + }), + }, + drawerPaperClose: { + overflowX: 'hidden', + transition: theme.transitions.create('width', { + easing: theme.transitions.easing.sharp, + duration: theme.transitions.duration.leavingScreen, + }), + width: theme.spacing(7), + [theme.breakpoints.up('sm')]: { + width: theme.spacing(9), + }, + }, + appBarSpacer: theme.mixins.toolbar, + content: { + flexGrow: 1, + height: '100vh', + overflow: 'auto', + }, + container: { + paddingTop: theme.spacing(4), + paddingBottom: theme.spacing(4), + }, + paper: { + padding: theme.spacing(2), + display: 'flex', + overflow: 'auto', + flexDirection: 'column', + }, + fixedHeight: { + height: 240, + }, +})); + + + +export default function Core() { + const { pathname } = useLocation(); + const classes = useStyles(); + const [user, setUser] = React.useState(null); + + useEffect(() => { + getUser().then(setUser) + }, []); + + const handleLogin = () => { + getUser().then(setUser) + } + + const userIsAdmin = isAdmin() + + let userDisplayName = '' + if (user) { + userDisplayName = userIsAdmin ? + user.username + " (Admin)" : + user.username + } + + const datasetsPath = "/" + const isDatasetPath = matchPath({path: datasetsPath, exact:true}, pathname) !== null + const harvestersPath = "/harvesters" + const isHarvestersPath = matchPath({path: harvestersPath, exact:true}, pathname) !== null + const cellsPath = "/cells" + const isCellsPath = matchPath({path: cellsPath, exact:true}, pathname) !== null + const equipmentPath = "/equipment" + const isEquipmentPath = matchPath({path: equipmentPath, exact:true}, pathname) !== null + console.log('paths:', isDatasetPath, isHarvestersPath) + + + const [open, setOpen] = React.useState(false); + const handleDrawerOpen = () => { + setOpen(true); + }; + const handleDrawerClose = () => { + setOpen(false); + }; + + const [tokenOpen, setTokenOpen] = React.useState(false); + const [token, setToken] = React.useState(); + + const handleTokenOpen = () => { + getToken().then(response => response.json()).then(data => { + setToken(data.access_token) + setTokenOpen(true); + }); + }; + + const handleTokenClose = () => { + setTokenOpen(false); + }; + + const tokenGenerator = ( + + + + + {"API Token"} + + + + {token} + + + + + + + + ) + + const mainListItems = ( +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ ); + + let navigate = useNavigate(); + + const Layout = ( +
+ + + + + + + + + + + + {tokenGenerator} + + + + +
+ + + +
+ + {mainListItems} + +
+
+ +
+
+ ); + + /* A looks through its children s and renders the first one that matches the current URL. */ + return ( + + }/> + + + + + + + + + ); +} + + diff --git a/frontend/src/DatasetDetail.js b/frontend/src/DatasetDetail.js index d623b5b0..ca92c1b6 100644 --- a/frontend/src/DatasetDetail.js +++ b/frontend/src/DatasetDetail.js @@ -1,14 +1,14 @@ import React, { useEffect, useState } from "react"; -import Typography from '@material-ui/core/Typography'; +import Typography from '@mui/material/Typography'; import { useForm } from "react-hook-form"; -import Card from "@material-ui/core/Card"; -import CardActions from "@material-ui/core/CardActions"; -import CardContent from "@material-ui/core/CardContent"; -import { makeStyles } from '@material-ui/core/styles'; -import SaveIcon from '@material-ui/icons/Save'; -import IconButton from '@material-ui/core/IconButton'; -import Alert from '@material-ui/lab/Alert'; -import Container from '@material-ui/core/Container'; +import Card from "@mui/material/Card"; +import CardActions from "@mui/material/CardActions"; +import CardContent from "@mui/material/CardContent"; +import { makeStyles } from '@mui/styles' +import SaveIcon from '@mui/icons-material/Save'; +import IconButton from '@mui/material/IconButton'; +import Alert from '@mui/lab/Alert'; +import Container from '@mui/material/Container'; import { useParams } from "react-router-dom"; import { FormTextField, FormSelectField, @@ -154,7 +154,7 @@ export default function DatasetDetail() { response.json().then((d) => { d['cell_id'] = d.cell ? d.cell.id : null d['owner_id'] = d.owner ? d.owner.id : null - d['equipment'] = d.equipment.map(x => x.id) + d['equipment'] = d.equipment? d.equipment.map(x => x.id) : [] setDataset(d); }); } diff --git a/frontend/src/Datasets.js b/frontend/src/Datasets.js index 1978d8b8..45797c81 100644 --- a/frontend/src/Datasets.js +++ b/frontend/src/Datasets.js @@ -1,17 +1,17 @@ import React, {useEffect, useState} from "react"; -import { DataGrid, GridRowsProp, GridColDef } from '@material-ui/data-grid'; -import Container from '@material-ui/core/Container'; +import { DataGrid, GridRowsProp, GridColDef } from '@mui/x-data-grid/'; +import Container from '@mui/material/Container'; import { datasets } from './Api'; -import { makeStyles } from '@material-ui/core/styles'; -import Button from '@material-ui/core/Button'; -import { useHistory } from "react-router-dom"; +import { makeStyles } from '@mui/styles' +import Button from '@mui/material/Button'; +import { useNavigate } from "react-router-dom"; import GetDatasetPython from "./GetDatasetPython" import GetDatasetMatlab from "./GetDatasetMatlab" -import Dialog from '@material-ui/core/Dialog'; -import DialogActions from '@material-ui/core/DialogActions'; -import DialogContent from '@material-ui/core/DialogContent'; -import DialogTitle from '@material-ui/core/DialogTitle'; +import Dialog from '@mui/material/Dialog'; +import DialogActions from '@mui/material/DialogActions'; +import DialogContent from '@mui/material/DialogContent'; +import DialogTitle from '@mui/material/DialogTitle'; const useStyles = makeStyles((theme) => ({ @@ -30,7 +30,7 @@ const useStyles = makeStyles((theme) => ({ export default function Datasets() { const [data, setData] = useState(null) const classes = useStyles(); - const history = useHistory(); + const navigate = useNavigate(); const [select, setSelect] = useState(null) @@ -92,7 +92,7 @@ export default function Datasets() { { field: 'name', headerName: 'Name', flex: true}, { field: 'date', headerName: 'Date', width: 110, - valueFormatter: (params: GridValueFormatterParams) => { + valueFormatter: (params: GridValueFormatterParams) => { return Intl.DateTimeFormat('en-GB').format(params.value); } }, @@ -132,7 +132,6 @@ export default function Datasets() { {history.push(`/dataset/${data[select].id}`);}} + onClick={()=>{navigate(`/dataset/${data[select].id}`);}} > Edit Metadata diff --git a/frontend/src/Equipment.js b/frontend/src/Equipment.js index 8d29684c..0f40374c 100644 --- a/frontend/src/Equipment.js +++ b/frontend/src/Equipment.js @@ -1,20 +1,20 @@ import React, { useEffect, useState } from 'react'; -import Typography from '@material-ui/core/Typography'; -import TextField from '@material-ui/core/TextField'; -import { makeStyles } from '@material-ui/core/styles'; -import Table from '@material-ui/core/Table'; -import TableBody from '@material-ui/core/TableBody'; -import Paper from '@material-ui/core/Paper'; -import Tooltip from '@material-ui/core/Tooltip'; -import AddIcon from '@material-ui/icons/Add'; -import IconButton from '@material-ui/core/IconButton'; -import TableCell from '@material-ui/core/TableCell'; -import Container from '@material-ui/core/Container'; -import SaveIcon from '@material-ui/icons/Save'; -import TableContainer from '@material-ui/core/TableContainer'; -import TableHead from '@material-ui/core/TableHead'; -import DeleteIcon from '@material-ui/icons/Delete'; -import TableRow from '@material-ui/core/TableRow'; +import Typography from '@mui/material/Typography'; +import TextField from '@mui/material/TextField'; +import { makeStyles } from '@mui/styles' +import Table from '@mui/material/Table'; +import TableBody from '@mui/material/TableBody'; +import Paper from '@mui/material/Paper'; +import Tooltip from '@mui/material/Tooltip'; +import AddIcon from '@mui/icons-material/Add'; +import IconButton from '@mui/material/IconButton'; +import TableCell from '@mui/material/TableCell'; +import Container from '@mui/material/Container'; +import SaveIcon from '@mui/icons-material/Save'; +import TableContainer from '@mui/material/TableContainer'; +import TableHead from '@mui/material/TableHead'; +import DeleteIcon from '@mui/icons-material/Delete'; +import TableRow from '@mui/material/TableRow'; import { equipment, add_equipment, update_equipment, delete_equipment diff --git a/frontend/src/Files.js b/frontend/src/Files.js index 68367235..ef8fd8c5 100644 --- a/frontend/src/Files.js +++ b/frontend/src/Files.js @@ -1,13 +1,13 @@ import React, { useEffect, useState } from 'react'; -import { makeStyles } from '@material-ui/core/styles'; -import Table from '@material-ui/core/Table'; -import TableBody from '@material-ui/core/TableBody'; -import Container from '@material-ui/core/Container'; -import TableCell from '@material-ui/core/TableCell'; -import TableContainer from '@material-ui/core/TableContainer'; -import TableHead from '@material-ui/core/TableHead'; -import TableRow from '@material-ui/core/TableRow'; -import Paper from '@material-ui/core/Paper'; +import { makeStyles } from '@mui/styles' +import Table from '@mui/material/Table'; +import TableBody from '@mui/material/TableBody'; +import Container from '@mui/material/Container'; +import TableCell from '@mui/material/TableCell'; +import TableContainer from '@mui/material/TableContainer'; +import TableHead from '@mui/material/TableHead'; +import TableRow from '@mui/material/TableRow'; +import Paper from '@mui/material/Paper'; import { files } from './Api' diff --git a/frontend/src/FormComponents.js b/frontend/src/FormComponents.js index b4cd46cc..1cc66f15 100644 --- a/frontend/src/FormComponents.js +++ b/frontend/src/FormComponents.js @@ -1,15 +1,15 @@ import React from "react"; -import TextField from '@material-ui/core/TextField'; -import { makeStyles } from '@material-ui/core/styles'; -import InputLabel from '@material-ui/core/InputLabel'; -import MenuItem from '@material-ui/core/MenuItem'; -import Autocomplete from '@material-ui/lab/Autocomplete'; -import FormControl from '@material-ui/core/FormControl'; -import Select from '@material-ui/core/Select'; +import TextField from '@mui/material/TextField'; +import { makeStyles } from '@mui/styles' +import InputLabel from '@mui/material/InputLabel'; +import MenuItem from '@mui/material/MenuItem'; +import Autocomplete from '@mui/lab/Autocomplete'; +import FormControl from '@mui/material/FormControl'; +import Select from '@mui/material/Select'; import { Controller } from "react-hook-form"; //import DateFnsUtils from '@date-io/date-fns'; // choose your lib -//import { DateTimePicker } from '@material-ui/pickers'; -import Chip from '@material-ui/core/Chip'; +//import { DateTimePicker } from '@mui/pickers'; +import Chip from '@mui/material/Chip'; const useStyles = makeStyles((theme) => ({ container: { diff --git a/frontend/src/GetDatasetMatlab.js b/frontend/src/GetDatasetMatlab.js index e933f5c8..f9be0d4c 100644 --- a/frontend/src/GetDatasetMatlab.js +++ b/frontend/src/GetDatasetMatlab.js @@ -2,7 +2,7 @@ import React, {useEffect, useState} from "react"; import SyntaxHighlighter from 'react-syntax-highlighter'; import { docco } from 'react-syntax-highlighter/dist/esm/styles/hljs'; import {getToken} from "./Api" -import Typography from '@material-ui/core/Typography'; +import Typography from '@mui/material/Typography'; export default function GetDatasetMatlab({dataset}) { diff --git a/frontend/src/GetDatasetPython.js b/frontend/src/GetDatasetPython.js index 79738061..2d1ea40d 100644 --- a/frontend/src/GetDatasetPython.js +++ b/frontend/src/GetDatasetPython.js @@ -2,7 +2,7 @@ import React, {useEffect, useState} from "react"; import SyntaxHighlighter from 'react-syntax-highlighter'; import { docco } from 'react-syntax-highlighter/dist/esm/styles/hljs'; import {getToken} from "./Api" -import Typography from '@material-ui/core/Typography'; +import Typography from '@mui/material/Typography'; export default function GetDatasetPython({dataset}) { diff --git a/frontend/src/HarvesterDetail.js b/frontend/src/HarvesterDetail.js index 670ae70e..d2803ae4 100644 --- a/frontend/src/HarvesterDetail.js +++ b/frontend/src/HarvesterDetail.js @@ -1,24 +1,24 @@ import React, { useEffect, useState, useCallback } from 'react'; -import TextField from '@material-ui/core/TextField'; -import Typography from '@material-ui/core/Typography'; -import Input from '@material-ui/core/Input'; -import InputAdornment from '@material-ui/core/InputAdornment'; -import { makeStyles } from '@material-ui/core/styles'; -import Table from '@material-ui/core/Table'; -import TableBody from '@material-ui/core/TableBody'; -import Paper from '@material-ui/core/Paper'; -import Tooltip from '@material-ui/core/Tooltip'; -import AddIcon from '@material-ui/icons/Add'; -import IconButton from '@material-ui/core/IconButton'; -import TableCell from '@material-ui/core/TableCell'; -import MenuItem from '@material-ui/core/MenuItem'; -import Select from '@material-ui/core/Select'; -import Chip from '@material-ui/core/Chip'; -import SaveIcon from '@material-ui/icons/Save'; -import TableContainer from '@material-ui/core/TableContainer'; -import TableHead from '@material-ui/core/TableHead'; -import DeleteIcon from '@material-ui/icons/Delete'; -import TableRow from '@material-ui/core/TableRow'; +import TextField from '@mui/material/TextField'; +import Typography from '@mui/material/Typography'; +import Input from '@mui/material/Input'; +import InputAdornment from '@mui/material/InputAdornment'; +import { makeStyles } from '@mui/styles' +import Table from '@mui/material/Table'; +import TableBody from '@mui/material/TableBody'; +import Paper from '@mui/material/Paper'; +import Tooltip from '@mui/material/Tooltip'; +import AddIcon from '@mui/icons-material/Add'; +import IconButton from '@mui/material/IconButton'; +import TableCell from '@mui/material/TableCell'; +import MenuItem from '@mui/material/MenuItem'; +import Select from '@mui/material/Select'; +import Chip from '@mui/material/Chip'; +import SaveIcon from '@mui/icons-material/Save'; +import TableContainer from '@mui/material/TableContainer'; +import TableHead from '@mui/material/TableHead'; +import DeleteIcon from '@mui/icons-material/Delete'; +import TableRow from '@mui/material/TableRow'; import Files from './Files' import { diff --git a/frontend/src/Harvesters.js b/frontend/src/Harvesters.js index 76fcdaed..bfa3f1c0 100644 --- a/frontend/src/Harvesters.js +++ b/frontend/src/Harvesters.js @@ -1,21 +1,21 @@ import React, { useEffect, useState } from 'react'; -import TextField from '@material-ui/core/TextField'; -import { makeStyles } from '@material-ui/core/styles'; -import Table from '@material-ui/core/Table'; -import TableBody from '@material-ui/core/TableBody'; -import Paper from '@material-ui/core/Paper'; -import Typography from '@material-ui/core/Typography'; -import PlayArrowIcon from '@material-ui/icons/PlayArrow'; -import Tooltip from '@material-ui/core/Tooltip'; -import AddIcon from '@material-ui/icons/Add'; -import IconButton from '@material-ui/core/IconButton'; -import TableCell from '@material-ui/core/TableCell'; -import Container from '@material-ui/core/Container'; -import SaveIcon from '@material-ui/icons/Save'; -import TableContainer from '@material-ui/core/TableContainer'; -import TableHead from '@material-ui/core/TableHead'; -import DeleteIcon from '@material-ui/icons/Delete'; -import TableRow from '@material-ui/core/TableRow'; +import TextField from '@mui/material/TextField'; +import { makeStyles } from '@mui/styles' +import Table from '@mui/material/Table'; +import TableBody from '@mui/material/TableBody'; +import Paper from '@mui/material/Paper'; +import Typography from '@mui/material/Typography'; +import PlayArrowIcon from '@mui/icons-material/PlayArrow'; +import Tooltip from '@mui/material/Tooltip'; +import AddIcon from '@mui/icons-material/Add'; +import IconButton from '@mui/material/IconButton'; +import TableCell from '@mui/material/TableCell'; +import Container from '@mui/material/Container'; +import SaveIcon from '@mui/icons-material/Save'; +import TableContainer from '@mui/material/TableContainer'; +import TableHead from '@mui/material/TableHead'; +import DeleteIcon from '@mui/icons-material/Delete'; +import TableRow from '@mui/material/TableRow'; import HarvesterDetail from './HarvesterDetail'; import { diff --git a/frontend/src/Login.js b/frontend/src/Login.js index 6f1d344a..a8379dfc 100644 --- a/frontend/src/Login.js +++ b/frontend/src/Login.js @@ -1,13 +1,13 @@ import {login} from "./Api" -import { makeStyles } from '@material-ui/core/styles'; +import { makeStyles } from '@mui/styles' import React, { useState } from "react"; -import Button from '@material-ui/core/Button'; -import CssBaseline from '@material-ui/core/CssBaseline'; -import Alert from '@material-ui/lab/Alert'; -import TextField from '@material-ui/core/TextField'; -import Typography from '@material-ui/core/Typography'; -import Container from '@material-ui/core/Container'; -import { useHistory } from "react-router-dom"; +import Button from '@mui/material/Button'; +import CssBaseline from '@mui/material/CssBaseline'; +import Alert from '@mui/lab/Alert'; +import TextField from '@mui/material/TextField'; +import Typography from '@mui/material/Typography'; +import Container from '@mui/material/Container'; +import { useNavigate } from "react-router-dom"; import { ReactComponent as GalvanalyserIcon} from './Galvanalyser-icon.svg'; const useStyles = makeStyles((theme) => ({ @@ -38,7 +38,7 @@ export default function Login({ onLogin }) { const [password, setPassword] = useState('') const [error, setError] = useState('') - const history = useHistory(); + const navigate =useNavigate(); const onSubmitClick = (e)=>{ e.preventDefault() @@ -51,7 +51,7 @@ export default function Login({ onLogin }) { return r.json().then(data => { setError('') onLogin() - history.push('/'); + navigate('/'); }) }); } diff --git a/frontend/src/index.js b/frontend/src/index.js index 5c92e68d..3b72e314 100644 --- a/frontend/src/index.js +++ b/frontend/src/index.js @@ -1,17 +1,18 @@ import React from 'react'; -import ReactDOM from 'react-dom'; +import { createRoot } from 'react-dom/client'; import './index.css'; import App from './App'; import reportWebVitals from './reportWebVitals'; import { BrowserRouter as Router } from 'react-router-dom' -ReactDOM.render( +const root = createRoot(document.getElementById('root')) + +root.render( - , - document.getElementById('root') + ); // If you want to start measuring performance in your app, pass a function diff --git a/frontend/yarn.lock b/frontend/yarn.lock index ead7779b..ad5042cc 100644 --- a/frontend/yarn.lock +++ b/frontend/yarn.lock @@ -1033,7 +1033,7 @@ core-js-pure "^3.25.1" regenerator-runtime "^0.13.10" -"@babel/runtime@^7.10.2", "@babel/runtime@^7.11.2", "@babel/runtime@^7.12.5", "@babel/runtime@^7.16.3", "@babel/runtime@^7.18.3", "@babel/runtime@^7.18.9", "@babel/runtime@^7.20.1", "@babel/runtime@^7.3.1", "@babel/runtime@^7.5.5", "@babel/runtime@^7.7.6", "@babel/runtime@^7.8.4", "@babel/runtime@^7.8.7", "@babel/runtime@^7.9.2": +"@babel/runtime@^7.10.2", "@babel/runtime@^7.11.2", "@babel/runtime@^7.12.5", "@babel/runtime@^7.16.3", "@babel/runtime@^7.18.3", "@babel/runtime@^7.18.9", "@babel/runtime@^7.20.1", "@babel/runtime@^7.3.1", "@babel/runtime@^7.5.5", "@babel/runtime@^7.7.6", "@babel/runtime@^7.8.3", "@babel/runtime@^7.8.4", "@babel/runtime@^7.8.7", "@babel/runtime@^7.9.2": version "7.20.1" resolved "https://registry.yarnpkg.com/@babel/runtime/-/runtime-7.20.1.tgz#1148bb33ab252b165a06698fde7576092a78b4a9" integrity sha512-mrzLkl6U9YLF8qpqI7TB82PESyEGjm/0Ly91jG575eVxMMlb8fYfOXFZIJ8XfLrJZQbm7dlKry2bJmXBUEkdFg== @@ -1667,6 +1667,27 @@ resolved "https://registry.yarnpkg.com/@mui/core-downloads-tracker/-/core-downloads-tracker-5.10.15.tgz#490f3dea5327c892f063496a0219c48301da0fa0" integrity sha512-xFcS0LpdF0Q1qJrrNsYUv9PU+ovvhCEPTOMw2jcpEFtl3CA87dLpvztORR5oE2UBFjWF7qLQLOwboQU1+xC7Cw== +"@mui/icons-material@^5.10.15": + version "5.10.15" + resolved "https://registry.yarnpkg.com/@mui/icons-material/-/icons-material-5.10.15.tgz#c93f1ba8d2b55fe0a16f559a568304df172cbbcb" + integrity sha512-fXkz7CtYTt4AH4YYT67VFhM/A3YCUqZGGLp/3BlzRPQRNEfFKknw3MgG1S5UYrY5weti8jxMx3mwwfhVP8OMhQ== + dependencies: + "@babel/runtime" "^7.20.1" + +"@mui/lab@^5.0.0-alpha.109": + version "5.0.0-alpha.109" + resolved "https://registry.yarnpkg.com/@mui/lab/-/lab-5.0.0-alpha.109.tgz#e0004174be4c3bcefcdbe674955e201d24ce96e0" + integrity sha512-9ZyzM4AHA1qWh48ZcvqxqwWRH1CzBhQuP9VYP2eEprEjEeraiuvvsZILCNhCemc9WWN04GJh8UiD1FeCaU4kWg== + dependencies: + "@babel/runtime" "^7.20.1" + "@mui/base" "5.0.0-alpha.107" + "@mui/system" "^5.10.15" + "@mui/types" "^7.2.1" + "@mui/utils" "^5.10.15" + clsx "^1.2.1" + prop-types "^15.8.1" + react-is "^18.2.0" + "@mui/material@^5.10.15": version "5.10.15" resolved "https://registry.yarnpkg.com/@mui/material/-/material-5.10.15.tgz#37345f5a3d71c662703af7b5be0cca229b2a1416" @@ -1704,6 +1725,29 @@ csstype "^3.1.1" prop-types "^15.8.1" +"@mui/styles@^5.10.15": + version "5.10.15" + resolved "https://registry.yarnpkg.com/@mui/styles/-/styles-5.10.15.tgz#d7af4c17e8699e6b768f3c11b69c02cdc8cc3541" + integrity sha512-q8OW8Cyq2C9wGJMcDWXYtFa7qgIIZPAZ15JShDQXBLvyib4qDop5wV3+olQoJdwU5ARjmfPd67IsbORWxG3abQ== + dependencies: + "@babel/runtime" "^7.20.1" + "@emotion/hash" "^0.9.0" + "@mui/private-theming" "^5.10.15" + "@mui/types" "^7.2.1" + "@mui/utils" "^5.10.15" + clsx "^1.2.1" + csstype "^3.1.1" + hoist-non-react-statics "^3.3.2" + jss "^10.9.2" + jss-plugin-camel-case "^10.9.2" + jss-plugin-default-unit "^10.9.2" + jss-plugin-global "^10.9.2" + jss-plugin-nested "^10.9.2" + jss-plugin-props-sort "^10.9.2" + jss-plugin-rule-value-function "^10.9.2" + jss-plugin-vendor-prefixer "^10.9.2" + prop-types "^15.8.1" + "@mui/system@^5.10.15": version "5.10.15" resolved "https://registry.yarnpkg.com/@mui/system/-/system-5.10.15.tgz#4bb58d1d1a531137559b775038a18d6050d9ee57" @@ -1723,7 +1767,7 @@ resolved "https://registry.yarnpkg.com/@mui/types/-/types-7.2.1.tgz#1eb2bc182c595029884047f2525ad4dbefea318e" integrity sha512-c5mSM7ivD8EsqK6HUi9hQPr5V7TJ/IRThUQ9nWNYPdhCGriTSQV4vL6DflT99LkM+wLiIS1rVjphpEWxERep7A== -"@mui/utils@^5.10.15": +"@mui/utils@^5.10.15", "@mui/utils@^5.10.3": version "5.10.15" resolved "https://registry.yarnpkg.com/@mui/utils/-/utils-5.10.15.tgz#54fc1b373508d20dd5568070b2dcc0818e6bebba" integrity sha512-6AW4MLBUijJi31hxx+6utTJM2q/4hbO+QiMdtwM+f4Iy+BfFnh/elhb08apxNYLfuugPnXXpkDmzEjg+8uDU9g== @@ -1734,6 +1778,17 @@ prop-types "^15.8.1" react-is "^18.2.0" +"@mui/x-data-grid@^5.17.12": + version "5.17.12" + resolved "https://registry.yarnpkg.com/@mui/x-data-grid/-/x-data-grid-5.17.12.tgz#b57c32605f1964c2eb8b25136fe51d7165e22112" + integrity sha512-Q7lFxapa9oc8j3LVm3JAS+jmJftcaSLYcvhApYLKYWej9LKMQYov8hUPdIjzSta3E0WTINfiHaTcO1b6W4UMvQ== + dependencies: + "@babel/runtime" "^7.18.9" + "@mui/utils" "^5.10.3" + clsx "^1.2.1" + prop-types "^15.8.1" + reselect "^4.1.6" + "@nicolo-ribaudo/eslint-scope-5-internals@5.1.1-v1": version "5.1.1-v1" resolved "https://registry.yarnpkg.com/@nicolo-ribaudo/eslint-scope-5-internals/-/eslint-scope-5-internals-5.1.1-v1.tgz#dbf733a965ca47b1973177dc0bb6c889edcfb129" @@ -3959,6 +4014,14 @@ css-tree@^1.1.2, css-tree@^1.1.3: mdn-data "2.0.14" source-map "^0.6.1" +css-vendor@^2.0.8: + version "2.0.8" + resolved "https://registry.yarnpkg.com/css-vendor/-/css-vendor-2.0.8.tgz#e47f91d3bd3117d49180a3c935e62e3d9f7f449d" + integrity sha512-x9Aq0XTInxrkuFeHKbYC7zWY8ai7qJ04Kxd9MnvbC1uO5DagxoHQjm4JvG+vCdXOoFtCjbL2XSZfxmoYa9uQVQ== + dependencies: + "@babel/runtime" "^7.8.3" + is-in-browser "^1.0.2" + css-what@^3.2.1: version "3.4.2" resolved "https://registry.yarnpkg.com/css-what/-/css-what-3.4.2.tgz#ea7026fcb01777edbde52124e21f327e7ae950e4" @@ -5597,7 +5660,7 @@ highlight.js@^10.4.1, highlight.js@~10.7.0: resolved "https://registry.yarnpkg.com/highlight.js/-/highlight.js-10.7.3.tgz#697272e3991356e40c3cac566a74eef681756531" integrity sha512-tzcUFauisWKNHaRkN4Wjl/ZA07gENAjFl3J/c480dprkGTg5EQstgaNFqBfUqCq54kZRIEcreTsAgF/m2quD7A== -hoist-non-react-statics@^3.3.1: +hoist-non-react-statics@^3.3.1, hoist-non-react-statics@^3.3.2: version "3.3.2" resolved "https://registry.yarnpkg.com/hoist-non-react-statics/-/hoist-non-react-statics-3.3.2.tgz#ece0acaf71d62c2969c2ec59feff42a4b1a85b45" integrity sha512-/gGivxi8JPKWNm/W0jSmzcMPpfpPLc3dY/6GxhX2hQ9iGj3aDfklV4ET7NjKpSinLpJ5vafa9iiGIEZg10SfBw== @@ -5976,7 +6039,7 @@ is-hexadecimal@^1.0.0: resolved "https://registry.yarnpkg.com/is-hexadecimal/-/is-hexadecimal-1.0.4.tgz#cc35c97588da4bd49a8eedd6bc4082d44dcb23a7" integrity sha512-gyPJuv83bHMpocVYoqof5VDiZveEoGoFL8m3BXNb2VW8Xs+rz9kqO8LOQ5DH6EsuvilT1ApazU0pyl+ytbPtlw== -is-in-browser@^1.1.3: +is-in-browser@^1.0.2, is-in-browser@^1.1.3: version "1.1.3" resolved "https://registry.yarnpkg.com/is-in-browser/-/is-in-browser-1.1.3.tgz#56ff4db683a078c6082eb95dad7dc62e1d04f835" integrity sha512-FeXIBgG/CPGd/WUxuEyvgGTEfwiG9Z4EKGxjNMRqviiIIfsmgrpnHLffEDdwUHqNva1VEW91o3xBT/m8Elgl9g== @@ -6886,7 +6949,7 @@ jsonpointer@^5.0.0: resolved "https://registry.yarnpkg.com/jsonpointer/-/jsonpointer-5.0.1.tgz#2110e0af0900fd37467b5907ecd13a7884a1b559" integrity sha512-p/nXbhSEcu3pZRdkW1OfJhpsVtW1gd4Wa1fnQc9YLiTfAjn0312eMKimbdIQzuZl9aa9xUGaRlP9T/CJE/ditQ== -jss-plugin-camel-case@^10.9.0: +jss-plugin-camel-case@^10.9.0, jss-plugin-camel-case@^10.9.2: version "10.9.2" resolved "https://registry.yarnpkg.com/jss-plugin-camel-case/-/jss-plugin-camel-case-10.9.2.tgz#76dddfa32f9e62d17daa4e3504991fd0933b89e1" integrity sha512-wgBPlL3WS0WDJ1lPJcgjux/SHnDuu7opmgQKSraKs4z8dCCyYMx9IDPFKBXQ8Q5dVYij1FFV0WdxyhuOOAXuTg== @@ -6904,7 +6967,7 @@ jss-plugin-compose@^10.9.0: jss "10.9.2" tiny-warning "^1.0.2" -jss-plugin-default-unit@^10.9.0: +jss-plugin-default-unit@^10.9.0, jss-plugin-default-unit@^10.9.2: version "10.9.2" resolved "https://registry.yarnpkg.com/jss-plugin-default-unit/-/jss-plugin-default-unit-10.9.2.tgz#3e7f4a1506b18d8fe231554fd982439feb2a9c53" integrity sha512-pYg0QX3bBEFtTnmeSI3l7ad1vtHU42YEEpgW7pmIh+9pkWNWb5dwS/4onSfAaI0kq+dOZHzz4dWe+8vWnanoSg== @@ -6912,7 +6975,7 @@ jss-plugin-default-unit@^10.9.0: "@babel/runtime" "^7.3.1" jss "10.9.2" -jss-plugin-global@^10.9.0: +jss-plugin-global@^10.9.0, jss-plugin-global@^10.9.2: version "10.9.2" resolved "https://registry.yarnpkg.com/jss-plugin-global/-/jss-plugin-global-10.9.2.tgz#e7f2ad4a5e8e674fb703b04b57a570b8c3e5c2c2" integrity sha512-GcX0aE8Ef6AtlasVrafg1DItlL/tWHoC4cGir4r3gegbWwF5ZOBYhx04gurPvWHC8F873aEGqge7C17xpwmp2g== @@ -6929,7 +6992,7 @@ jss-plugin-isolate@^10.9.0: css-initials "^0.3.1" jss "10.9.2" -jss-plugin-nested@^10.9.0: +jss-plugin-nested@^10.9.0, jss-plugin-nested@^10.9.2: version "10.9.2" resolved "https://registry.yarnpkg.com/jss-plugin-nested/-/jss-plugin-nested-10.9.2.tgz#3aa2502816089ecf3981e1a07c49b276d67dca63" integrity sha512-VgiOWIC6bvgDaAL97XCxGD0BxOKM0K0zeB/ECyNaVF6FqvdGB9KBBWRdy2STYAss4VVA7i5TbxFZN+WSX1kfQA== @@ -6938,7 +7001,33 @@ jss-plugin-nested@^10.9.0: jss "10.9.2" tiny-warning "^1.0.2" -jss@10.9.2, jss@^10.9.0: +jss-plugin-props-sort@^10.9.2: + version "10.9.2" + resolved "https://registry.yarnpkg.com/jss-plugin-props-sort/-/jss-plugin-props-sort-10.9.2.tgz#645f6c8f179309667b3e6212f66b59a32fb3f01f" + integrity sha512-AP1AyUTbi2szylgr+O0OB7gkIxEGzySLITZ2GpsaoX72YMCGI2jYAc+WUhPfvUnZYiauF4zTnN4V4TGuvFjJlw== + dependencies: + "@babel/runtime" "^7.3.1" + jss "10.9.2" + +jss-plugin-rule-value-function@^10.9.2: + version "10.9.2" + resolved "https://registry.yarnpkg.com/jss-plugin-rule-value-function/-/jss-plugin-rule-value-function-10.9.2.tgz#9afe07596e477123cbf11120776be6a64494541f" + integrity sha512-vf5ms8zvLFMub6swbNxvzsurHfUZ5Shy5aJB2gIpY6WNA3uLinEcxYyraQXItRHi5ivXGqYciFDRM2ZoVoRZ4Q== + dependencies: + "@babel/runtime" "^7.3.1" + jss "10.9.2" + tiny-warning "^1.0.2" + +jss-plugin-vendor-prefixer@^10.9.2: + version "10.9.2" + resolved "https://registry.yarnpkg.com/jss-plugin-vendor-prefixer/-/jss-plugin-vendor-prefixer-10.9.2.tgz#410a0f3b9f8dbbfba58f4d329134df4849aa1237" + integrity sha512-SxcEoH+Rttf9fEv6KkiPzLdXRmI6waOTcMkbbEFgdZLDYNIP9UKNHFy6thhbRKqv0XMQZdrEsbDyV464zE/dUA== + dependencies: + "@babel/runtime" "^7.3.1" + css-vendor "^2.0.8" + jss "10.9.2" + +jss@10.9.2, jss@^10.9.0, jss@^10.9.2: version "10.9.2" resolved "https://registry.yarnpkg.com/jss/-/jss-10.9.2.tgz#9379be1f195ef98011dfd31f9448251bd61b95a9" integrity sha512-b8G6rWpYLR4teTUbGd4I4EsnWjg7MN0Q5bSsjKhVkJVjhQDy2KzkbD2AW3TuT0RYZVmZZHKIrXDn6kjU14qkUg== @@ -9108,6 +9197,11 @@ requires-port@^1.0.0: resolved "https://registry.yarnpkg.com/requires-port/-/requires-port-1.0.0.tgz#925d2601d39ac485e091cf0da5c6e694dc3dcaff" integrity sha512-KigOCHcocU3XODJxsu8i/j8T9tzT4adHiecwORRQ0ZZFcp7ahwXuRU1m+yuO90C5ZUyGeGfocHDI14M3L3yDAQ== +reselect@^4.1.6: + version "4.1.7" + resolved "https://registry.yarnpkg.com/reselect/-/reselect-4.1.7.tgz#56480d9ff3d3188970ee2b76527bd94a95567a42" + integrity sha512-Zu1xbUt3/OPwsXL46hvOOoQrap2azE7ZQbokq61BQfiXvhewsKDwhMeZjTX9sX0nvw1t/U5Audyn1I9P/m9z0A== + resolve-cwd@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/resolve-cwd/-/resolve-cwd-3.0.0.tgz#0f0075f1bb2544766cf73ba6a6e2adfebcb13f2d" From 9bc5400e0d82aca1e7811959ecee48a8a36d48d9 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Thu, 1 Dec 2022 17:18:51 +0000 Subject: [PATCH 03/79] add django project --- backend/test/test_biologic.py | 1 - django/Dockerfile | 17 ++ django/backend_django/__init__.py | 1 + django/backend_django/asgi.py | 16 ++ .../backend_django/backend_django/__init__.py | 0 django/backend_django/backend_django/asgi.py | 16 ++ .../backend_django/backend_django/settings.py | 123 ++++++++++++++ django/backend_django/backend_django/urls.py | 21 +++ django/backend_django/backend_django/wsgi.py | 16 ++ .../backend_django/galvanalyser/__init__.py | 0 django/backend_django/galvanalyser/admin.py | 3 + django/backend_django/galvanalyser/apps.py | 6 + .../galvanalyser/migrations/__init__.py | 0 django/backend_django/galvanalyser/models.py | 153 ++++++++++++++++++ django/backend_django/galvanalyser/tests.py | 3 + django/backend_django/galvanalyser/views.py | 3 + django/backend_django/manage.py | 22 +++ django/backend_django/settings.py | 123 ++++++++++++++ django/backend_django/urls.py | 21 +++ django/backend_django/wsgi.py | 16 ++ django/db.sqlite3 | Bin 0 -> 131072 bytes django/manage.py | 22 +++ django/requirements.txt | 3 + django/server.sh | 31 ++++ django/worker.sh | 11 ++ docker-compose.override.yml | 36 +++++ docker-compose.yml | 2 +- frontend/.env | 1 + frontend/src/Datasets.js | 16 +- 29 files changed, 673 insertions(+), 10 deletions(-) create mode 100644 django/Dockerfile create mode 100644 django/backend_django/__init__.py create mode 100644 django/backend_django/asgi.py create mode 100644 django/backend_django/backend_django/__init__.py create mode 100644 django/backend_django/backend_django/asgi.py create mode 100644 django/backend_django/backend_django/settings.py create mode 100644 django/backend_django/backend_django/urls.py create mode 100644 django/backend_django/backend_django/wsgi.py create mode 100644 django/backend_django/galvanalyser/__init__.py create mode 100644 django/backend_django/galvanalyser/admin.py create mode 100644 django/backend_django/galvanalyser/apps.py create mode 100644 django/backend_django/galvanalyser/migrations/__init__.py create mode 100644 django/backend_django/galvanalyser/models.py create mode 100644 django/backend_django/galvanalyser/tests.py create mode 100644 django/backend_django/galvanalyser/views.py create mode 100644 django/backend_django/manage.py create mode 100644 django/backend_django/settings.py create mode 100644 django/backend_django/urls.py create mode 100644 django/backend_django/wsgi.py create mode 100644 django/db.sqlite3 create mode 100644 django/manage.py create mode 100644 django/requirements.txt create mode 100644 django/server.sh create mode 100644 django/worker.sh create mode 100644 frontend/.env diff --git a/backend/test/test_biologic.py b/backend/test/test_biologic.py index c3ab570b..0fcffbe3 100644 --- a/backend/test/test_biologic.py +++ b/backend/test/test_biologic.py @@ -22,4 +22,3 @@ def test_read_mpr_files(self): ) num_samples = sum(1 for d in data_generator) self.assertEqual(num_samples, metadata['num_rows']) - diff --git a/django/Dockerfile b/django/Dockerfile new file mode 100644 index 00000000..1f26bf56 --- /dev/null +++ b/django/Dockerfile @@ -0,0 +1,17 @@ +FROM python:3.10.4-slim@sha256:a2e8240faa44748fe18c5b37f83e14101a38dd3f4a1425d18e9e0e913f89b562 + +ENV PYTHONDONTWRITEBYTECODE=1 +ENV PYTHONUNBUFFERED=1 + +# Install postgresql-client for healthchecking +RUN apt-get update && \ + apt-get install -y \ + postgresql-client && \ + apt-get autoremove && \ + apt-get autoclean + +RUN mkdir -p /usr/app +WORKDIR /usr/app +COPY requirements.txt /requirements.txt +RUN pip install -r /requirements.txt +COPY . /usr/app diff --git a/django/backend_django/__init__.py b/django/backend_django/__init__.py new file mode 100644 index 00000000..38ab64fd --- /dev/null +++ b/django/backend_django/__init__.py @@ -0,0 +1 @@ +import celery \ No newline at end of file diff --git a/django/backend_django/asgi.py b/django/backend_django/asgi.py new file mode 100644 index 00000000..9df576b4 --- /dev/null +++ b/django/backend_django/asgi.py @@ -0,0 +1,16 @@ +""" +ASGI config for backend_django project. + +It exposes the ASGI callable as a module-level variable named ``application``. + +For more information on this file, see +https://docs.djangoproject.com/en/4.1/howto/deployment/asgi/ +""" + +import os + +from django.core.asgi import get_asgi_application + +os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') + +application = get_asgi_application() diff --git a/django/backend_django/backend_django/__init__.py b/django/backend_django/backend_django/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/django/backend_django/backend_django/asgi.py b/django/backend_django/backend_django/asgi.py new file mode 100644 index 00000000..9df576b4 --- /dev/null +++ b/django/backend_django/backend_django/asgi.py @@ -0,0 +1,16 @@ +""" +ASGI config for backend_django project. + +It exposes the ASGI callable as a module-level variable named ``application``. + +For more information on this file, see +https://docs.djangoproject.com/en/4.1/howto/deployment/asgi/ +""" + +import os + +from django.core.asgi import get_asgi_application + +os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') + +application = get_asgi_application() diff --git a/django/backend_django/backend_django/settings.py b/django/backend_django/backend_django/settings.py new file mode 100644 index 00000000..6f323836 --- /dev/null +++ b/django/backend_django/backend_django/settings.py @@ -0,0 +1,123 @@ +""" +Django settings for backend_django project. + +Generated by 'django-admin startproject' using Django 4.1.3. + +For more information on this file, see +https://docs.djangoproject.com/en/4.1/topics/settings/ + +For the full list of settings and their values, see +https://docs.djangoproject.com/en/4.1/ref/settings/ +""" + +from pathlib import Path + +# Build paths inside the project like this: BASE_DIR / 'subdir'. +BASE_DIR = Path(__file__).resolve().parent.parent + + +# Quick-start development settings - unsuitable for production +# See https://docs.djangoproject.com/en/4.1/howto/deployment/checklist/ + +# SECURITY WARNING: keep the secret key used in production secret! +SECRET_KEY = 'django-insecure-@+e142%m^c6ka7g&8avn(!^@b4##!7f++fbfsq^10^$0oul)a@' + +# SECURITY WARNING: don't run with debug turned on in production! +DEBUG = True + +ALLOWED_HOSTS = [] + + +# Application definition + +INSTALLED_APPS = [ + 'django.contrib.admin', + 'django.contrib.auth', + 'django.contrib.contenttypes', + 'django.contrib.sessions', + 'django.contrib.messages', + 'django.contrib.staticfiles', +] + +MIDDLEWARE = [ + 'django.middleware.security.SecurityMiddleware', + 'django.contrib.sessions.middleware.SessionMiddleware', + 'django.middleware.common.CommonMiddleware', + 'django.middleware.csrf.CsrfViewMiddleware', + 'django.contrib.auth.middleware.AuthenticationMiddleware', + 'django.contrib.messages.middleware.MessageMiddleware', + 'django.middleware.clickjacking.XFrameOptionsMiddleware', +] + +ROOT_URLCONF = 'backend_django.urls' + +TEMPLATES = [ + { + 'BACKEND': 'django.template.backends.django.DjangoTemplates', + 'DIRS': [], + 'APP_DIRS': True, + 'OPTIONS': { + 'context_processors': [ + 'django.template.context_processors.debug', + 'django.template.context_processors.request', + 'django.contrib.auth.context_processors.auth', + 'django.contrib.messages.context_processors.messages', + ], + }, + }, +] + +WSGI_APPLICATION = 'backend_django.wsgi.application' + + +# Database +# https://docs.djangoproject.com/en/4.1/ref/settings/#databases + +DATABASES = { + 'default': { + 'ENGINE': 'django.db.backends.sqlite3', + 'NAME': BASE_DIR / 'db.sqlite3', + } +} + + +# Password validation +# https://docs.djangoproject.com/en/4.1/ref/settings/#auth-password-validators + +AUTH_PASSWORD_VALIDATORS = [ + { + 'NAME': 'django.contrib.auth.password_validation.UserAttributeSimilarityValidator', + }, + { + 'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator', + }, + { + 'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator', + }, + { + 'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator', + }, +] + + +# Internationalization +# https://docs.djangoproject.com/en/4.1/topics/i18n/ + +LANGUAGE_CODE = 'en-us' + +TIME_ZONE = 'UTC' + +USE_I18N = True + +USE_TZ = True + + +# Static files (CSS, JavaScript, Images) +# https://docs.djangoproject.com/en/4.1/howto/static-files/ + +STATIC_URL = 'static/' + +# Default primary key field type +# https://docs.djangoproject.com/en/4.1/ref/settings/#default-auto-field + +DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField' diff --git a/django/backend_django/backend_django/urls.py b/django/backend_django/backend_django/urls.py new file mode 100644 index 00000000..5fefc865 --- /dev/null +++ b/django/backend_django/backend_django/urls.py @@ -0,0 +1,21 @@ +"""backend_django URL Configuration + +The `urlpatterns` list routes URLs to views. For more information please see: + https://docs.djangoproject.com/en/4.1/topics/http/urls/ +Examples: +Function views + 1. Add an import: from my_app import views + 2. Add a URL to urlpatterns: path('', views.home, name='home') +Class-based views + 1. Add an import: from other_app.views import Home + 2. Add a URL to urlpatterns: path('', Home.as_view(), name='home') +Including another URLconf + 1. Import the include() function: from django.urls import include, path + 2. Add a URL to urlpatterns: path('blog/', include('blog.urls')) +""" +from django.contrib import admin +from django.urls import path + +urlpatterns = [ + path('admin/', admin.site.urls), +] diff --git a/django/backend_django/backend_django/wsgi.py b/django/backend_django/backend_django/wsgi.py new file mode 100644 index 00000000..984d982b --- /dev/null +++ b/django/backend_django/backend_django/wsgi.py @@ -0,0 +1,16 @@ +""" +WSGI config for backend_django project. + +It exposes the WSGI callable as a module-level variable named ``application``. + +For more information on this file, see +https://docs.djangoproject.com/en/4.1/howto/deployment/wsgi/ +""" + +import os + +from django.core.wsgi import get_wsgi_application + +os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') + +application = get_wsgi_application() diff --git a/django/backend_django/galvanalyser/__init__.py b/django/backend_django/galvanalyser/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/django/backend_django/galvanalyser/admin.py b/django/backend_django/galvanalyser/admin.py new file mode 100644 index 00000000..8c38f3f3 --- /dev/null +++ b/django/backend_django/galvanalyser/admin.py @@ -0,0 +1,3 @@ +from django.contrib import admin + +# Register your models here. diff --git a/django/backend_django/galvanalyser/apps.py b/django/backend_django/galvanalyser/apps.py new file mode 100644 index 00000000..bbf26faf --- /dev/null +++ b/django/backend_django/galvanalyser/apps.py @@ -0,0 +1,6 @@ +from django.apps import AppConfig + + +class GalvanalyserConfig(AppConfig): + default_auto_field = 'django.db.models.BigAutoField' + name = 'galvanalyser' diff --git a/django/backend_django/galvanalyser/migrations/__init__.py b/django/backend_django/galvanalyser/migrations/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py new file mode 100644 index 00000000..e375792f --- /dev/null +++ b/django/backend_django/galvanalyser/models.py @@ -0,0 +1,153 @@ +from django.db import models +from django.core.validators import MaxValueValidator, MinValueValidator +from django.contrib.auth.models import User, Group + + +class FileState(models.IntegerChoices): + IMPORT_FAILED = -1 + UNSTABLE = 0 + GROWING = 1 + STABLE = 2 + IMPORTING = 3 + IMPORTED = 4 + + +class Machine(models.Model): + pass + + +class Harvester(models.Model): + machine_id = models.ForeignKey(to=Machine, on_delete=models.CASCADE, unique=True) + name = models.TextField() + last_successful_run = models.DateTimeField() + is_running = models.BooleanField(default=False) + periodic_hour = models.IntegerField(validators=[ + MinValueValidator(1), MaxValueValidator(24) + ]) + + +class MonitoredPath(models.Model): + harvester = models.ForeignKey(to=Harvester, on_delete=models.CASCADE, unique=True) + path = models.TextField(unique=True) + + +class MonitoredFor(models.Model): + path = models.ForeignKey(to=MonitoredPath, on_delete=models.CASCADE) + user_id = models.ForeignKey(to=User, on_delete=models.CASCADE) + + +class ObservedFile(models.Model): + monitored_path = models.ForeignKey(to=MonitoredPath, on_delete=models.DO_NOTHING) + relative_path = models.TextField() + last_observed_size = models.PositiveBigIntegerField(null=False) + last_observed_time = models.DateTimeField() + file_state = models.SmallIntegerField(choices=FileState.choices, default=FileState.UNSTABLE, null=False) + + class Meta: + unique_together = [['monitored_path', 'relative_path']] + + +class CellData(models.Model): + name = models.TextField(null=False, unique=True) + form_factor = models.TextField() + link_to_datasheet = models.TextField() + anode_chemistry = models.TextField() + cathode_chemistry = models.TextField() + nominal_capacity = models.FloatField() + nominal_cell_weight = models.FloatField() + manufacturer = models.TextField() + + +class Dataset(models.Model): + cell_id = models.ForeignKey(to=CellData, on_delete=models.SET_NULL) + owner_id = models.ForeignKey(to=User, on_delete=models.SET_NULL) + access_group = models.ForeignKey(to=Group, on_delete=models.CASCADE) + name = models.TextField(null=False) + date = models.DateTimeField(null=False) + type = models.TextField(null=False) + purpose = models.TextField() + json_data = models.JSONField() + + class Meta: + unique_together = [['name', 'date']] + + +class Equipment(models.Model): + name = models.TextField(null=False, unique=True) + type = models.TextField() + + +class DatasetEquipment(models.Model): + dataset = models.ForeignKey(to=Dataset, on_delete=models.CASCADE) + equipment = models.ForeignKey(to=Equipment, on_delete=models.CASCADE) + + class Meta: + unique_together = [['dataset', 'equipment']] + + +class DataUnit(models.Model): + name = models.TextField(null=False) + symbol = models.TextField(null=False) + description = models.TextField() + + +class DataColumType(models.Model): + unit = models.ForeignKey(to=DataUnit, on_delete=models.SET_NULL) + name = models.TextField(null=False) + description = models.TextField() + + +class DataColumn(models.Model): + dataset = models.ForeignKey(to=Dataset, on_delete=models.CASCADE) + type = models.ForeignKey(to=DataColumType, on_delete=models.RESTRICT) + name = models.TextField(null=False) + + class Meta: + unique_together = [['dataset', 'name']] + + +class TimeseriesData(models.Model): + sample = models.PositiveBigIntegerField(null=False) + column = models.ForeignKey(to=DataColumn, null=False, on_delete=models.RESTRICT) + value = models.FloatField(null=False) + + class Meta: + unique_together = [['sample', 'column']] + + +class TimeseriesRangeLabel(models.Model): + dataset = models.ForeignKey(to=Dataset, null=False, on_delete=models.CASCADE) + label = models.TextField(null=False) + range_start = models.PositiveBigIntegerField(null=False) + range_end = models.PositiveBigIntegerField(null=False) + info = models.TextField() + + +# -- Add required column +# +# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (0, 'Unitless', '', 'A value with no units'); +# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (1, 'Time', 's', 'Time in seconds'); +# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (2, 'Volts', 'V', 'Voltage'); +# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (3, 'Amps', 'A', 'Current'); +# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (4, 'Energy', 'Wh', 'Energy in Watt-Hours'); +# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (5, 'Charge', 'Ah', 'Charge in Amp-Hours'); +# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (6, 'Temperature', '°c', 'Temperature in Centigrade'); +# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (7, 'Power', 'W', 'Power in Watts'); +# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (8, 'Ohm', 'Ω', 'Resistance or impediance in Ohms'); +# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (9, 'Degrees', '°', 'Angle in degrees'); +# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (10, 'Frequency', 'Hz', 'Frequency in Hz'); +# SELECT setval('experiment.unit_id_seq'::regclass, 10); +# +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (-1, 'Unknown', 'unknown column type', NULL); +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (0, 'Sample Number', 'The sample or record number. Is increased by one each time a test machine records a reading. Usually counts from 1 at the start of a test', 0); +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (1, 'Time', 'The time in seconds since the test run began.', 1); +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (2, 'Volts', 'The voltage of the cell.', 2); +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (3, 'Amps', 'The current current.', 3); +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (4, 'Energy Capacity', 'The Energy Capacity.', 4); +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (5, 'Charge Capacity', 'The Charge Capacity.', 5); +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (6, 'Temperature', 'The temperature.', 6); +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (7, 'Step Time', 'The time in seconds since the current step began.', 1); +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (8, 'Impedence Magnitude', 'The magnitude of the impedence (EIS).', 8); +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (9, 'Impedence Phase', 'The phase of the impedence (EIS).', 9); +# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (10, 'Frequency', 'The frequency of the input EIS voltage signal.', 10); +# SELECT setval('experiment.column_type_id_seq'::regclass, 10); \ No newline at end of file diff --git a/django/backend_django/galvanalyser/tests.py b/django/backend_django/galvanalyser/tests.py new file mode 100644 index 00000000..7ce503c2 --- /dev/null +++ b/django/backend_django/galvanalyser/tests.py @@ -0,0 +1,3 @@ +from django.test import TestCase + +# Create your tests here. diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py new file mode 100644 index 00000000..91ea44a2 --- /dev/null +++ b/django/backend_django/galvanalyser/views.py @@ -0,0 +1,3 @@ +from django.shortcuts import render + +# Create your views here. diff --git a/django/backend_django/manage.py b/django/backend_django/manage.py new file mode 100644 index 00000000..f5d21900 --- /dev/null +++ b/django/backend_django/manage.py @@ -0,0 +1,22 @@ +#!/usr/bin/env python +"""Django's command-line utility for administrative tasks.""" +import os +import sys + + +def main(): + """Run administrative tasks.""" + os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') + try: + from django.core.management import execute_from_command_line + except ImportError as exc: + raise ImportError( + "Couldn't import Django. Are you sure it's installed and " + "available on your PYTHONPATH environment variable? Did you " + "forget to activate a virtual environment?" + ) from exc + execute_from_command_line(sys.argv) + + +if __name__ == '__main__': + main() diff --git a/django/backend_django/settings.py b/django/backend_django/settings.py new file mode 100644 index 00000000..111c42e7 --- /dev/null +++ b/django/backend_django/settings.py @@ -0,0 +1,123 @@ +""" +Django settings for backend_django project. + +Generated by 'django-admin startproject' using Django 4.1.3. + +For more information on this file, see +https://docs.djangoproject.com/en/4.1/topics/settings/ + +For the full list of settings and their values, see +https://docs.djangoproject.com/en/4.1/ref/settings/ +""" + +from pathlib import Path + +# Build paths inside the project like this: BASE_DIR / 'subdir'. +BASE_DIR = Path(__file__).resolve().parent.parent + + +# Quick-start development settings - unsuitable for production +# See https://docs.djangoproject.com/en/4.1/howto/deployment/checklist/ + +# SECURITY WARNING: keep the secret key used in production secret! +SECRET_KEY = 'django-insecure-o^%u2n5a1agn%(nwdi^#%r%mp2g^&i11e@p4tx0dpcha*=c_@(' + +# SECURITY WARNING: don't run with debug turned on in production! +DEBUG = True + +ALLOWED_HOSTS = [] + + +# Application definition + +INSTALLED_APPS = [ + 'django.contrib.admin', + 'django.contrib.auth', + 'django.contrib.contenttypes', + 'django.contrib.sessions', + 'django.contrib.messages', + 'django.contrib.staticfiles', +] + +MIDDLEWARE = [ + 'django.middleware.security.SecurityMiddleware', + 'django.contrib.sessions.middleware.SessionMiddleware', + 'django.middleware.common.CommonMiddleware', + 'django.middleware.csrf.CsrfViewMiddleware', + 'django.contrib.auth.middleware.AuthenticationMiddleware', + 'django.contrib.messages.middleware.MessageMiddleware', + 'django.middleware.clickjacking.XFrameOptionsMiddleware', +] + +ROOT_URLCONF = 'backend_django.urls' + +TEMPLATES = [ + { + 'BACKEND': 'django.template.backends.django.DjangoTemplates', + 'DIRS': [], + 'APP_DIRS': True, + 'OPTIONS': { + 'context_processors': [ + 'django.template.context_processors.debug', + 'django.template.context_processors.request', + 'django.contrib.auth.context_processors.auth', + 'django.contrib.messages.context_processors.messages', + ], + }, + }, +] + +WSGI_APPLICATION = 'backend_django.wsgi.application' + + +# Database +# https://docs.djangoproject.com/en/4.1/ref/settings/#databases + +DATABASES = { + 'default': { + 'ENGINE': 'django.db.backends.sqlite3', + 'NAME': BASE_DIR / 'db.sqlite3', + } +} + + +# Password validation +# https://docs.djangoproject.com/en/4.1/ref/settings/#auth-password-validators + +AUTH_PASSWORD_VALIDATORS = [ + { + 'NAME': 'django.contrib.auth.password_validation.UserAttributeSimilarityValidator', + }, + { + 'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator', + }, + { + 'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator', + }, + { + 'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator', + }, +] + + +# Internationalization +# https://docs.djangoproject.com/en/4.1/topics/i18n/ + +LANGUAGE_CODE = 'en-us' + +TIME_ZONE = 'UTC' + +USE_I18N = True + +USE_TZ = True + + +# Static files (CSS, JavaScript, Images) +# https://docs.djangoproject.com/en/4.1/howto/static-files/ + +STATIC_URL = 'static/' + +# Default primary key field type +# https://docs.djangoproject.com/en/4.1/ref/settings/#default-auto-field + +DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField' diff --git a/django/backend_django/urls.py b/django/backend_django/urls.py new file mode 100644 index 00000000..5fefc865 --- /dev/null +++ b/django/backend_django/urls.py @@ -0,0 +1,21 @@ +"""backend_django URL Configuration + +The `urlpatterns` list routes URLs to views. For more information please see: + https://docs.djangoproject.com/en/4.1/topics/http/urls/ +Examples: +Function views + 1. Add an import: from my_app import views + 2. Add a URL to urlpatterns: path('', views.home, name='home') +Class-based views + 1. Add an import: from other_app.views import Home + 2. Add a URL to urlpatterns: path('', Home.as_view(), name='home') +Including another URLconf + 1. Import the include() function: from django.urls import include, path + 2. Add a URL to urlpatterns: path('blog/', include('blog.urls')) +""" +from django.contrib import admin +from django.urls import path + +urlpatterns = [ + path('admin/', admin.site.urls), +] diff --git a/django/backend_django/wsgi.py b/django/backend_django/wsgi.py new file mode 100644 index 00000000..984d982b --- /dev/null +++ b/django/backend_django/wsgi.py @@ -0,0 +1,16 @@ +""" +WSGI config for backend_django project. + +It exposes the WSGI callable as a module-level variable named ``application``. + +For more information on this file, see +https://docs.djangoproject.com/en/4.1/howto/deployment/wsgi/ +""" + +import os + +from django.core.wsgi import get_wsgi_application + +os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') + +application = get_wsgi_application() diff --git a/django/db.sqlite3 b/django/db.sqlite3 new file mode 100644 index 0000000000000000000000000000000000000000..46b5aa945b96a89b990271da4f668de37b670c1f GIT binary patch literal 131072 zcmeI5du$^~UdOxbww;IV%5xlUCL71u?2O4Kakn3dcUjo%Y;GpZY-V>J?2W{!Y1^Gl z&-szDoq6aagmW_-+5;p&cM?dj{DTC7Ki~k}A9p7q5JG_90No++I0Sz!Al)4T!TkXz zQC0o4-Ep#Wx6+RF^=LX>RloZ6w?6gguBw)O~xGeof>~rAb&zWM=E47{5%u4^AT^ujF!a_EMZWxn()Y6ukwiYNsntE>pOp9HuE_} zz7nN=K5qNju>9QDss`oLXtq?XQc?A0v(Z#*wCc2dz2%2Uri^kMTjSK(j_s_VHuZal zMpIYIje1+Jx7&{n^p;9%Uh#90$z?P7&DX}Liz~K^ytiB&P_?md)YbZ7)u+`cwAIM6 zy!q-V^*& ziQRZJcH?#1+R3d(S<7!KN>;uc4hhSbw!9b_Mas9 zf@-SNj5>9ZRVhzeGtEc5p0#qD_DyxKs_m=gI}M}kSJ}#1R?coH#Vv`tqLeLHitEaf zMSE?7x$RdY(~6=UypRb}7t4-|0Rw`(wwcT1bJ_I(WlD4K0b$SxBCi#cTp^p=5GlIl zUUUPml-(>A3z-=Cbs)0nO!r(WAqBHy<*ruWZ`eyu zd~GB=9SE+DSP6XHf~{H1iotc;x@PP*HMR!Qni``{!{jpp`6l^u^7rJ+GA1R=z=~`~P9`jzGRa{*L?^`4V}T2Jis^5C8!X z009sH0T2KI5C8!X009vAfCx;7C1L(-&;0*vND`KpJahh*=R7J&!t5-2V}Q;7V?i29 zun?dBPX%ajkpp6n~}t{7_R75oqn-|6`3$2%XjF@=uYIBNl9E1!|atew2<;F+M zc*~(1ALdj8%&Qw2nvzD(i`=ulhcC@Yqbs82){YGFNXw@k8JLhpm+1=t73W(F*#1BL z(tmtF00ck)1V8`;KmY_l00ck)1V8`;hL`}`|Hu4)h$|RH0|5{K0T2KI5C8!X009sH z0T2KIN&x%+Xa*nv0w4eaAOHd&00JNY0w4eaATay{F#jL^Iz|aW00ck)1V8`;KmY_l z00ck)1V8}q|Dz3n00@8p2!H?xfB*=900@8p2!O!w6Ttre@YgX)2m&Ag0w4eaAOHd& z00JNY0w4eanE#^}Ka4$yz7w7ay)Auq{M+`wz;^=I#Ge=bN_eHm*Z4QXPkN#d1OX5Lf$xey=ZB^u ziBGJGot9Cr=nu8S_8s-Gr8m|6X5;XnWu6-qGpN#&VlJD{lrv@Zux{MzHJ`qCeS7QX zcJkKl&Re&(lRLYwZ+|SA>a{w-X)1Ybw?9)Vc_GDx8I{zF$rP7I^`z3BmnI{L{i4{> z+!C0n2YRz+v|2`^-csFjR*219IbSX+I#^$DeOXu$x^z(SD-)5# z$Eo-?28lO4QQak3$&^cbMStCsr_$Z$>?Fx{hE)0}GagB-u8NPR+ghn=((^Qy-g=H& zdTwsLc6HmoMrj2mje1+(*PF@RYd4d-x2|4IzIlD;jjijqlUKHHC%10hytcDT9lf!= zdz03?-30n`UElub_Vw-Ei`zFmmtx3SBT2r_Qm=C%JG(nKcebuxy=_HqzwT{Mr*O=H zoX&H4`~~r!zpD<4%pYn3N4q1DM6oD7-f+8w*@c*p|N28+We%bAzoCH6(MKgP;Z%WLk zr}`Q`Rd3~FN4WABPX3uf7=wCstO(+Z=4`Ue##pYD>R&sMpJSPcYbpuqW|C zU90IY(wyneZ84HqUl)%w?z3`NtM50|nz7&1+Uz;5FCx(8H`SN^R5hX<9Hf%>wPyK_ z*1VwP^J(YVgkoh{k58pptA8<$_WuWV=n0 z*6NP66W5*So8Me0>^5X;K%Q&SUAKZ9Nu<-_(RuGGlO?M=@0joUl4Z&q+lBdr{>WVw z%4OUoBky(=T|TnyX{ohTvaLUCJ1ayq)hp9y3F&1eoVb=21y0jiM5F7)4IWmzm8)`h zcwEke6Wa^NWp z__M-PcVo=1g%g(+2Nuj+A2v(I&lji*rQ6L(p-+APdL*&1ApYc%3xh4lI=CV}C_F2+ z{VTA8_HYigR_j5dNmml>g-BW1bXyf|D^;!4R;!JDqwZa8q#LL-&1k8uL%OzYUcS_5 zRK2Z?#hy&szQh1a)?#a#QFTQs`COMsCZw(H?WK~vB4~ut6D=s;(C8p>X7qoC)^%@@}$Zq=yw zO#nCbSTCO43fG$Thn~yQk?6)!B=KlPJR#?2MB zMEh*MxJIXRed?0XO0mV!_XL(x5wCI$a_2kzEoHDz;G~*ewD3$I;+O?UG?p$7sBpO+<^GWaR(JMry`w41QE9q6WM(e(+ zZWKzDY$aRb74M^5@~wOy!@-`rZlhj7jEtj+?Y41Qv?1>#BZ+KQJSuu`sotDE8baMw z?_=>))$i&%wpL8l{>kai#JqRM){>=FYDS%nx6Y1jIbX=>C9TkFaLy`L_fyO9`MY2{ zW~}IJpk^EG>CT07k%US&k>B#R6vwu|H|I)aeN!*>N;`XkG;f8maj|UqIbLET-hcXD4Ni9JalPAbSb4ADJib_{PagEFBD391?~{k+Jl*->1Rd43 z#LhkUp2nr{gFCeMzLY2Ll}hb;cQao>jDUMNv*T@^ zi6qLjFt<-Cj73}3ig{hD$e#B&ddvNNr!GdX&(jpZ%0tJD2eb4okI^mhX#KR>y9%$$ zIjvACWEJ-zgZu6+&YV>opXUu`ClqY$^Ib(XU2-EBcsbzy}0C00ck)1V8`;KmY_l00epnq~=0`xV##^Z|D!` z&#?2~*t)3IlPsLH!Y?GKOBC9G8{ z-b>P;ZLu;#Emk)|T$S~^2kcjO9A#Eql0~jhQ)Bt%kR`9j+>+RpVam*4>Fmj1Y4v7E zPtpu4`4AJ_W6eZ+P0vkG(}nXASI)l4-jU1#NkUVXRwPTRoo;F57ID+U(q>y&qFC@F zF={ctEHN>5GE>3MpNrD8#dMHgoqvhEb9o+0jnnky)u45K$HEd|+KibtmIBAdlEA~~ zMybuh`5@Ea7%&k$aAAa|u4DsTh5If0jubcQ#R#=r-w0TG+yrK8iE<-f44c-LGB<%) zTk_n<7edrJEeDuJHE9cQb-s*FLSZi#ezr>009sH0T2KI5C8!X O009sH0T37}0{;&=mG%Gt literal 0 HcmV?d00001 diff --git a/django/manage.py b/django/manage.py new file mode 100644 index 00000000..f5d21900 --- /dev/null +++ b/django/manage.py @@ -0,0 +1,22 @@ +#!/usr/bin/env python +"""Django's command-line utility for administrative tasks.""" +import os +import sys + + +def main(): + """Run administrative tasks.""" + os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') + try: + from django.core.management import execute_from_command_line + except ImportError as exc: + raise ImportError( + "Couldn't import Django. Are you sure it's installed and " + "available on your PYTHONPATH environment variable? Did you " + "forget to activate a virtual environment?" + ) from exc + execute_from_command_line(sys.argv) + + +if __name__ == '__main__': + main() diff --git a/django/requirements.txt b/django/requirements.txt new file mode 100644 index 00000000..00c32049 --- /dev/null +++ b/django/requirements.txt @@ -0,0 +1,3 @@ +celery==5.2.7 +Django==4.1.3 +djangorestframework==3.14.0 diff --git a/django/server.sh b/django/server.sh new file mode 100644 index 00000000..30976a26 --- /dev/null +++ b/django/server.sh @@ -0,0 +1,31 @@ +#!/bin/sh +# init.sh + +# adapted from https://docs.docker.com/compose/startup-order/ + +set -e +PGUP=1 + +while [ $PGUP -ne 0 ]; do + pg_isready -d "postgresql://postgres:galvanalyser@postgres:5433/postgres" + PGUP=$? + >&2 echo "Postgres is unavailable - sleeping" + sleep 1 +done + +>&2 echo "Postgres ready - initialising" +python manage.py makemigrations +python manage.py migrate + +>&2 echo "Initialisation complete - starting server" +#exec "$@" + +mkdir -p /var/run/celery /var/log/celery +chown -R nobody:nogroup /var/run/celery /var/log/celery + +python manage.py runserver 0.0.0.0:5000 & \ +celery -A backend_django.celery beat \ + --loglevel=DEBUG \ + --logfile=/var/log/celery/scheduler.log \ + -s /var/run/celery/celerybeat-schedule \ + --uid=nobody --gid=nogroup diff --git a/django/worker.sh b/django/worker.sh new file mode 100644 index 00000000..0dce27dd --- /dev/null +++ b/django/worker.sh @@ -0,0 +1,11 @@ +#!/usr/bin/env bash + +mkdir -p /var/run/celery /var/log/celery +chown -R nobody:nogroup /var/run/celery /var/log/celery + +exec celery -A backend_django.celery worker \ + --loglevel=INFO \ + --logfile=/var/log/celery/worker.log \ + -O fair \ + -Q $HARVESTER_USERNAME \ + --uid=nobody --gid=nogroup diff --git a/docker-compose.override.yml b/docker-compose.override.yml index de9592e1..7b35b20e 100644 --- a/docker-compose.override.yml +++ b/docker-compose.override.yml @@ -1,5 +1,41 @@ version: "2" services: + app: + image: app + build: + dockerfile: Dockerfile + context: ./django + depends_on: + - redis + - rabbitmq + - postgres + ports: + - "5001:5000" + volumes: + - ./django:/usr/app + - "${GALVANALYSER_HARVESTER_TEST_PATH}:/usr/test_data" + - "${GALVANALYSER_HARVESTER_BASE_PATH}:/usr/data" + - "${CELERY_LOG_DIR}:/var/log/celery" + restart: unless-stopped + working_dir: /usr/app + command: ./server.sh +# command: tail -F anything + env_file: + - ./.env + worker: + image: app + command: ./worker.sh + depends_on: + - app + volumes: + - ./django:/usr/app + - "${GALVANALYSER_HARVESTER_BASE_PATH}:/usr/data" + - "${CELERY_LOG_DIR}:/var/log/celery" + + working_dir: /usr/app + restart: unless-stopped + env_file: + - ./.env frontend: image: frontend_dev build: diff --git a/docker-compose.yml b/docker-compose.yml index 9821d127..d68d2984 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,7 +1,7 @@ version: "2" services: app: - image: app +# image: app build: dockerfile: Dockerfile context: ./backend diff --git a/frontend/.env b/frontend/.env new file mode 100644 index 00000000..98a4f13c --- /dev/null +++ b/frontend/.env @@ -0,0 +1 @@ +CHOKIDAR_USEPOLLING=true \ No newline at end of file diff --git a/frontend/src/Datasets.js b/frontend/src/Datasets.js index 45797c81..f6531c05 100644 --- a/frontend/src/Datasets.js +++ b/frontend/src/Datasets.js @@ -85,12 +85,12 @@ export default function Datasets() { setMatlabCodeOpen(false); }; - + const columns: GridColDef[] = [ { field: 'dataset_id', headerName: 'ID', width: 70}, { field: 'name', headerName: 'Name', flex: true}, - { + { field: 'date', headerName: 'Date', width: 110, valueFormatter: (params: GridValueFormatterParams) => { return Intl.DateTimeFormat('en-GB').format(params.value); @@ -124,13 +124,13 @@ export default function Datasets() { let autoHeight = true; let divStyle = { width: '100%' }; console.log('datasets', rows) - + return (
-
{data && data[select] && - From 5df96c706860917b2872398adb9386bbceb39e42 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Fri, 2 Dec 2022 12:06:51 +0000 Subject: [PATCH 04/79] django database model --- django/.env.secret | 1 + django/backend_django/asgi.py | 16 -- .../backend_django/backend_django/__init__.py | 0 django/backend_django/backend_django/asgi.py | 16 -- .../backend_django/backend_django/settings.py | 123 ------------ django/backend_django/backend_django/urls.py | 21 --- django/backend_django/backend_django/wsgi.py | 16 -- .../galvanalyser/fixtures/DataColumnType.json | 109 +++++++++++ .../galvanalyser/fixtures/DataUnit.json | 101 ++++++++++ .../galvanalyser/migrations/0001_initial.py | 175 ++++++++++++++++++ django/backend_django/galvanalyser/models.py | 20 +- django/backend_django/manage.py | 2 +- django/backend_django/settings.py | 123 ------------ django/backend_django/urls.py | 21 --- django/backend_django/wsgi.py | 16 -- django/manage.py | 22 --- django/requirements.txt | 1 + django/server.sh | 6 + docker-compose.override.yml | 1 + 19 files changed, 408 insertions(+), 382 deletions(-) create mode 100644 django/.env.secret delete mode 100644 django/backend_django/asgi.py delete mode 100644 django/backend_django/backend_django/__init__.py delete mode 100644 django/backend_django/backend_django/asgi.py delete mode 100644 django/backend_django/backend_django/settings.py delete mode 100644 django/backend_django/backend_django/urls.py delete mode 100644 django/backend_django/backend_django/wsgi.py create mode 100644 django/backend_django/galvanalyser/fixtures/DataColumnType.json create mode 100644 django/backend_django/galvanalyser/fixtures/DataUnit.json create mode 100644 django/backend_django/galvanalyser/migrations/0001_initial.py delete mode 100644 django/backend_django/settings.py delete mode 100644 django/backend_django/urls.py delete mode 100644 django/backend_django/wsgi.py delete mode 100644 django/manage.py diff --git a/django/.env.secret b/django/.env.secret new file mode 100644 index 00000000..8e8f475d --- /dev/null +++ b/django/.env.secret @@ -0,0 +1 @@ +DJANGO_SECRET_KEY=django-insecure-o^%u2n5a1agn%(nwdi^!%r%mp2g^&i11e@p4tx0dpcha*=c_@( diff --git a/django/backend_django/asgi.py b/django/backend_django/asgi.py deleted file mode 100644 index 9df576b4..00000000 --- a/django/backend_django/asgi.py +++ /dev/null @@ -1,16 +0,0 @@ -""" -ASGI config for backend_django project. - -It exposes the ASGI callable as a module-level variable named ``application``. - -For more information on this file, see -https://docs.djangoproject.com/en/4.1/howto/deployment/asgi/ -""" - -import os - -from django.core.asgi import get_asgi_application - -os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') - -application = get_asgi_application() diff --git a/django/backend_django/backend_django/__init__.py b/django/backend_django/backend_django/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/django/backend_django/backend_django/asgi.py b/django/backend_django/backend_django/asgi.py deleted file mode 100644 index 9df576b4..00000000 --- a/django/backend_django/backend_django/asgi.py +++ /dev/null @@ -1,16 +0,0 @@ -""" -ASGI config for backend_django project. - -It exposes the ASGI callable as a module-level variable named ``application``. - -For more information on this file, see -https://docs.djangoproject.com/en/4.1/howto/deployment/asgi/ -""" - -import os - -from django.core.asgi import get_asgi_application - -os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') - -application = get_asgi_application() diff --git a/django/backend_django/backend_django/settings.py b/django/backend_django/backend_django/settings.py deleted file mode 100644 index 6f323836..00000000 --- a/django/backend_django/backend_django/settings.py +++ /dev/null @@ -1,123 +0,0 @@ -""" -Django settings for backend_django project. - -Generated by 'django-admin startproject' using Django 4.1.3. - -For more information on this file, see -https://docs.djangoproject.com/en/4.1/topics/settings/ - -For the full list of settings and their values, see -https://docs.djangoproject.com/en/4.1/ref/settings/ -""" - -from pathlib import Path - -# Build paths inside the project like this: BASE_DIR / 'subdir'. -BASE_DIR = Path(__file__).resolve().parent.parent - - -# Quick-start development settings - unsuitable for production -# See https://docs.djangoproject.com/en/4.1/howto/deployment/checklist/ - -# SECURITY WARNING: keep the secret key used in production secret! -SECRET_KEY = 'django-insecure-@+e142%m^c6ka7g&8avn(!^@b4##!7f++fbfsq^10^$0oul)a@' - -# SECURITY WARNING: don't run with debug turned on in production! -DEBUG = True - -ALLOWED_HOSTS = [] - - -# Application definition - -INSTALLED_APPS = [ - 'django.contrib.admin', - 'django.contrib.auth', - 'django.contrib.contenttypes', - 'django.contrib.sessions', - 'django.contrib.messages', - 'django.contrib.staticfiles', -] - -MIDDLEWARE = [ - 'django.middleware.security.SecurityMiddleware', - 'django.contrib.sessions.middleware.SessionMiddleware', - 'django.middleware.common.CommonMiddleware', - 'django.middleware.csrf.CsrfViewMiddleware', - 'django.contrib.auth.middleware.AuthenticationMiddleware', - 'django.contrib.messages.middleware.MessageMiddleware', - 'django.middleware.clickjacking.XFrameOptionsMiddleware', -] - -ROOT_URLCONF = 'backend_django.urls' - -TEMPLATES = [ - { - 'BACKEND': 'django.template.backends.django.DjangoTemplates', - 'DIRS': [], - 'APP_DIRS': True, - 'OPTIONS': { - 'context_processors': [ - 'django.template.context_processors.debug', - 'django.template.context_processors.request', - 'django.contrib.auth.context_processors.auth', - 'django.contrib.messages.context_processors.messages', - ], - }, - }, -] - -WSGI_APPLICATION = 'backend_django.wsgi.application' - - -# Database -# https://docs.djangoproject.com/en/4.1/ref/settings/#databases - -DATABASES = { - 'default': { - 'ENGINE': 'django.db.backends.sqlite3', - 'NAME': BASE_DIR / 'db.sqlite3', - } -} - - -# Password validation -# https://docs.djangoproject.com/en/4.1/ref/settings/#auth-password-validators - -AUTH_PASSWORD_VALIDATORS = [ - { - 'NAME': 'django.contrib.auth.password_validation.UserAttributeSimilarityValidator', - }, - { - 'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator', - }, - { - 'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator', - }, - { - 'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator', - }, -] - - -# Internationalization -# https://docs.djangoproject.com/en/4.1/topics/i18n/ - -LANGUAGE_CODE = 'en-us' - -TIME_ZONE = 'UTC' - -USE_I18N = True - -USE_TZ = True - - -# Static files (CSS, JavaScript, Images) -# https://docs.djangoproject.com/en/4.1/howto/static-files/ - -STATIC_URL = 'static/' - -# Default primary key field type -# https://docs.djangoproject.com/en/4.1/ref/settings/#default-auto-field - -DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField' diff --git a/django/backend_django/backend_django/urls.py b/django/backend_django/backend_django/urls.py deleted file mode 100644 index 5fefc865..00000000 --- a/django/backend_django/backend_django/urls.py +++ /dev/null @@ -1,21 +0,0 @@ -"""backend_django URL Configuration - -The `urlpatterns` list routes URLs to views. For more information please see: - https://docs.djangoproject.com/en/4.1/topics/http/urls/ -Examples: -Function views - 1. Add an import: from my_app import views - 2. Add a URL to urlpatterns: path('', views.home, name='home') -Class-based views - 1. Add an import: from other_app.views import Home - 2. Add a URL to urlpatterns: path('', Home.as_view(), name='home') -Including another URLconf - 1. Import the include() function: from django.urls import include, path - 2. Add a URL to urlpatterns: path('blog/', include('blog.urls')) -""" -from django.contrib import admin -from django.urls import path - -urlpatterns = [ - path('admin/', admin.site.urls), -] diff --git a/django/backend_django/backend_django/wsgi.py b/django/backend_django/backend_django/wsgi.py deleted file mode 100644 index 984d982b..00000000 --- a/django/backend_django/backend_django/wsgi.py +++ /dev/null @@ -1,16 +0,0 @@ -""" -WSGI config for backend_django project. - -It exposes the WSGI callable as a module-level variable named ``application``. - -For more information on this file, see -https://docs.djangoproject.com/en/4.1/howto/deployment/wsgi/ -""" - -import os - -from django.core.wsgi import get_wsgi_application - -os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') - -application = get_wsgi_application() diff --git a/django/backend_django/galvanalyser/fixtures/DataColumnType.json b/django/backend_django/galvanalyser/fixtures/DataColumnType.json new file mode 100644 index 00000000..23e8b24f --- /dev/null +++ b/django/backend_django/galvanalyser/fixtures/DataColumnType.json @@ -0,0 +1,109 @@ +[ + { + "pk": 1, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Unknown", + "description": "unknown column type" + } + }, + { + "pk": 2, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Sample Number", + "description": "The sample or record number. Is increased by one each time a test machine records a reading. Usually counts from 1 at the start of a test", + "unit": 1 + } + }, + { + "pk": 3, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Time", + "description": "The time in seconds since the test run began.", + "unit": 2 + } + }, + { + "pk": 4, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Volts", + "description": "The voltage of the cell.", + "unit": 3 + } + }, + { + "pk": 5, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Amps", + "description": "The current current.", + "unit": 4 + } + }, + { + "pk": 6, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Energy Capacity", + "description": "The Energy Capacity.", + "unit": 5 + } + }, + { + "pk": 7, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Charge Capacity", + "description": "The Charge Capacity.", + "unit": 6 + } + }, + { + "pk": 8, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Temperature", + "description": "The temperature.", + "unit": 7 + } + }, + { + "pk": 9, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Step Time", + "description": "The time in seconds since the current step began.", + "unit": 8 + } + }, + { + "pk": 10, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Impedence Magnitude", + "description": "The magnitude of the impedence (EIS).", + "unit": 9 + } + }, + { + "pk": 11, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Impedence Phase", + "description": "The phase of the impedence (EIS).", + "unit": 10 + } + }, + { + "pk": 12, + "model": "galvanalyser.DataColumnType", + "fields": { + "name": "Frequency", + "description": "The frequency of the input EIS voltage signal.", + "unit": 11 + } + } +] \ No newline at end of file diff --git a/django/backend_django/galvanalyser/fixtures/DataUnit.json b/django/backend_django/galvanalyser/fixtures/DataUnit.json new file mode 100644 index 00000000..53b68f33 --- /dev/null +++ b/django/backend_django/galvanalyser/fixtures/DataUnit.json @@ -0,0 +1,101 @@ +[ + { + "pk": 1, + "model": "galvanalyser.DataUnit", + "fields": { + "name": "Unitless", + "symbol": "", + "description": "A value with no units" + } + }, + { + "pk": 2, + "model": "galvanalyser.DataUnit", + "fields": { + "name": "Time", + "symbol": "s", + "description": "Time in seconds" + } + }, + { + "pk": 3, + "model": "galvanalyser.DataUnit", + "fields": { + "name": "Volts", + "symbol": "V", + "description": "Voltage" + } + }, + { + "pk": 4, + "model": "galvanalyser.DataUnit", + "fields": { + "name": "Amps", + "symbol": "A", + "description": "Current" + } + }, + { + "pk": 5, + "model": "galvanalyser.DataUnit", + "fields": { + "name": "Energy", + "symbol": "Wh", + "description": "Energy in Watt-Hours" + } + }, + { + "pk": 6, + "model": "galvanalyser.DataUnit", + "fields": { + "name": "Charge", + "symbol": "Ah", + "description": "Charge in Amp-Hours" + } + }, + { + "pk": 7, + "model": "galvanalyser.DataUnit", + "fields": { + "name": "Temperature", + "symbol": "°c", + "description": "Temperature in Centigrade" + } + }, + { + "pk": 8, + "model": "galvanalyser.DataUnit", + "fields": { + "name": "Power", + "symbol": "W", + "description": "Power in Watts" + } + }, + { + "pk": 9, + "model": "galvanalyser.DataUnit", + "fields": { + "name": "Ohm", + "symbol": "Ω", + "description": "Resistance or impediance in Ohms" + } + }, + { + "pk": 10, + "model": "galvanalyser.DataUnit", + "fields": { + "name": "Degrees", + "symbol": "°", + "description": "Angle in degrees" + } + }, + { + "pk": 11, + "model": "galvanalyser.DataUnit", + "fields": { + "name": "Frequency", + "symbol": "Hz", + "description": "Frequency in Hz" + } + } +] \ No newline at end of file diff --git a/django/backend_django/galvanalyser/migrations/0001_initial.py b/django/backend_django/galvanalyser/migrations/0001_initial.py new file mode 100644 index 00000000..f171c3bb --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0001_initial.py @@ -0,0 +1,175 @@ +# Generated by Django 4.1.3 on 2022-12-02 12:00 + +from django.conf import settings +import django.core.validators +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + initial = True + + dependencies = [ + migrations.swappable_dependency(settings.AUTH_USER_MODEL), + ('auth', '0012_alter_user_first_name_max_length'), + ] + + operations = [ + migrations.CreateModel( + name='CellData', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField(unique=True)), + ('form_factor', models.TextField()), + ('link_to_datasheet', models.TextField()), + ('anode_chemistry', models.TextField()), + ('cathode_chemistry', models.TextField()), + ('nominal_capacity', models.FloatField()), + ('nominal_cell_weight', models.FloatField()), + ('manufacturer', models.TextField()), + ], + ), + migrations.CreateModel( + name='Dataset', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField()), + ('date', models.DateTimeField()), + ('type', models.TextField()), + ('purpose', models.TextField()), + ('json_data', models.JSONField()), + ('access_group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='auth.group')), + ('cell_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='galvanalyser.celldata')), + ('owner_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL)), + ], + options={ + 'unique_together': {('name', 'date')}, + }, + ), + migrations.CreateModel( + name='DataUnit', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField()), + ('symbol', models.TextField()), + ('description', models.TextField()), + ], + ), + migrations.CreateModel( + name='Equipment', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField(unique=True)), + ('type', models.TextField()), + ], + ), + migrations.CreateModel( + name='Harvester', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('machine_id', models.TextField(unique=True)), + ('name', models.TextField()), + ('last_successful_run', models.DateTimeField()), + ('is_running', models.BooleanField(default=False)), + ('periodic_hour', models.IntegerField(validators=[django.core.validators.MinValueValidator(1), django.core.validators.MaxValueValidator(24)])), + ], + ), + migrations.CreateModel( + name='Machine', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ], + ), + migrations.CreateModel( + name='MonitoredPath', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('path', models.TextField(unique=True)), + ('harvester', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.harvester')), + ], + options={ + 'unique_together': {('harvester', 'path')}, + }, + ), + migrations.CreateModel( + name='TimeseriesRangeLabel', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('label', models.TextField()), + ('range_start', models.PositiveBigIntegerField()), + ('range_end', models.PositiveBigIntegerField()), + ('info', models.TextField()), + ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.dataset')), + ], + ), + migrations.CreateModel( + name='MonitoredFor', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('path', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.monitoredpath')), + ('user_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ], + ), + migrations.CreateModel( + name='DataColumnType', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField()), + ('description', models.TextField()), + ('unit', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='galvanalyser.dataunit')), + ], + options={ + 'unique_together': {('unit', 'name')}, + }, + ), + migrations.CreateModel( + name='DataColumn', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField()), + ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.dataset')), + ('type', models.ForeignKey(on_delete=django.db.models.deletion.RESTRICT, to='galvanalyser.datacolumntype')), + ], + options={ + 'unique_together': {('dataset', 'name')}, + }, + ), + migrations.CreateModel( + name='TimeseriesData', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample', models.PositiveBigIntegerField()), + ('value', models.FloatField()), + ('column', models.ForeignKey(on_delete=django.db.models.deletion.RESTRICT, to='galvanalyser.datacolumn')), + ], + options={ + 'unique_together': {('sample', 'column')}, + }, + ), + migrations.CreateModel( + name='ObservedFile', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('relative_path', models.TextField()), + ('last_observed_size', models.PositiveBigIntegerField()), + ('last_observed_time', models.DateTimeField()), + ('file_state', models.SmallIntegerField(choices=[(-1, 'Import Failed'), (0, 'Unstable'), (1, 'Growing'), (2, 'Stable'), (3, 'Importing'), (4, 'Imported')], default=0)), + ('monitored_path', models.ForeignKey(on_delete=django.db.models.deletion.DO_NOTHING, to='galvanalyser.monitoredpath')), + ], + options={ + 'unique_together': {('monitored_path', 'relative_path')}, + }, + ), + migrations.CreateModel( + name='DatasetEquipment', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.dataset')), + ('equipment', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.equipment')), + ], + options={ + 'unique_together': {('dataset', 'equipment')}, + }, + ), + ] diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index e375792f..9b401897 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -17,7 +17,7 @@ class Machine(models.Model): class Harvester(models.Model): - machine_id = models.ForeignKey(to=Machine, on_delete=models.CASCADE, unique=True) + machine_id = models.TextField(unique=True) name = models.TextField() last_successful_run = models.DateTimeField() is_running = models.BooleanField(default=False) @@ -27,9 +27,12 @@ class Harvester(models.Model): class MonitoredPath(models.Model): - harvester = models.ForeignKey(to=Harvester, on_delete=models.CASCADE, unique=True) + harvester = models.ForeignKey(to=Harvester, on_delete=models.CASCADE) path = models.TextField(unique=True) + class Meta: + unique_together = [['harvester', 'path']] + class MonitoredFor(models.Model): path = models.ForeignKey(to=MonitoredPath, on_delete=models.CASCADE) @@ -59,8 +62,8 @@ class CellData(models.Model): class Dataset(models.Model): - cell_id = models.ForeignKey(to=CellData, on_delete=models.SET_NULL) - owner_id = models.ForeignKey(to=User, on_delete=models.SET_NULL) + cell_id = models.ForeignKey(to=CellData, on_delete=models.SET_NULL, null=True) + owner_id = models.ForeignKey(to=User, on_delete=models.SET_NULL, null=True) access_group = models.ForeignKey(to=Group, on_delete=models.CASCADE) name = models.TextField(null=False) date = models.DateTimeField(null=False) @@ -91,15 +94,18 @@ class DataUnit(models.Model): description = models.TextField() -class DataColumType(models.Model): - unit = models.ForeignKey(to=DataUnit, on_delete=models.SET_NULL) +class DataColumnType(models.Model): + unit = models.ForeignKey(to=DataUnit, on_delete=models.SET_NULL, null=True) name = models.TextField(null=False) description = models.TextField() + class Meta: + unique_together = [['unit', 'name']] + class DataColumn(models.Model): dataset = models.ForeignKey(to=Dataset, on_delete=models.CASCADE) - type = models.ForeignKey(to=DataColumType, on_delete=models.RESTRICT) + type = models.ForeignKey(to=DataColumnType, on_delete=models.RESTRICT) name = models.TextField(null=False) class Meta: diff --git a/django/backend_django/manage.py b/django/backend_django/manage.py index f5d21900..8e7ac79b 100644 --- a/django/backend_django/manage.py +++ b/django/backend_django/manage.py @@ -6,7 +6,7 @@ def main(): """Run administrative tasks.""" - os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') + os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'config.settings') try: from django.core.management import execute_from_command_line except ImportError as exc: diff --git a/django/backend_django/settings.py b/django/backend_django/settings.py deleted file mode 100644 index 111c42e7..00000000 --- a/django/backend_django/settings.py +++ /dev/null @@ -1,123 +0,0 @@ -""" -Django settings for backend_django project. - -Generated by 'django-admin startproject' using Django 4.1.3. - -For more information on this file, see -https://docs.djangoproject.com/en/4.1/topics/settings/ - -For the full list of settings and their values, see -https://docs.djangoproject.com/en/4.1/ref/settings/ -""" - -from pathlib import Path - -# Build paths inside the project like this: BASE_DIR / 'subdir'. -BASE_DIR = Path(__file__).resolve().parent.parent - - -# Quick-start development settings - unsuitable for production -# See https://docs.djangoproject.com/en/4.1/howto/deployment/checklist/ - -# SECURITY WARNING: keep the secret key used in production secret! -SECRET_KEY = 'django-insecure-o^%u2n5a1agn%(nwdi^#%r%mp2g^&i11e@p4tx0dpcha*=c_@(' - -# SECURITY WARNING: don't run with debug turned on in production! -DEBUG = True - -ALLOWED_HOSTS = [] - - -# Application definition - -INSTALLED_APPS = [ - 'django.contrib.admin', - 'django.contrib.auth', - 'django.contrib.contenttypes', - 'django.contrib.sessions', - 'django.contrib.messages', - 'django.contrib.staticfiles', -] - -MIDDLEWARE = [ - 'django.middleware.security.SecurityMiddleware', - 'django.contrib.sessions.middleware.SessionMiddleware', - 'django.middleware.common.CommonMiddleware', - 'django.middleware.csrf.CsrfViewMiddleware', - 'django.contrib.auth.middleware.AuthenticationMiddleware', - 'django.contrib.messages.middleware.MessageMiddleware', - 'django.middleware.clickjacking.XFrameOptionsMiddleware', -] - -ROOT_URLCONF = 'backend_django.urls' - -TEMPLATES = [ - { - 'BACKEND': 'django.template.backends.django.DjangoTemplates', - 'DIRS': [], - 'APP_DIRS': True, - 'OPTIONS': { - 'context_processors': [ - 'django.template.context_processors.debug', - 'django.template.context_processors.request', - 'django.contrib.auth.context_processors.auth', - 'django.contrib.messages.context_processors.messages', - ], - }, - }, -] - -WSGI_APPLICATION = 'backend_django.wsgi.application' - - -# Database -# https://docs.djangoproject.com/en/4.1/ref/settings/#databases - -DATABASES = { - 'default': { - 'ENGINE': 'django.db.backends.sqlite3', - 'NAME': BASE_DIR / 'db.sqlite3', - } -} - - -# Password validation -# https://docs.djangoproject.com/en/4.1/ref/settings/#auth-password-validators - -AUTH_PASSWORD_VALIDATORS = [ - { - 'NAME': 'django.contrib.auth.password_validation.UserAttributeSimilarityValidator', - }, - { - 'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator', - }, - { - 'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator', - }, - { - 'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator', - }, -] - - -# Internationalization -# https://docs.djangoproject.com/en/4.1/topics/i18n/ - -LANGUAGE_CODE = 'en-us' - -TIME_ZONE = 'UTC' - -USE_I18N = True - -USE_TZ = True - - -# Static files (CSS, JavaScript, Images) -# https://docs.djangoproject.com/en/4.1/howto/static-files/ - -STATIC_URL = 'static/' - -# Default primary key field type -# https://docs.djangoproject.com/en/4.1/ref/settings/#default-auto-field - -DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField' diff --git a/django/backend_django/urls.py b/django/backend_django/urls.py deleted file mode 100644 index 5fefc865..00000000 --- a/django/backend_django/urls.py +++ /dev/null @@ -1,21 +0,0 @@ -"""backend_django URL Configuration - -The `urlpatterns` list routes URLs to views. For more information please see: - https://docs.djangoproject.com/en/4.1/topics/http/urls/ -Examples: -Function views - 1. Add an import: from my_app import views - 2. Add a URL to urlpatterns: path('', views.home, name='home') -Class-based views - 1. Add an import: from other_app.views import Home - 2. Add a URL to urlpatterns: path('', Home.as_view(), name='home') -Including another URLconf - 1. Import the include() function: from django.urls import include, path - 2. Add a URL to urlpatterns: path('blog/', include('blog.urls')) -""" -from django.contrib import admin -from django.urls import path - -urlpatterns = [ - path('admin/', admin.site.urls), -] diff --git a/django/backend_django/wsgi.py b/django/backend_django/wsgi.py deleted file mode 100644 index 984d982b..00000000 --- a/django/backend_django/wsgi.py +++ /dev/null @@ -1,16 +0,0 @@ -""" -WSGI config for backend_django project. - -It exposes the WSGI callable as a module-level variable named ``application``. - -For more information on this file, see -https://docs.djangoproject.com/en/4.1/howto/deployment/wsgi/ -""" - -import os - -from django.core.wsgi import get_wsgi_application - -os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') - -application = get_wsgi_application() diff --git a/django/manage.py b/django/manage.py deleted file mode 100644 index f5d21900..00000000 --- a/django/manage.py +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env python -"""Django's command-line utility for administrative tasks.""" -import os -import sys - - -def main(): - """Run administrative tasks.""" - os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'backend_django.settings') - try: - from django.core.management import execute_from_command_line - except ImportError as exc: - raise ImportError( - "Couldn't import Django. Are you sure it's installed and " - "available on your PYTHONPATH environment variable? Did you " - "forget to activate a virtual environment?" - ) from exc - execute_from_command_line(sys.argv) - - -if __name__ == '__main__': - main() diff --git a/django/requirements.txt b/django/requirements.txt index 00c32049..4816fa9f 100644 --- a/django/requirements.txt +++ b/django/requirements.txt @@ -1,3 +1,4 @@ celery==5.2.7 Django==4.1.3 djangorestframework==3.14.0 +psycopg2-binary==2.9.5 diff --git a/django/server.sh b/django/server.sh index 30976a26..3a8ef2e3 100644 --- a/django/server.sh +++ b/django/server.sh @@ -14,9 +14,14 @@ while [ $PGUP -ne 0 ]; do done >&2 echo "Postgres ready - initialising" +cd backend_django python manage.py makemigrations python manage.py migrate +>&2 echo "... populating database" +python manage.py loaddata galvanalyser/fixtures/DataUnit.json +python manage.py loaddata galvanalyser/fixtures/DataColumnType.json + >&2 echo "Initialisation complete - starting server" #exec "$@" @@ -24,6 +29,7 @@ mkdir -p /var/run/celery /var/log/celery chown -R nobody:nogroup /var/run/celery /var/log/celery python manage.py runserver 0.0.0.0:5000 & \ +cd .. && \ celery -A backend_django.celery beat \ --loglevel=DEBUG \ --logfile=/var/log/celery/scheduler.log \ diff --git a/docker-compose.override.yml b/docker-compose.override.yml index 7b35b20e..e987c111 100644 --- a/docker-compose.override.yml +++ b/docker-compose.override.yml @@ -22,6 +22,7 @@ services: # command: tail -F anything env_file: - ./.env + - ./django/.env.secret worker: image: app command: ./worker.sh From 78a79f06d5f1407fa395533e2f8f150f3ae78045 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Fri, 2 Dec 2022 12:14:20 +0000 Subject: [PATCH 05/79] untrack secrets --- .gitignore | 2 ++ django/.env.secret | 1 - 2 files changed, 2 insertions(+), 1 deletion(-) delete mode 100644 django/.env.secret diff --git a/.gitignore b/.gitignore index dba05bd4..b1252dc9 100644 --- a/.gitignore +++ b/.gitignore @@ -19,3 +19,5 @@ env .test-data/ frontend/src/demo_matlab_code.m + +**/.env.secret \ No newline at end of file diff --git a/django/.env.secret b/django/.env.secret deleted file mode 100644 index 8e8f475d..00000000 --- a/django/.env.secret +++ /dev/null @@ -1 +0,0 @@ -DJANGO_SECRET_KEY=django-insecure-o^%u2n5a1agn%(nwdi^!%r%mp2g^&i11e@p4tx0dpcha*=c_@( From 1806fadcfed36a6fd2bd64d2adef34728ab321b7 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Fri, 2 Dec 2022 12:40:13 +0000 Subject: [PATCH 06/79] djangorestframework running --- .../migrations/0002_delete_machine.py | 16 ++ django/backend_django/galvanalyser/models.py | 34 ---- .../galvanalyser/serializers.py | 105 +++++++++++ django/backend_django/galvanalyser/views.py | 165 +++++++++++++++++- 4 files changed, 284 insertions(+), 36 deletions(-) create mode 100644 django/backend_django/galvanalyser/migrations/0002_delete_machine.py create mode 100644 django/backend_django/galvanalyser/serializers.py diff --git a/django/backend_django/galvanalyser/migrations/0002_delete_machine.py b/django/backend_django/galvanalyser/migrations/0002_delete_machine.py new file mode 100644 index 00000000..e7d2c46b --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0002_delete_machine.py @@ -0,0 +1,16 @@ +# Generated by Django 4.1.3 on 2022-12-02 12:31 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0001_initial'), + ] + + operations = [ + migrations.DeleteModel( + name='Machine', + ), + ] diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index 9b401897..fcf24cbe 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -12,10 +12,6 @@ class FileState(models.IntegerChoices): IMPORTED = 4 -class Machine(models.Model): - pass - - class Harvester(models.Model): machine_id = models.TextField(unique=True) name = models.TextField() @@ -127,33 +123,3 @@ class TimeseriesRangeLabel(models.Model): range_start = models.PositiveBigIntegerField(null=False) range_end = models.PositiveBigIntegerField(null=False) info = models.TextField() - - -# -- Add required column -# -# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (0, 'Unitless', '', 'A value with no units'); -# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (1, 'Time', 's', 'Time in seconds'); -# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (2, 'Volts', 'V', 'Voltage'); -# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (3, 'Amps', 'A', 'Current'); -# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (4, 'Energy', 'Wh', 'Energy in Watt-Hours'); -# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (5, 'Charge', 'Ah', 'Charge in Amp-Hours'); -# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (6, 'Temperature', '°c', 'Temperature in Centigrade'); -# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (7, 'Power', 'W', 'Power in Watts'); -# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (8, 'Ohm', 'Ω', 'Resistance or impediance in Ohms'); -# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (9, 'Degrees', '°', 'Angle in degrees'); -# INSERT INTO experiment.unit (id, name, symbol, description) VALUES (10, 'Frequency', 'Hz', 'Frequency in Hz'); -# SELECT setval('experiment.unit_id_seq'::regclass, 10); -# -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (-1, 'Unknown', 'unknown column type', NULL); -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (0, 'Sample Number', 'The sample or record number. Is increased by one each time a test machine records a reading. Usually counts from 1 at the start of a test', 0); -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (1, 'Time', 'The time in seconds since the test run began.', 1); -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (2, 'Volts', 'The voltage of the cell.', 2); -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (3, 'Amps', 'The current current.', 3); -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (4, 'Energy Capacity', 'The Energy Capacity.', 4); -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (5, 'Charge Capacity', 'The Charge Capacity.', 5); -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (6, 'Temperature', 'The temperature.', 6); -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (7, 'Step Time', 'The time in seconds since the current step began.', 1); -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (8, 'Impedence Magnitude', 'The magnitude of the impedence (EIS).', 8); -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (9, 'Impedence Phase', 'The phase of the impedence (EIS).', 9); -# INSERT INTO experiment.column_type (id, name, description, unit_id) VALUES (10, 'Frequency', 'The frequency of the input EIS voltage signal.', 10); -# SELECT setval('experiment.column_type_id_seq'::regclass, 10); \ No newline at end of file diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py new file mode 100644 index 00000000..c0f6cbbe --- /dev/null +++ b/django/backend_django/galvanalyser/serializers.py @@ -0,0 +1,105 @@ +from .models import Harvester, \ + MonitoredPath, \ + MonitoredFor, \ + ObservedFile, \ + CellData, \ + Dataset, \ + Equipment, \ + DatasetEquipment, \ + DataUnit, \ + DataColumnType, \ + DataColumn, \ + TimeseriesData, \ + TimeseriesRangeLabel +from django.contrib.auth.models import User, Group +from rest_framework import serializers + + +class HarvesterSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = Harvester + fields = '__all__' + + +class MonitoredPathSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = MonitoredPath + fields = '__all__' + + +class MonitoredForSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = MonitoredFor + fields = '__all__' + + +class ObservedFileSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = ObservedFile + fields = '__all__' + + +class CellDataSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = CellData + fields = '__all__' + + +class DatasetSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = Dataset + fields = '__all__' + + +class EquipmentSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = Equipment + fields = '__all__' + + +class DatasetEquipmentSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = DatasetEquipment + fields = '__all__' + + +class DataUnitSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = DataUnit + fields = '__all__' + + +class DataColumnTypeSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = DataColumnType + fields = '__all__' + + +class DataColumnSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = DataColumn + fields = '__all__' + + +class TimeseriesDataSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = TimeseriesData + fields = '__all__' + + +class TimeseriesRangeLabelSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = TimeseriesRangeLabel + fields = '__all__' + + +class UserSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = User + fields = '__all__' + + +class GroupSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = Group + fields = '__all__' diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 91ea44a2..310ceb38 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -1,3 +1,164 @@ -from django.shortcuts import render +from .serializers import HarvesterSerializer, \ + MonitoredPathSerializer, \ + MonitoredForSerializer, \ + ObservedFileSerializer, \ + CellDataSerializer, \ + DatasetSerializer, \ + EquipmentSerializer, \ + DatasetEquipmentSerializer, \ + DataUnitSerializer, \ + DataColumnTypeSerializer, \ + DataColumnSerializer, \ + TimeseriesDataSerializer, \ + TimeseriesRangeLabelSerializer, \ + UserSerializer, \ + GroupSerializer +from .models import Harvester, \ + MonitoredPath, \ + MonitoredFor, \ + ObservedFile, \ + CellData, \ + Dataset, \ + Equipment, \ + DatasetEquipment, \ + DataUnit, \ + DataColumnType, \ + DataColumn, \ + TimeseriesData, \ + TimeseriesRangeLabel +from django.contrib.auth.models import User, Group +from rest_framework import viewsets +from rest_framework import permissions + +class HarvesterViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = HarvesterSerializer + queryset = Harvester.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class MonitoredPathViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = MonitoredPathSerializer + queryset = MonitoredPath.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class MonitoredForViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = MonitoredForSerializer + queryset = MonitoredFor.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class ObservedFileViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = ObservedFileSerializer + queryset = ObservedFile.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class CellDataViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = CellDataSerializer + queryset = CellData.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class DatasetViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = DatasetSerializer + queryset = Dataset.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class EquipmentViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = EquipmentSerializer + queryset = Equipment.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class DatasetEquipmentViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = DatasetEquipmentSerializer + queryset = DatasetEquipment.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class DataUnitViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = DataUnitSerializer + queryset = DataUnit.objects.all() + + +class DataColumnTypeViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = DataColumnTypeSerializer + queryset = DataColumnType.objects.all() + + +class DataColumnViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = DataColumnSerializer + queryset = DataColumn.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class TimeseriesDataViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = TimeseriesDataSerializer + queryset = TimeseriesData.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class TimeseriesRangeLabelViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = TimeseriesRangeLabelSerializer + queryset = TimeseriesRangeLabel.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class UserViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = UserSerializer + queryset = User.objects.all() + permission_classes = [permissions.IsAuthenticated] + + +class GroupViewSet(viewsets.ModelViewSet): + """ + TODO: document + """ + serializer_class = GroupSerializer + queryset = Group.objects.all() + permission_classes = [permissions.IsAuthenticated] -# Create your views here. From 8d763f02e65ab0d1510a63d01b1ca14c76b867c3 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Thu, 8 Dec 2022 15:45:19 +0000 Subject: [PATCH 07/79] django-react integration --- backend/galvanalyser/routes.py | 32 +++--- django/Dockerfile | 3 +- .../galvanalyser/fixtures/Users.json | 13 +++ django/backend_django/galvanalyser/models.py | 5 + django/backend_django/galvanalyser/views.py | 25 ++--- django/requirements.txt | 4 +- django/server.sh | 1 + frontend/src/Api.js | 102 +++++++++--------- frontend/src/Core.js | 13 +-- frontend/src/GetDatasetMatlab.js | 2 +- frontend/src/Harvesters.js | 7 +- frontend/src/Login.js | 47 +++++--- frontend/src/auth/index.js | 5 +- 13 files changed, 146 insertions(+), 113 deletions(-) create mode 100644 django/backend_django/galvanalyser/fixtures/Users.json diff --git a/backend/galvanalyser/routes.py b/backend/galvanalyser/routes.py index b6561d04..4d7e0074 100644 --- a/backend/galvanalyser/routes.py +++ b/backend/galvanalyser/routes.py @@ -75,7 +75,7 @@ def refresh_expiring_jwts(response): return response -@app.route('/api/login', methods=['POST']) +@app.route('/api-auth/login', methods=['POST']) def login(): auth = request.authorization @@ -114,7 +114,7 @@ def login(): ) -@app.route("/api/logout", methods=["POST"]) +@app.route("/api-auth/logout", methods=["POST"]) def logout(): response = jsonify({"message": "logout successful"}) unset_jwt_cookies(response) @@ -192,8 +192,8 @@ def user(id_=None): return jsonify(session.get(User, id_)) -@app.route('/api/dataset', methods=['GET']) -@app.route('/api/dataset/', methods=['GET', 'PUT']) +@app.route('/Dataset', methods=['GET']) +@app.route('/Dataset/', methods=['GET', 'PUT']) @cross_origin() @jwt_required() def dataset(id_=None): @@ -292,8 +292,8 @@ def dataset(id_=None): return jsonify(dataset) -@ app.route('/api/equipment', methods=['GET', 'POST']) -@ app.route('/api/equipment/', methods=['GET', 'PUT', 'DELETE']) +@ app.route('/Equipment', methods=['GET', 'POST']) +@ app.route('/Equipment/', methods=['GET', 'PUT', 'DELETE']) @ cross_origin() @ jwt_required() def equipment(id_=None): @@ -345,8 +345,8 @@ def equipment(id_=None): return jsonify({'success': True}), 200 -@ app.route('/api/cell', methods=['GET', 'POST']) -@ app.route('/api/cell/', methods=['GET', 'PUT', 'DELETE']) +@ app.route('/CellData', methods=['GET', 'POST']) +@ app.route('/CellData/', methods=['GET', 'PUT', 'DELETE']) @ cross_origin() @ jwt_required() def cell(id_=None): @@ -419,8 +419,8 @@ def cell(id_=None): return jsonify({'success': True}), 200 -@ app.route('/api/manufacturer', methods=['GET', 'POST']) -@ app.route('/api/manufacturer/', methods=['GET', 'PUT', 'DELETE']) +@ app.route('/Manufacturer', methods=['GET', 'POST']) +@ app.route('/Manufacturer/', methods=['GET', 'PUT', 'DELETE']) @ jwt_required() @ cross_origin() def manufacturer(id_=None): @@ -481,7 +481,7 @@ def dataset_by_id(dataset_id): return DatasetRow.to_json(datasets) -@ app.route('/api/file', methods=['GET']) +@ app.route('/MonitoredPath', methods=['GET']) @ jwt_required() @ cross_origin() def file(): @@ -555,7 +555,7 @@ def get_env_celery(): return {env_var: os.getenv(env_var)} -@ app.route('/api/harvester//env', methods=['GET']) +@ app.route('/Harvester//env', methods=['GET']) @ jwt_required() @ cross_origin() def env_harvester(id_=None): @@ -584,8 +584,8 @@ def run_harvester(id_=None): return jsonify({'success': True}), 200 -@ app.route('/api/harvester', methods=['GET', 'POST']) -@ app.route('/api/harvester/', methods=['GET', 'PUT', 'DELETE']) +@ app.route('/Harvester', methods=['GET', 'POST']) +@ app.route('/Harvester/', methods=['GET', 'PUT', 'DELETE']) @ jwt_required() @ cross_origin() def harvester(id_=None): @@ -654,8 +654,8 @@ def harvester(id_=None): return jsonify({'success': True}), 200 -@ app.route('/api/monitored_path', methods=['GET', 'POST']) -@ app.route('/api/monitored_path/', methods=['GET', 'PUT', 'DELETE']) +@ app.route('/MonitoredPath', methods=['GET', 'POST']) +@ app.route('/MonitoredPath/', methods=['GET', 'PUT', 'DELETE']) @ jwt_required() @ cross_origin() def monitored_path(id_=None): diff --git a/django/Dockerfile b/django/Dockerfile index 1f26bf56..632b5a36 100644 --- a/django/Dockerfile +++ b/django/Dockerfile @@ -6,7 +6,8 @@ ENV PYTHONUNBUFFERED=1 # Install postgresql-client for healthchecking RUN apt-get update && \ apt-get install -y \ - postgresql-client && \ + postgresql-client \ + build-essential libssl-dev libffi-dev python3-dev python-dev && \ apt-get autoremove && \ apt-get autoclean diff --git a/django/backend_django/galvanalyser/fixtures/Users.json b/django/backend_django/galvanalyser/fixtures/Users.json new file mode 100644 index 00000000..45941f1a --- /dev/null +++ b/django/backend_django/galvanalyser/fixtures/Users.json @@ -0,0 +1,13 @@ +[ + { + "pk": 42, + "model": "auth.user", + "fields": { + "username": "admin", + "password": "pbkdf2_sha256$390000$RxLzqctUYIeEpAKWJWjRZV$jbeQqoCb6ZWs7HGGlG2nTdp4VRmRXCbkq7vXWykU2ug=", + "is_superuser": true, + "is_staff": true, + "is_active": true + } + } +] \ No newline at end of file diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index fcf24cbe..161ad64a 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -89,6 +89,11 @@ class DataUnit(models.Model): symbol = models.TextField(null=False) description = models.TextField() + def __str__(self): + if self.symbol: + return f"{self.symbol} | {self.name} - {self.description}" + return f"{self.name} - {self.description}" + class DataColumnType(models.Model): unit = models.ForeignKey(to=DataUnit, on_delete=models.SET_NULL, null=True) diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 310ceb38..2cda0a8e 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -28,15 +28,22 @@ TimeseriesRangeLabel from django.contrib.auth.models import User, Group from rest_framework import viewsets -from rest_framework import permissions +from rest_framework.permissions import AllowAny +from knox.views import LoginView as KnoxLoginView +from rest_framework.authentication import BasicAuthentication + + +class LoginView(KnoxLoginView): + permission_classes = [AllowAny] + authentication_classes = [BasicAuthentication] + class HarvesterViewSet(viewsets.ModelViewSet): """ TODO: document """ serializer_class = HarvesterSerializer - queryset = Harvester.objects.all() - permission_classes = [permissions.IsAuthenticated] + queryset = Harvester.objects.all().order_by('is_running', 'pk') class MonitoredPathViewSet(viewsets.ModelViewSet): @@ -45,7 +52,6 @@ class MonitoredPathViewSet(viewsets.ModelViewSet): """ serializer_class = MonitoredPathSerializer queryset = MonitoredPath.objects.all() - permission_classes = [permissions.IsAuthenticated] class MonitoredForViewSet(viewsets.ModelViewSet): @@ -54,7 +60,6 @@ class MonitoredForViewSet(viewsets.ModelViewSet): """ serializer_class = MonitoredForSerializer queryset = MonitoredFor.objects.all() - permission_classes = [permissions.IsAuthenticated] class ObservedFileViewSet(viewsets.ModelViewSet): @@ -63,7 +68,6 @@ class ObservedFileViewSet(viewsets.ModelViewSet): """ serializer_class = ObservedFileSerializer queryset = ObservedFile.objects.all() - permission_classes = [permissions.IsAuthenticated] class CellDataViewSet(viewsets.ModelViewSet): @@ -72,7 +76,6 @@ class CellDataViewSet(viewsets.ModelViewSet): """ serializer_class = CellDataSerializer queryset = CellData.objects.all() - permission_classes = [permissions.IsAuthenticated] class DatasetViewSet(viewsets.ModelViewSet): @@ -81,7 +84,6 @@ class DatasetViewSet(viewsets.ModelViewSet): """ serializer_class = DatasetSerializer queryset = Dataset.objects.all() - permission_classes = [permissions.IsAuthenticated] class EquipmentViewSet(viewsets.ModelViewSet): @@ -90,7 +92,6 @@ class EquipmentViewSet(viewsets.ModelViewSet): """ serializer_class = EquipmentSerializer queryset = Equipment.objects.all() - permission_classes = [permissions.IsAuthenticated] class DatasetEquipmentViewSet(viewsets.ModelViewSet): @@ -99,7 +100,6 @@ class DatasetEquipmentViewSet(viewsets.ModelViewSet): """ serializer_class = DatasetEquipmentSerializer queryset = DatasetEquipment.objects.all() - permission_classes = [permissions.IsAuthenticated] class DataUnitViewSet(viewsets.ModelViewSet): @@ -124,7 +124,6 @@ class DataColumnViewSet(viewsets.ModelViewSet): """ serializer_class = DataColumnSerializer queryset = DataColumn.objects.all() - permission_classes = [permissions.IsAuthenticated] class TimeseriesDataViewSet(viewsets.ModelViewSet): @@ -133,7 +132,6 @@ class TimeseriesDataViewSet(viewsets.ModelViewSet): """ serializer_class = TimeseriesDataSerializer queryset = TimeseriesData.objects.all() - permission_classes = [permissions.IsAuthenticated] class TimeseriesRangeLabelViewSet(viewsets.ModelViewSet): @@ -142,7 +140,6 @@ class TimeseriesRangeLabelViewSet(viewsets.ModelViewSet): """ serializer_class = TimeseriesRangeLabelSerializer queryset = TimeseriesRangeLabel.objects.all() - permission_classes = [permissions.IsAuthenticated] class UserViewSet(viewsets.ModelViewSet): @@ -151,7 +148,6 @@ class UserViewSet(viewsets.ModelViewSet): """ serializer_class = UserSerializer queryset = User.objects.all() - permission_classes = [permissions.IsAuthenticated] class GroupViewSet(viewsets.ModelViewSet): @@ -160,5 +156,4 @@ class GroupViewSet(viewsets.ModelViewSet): """ serializer_class = GroupSerializer queryset = Group.objects.all() - permission_classes = [permissions.IsAuthenticated] diff --git a/django/requirements.txt b/django/requirements.txt index 4816fa9f..abbb0c4f 100644 --- a/django/requirements.txt +++ b/django/requirements.txt @@ -1,4 +1,6 @@ celery==5.2.7 -Django==4.1.3 +Django==4.1.4 +django-cors-headers==3.13.0 djangorestframework==3.14.0 +django-rest-knox==4.2.0 psycopg2-binary==2.9.5 diff --git a/django/server.sh b/django/server.sh index 3a8ef2e3..2c05e773 100644 --- a/django/server.sh +++ b/django/server.sh @@ -21,6 +21,7 @@ python manage.py migrate >&2 echo "... populating database" python manage.py loaddata galvanalyser/fixtures/DataUnit.json python manage.py loaddata galvanalyser/fixtures/DataColumnType.json +python manage.py loaddata galvanalyser/fixtures/Users.json >&2 echo "Initialisation complete - starting server" #exec "$@" diff --git a/frontend/src/Api.js b/frontend/src/Api.js index fa2d0f06..fdd0d8d7 100644 --- a/frontend/src/Api.js +++ b/frontend/src/Api.js @@ -1,5 +1,5 @@ -const url = '/api/'; +const url = 'http://localhost:5001/'; const headers = { 'Accept': 'application/json', 'Content-Type': 'application/json' @@ -7,20 +7,14 @@ const headers = { let user = null; -export function getUser() { - return authFetch(url + 'user/current').then(response => { - if (!response.ok) { - return Promise.reject() - } - return response.json() - }).then(data => { - console.log('setUser ', data) - user = data - return data - }); +export function handleLogin(data) { + user = {...data.user, token: data.token}; } +export function getUser() {return user;} + export function isAdmin() { + return false; if (!user) { return false; } @@ -30,11 +24,14 @@ export function isAdmin() { export async function login(username, password) { let headers = new Headers(); headers.set('Authorization', 'Basic ' + btoa(username + ":" + password)); - return fetch(url + '/login', {method: 'POST', headers: headers}) + headers.set('Accept', 'application/json'); + return fetch(url + 'login/', {method: 'POST', headers: headers}) } export async function logout() { - return fetch(url + '/logout', {method: 'POST'}); + let headers = new Headers(); + headers.set('Accept', 'application/json'); + return fetch(url + 'logout/', {method: 'POST'}); } export function getCookie(name) { @@ -45,14 +42,19 @@ export function getCookie(name) { export function loggedIn() { const cookie = getCookie('csrf_access_token'); - return cookie !== undefined; + return cookie !== undefined && user; } async function authFetch(url, options) { + const token = user?.token; let newOptions = {...options}; newOptions.credentials = 'same-origin'; newOptions.headers = {...newOptions.headers}; + newOptions.headers['Content-Type'] = "application/json"; + newOptions.headers['Accept'] = "application/json"; + newOptions.headers['Authorization'] = `Token ${token}`; newOptions.headers['X-CSRF-TOKEN'] = getCookie('csrf_access_token'); + url = /\/$/.test(url) ? url : `${url}/`; return fetch(url, newOptions).then((response) => { if (response.status === 401) { return logout().then(() => { @@ -60,12 +62,12 @@ async function authFetch(url, options) { }); } return response; - });; + }); } export async function run_harvester(id) { return authFetch( - url + `harvester/${id}/run`, + url + `harvesters/${id}/run`, { method: 'PUT', headers: headers, @@ -78,19 +80,19 @@ export async function getToken() { } export async function env_harvester(id) { - return authFetch(url + `harvester/${id}/env`); + return authFetch(url + `harvesters/${id}/env`); } export async function harvesters(id) { if (id) { - return authFetch(url + `harvester/${id}`); + return authFetch(url + `harvesters/${id}`); } - return authFetch(url + 'harvester'); + return authFetch(url + 'harvesters/'); } export async function delete_harvester(id) { return authFetch( - url + `harvester/${id}`, + url + `harvesters/${id}`, { method: 'DELETE', } @@ -102,7 +104,7 @@ export async function delete_harvester(id) { // { machine_id: ? } export async function add_harvester(harvester) { return authFetch( - url + `harvester`, + url + `harvesters/`, { method: 'POST', headers: headers, @@ -116,7 +118,7 @@ export async function add_harvester(harvester) { // { machine_id: ? } export async function update_harvester(id, harvester) { return authFetch( - url + `harvester/${id}`, + url + `harvesters/${id}`, { method: 'PUT', headers: headers, @@ -130,7 +132,7 @@ export async function update_harvester(id, harvester) { // { path: ?, monitored_for: ?, harvester_id: ? } export async function update_monitored_path(id, path) { return authFetch( - url + `monitored_path/${id}`, + url + `monitored_paths/${id}`, { method: 'PUT', headers: headers, @@ -144,7 +146,7 @@ export async function update_monitored_path(id, path) { // { path: ?, monitored_for: ?, harvester_id: ? } export async function add_monitored_path(path) { return authFetch( - url + `monitored_path`, + url + `monitored_paths`, { method: 'POST', headers: headers, @@ -155,7 +157,7 @@ export async function add_monitored_path(path) { export async function delete_monitored_path(id) { return authFetch( - url + `monitored_path/${id}`, + url + `monitored_paths/${id}`, { method: 'DELETE', } @@ -164,23 +166,23 @@ export async function delete_monitored_path(id) { export async function monitored_paths(harvester_id) { return authFetch( - url + `monitored_path?harvester_id=${harvester_id}` + url + `monitored_paths?harvester_id=${harvester_id}` ); } export async function users() { - return authFetch(url + 'user'); + return authFetch(url + 'users/'); } export async function files(path_id) { - return authFetch(url + `file?path_id=${path_id}`); + return authFetch(url + `files?path_id=${path_id}`); } export async function datasets(id) { if (id) { - return authFetch(url + `dataset/${id}`); + return authFetch(url + `datasets/${id}`); } - return authFetch(url + 'dataset'); + return authFetch(url + 'datasets/'); } @@ -191,7 +193,7 @@ export async function datasets(id) { // purpose: ? } export async function update_dataset(id, dataset) { return authFetch( - url + `dataset/${id}`, + url + `datasets/${id}`, { method: 'PUT', headers: headers, @@ -208,7 +210,7 @@ export async function equipment(id) { if (id) { return authFetch(url + `equipment/${id}`); } - return authFetch(url + `equipment`); + return authFetch(url + `equipment/`); } //// equipment is object with fields: @@ -216,7 +218,7 @@ export async function equipment(id) { // { name: ?, type: ?, } export async function add_equipment(equipment) { return authFetch( - url + `equipment`, + url + `equipment/`, { method: 'POST', headers: headers, @@ -250,9 +252,9 @@ export async function delete_equipment(id) { export async function cells(id) { if (id) { - return authFetch(url + `cell/${id}`); + return authFetch(url + `cells/${id}`); } - return authFetch(url + `cell`); + return authFetch(url + `cells/`); } //// cell is object with fields: @@ -262,7 +264,7 @@ export async function cells(id) { // nominal_capacity: ?, nominal_cell_weight: ? } export async function add_cell(cell) { return authFetch( - url + `cell`, + url + `cells/`, { method: 'POST', headers: headers, @@ -278,7 +280,7 @@ export async function add_cell(cell) { // nominal_capacity: ?, nominal_cell_weight: ? } export async function update_cell(id, cell) { return authFetch( - url + `cell/${id}`, + url + `cells/${id}`, { method: 'PUT', headers: headers, @@ -289,7 +291,7 @@ export async function update_cell(id, cell) { export async function delete_cell(id) { return authFetch( - url + `cell/${id}`, + url + `cells/${id}`, { method: 'DELETE', } @@ -298,14 +300,14 @@ export async function delete_cell(id) { export async function manufacturers(id) { if (id) { - return authFetch(url + `manufacturer/${id}`); + return authFetch(url + `manufacturers/${id}`); } - return authFetch(url + `manufacturer`); + return authFetch(url + `manufacturers/`); } export async function delete_manufacturer(id) { return authFetch( - url + `manufacturer/${id}`, + url + `manufacturers/${id}`, { method: 'DELETE', } @@ -317,7 +319,7 @@ export async function delete_manufacturer(id) { // { name: ? } export async function add_manufacturer(manufacturer) { return authFetch( - url + `manufacturer`, + url + `manufacturers/`, { method: 'POST', headers: headers, @@ -331,7 +333,7 @@ export async function add_manufacturer(manufacturer) { // { path: ?, monitored_for: ?, harvester_id: ? } export async function update_manufacturer(id, manufacturer) { return authFetch( - url + `manufacturer/${id}`, + url + `manufacturers/${id}`, { method: 'PUT', headers: headers, @@ -342,14 +344,14 @@ export async function update_manufacturer(id, manufacturer) { export async function institutions(id) { if (id) { - return authFetch(url + `institution/${id}`); + return authFetch(url + `institutions/${id}`); } - return authFetch(url + `institution`); + return authFetch(url + `institutions/`); } export async function delete_institution(id) { return authFetch( - url + `institution/${id}`, + url + `institutions/${id}`, { method: 'DELETE', } @@ -361,7 +363,7 @@ export async function delete_institution(id) { // { name: ? } export async function add_institution(institution) { return authFetch( - url + `institution`, + url + `institutions/`, { method: 'POST', headers: headers, @@ -375,7 +377,7 @@ export async function add_institution(institution) { // { path: ?, monitored_for: ?, harvester_id: ? } export async function update_institution(id, institution) { return authFetch( - url + `institution/${id}`, + url + `institutions/${id}`, { method: 'PUT', headers: headers, @@ -407,7 +409,7 @@ export async function update_metadata(dataset_id, metadata) { } export async function timeseries_column(dataset_id, col_id) { - return authFetch(url + `dataset/${dataset_id}/${col_id}`, + return authFetch(url + `datasets/${dataset_id}/${col_id}`, { responseType: 'arraybuffer', headers: { diff --git a/frontend/src/Core.js b/frontend/src/Core.js index 200f856a..8ddcbe1c 100644 --- a/frontend/src/Core.js +++ b/frontend/src/Core.js @@ -24,7 +24,7 @@ import DialogContentText from '@mui/material/DialogContentText'; import DialogTitle from '@mui/material/DialogTitle'; import BatteryUnknownIcon from '@mui/icons-material/BatteryUnknown'; import BackupIcon from '@mui/icons-material/Backup'; -import {loggedIn, logout, getToken, getUser, isAdmin} from "./Api" +import {loggedIn, handleLogin, logout, getToken, getUser, isAdmin} from "./Api" import { makeStyles} from "@mui/styles"; import CssBaseline from '@mui/material/CssBaseline'; @@ -141,15 +141,8 @@ const useStyles = makeStyles((theme) => ({ export default function Core() { const { pathname } = useLocation(); const classes = useStyles(); - const [user, setUser] = React.useState(null); - useEffect(() => { - getUser().then(setUser) - }, []); - - const handleLogin = () => { - getUser().then(setUser) - } + const user = getUser() const userIsAdmin = isAdmin() @@ -253,8 +246,6 @@ export default function Core() { - - ); diff --git a/frontend/src/GetDatasetMatlab.js b/frontend/src/GetDatasetMatlab.js index f9be0d4c..3793e500 100644 --- a/frontend/src/GetDatasetMatlab.js +++ b/frontend/src/GetDatasetMatlab.js @@ -33,7 +33,7 @@ export default function GetDatasetMatlab({dataset}) { % login to galvanalyser > Generate API Token token = '${token}'; -apiURL = '${host}/api/dataset'; +apiURL = '${host}/Dataset'; options = weboptions('HeaderFields', {'Authorization' ['Bearer ' token]}); % Datasets can be referenced by name or by id. diff --git a/frontend/src/Harvesters.js b/frontend/src/Harvesters.js index bfa3f1c0..6cd9e362 100644 --- a/frontend/src/Harvesters.js +++ b/frontend/src/Harvesters.js @@ -147,7 +147,7 @@ export default function Harvesters() { useEffect(() => { refreshHarvesters(); const interval = setInterval(() => { - refreshHarvesters(); + // refreshHarvesters(); }, 5000); return () => clearInterval(interval); }, []); @@ -156,9 +156,10 @@ export default function Harvesters() { harvesters().then((response) => { if (response.ok) { return response.json().then((result) => { - setHarvesterData(result.sort((arg1, arg2) => arg1.id - arg2.id)); + const results = result.results; + setHarvesterData(results.sort((arg1, arg2) => arg1.id - arg2.id)); setSelected(oldSelected => { - const newSelected = result.find(x => x.id === oldSelected.id) + const newSelected = results.find(x => x.id === oldSelected.id) return newSelected || {id: null}; }); }); diff --git a/frontend/src/Login.js b/frontend/src/Login.js index a8379dfc..a552f349 100644 --- a/frontend/src/Login.js +++ b/frontend/src/Login.js @@ -1,6 +1,6 @@ import {login} from "./Api" import { makeStyles } from '@mui/styles' -import React, { useState } from "react"; +import React, { useState, useRef } from "react"; import Button from '@mui/material/Button'; import CssBaseline from '@mui/material/CssBaseline'; import Alert from '@mui/lab/Alert'; @@ -38,22 +38,38 @@ export default function Login({ onLogin }) { const [password, setPassword] = useState('') const [error, setError] = useState('') - const navigate =useNavigate(); + const navigate = useNavigate(); + + const submit = useRef(null); + const username_input = useRef(null); + const password_input = useRef(null); + + const handleEnterKey = (e) => { + if(e.key === "Enter") { + if (username === "") username_input.current.focus(); + else if (password === "") password_input.current.focus(); + else submit.current.click(); + } + } const onSubmitClick = (e)=>{ e.preventDefault() console.log("You pressed login") - login(username, password).then(r => { - if (!r.ok) { - console.log(r, r.data) - return r.json().then(data=>setError(data.message)); - } - return r.json().then(data => { - setError('') - onLogin() - navigate('/'); - }) - }); + if (username === "") username_input.current.focus(); + else if (password === "") password_input.current.focus(); + else { + login(username, password).then(r => { + if (!r.ok) { + console.log(r, r.data) + return r.json().then(data=>setError(data.message)); + } + return r.json().then(data => { + setError('') + onLogin(data) + navigate('/'); + }) + }); + } } const handleUsernameChange = (e) => { @@ -83,6 +99,8 @@ export default function Login({ onLogin }) { name="username" autoComplete="username" onChange={handleUsernameChange} + onKeyDown={handleEnterKey} + ref={username_input} autoFocus /> @@ -104,6 +124,7 @@ export default function Login({ onLogin }) { } + + + + { + // @ts-ignore + + {this.header} + { + // @ts-ignore + + {this.state.row_data.map(this.row_fun)} + {this.new_entry_row} + } + } + + ); + }; + return PaginatedTable; +}(react_1.Component)); +exports.default = PaginatedTable; diff --git a/frontend/src/PaginatedTable.tsx b/frontend/src/PaginatedTable.tsx new file mode 100644 index 00000000..f30a1ddb --- /dev/null +++ b/frontend/src/PaginatedTable.tsx @@ -0,0 +1,155 @@ +/** + * Offer a table with previous/next links. + */ +import classNames from 'classnames' +import {TableHead, TableRow} from "@mui/material"; +import {Component} from "react"; +import TableContainer from "@mui/material/TableContainer"; +import Table from "@mui/material/Table"; +import TableBody from "@mui/material/TableBody"; +import Connection, {APIResponse} from "./APIConnection"; + +type RowFunOptions = { + savedRow: any, + onRowSave: (row: any) => void, + selected: boolean, + onSelectRow: (id: number) => void, + disabledSave: boolean, + addIcon?: boolean, + [key: string]: any +} + +type RowFun = (row: any) => (options: RowFunOptions) => typeof TableRow + +export type PaginationLinks = { + previous?: string | null, + next?: string | null, +} + +type PaginationDataFun = (url?: string | null) => APIResponse + +type PaginationProps = PaginationLinks & { get_data_fun: PaginationDataFun; position: string } + + +class Pagination extends Component { + render() { + return ( +
+ + +
+ ) + } +} + +export type PaginatedTableProps = { + header: typeof TableHead, + row_fun: RowFun, + initial_url: string, + new_entry_row?: typeof TableRow, + styles?: any, + [key: string]: any +} + +type PaginatedTableState = { + row_data: any[], + links: PaginationLinks +} + +export default class PaginatedTable extends Component { + header: typeof TableHead; + row_fun: RowFun; + new_entry_row: typeof TableRow | undefined; + styles: any; + initial_url: string; + + state = { + row_data: [], + links: {previous: null, next: null} + } + + constructor(props: PaginatedTableProps) { + super(props) + this.header = props.data.header + this.row_fun = props.data.row_fun + this.new_entry_row = props.data.new_entry_row + this.styles = props.data.styles + this.initial_url = props.data.initial_url + } + + componentDidMount() { + this.get_data(this.initial_url) + } + + get_data: PaginationDataFun = async (url) => { + if (!url) return; + await Connection.fetch(url) + // @ts-ignore + .then((res: APIResponse) => { + console.log(res); + this.setState({ + row_data: res.results, + links: { + next: res.next, + previous: res.previous + }, + }) + }) + .catch(e => { + console.error('Paginated Table error', e) + }) + } + + render() { + return ( +
+ + + { + // @ts-ignore + + {this.header} + { + // @ts-ignore + + {this.state.row_data.map(this.row_fun)} + {this.new_entry_row} + + } +
+ } + + +
+ ) + } +} \ No newline at end of file diff --git a/frontend/src/react-app-env.d.ts b/frontend/src/react-app-env.d.ts new file mode 100644 index 00000000..6431bc5f --- /dev/null +++ b/frontend/src/react-app-env.d.ts @@ -0,0 +1 @@ +/// diff --git a/frontend/tsconfig.json b/frontend/tsconfig.json new file mode 100644 index 00000000..78701d78 --- /dev/null +++ b/frontend/tsconfig.json @@ -0,0 +1,27 @@ +{ + "compilerOptions": { + "jsx": "react-jsx", + "target": "es5", + "lib": [ + "dom", + "dom.iterable", + "esnext" + ], + "allowJs": true, + "skipLibCheck": true, + "esModuleInterop": true, + "allowSyntheticDefaultImports": true, + "strict": true, + "forceConsistentCasingInFileNames": true, + "noFallthroughCasesInSwitch": true, + "module": "esnext", + "moduleResolution": "node", + "resolveJsonModule": true, + "isolatedModules": true, + "noEmit": true + }, + "include": [ + "src/*", + "src/**/*" + ] +} diff --git a/frontend/yarn.lock b/frontend/yarn.lock index cf9f1b80..905d82c5 100644 --- a/frontend/yarn.lock +++ b/frontend/yarn.lock @@ -2359,6 +2359,14 @@ expect "^29.0.0" pretty-format "^29.0.0" +"@types/jest@^29.2.5": + version "29.2.5" + resolved "https://registry.yarnpkg.com/@types/jest/-/jest-29.2.5.tgz#c27f41a9d6253f288d1910d3c5f09484a56b73c0" + integrity sha512-H2cSxkKgVmqNHXP7TC2L/WUorrZu8ZigyRywfVzv6EyBlxj39n4C00hjXYQWsbwqgElaj/CiAeSRmk5GoaKTgw== + dependencies: + expect "^29.0.0" + pretty-format "^29.0.0" + "@types/json-schema@*", "@types/json-schema@^7.0.3", "@types/json-schema@^7.0.4", "@types/json-schema@^7.0.5", "@types/json-schema@^7.0.7", "@types/json-schema@^7.0.8", "@types/json-schema@^7.0.9": version "7.0.11" resolved "https://registry.yarnpkg.com/@types/json-schema/-/json-schema-7.0.11.tgz#d421b6c527a3037f7c84433fd2c4229e016863d3" @@ -2391,6 +2399,11 @@ resolved "https://registry.yarnpkg.com/@types/node/-/node-18.11.9.tgz#02d013de7058cea16d36168ef2fc653464cfbad4" integrity sha512-CRpX21/kGdzjOpFsZSkcrXMGIBWMGNIHXXBVFSH+ggkftxg+XYP20TESbh+zFvFj3EQOl5byk0HTRn1IL6hbqg== +"@types/node@^18.11.18": + version "18.11.18" + resolved "https://registry.yarnpkg.com/@types/node/-/node-18.11.18.tgz#8dfb97f0da23c2293e554c5a50d61ef134d7697f" + integrity sha512-DHQpWGjyQKSHj3ebjFI/wRKcqQcdR+MoFBygntYOZytCqNfkd2ZC4ARDJ2DQqhjH5p85Nnd3jhUJIXrszFX/JA== + "@types/normalize-package-data@^2.4.0": version "2.4.1" resolved "https://registry.yarnpkg.com/@types/normalize-package-data/-/normalize-package-data-2.4.1.tgz#d3357479a0fdfdd5907fe67e17e0a85c906e1301" @@ -2426,6 +2439,13 @@ resolved "https://registry.yarnpkg.com/@types/range-parser/-/range-parser-1.2.4.tgz#cd667bcfdd025213aafb7ca5915a932590acdcdc" integrity sha512-EEhsLsD6UsDM1yFhAvy0Cjr6VwmpMWqFBCb9w07wVugF7w9nfajxLuVmngTIpgS6svCnm6Vaw+MZhoDCKnOfsw== +"@types/react-dom@^18.0.10": + version "18.0.10" + resolved "https://registry.yarnpkg.com/@types/react-dom/-/react-dom-18.0.10.tgz#3b66dec56aa0f16a6cc26da9e9ca96c35c0b4352" + integrity sha512-E42GW/JA4Qv15wQdqJq8DL4JhNpB3prJgjgapN3qJT9K2zO5IIAQh4VXvCEDupoqAwnz0cY4RlXeC/ajX5SFHg== + dependencies: + "@types/react" "*" + "@types/react-is@^16.7.1 || ^17.0.0": version "17.0.3" resolved "https://registry.yarnpkg.com/@types/react-is/-/react-is-17.0.3.tgz#2d855ba575f2fc8d17ef9861f084acc4b90a137a" @@ -2449,6 +2469,15 @@ "@types/scheduler" "*" csstype "^3.0.2" +"@types/react@^18.0.26": + version "18.0.26" + resolved "https://registry.yarnpkg.com/@types/react/-/react-18.0.26.tgz#8ad59fc01fef8eaf5c74f4ea392621749f0b7917" + integrity sha512-hCR3PJQsAIXyxhTNSiDFY//LhnMZWpNNr5etoCqx/iUfGc5gXWtQR2Phl908jVR6uPXacojQWTg4qRpkxTuGug== + dependencies: + "@types/prop-types" "*" + "@types/scheduler" "*" + csstype "^3.0.2" + "@types/resolve@0.0.8": version "0.0.8" resolved "https://registry.yarnpkg.com/@types/resolve/-/resolve-0.0.8.tgz#f26074d238e02659e323ce1a13d041eee280e194" @@ -12863,6 +12892,11 @@ typedarray@^0.0.6: resolved "https://registry.yarnpkg.com/typedarray/-/typedarray-0.0.6.tgz#867ac74e3864187b1d3d47d996a78ec5c8830777" integrity sha512-/aCDEGatGvZ2BIk+HmLf4ifCJFwvKFNb9/JeZPMulfgFracn9QFcAf5GO8B/mweUjSoblS5In0cWhqpfs/5PQA== +typescript@^4.9.4: + version "4.9.4" + resolved "https://registry.yarnpkg.com/typescript/-/typescript-4.9.4.tgz#a2a3d2756c079abda241d75f149df9d561091e78" + integrity sha512-Uz+dTXYzxXXbsFpM86Wh3dKCxrQqUcVMxwU54orwlJjOpO3ao8L7j5lH+dWfTwgCwIuM9GQ2kvVotzYJMXTBZg== + unbox-primitive@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/unbox-primitive/-/unbox-primitive-1.0.2.tgz#29032021057d5e6cdbd08c5129c226dff8ed6f9e" From 8fccfe17c2dbadcc6e7ea714e7bd23d16430f592 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Thu, 5 Jan 2023 17:12:12 +0000 Subject: [PATCH 16/79] harvester setup tweaks --- docker-compose.override.yml | 2 +- harvester/harvest.py | 41 +++++++++++++++++++++++-------------- harvester/init.py | 13 ++++++++++-- harvester/settings.py | 16 ++++++++++----- 4 files changed, 49 insertions(+), 23 deletions(-) diff --git a/docker-compose.override.yml b/docker-compose.override.yml index 8f0db530..3c9563f7 100644 --- a/docker-compose.override.yml +++ b/docker-compose.override.yml @@ -27,7 +27,7 @@ services: build: dockerfile: Dockerfile context: ./harvester - command: python init.py --name "Harvester03" --url http://app:5000/ --user_id 42 --run_foreground + command: python init.py --name "Harvester03" --url http://app:5000/ --user_id 42 --run_foreground --restart # command: tail -F anything depends_on: - app diff --git a/harvester/harvest.py b/harvester/harvest.py index 7d382482..e2eb010e 100644 --- a/harvester/harvest.py +++ b/harvester/harvest.py @@ -4,7 +4,7 @@ import requests import logging import json -from settings import get_logfile, get_setting, get_settings_file +from settings import get_logfile, get_setting, get_settings, get_settings_file from parse.harvester import import_file @@ -41,19 +41,30 @@ def update_config(): result = requests.get(f"{url}config/", headers={'Authorization': f"Harvester {key}"}) if result.status_code == 200: dirty = False - for setting, value in result.json().items(): - old_value = get_setting(setting) - if old_value is None: - old = "[not set]" - else: - old = json.dumps(get_setting(setting)) - new = json.dumps(value) - if new != old: - logger.info(f"Updating value for setting '{setting}'") - logger.info(f"Old value: {old}") - logger.info(f"New value: {new}") + new = result.json() + old = get_settings() + if old is None: + old = {} + all_keys = [*new.keys(), *old.keys()] + for key in all_keys: + if key in old.keys() and key in new.keys(): + if json.dumps(old[key]) == json.dumps(new[key]): + continue + logger.info(f"Updating value for setting '{key}'") + logger.info(f"Old value: {json.dumps(old[key])}") + logger.info(f"New value: {json.dumps(new[key])}") dirty = True - # TODO: handle removed values + if key in old.keys(): + logger.info(f"Updating value for setting '{key}'") + logger.info(f"Old value: {json.dumps(old[key])}") + logger.info(f"New value: [not set]") + dirty = True + if key in new.keys(): + logger.info(f"Updating value for setting '{key}'") + logger.info(f"Old value: [not set]") + logger.info(f"New value: {json.dumps(new[key])}") + dirty = True + if dirty: with open(get_settings_file(), 'w') as f: json.dump(result.json(), f) @@ -82,10 +93,10 @@ def harvest_path(path: str): logger.info(f"Reporting stats for {filename}") result = report_harvest_result( path=path, + file=filename, content={ 'task': 'file_size', - 'file': filename, - 'stat': os.stat(filename) + 'size': os.stat(filename).st_size } ) if result is not None: diff --git a/harvester/init.py b/harvester/init.py index b2f4c374..18845623 100644 --- a/harvester/init.py +++ b/harvester/init.py @@ -175,10 +175,19 @@ def register(url: str = None, name: str = None, user_id: int = None, run_foregro "(will not close the thread, useful for Dockerized application)." ) ) -def click_wrapper(url: str, name: str, user_id: int, run_foreground: bool): - register(url=url, name=name, user_id=user_id, run_foreground=run_foreground) +@click.option( + '--restart', + is_flag=True, + help="Ignore other options and run harvester if config file already exists." +) +def click_wrapper(url: str, name: str, user_id: int, run_foreground: bool, restart: bool): + if click.option('restart') and settings.get_setting('url'): + harvest.run_cycle() + else: + register(url=url, name=name, user_id=user_id, run_foreground=run_foreground) if __name__ == "__main__": + # Check whether a config file already exists, if so, use it click.echo("Welcome to Harvester setup.") click_wrapper() diff --git a/harvester/settings.py b/harvester/settings.py index da42c97b..052d962e 100644 --- a/harvester/settings.py +++ b/harvester/settings.py @@ -11,17 +11,23 @@ def get_logfile() -> pathlib.Path: return pathlib.Path(os.getenv('LOG_FILE', "/harvester_files/harvester.log")) -def get_setting(*args): +def get_settings(): with open(get_settings_file(), 'r') as f: try: - settings = json.load(f) + return json.load(f) except json.JSONDecodeError as e: print(f"Error decoding json file {f.name}", e) f.seek(0) print(f.readlines()) - if len(args) == 1: - return None - return [None for _ in args] + return None + + +def get_setting(*args): + settings = get_settings() + if not settings: + if len(args) == 1: + return None + return [None for _ in args] if len(args) == 1: return settings.get(args[0]) return [settings.get(arg) for arg in args] From 5f95b79f1cda9ade87042554a6da2883b177d782 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Thu, 5 Jan 2023 17:28:00 +0000 Subject: [PATCH 17/79] classnames dependency --- frontend/package.json | 1 + frontend/yarn.lock | 5 +++++ 2 files changed, 6 insertions(+) diff --git a/frontend/package.json b/frontend/package.json index bb209fd7..60d7616b 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -20,6 +20,7 @@ "@types/node": "^18.11.18", "@types/react": "^18.0.26", "@types/react-dom": "^18.0.10", + "classnames": "^2.3.2", "react": "^18.2.0", "react-dom": "^18.2.0", "react-hook-form": "^7.6.3", diff --git a/frontend/yarn.lock b/frontend/yarn.lock index 905d82c5..ab1338f4 100644 --- a/frontend/yarn.lock +++ b/frontend/yarn.lock @@ -4114,6 +4114,11 @@ class-utils@^0.3.5: isobject "^3.0.0" static-extend "^0.1.1" +classnames@^2.3.2: + version "2.3.2" + resolved "https://registry.yarnpkg.com/classnames/-/classnames-2.3.2.tgz#351d813bf0137fcc6a76a16b88208d2560a0d924" + integrity sha512-CSbhY4cFEJRe6/GQzIk5qXZ4Jeg5pcsP7b5peFSDpffpe1cqjASH/n9UTjBwOp6XpMSTwQ8Za2K5V02ueA7Tmw== + clean-css@^4.2.3: version "4.2.4" resolved "https://registry.yarnpkg.com/clean-css/-/clean-css-4.2.4.tgz#733bf46eba4e607c6891ea57c24a989356831178" From 2c5d58a80c7e16b5c2e954cfd9bcdc94739cb70e Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Fri, 6 Jan 2023 16:56:31 +0000 Subject: [PATCH 18/79] Harvesters typescript --- frontend/src/Api.js | 21 ++- .../src/{Harvesters.jsx => Harvesters.tsx} | 108 ++++++++------- frontend/src/PaginatedTable.jsx | 126 ------------------ frontend/src/PaginatedTable.tsx | 97 +++++++------- frontend/src/index.d.ts | 6 + 5 files changed, 131 insertions(+), 227 deletions(-) rename frontend/src/{Harvesters.jsx => Harvesters.tsx} (69%) delete mode 100644 frontend/src/PaginatedTable.jsx create mode 100644 frontend/src/index.d.ts diff --git a/frontend/src/Api.js b/frontend/src/Api.js index 7c847884..975b6761 100644 --- a/frontend/src/Api.js +++ b/frontend/src/Api.js @@ -1,5 +1,5 @@ -const url = 'http://localhost:5001/'; +export const url = 'http://localhost:5001/'; const headers = { 'Accept': 'application/json', 'Content-Type': 'application/json' @@ -49,7 +49,7 @@ export async function loggedIn(skip = true) { return cookie !== undefined && user; } -async function authFetch(url, options) { +export async function authFetch(url, options) { const token = user?.token; let newOptions = {...options}; newOptions.credentials = 'same-origin'; @@ -61,14 +61,21 @@ async function authFetch(url, options) { url = /\/$/.test(url) ? url : `${url}/`; return fetch(url, newOptions).then((response) => { if (response.status === 401) { - return logout().then(() => { - return response; - }); + throw new Error(`Server said 'unauthorised'`) + // return logout().then(() => { + // return response; + // }); } return response; }).catch(e => { - console.error(e); - return null; + // console.error(e); + return { + count: 0, + previous: null, + next: null, + results: [], + error: "Unauthorised" + }; }); } diff --git a/frontend/src/Harvesters.jsx b/frontend/src/Harvesters.tsx similarity index 69% rename from frontend/src/Harvesters.jsx rename to frontend/src/Harvesters.tsx index 88882993..abad2d17 100644 --- a/frontend/src/Harvesters.jsx +++ b/frontend/src/Harvesters.tsx @@ -13,13 +13,25 @@ import SaveIcon from '@mui/icons-material/Save'; import TableHead from '@mui/material/TableHead'; import DeleteIcon from '@mui/icons-material/Delete'; import TableRow from '@mui/material/TableRow'; -import PaginatedTable from './PaginatedTable'; +import PaginatedTable, {RowFunProps} from './PaginatedTable'; import HarvesterDetail from './HarvesterDetail'; import { url, run_harvester, harvesters, add_harvester, update_harvester, delete_harvester, isAdmin } from './Api' +import Connection from "./APIConnection"; + +export type HarvesterWriteableFields = { + name: string; + sleep_time: number; +} + +export type HarvesterFields = HarvesterWriteableFields & { + url: string; + id: number; + last_check_in: string | null; +} const useStyles = makeStyles((theme) => ({ container: { @@ -39,21 +51,27 @@ const useStyles = makeStyles((theme) => ({ iconButton: { padding: 10, }, + paper: {} })); export default function Harvesters() { const classes = useStyles(); + const [lastUpdated, setLastUpdated] = useState(new Date()) + const [selected, setSelected] = useState({id: null}) const userIsAdmin = isAdmin() - const addNewHarvester = (data) => { - add_harvester({name: data.name, sleep_time: data.sleep_time}); + const addNewHarvester = (data: HarvesterFields) => { + const insert_data: HarvesterWriteableFields = {name: data.name, sleep_time: data.sleep_time} + Connection.fetch('harvesters', {body: JSON.stringify(insert_data), method: 'POST'}) + .then(() => setLastUpdated(new Date())) }; + const deleteHarvester= () => { delete_harvester(selected.id); }; - const updateHarvester= (value) => { + const updateHarvester= (value: any) => { update_harvester(value.id, value); }; @@ -61,8 +79,8 @@ export default function Harvesters() { run_harvester(selected.id); }; - function table_row_generator(row) { - return () } - function MyTableRow({savedRow, onRowSave, selected, onSelectRow, disableSave, addIcon}) { + function MyTableRow(props: RowFunProps) { const classes = useStyles(); - const [row, setRow] = useState([]) - const [dirty, setDirty] = useState(false) + const [row, setRow] = useState({ + id: -1, + url: "", + name: "", + last_check_in: null, + sleep_time: 3600 + }) + const [dirty, setDirty] = useState(false) useEffect(() => { - if (!dirty) { - setRow(savedRow); + if (!dirty && props.savedRow) { + setRow(props.savedRow); } - }, [dirty, savedRow]); - + }, [dirty, props.savedRow]); let useRow = row; - if (useRow.id === undefined) { - useRow = savedRow; - } + if (row.id === -1 && props.savedRow) + useRow = props.savedRow; - const Icon = addIcon ? : ; + const Icon = props.addIcon ? : ; return ( {onSelectRow(savedRow);}} + onClick={() => {props.onSelectRow(props.savedRow);}} hover - selected={selected} + selected={props.selected} > - {savedRow.id} + {props.savedRow?.id || ""} @@ -119,15 +141,10 @@ export default function Harvesters() { - {(savedRow.is_running && (Yes)) || - (No) - } - - - {(savedRow.last_successful_run && + {(props.savedRow?.last_check_in && Intl.DateTimeFormat('en-GB', { dateStyle: 'long', timeStyle: 'long' }).format( - Date.parse(savedRow.last_successful_run) + Date.parse(props.savedRow.last_check_in) )) || (None)} @@ -141,18 +158,18 @@ export default function Harvesters() { value={useRow.sleep_time ? useRow.sleep_time : ''} onChange={(e) => { setDirty(true); - setRow({...row, sleep_time: e.target.value}); + setRow({...row, sleep_time: parseInt(e.target.value)}); }} > - + { - onRowSave(row); + props.onRowSave(row); setDirty(false); }} > @@ -169,13 +186,6 @@ export default function Harvesters() { const new_row = ( {}} @@ -187,8 +197,7 @@ export default function Harvesters() { const column_headings = [ {label: 'ID', help: 'Harvester id in database'}, {label: 'Name', help: 'Harvester name'}, - {label: 'Is Running', help: 'Displays "True" if harvester is currently running'}, - {label: 'Last Completed Run', help: 'Datetime of last harvester run that successfully ran until completion'}, + {label: 'Last Check In', help: 'Datetime of last harvester run that successfully contacted the database'}, {label: 'Sleep Time (s)', help: 'If set, harvester is run every day on this hour'}, {label: 'Save', help: 'Click to save edits to a row'}, ] @@ -205,16 +214,19 @@ export default function Harvesters() { const isSelected = selected.id !== null; + const paginated_table = ({table_head})} + row_fun= {table_row_generator} + initial_url={`${url}harvesters/`} + new_entry_row={new_row} + styles={classes} + last_updated={lastUpdated} + />) + return ( - {table_head}), - row_fun: table_row_generator, - initial_url: `${url}harvesters/`, - new_entry_row: new_row, - styles: classes, - }}/> + {paginated_table} diff --git a/frontend/src/PaginatedTable.jsx b/frontend/src/PaginatedTable.jsx deleted file mode 100644 index 93b92cb4..00000000 --- a/frontend/src/PaginatedTable.jsx +++ /dev/null @@ -1,126 +0,0 @@ -"use strict"; -var __extends = (this && this.__extends) || (function () { - var extendStatics = function (d, b) { - extendStatics = Object.setPrototypeOf || - ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) || - function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; }; - return extendStatics(d, b); - }; - return function (d, b) { - if (typeof b !== "function" && b !== null) - throw new TypeError("Class extends value " + String(b) + " is not a constructor or null"); - extendStatics(d, b); - function __() { this.constructor = d; } - d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __()); - }; -})(); -var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) { - function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); } - return new (P || (P = Promise))(function (resolve, reject) { - function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } } - function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } } - function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); } - step((generator = generator.apply(thisArg, _arguments || [])).next()); - }); -}; -var __generator = (this && this.__generator) || function (thisArg, body) { - var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g; - return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g; - function verb(n) { return function (v) { return step([n, v]); }; } - function step(op) { - if (f) throw new TypeError("Generator is already executing."); - while (g && (g = 0, op[0] && (_ = 0)), _) try { - if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t; - if (y = 0, t) op = [op[0] & 2, t.value]; - switch (op[0]) { - case 0: case 1: t = op; break; - case 4: _.label++; return { value: op[1], done: false }; - case 5: _.label++; y = op[1]; op = [0]; continue; - case 7: op = _.ops.pop(); _.trys.pop(); continue; - default: - if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; } - if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; } - if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; } - if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; } - if (t[2]) _.ops.pop(); - _.trys.pop(); continue; - } - op = body.call(thisArg, _); - } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; } - if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true }; - } -}; -Object.defineProperty(exports, "__esModule", { value: true }); -var react_1 = require("react"); -var TableContainer_1 = require("@mui/material/TableContainer"); -var Table_1 = require("@mui/material/Table"); -var TableBody_1 = require("@mui/material/TableBody"); -var Api_1 = require("./Api"); -var PaginatedTable = /** @class */ (function (_super) { - __extends(PaginatedTable, _super); - function PaginatedTable(props) { - var _this = _super.call(this, props) || this; - _this.state = { - row_data: [], - links: { previous: null, next: null } - }; - _this.get_data = function (url) { return __awaiter(_this, void 0, void 0, function () { - var _this = this; - return __generator(this, function (_a) { - switch (_a.label) { - case 0: return [4 /*yield*/, (0, Api_1.authFetch)(url) - .then(function (res) { - console.log(res); - _this.setState({ - row_data: res.results, - links: { - next: res.next, - previous: res.previous - }, - }); - })]; - case 1: - _a.sent(); - return [2 /*return*/]; - } - }); - }); }; - _this.header = props.data.header; - _this.row_fun = props.data.row_fun; - _this.new_entry_row = props.data.new_entry_row; - _this.styles = props.data.styles; - _this.initial_url = props.data.initial_url; - return _this; - } - PaginatedTable.prototype.componentDidMount = function () { - this.get_data(this.initial_url); - }; - PaginatedTable.prototype.render = function () { - var _this = this; - return (
-
- - -
- - { - // @ts-ignore - - {this.header} - { - // @ts-ignore - - {this.state.row_data.map(this.row_fun)} - {this.new_entry_row} - } - } - -
); - }; - return PaginatedTable; -}(react_1.Component)); -exports.default = PaginatedTable; diff --git a/frontend/src/PaginatedTable.tsx b/frontend/src/PaginatedTable.tsx index f30a1ddb..eeff5eeb 100644 --- a/frontend/src/PaginatedTable.tsx +++ b/frontend/src/PaginatedTable.tsx @@ -2,24 +2,39 @@ * Offer a table with previous/next links. */ import classNames from 'classnames' -import {TableHead, TableRow} from "@mui/material"; -import {Component} from "react"; +import {Component, ReactComponentElement} from "react"; import TableContainer from "@mui/material/TableContainer"; import Table from "@mui/material/Table"; import TableBody from "@mui/material/TableBody"; +import Button from '@mui/material/Button'; import Connection, {APIResponse} from "./APIConnection"; -type RowFunOptions = { - savedRow: any, - onRowSave: (row: any) => void, - selected: boolean, - onSelectRow: (id: number) => void, - disabledSave: boolean, - addIcon?: boolean, +export type RowFunProps = { + savedRow?: T; + onRowSave: (row: any) => void; + selected: boolean; + onSelectRow: (id: any) => void; + disabledSave?: boolean; + addIcon?: boolean; + [key: string]: any; +} + +type RowFun = (row: any) => ReactComponentElement + +export type PaginatedTableProps = { + header: ReactComponentElement, + row_fun: RowFun, + initial_url: string, + new_entry_row?: ReactComponentElement, + styles?: any, [key: string]: any } -type RowFun = (row: any) => (options: RowFunOptions) => typeof TableRow +type PaginatedTableState = { + row_data: any[]; + links: PaginationLinks; + last_updated: Date; +} export type PaginationLinks = { previous?: string | null, @@ -28,7 +43,10 @@ export type PaginationLinks = { type PaginationDataFun = (url?: string | null) => APIResponse -type PaginationProps = PaginationLinks & { get_data_fun: PaginationDataFun; position: string } +type PaginationProps = PaginationLinks & { + get_data_fun: PaginationDataFun; + position: string; +} class Pagination extends Component { @@ -39,15 +57,15 @@ class Pagination extends Component { 'pagination-above': this.props.position === 'above', 'pagination-below': this.props.position === 'below', })}> - - + ) } } -export type PaginatedTableProps = { - header: typeof TableHead, - row_fun: RowFun, - initial_url: string, - new_entry_row?: typeof TableRow, - styles?: any, - [key: string]: any -} - -type PaginatedTableState = { - row_data: any[], - links: PaginationLinks -} - export default class PaginatedTable extends Component { - header: typeof TableHead; - row_fun: RowFun; - new_entry_row: typeof TableRow | undefined; - styles: any; - initial_url: string; + current_url: string = ""; state = { row_data: [], - links: {previous: null, next: null} + links: {previous: null, next: null}, + last_updated: new Date(0) } constructor(props: PaginatedTableProps) { super(props) - this.header = props.data.header - this.row_fun = props.data.row_fun - this.new_entry_row = props.data.new_entry_row - this.styles = props.data.styles - this.initial_url = props.data.initial_url + if (!this.current_url) this.current_url = props.initial_url } componentDidMount() { - this.get_data(this.initial_url) + this.get_data(this.props.initial_url) + } + + componentDidUpdate(prevProps: PaginatedTableProps) { + // Typical usage (don't forget to compare props): + if (this.props.last_updated !== prevProps.last_updated) { + this.get_data(this.props.initial_url); + } } get_data: PaginationDataFun = async (url) => { if (!url) return; + this.current_url = url; await Connection.fetch(url) // @ts-ignore .then((res: APIResponse) => { @@ -111,7 +116,7 @@ export default class PaginatedTable extends Component { @@ -131,13 +136,13 @@ export default class PaginatedTable extends Component { // @ts-ignore - - {this.header} +
+ {this.props.header} { // @ts-ignore - {this.state.row_data.map(this.row_fun)} - {this.new_entry_row} + {this.state.row_data.map(this.props.row_fun)} + {this.props.new_entry_row} }
diff --git a/frontend/src/index.d.ts b/frontend/src/index.d.ts new file mode 100644 index 00000000..bf5433df --- /dev/null +++ b/frontend/src/index.d.ts @@ -0,0 +1,6 @@ +// Prevent complaints that 'spacing' isn't a DefaultTheme property +declare module "@mui/private-theming" { + import type { Theme } from "@mui/material/styles"; + + interface DefaultTheme extends Theme {} +} \ No newline at end of file From 0f0760f4059746c8ab52b46aee7866d223dbed25 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Fri, 6 Jan 2023 16:57:06 +0000 Subject: [PATCH 19/79] django filtering --- django/backend_django/galvanalyser/models.py | 43 ++-- .../galvanalyser/serializers.py | 63 +++++- django/backend_django/galvanalyser/tasks.py | 6 + django/backend_django/galvanalyser/views.py | 203 ++++++++++++++++-- django/requirements.txt | 4 +- 5 files changed, 270 insertions(+), 49 deletions(-) diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index 8d626f07..a3b21537 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -26,13 +26,13 @@ class Harvester(models.Model): to=Group, on_delete=models.CASCADE, null=True, - related_name='harvester_admins' + related_name='editable_harvesters' ) user_group = models.ForeignKey( to=Group, on_delete=models.CASCADE, null=True, - related_name='harvester_users' + related_name='readable_harvesters' ) def save(self, *args, **kwargs): @@ -59,20 +59,36 @@ def run(self): class MonitoredPath(models.Model): harvester = models.ForeignKey(to=Harvester, on_delete=models.CASCADE) path = models.TextField(unique=True) + stable_time = models.PositiveSmallIntegerField(default=60) # seconds files must remain stable to be processed + admin_group = models.ForeignKey( + to=Group, + on_delete=models.CASCADE, + null=True, + related_name='editable_paths' + ) + user_group = models.ForeignKey( + to=Group, + on_delete=models.CASCADE, + null=True, + related_name='readable_paths' + ) class Meta: unique_together = [['harvester', 'path']] -class MonitoredFor(models.Model): - path = models.ForeignKey(to=MonitoredPath, on_delete=models.CASCADE) - user = models.ForeignKey(to=User, on_delete=models.CASCADE) +class HarvestError(models.Model): + harvester = models.ForeignKey(to=Harvester, related_name='paths', on_delete=models.CASCADE) + path = models.ForeignKey(to=MonitoredPath, on_delete=models.DO_NOTHING) + file = models.TextField(null=True) + error = models.TextField() + timestamp = models.DateTimeField(auto_created=True) class ObservedFile(models.Model): - monitored_path = models.ForeignKey(to=MonitoredPath, on_delete=models.DO_NOTHING) + monitored_path = models.ForeignKey(to=MonitoredPath, related_name='files', on_delete=models.DO_NOTHING) relative_path = models.TextField() - last_observed_size = models.PositiveBigIntegerField(null=False) + last_observed_size = models.PositiveBigIntegerField(null=False, default=0) last_observed_time = models.DateTimeField() state = models.SmallIntegerField(choices=FileState.choices, default=FileState.UNSTABLE, null=False) @@ -90,19 +106,6 @@ def inspect_size(self): self.last_observed_time = timezone.now() - def import_content(self): - path = Path(os.path.join(self.monitored_path.path, self.relative_path)) - self.state = FileState.IMPORTING - try: - if not os.path.isfile(path): - raise FileNotFoundError - print(f"Importing {path}") - parse(path, DataColumnType.objects.filter(is_default=True)) - self.state = FileState.IMPORTED - except BaseException as e: - self.state = FileState.IMPORT_FAILED - raise e - class Meta: unique_together = [['monitored_path', 'relative_path']] diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py index 5fbd0adc..241192b2 100644 --- a/django/backend_django/galvanalyser/serializers.py +++ b/django/backend_django/galvanalyser/serializers.py @@ -1,6 +1,5 @@ from .models import Harvester, \ MonitoredPath, \ - MonitoredFor, \ ObservedFile, \ CellData, \ Dataset, \ @@ -13,24 +12,70 @@ TimeseriesRangeLabel from django.contrib.auth.models import User, Group from rest_framework import serializers +from rest_framework.reverse import reverse_lazy class HarvesterSerializer(serializers.HyperlinkedModelSerializer): + links = serializers.SerializerMethodField() + + def get_links(self, harvester): + return { + 'monitored_paths': reverse_lazy( + 'harvester-paths', + request=self.context.get('request'), + kwargs={'pk': harvester.id} + ), + 'users': reverse_lazy( + 'harvester-users', + request=self.context.get('request'), + kwargs={'pk': harvester.id} + ), + 'admins': reverse_lazy( + 'harvester-admins', + request=self.context.get('request'), + kwargs={'pk': harvester.id} + ), + } + class Meta: model = Harvester - fields = ['url', 'name', 'api_key', 'last_check_in', 'sleep_time'] + fields = ['url', 'id', 'name', 'sleep_time', 'last_check_in', 'links'] + read_only_fields = ['url', 'id', 'last_check_in'] -class MonitoredPathSerializer(serializers.HyperlinkedModelSerializer): +class HarvesterConfigSerializer(serializers.HyperlinkedModelSerializer): class Meta: - model = MonitoredPath - fields = '__all__' + model = Harvester + fields = ['url', 'id', 'api_key', 'name', 'last_check_in', 'sleep_time', 'paths'] + depth = 10 # max depth -class MonitoredForSerializer(serializers.HyperlinkedModelSerializer): +class MonitoredPathSerializer(serializers.HyperlinkedModelSerializer): + links = serializers.SerializerMethodField() + + def get_links(self, monitored_path): + return { + 'files': reverse_lazy( + 'monitored_path-files', + request=self.context.get('request'), + kwargs={'pk': monitored_path.id} + ), + 'users': reverse_lazy( + 'monitored_path-users', + request=self.context.get('request'), + kwargs={'pk': monitored_path.id} + ), + 'admins': reverse_lazy( + 'monitored_path-admins', + request=self.context.get('request'), + kwargs={'pk': monitored_path.id} + ), + } + class Meta: - model = MonitoredFor + model = MonitoredPath fields = '__all__' + read_only_fields = ['admin_group', 'user_group'] class ObservedFileSerializer(serializers.HyperlinkedModelSerializer): @@ -100,9 +145,6 @@ class Meta: class UserSerializer(serializers.HyperlinkedModelSerializer): - groups = serializers.PrimaryKeyRelatedField(many=True, read_only=True) - groups = GroupSerializer(groups, many=True) - class Meta: model = User fields = [ @@ -114,3 +156,4 @@ class Meta: 'is_superuser', 'groups', ] + depth = 1 diff --git a/django/backend_django/galvanalyser/tasks.py b/django/backend_django/galvanalyser/tasks.py index 5032511a..f26cff73 100644 --- a/django/backend_django/galvanalyser/tasks.py +++ b/django/backend_django/galvanalyser/tasks.py @@ -1,4 +1,5 @@ from celery import shared_task +from .models import Harvester import os @@ -6,3 +7,8 @@ def get_env(): env_var = 'GALVANALYSER_HARVESTER_BASE_PATH' return {env_var: os.getenv(env_var)} + + +@shared_task +def run_harvester(harvester_id): + Harvester.objects.get(id=harvester_id).run() diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index d5461cb5..efe4fe84 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -1,6 +1,8 @@ +from django.db.models import Q + from .serializers import HarvesterSerializer, \ + HarvesterConfigSerializer, \ MonitoredPathSerializer, \ - MonitoredForSerializer, \ ObservedFileSerializer, \ CellDataSerializer, \ DatasetSerializer, \ @@ -14,8 +16,8 @@ UserSerializer, \ GroupSerializer from .models import Harvester, \ + HarvestError, \ MonitoredPath, \ - MonitoredFor, \ ObservedFile, \ CellData, \ Dataset, \ @@ -25,14 +27,18 @@ DataColumnType, \ DataColumn, \ TimeseriesData, \ - TimeseriesRangeLabel + TimeseriesRangeLabel, \ + FileState from django.contrib.auth.models import User, Group +from django.shortcuts import get_object_or_404 +from django.utils import timezone from rest_framework import viewsets from rest_framework.permissions import AllowAny from rest_framework.decorators import action from rest_framework.response import Response from knox.views import LoginView as KnoxLoginView from rest_framework.authentication import BasicAuthentication +import json from .tasks import get_env @@ -43,12 +49,28 @@ class LoginView(KnoxLoginView): class HarvesterViewSet(viewsets.ModelViewSet): """ - TODO: document + Harvesters monitor a set of MonitoredPaths and send reports about ObservedFiles + within those paths. + A Harvester has Users and Admins, managed by Django's inbuilt User and Group models. + + When Harvesters communicate with the API they do so using special Harvester API Keys. + These provide access to the report and configuration endpoints. """ serializer_class = HarvesterSerializer - queryset = Harvester.objects.all().order_by('last_check_in', 'id') + filterset_fields = ['name'] + search_fields = ['@name'] + + def get_queryset(self): + return Harvester.objects.complex_filter( + Q(user_group__user_set__username__contains=self.request.user.username) | + Q(admin_group__user_set__username__contains=self.request.user.username) + ).order_by('last_check_in', 'id') def create(self, request, *args, **kwargs): + """ + Create a Harvester and the user Groups required to control it. + """ + # Validate input if not request.data['name']: return Response({'error': 'No name specified for Harvester.'}, status=400) @@ -78,15 +100,104 @@ def env(self, request, pk: int = None): result = get_env.apply_async(queue=harvester.name) return Response(result.get()) - @action(detail=False, methods=['GET']) - def by_name(self, request): + @action(detail=True, methods=['GET']) + def config(self, request, pk: int = None): + """ + Return a full configuration file including MonitoredPaths under paths. + Used by the API for updating the Harvester. + """ + # TODO: Restrict access to Harvester or harvester user + harvester = get_object_or_404(Harvester, id=pk) + return Response(HarvesterConfigSerializer(harvester, context={'request': request}).data) + + @action(detail=True, methods=['GET']) + def paths(self, request, pk: int = None): """ - Used by the harvesters' init.py call to check their prospective name is free. - Returns a list of Harvesters with the specified name (should be length 1 or 0). + MonitoredPaths for the Harvester. + """ + # TODO: Restrict access to Harvester or harvester user + harvester = get_object_or_404(Harvester, id=pk) + paths = MonitoredPath.objects.filter(harvester=harvester).order_by('id') + paths = self.paginate_queryset(paths) + return self.get_paginated_response(MonitoredPathSerializer(paths, many=True).data) + + @action(detail=True, methods=['GET']) + def users(self, request, pk: int = None): + """ + Users able to access the Harvester. Users can create MonitoredPaths. + """ + # TODO: Restrict access to Harvester or harvester user + harvester = get_object_or_404(Harvester, id=pk) + users = User.objects.filter(groups__in=[harvester.admin_group, harvester.user_group]) + users = self.paginate_queryset(users) + return self.get_paginated_response(UserSerializer(users, context={'request': request}, many=True).data) + + @action(detail=True, methods=['GET']) + def admins(self, request, pk: int = None): + """ + Users able to edit the Harvester. + """ + # TODO: Restrict access to Harvester or harvester user + harvester = get_object_or_404(Harvester, id=pk) + admins = User.objects.filter(groups__in=[harvester.admin_group]) + admins = self.paginate_queryset(admins) + return self.get_paginated_response(UserSerializer(admins, context={'request': request}, many=True).data) + + @action(detail=True, methods=['POST']) + def report(self, request, pk: int = None): + """ + Process a harvester's report on its activity. + This will spawn various other database updates depending on payload content. + + Only harvesters are authorised to issue reports. """ - name = request.query_params.get('name', '') - harvester = self.paginate_queryset(Harvester.objects.filter(name=name)) - return self.get_paginated_response(self.get_serializer(harvester, many=True).data) + # TODO access class Harvester + harvester = Harvester.objects.get(id=pk) + if request.data.get('status') is None: + return Response({'error': 'Badly formatted request'}, status=400) + try: + path = MonitoredPath.objects.get(path=request.data['path'], harvester=harvester) + except MonitoredPath.DoesNotExist: + return Response({'error': 'Unrecognized path'}, status=400) + if request.data['status'] == 'error': + error = request.data['error'] + if not isinstance(error, str): + try: + error = json.dumps(error) + except json.JSONDecodeError: + error = str(error) + HarvestError.objects.create( + harvester=harvester, + path=path, + error=str(error) + ) + elif request.data['status'] == 'success': + # Figure out what we succeeded in doing! + content = request.data['content'] + if content['task'] == 'file_size': + # Harvester is reporting the size of a file + # Update our database record and return a file status + file, _ = ObservedFile.objects.get_or_create(monitored_path=path) + size = content['size'] + if size < file.last_observed_size: + file.state = FileState.UNSTABLE + elif size > file.last_observed_size: + file.state = FileState.GROWING + else: + # Recent changes + if file.last_observed_time + timezone.timedelta(seconds=path.stable_time) > timezone.now(): + file.state = FileState.UNSTABLE + # Stable file -- already imported? + elif file.state not in [FileState.IMPORTED, FileState.IMPORT_FAILED]: + file.state = FileState.UNSTABLE + file.last_observed_size = size + file.last_observed_time = timezone.now() + file.save() + return Response(ObservedFileSerializer(file).data) + else: + return Response({'error': 'Unrecognised task'}, status=400) + else: + return Response({'error': 'Unrecognised status'}, status=400) class MonitoredPathViewSet(viewsets.ModelViewSet): @@ -96,13 +207,69 @@ class MonitoredPathViewSet(viewsets.ModelViewSet): serializer_class = MonitoredPathSerializer queryset = MonitoredPath.objects.all().order_by('id') + def create(self, request, *args, **kwargs): + """ + Create a MonitoredPath for a Harvester and the user Groups required to control it. + """ -class MonitoredForViewSet(viewsets.ModelViewSet): - """ - TODO: document - """ - serializer_class = MonitoredForSerializer - queryset = MonitoredFor.objects.all() + # Validate input + path = str(request.data['path']).lower().lstrip().rstrip() + if not path: + return Response({'error': 'No path specified.'}, status=400) + try: + harvester = Harvester.objects.get(id=request.data['harvester']) + except (Harvester.DoesNotExist, AttributeError): + return Response({'error': 'Harvester not found.'}) + if len(MonitoredPath.objects.filter(path=path, harvester=harvester)): + return Response({'error': 'Path already exists on Harvester.'}, status=400) + # Check user is authorised to create paths on Harvester + if harvester.user_group not in request.user.groups and harvester.admin_group not in request.user.groups: + return Response({'error': f'Permission denied to {request.user.username} for {harvester.name}'}) + + # Create Path + monitored_path = MonitoredPath.objects.create(path=path, harvester=harvester) + # Create user/admin groups + monitored_path.user_group = Group.objects.create(name=f"path_{harvester.id}_{monitored_path.id}_users") + monitored_path.admin_group = Group.objects.create(name=f"path_{harvester.id}_{monitored_path.id}_admins") + monitored_path.save() + # Add user as admin + request.user.groups.add(monitored_path.admin_group) + request.user.save() + + return Response(self.get_serializer(monitored_path).data) + + @action(detail=True, methods=['GET']) + def files(self, request, pk: int = None): + """ + ObservedFiles for the MonitoredPath. + """ + # TODO: Restrict access to Harvester or harvester user + monitored_path = get_object_or_404(MonitoredPath, id=pk) + paths = ObservedFile.objects.filter(monitored_path=monitored_path).order_by('id') + paths = self.paginate_queryset(paths) + return self.get_paginated_response(ObservedFileSerializer(paths, many=True).data) + + @action(detail=True, methods=['GET']) + def users(self, request, pk: int = None): + """ + Users able to access the Harvester. Users can create MonitoredPaths. + """ + # TODO: Restrict access to Harvester or harvester user + monitored_path = get_object_or_404(Harvester, id=pk) + users = User.objects.filter(groups__in=[monitored_path.admin_group, monitored_path.user_group]) + users = self.paginate_queryset(users) + return self.get_paginated_response(UserSerializer(users, context={'request': request}, many=True).data) + + @action(detail=True, methods=['GET']) + def admins(self, request, pk: int = None): + """ + Users able to edit the Harvester. + """ + # TODO: Restrict access to Harvester or harvester user + monitored_path = get_object_or_404(Harvester, id=pk) + admins = User.objects.filter(groups__in=[monitored_path.admin_group]) + admins = self.paginate_queryset(admins) + return self.get_paginated_response(UserSerializer(admins, context={'request': request}, many=True).data) class ObservedFileViewSet(viewsets.ModelViewSet): diff --git a/django/requirements.txt b/django/requirements.txt index 12347579..a85cb07c 100644 --- a/django/requirements.txt +++ b/django/requirements.txt @@ -1,7 +1,9 @@ celery==5.2.7 Django==4.1.4 +django-celery-beat==2.4.0 django-cors-headers==3.13.0 +django-filter==22.1 djangorestframework==3.14.0 django-rest-knox==4.2.0 psycopg2-binary==2.9.5 -redis==4.4.0 +redis==4.4.0 \ No newline at end of file From 7fc3a5d42ea8d4c3a592fd3d2501a3c7158906e3 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Fri, 6 Jan 2023 17:54:02 +0000 Subject: [PATCH 20/79] restrict harvester list view --- .../galvanalyser/serializers.py | 34 +++++++++---------- django/backend_django/galvanalyser/views.py | 5 +-- 2 files changed, 20 insertions(+), 19 deletions(-) diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py index 241192b2..44ce3c91 100644 --- a/django/backend_django/galvanalyser/serializers.py +++ b/django/backend_django/galvanalyser/serializers.py @@ -19,23 +19,23 @@ class HarvesterSerializer(serializers.HyperlinkedModelSerializer): links = serializers.SerializerMethodField() def get_links(self, harvester): - return { - 'monitored_paths': reverse_lazy( - 'harvester-paths', - request=self.context.get('request'), - kwargs={'pk': harvester.id} - ), - 'users': reverse_lazy( - 'harvester-users', - request=self.context.get('request'), - kwargs={'pk': harvester.id} - ), - 'admins': reverse_lazy( - 'harvester-admins', - request=self.context.get('request'), - kwargs={'pk': harvester.id} - ), - } + return {} + # 'monitored_paths': reverse_lazy( + # 'harvester-paths', + # request=self.context.get('request'), + # kwargs={'pk': harvester.id} + # ), + # 'users': reverse_lazy( + # 'harvester-users', + # request=self.context.get('request'), + # kwargs={'pk': harvester.id} + # ), + # 'admins': reverse_lazy( + # 'harvester-admins', + # request=self.context.get('request'), + # kwargs={'pk': harvester.id} + # ), + # } class Meta: model = Harvester diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index efe4fe84..5e39752f 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -59,11 +59,12 @@ class HarvesterViewSet(viewsets.ModelViewSet): serializer_class = HarvesterSerializer filterset_fields = ['name'] search_fields = ['@name'] + queryset = Harvester.objects.none().order_by('last_check_in', 'id') def get_queryset(self): return Harvester.objects.complex_filter( - Q(user_group__user_set__username__contains=self.request.user.username) | - Q(admin_group__user_set__username__contains=self.request.user.username) + Q(user_group__in=self.request.user.groups.all()) | + Q(admin_group__in=self.request.user.groups.all()) ).order_by('last_check_in', 'id') def create(self, request, *args, **kwargs): From 7ebad34258b5f70e8b0df703c92d74c9f9f4df6e Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Mon, 9 Jan 2023 14:30:41 +0000 Subject: [PATCH 21/79] harvester + path editing --- README.md | 19 ++ django/backend_django/galvanalyser/models.py | 2 +- .../galvanalyser/serializers.py | 79 ++--- django/backend_django/galvanalyser/views.py | 119 ++++--- frontend/src/APIConnection.ts | 11 +- frontend/src/HarvesterDetail.js | 307 ------------------ frontend/src/HarvesterDetail.tsx | 283 ++++++++++++++++ frontend/src/Harvesters.tsx | 57 ++-- frontend/src/PaginatedTable.tsx | 4 +- 9 files changed, 444 insertions(+), 437 deletions(-) delete mode 100644 frontend/src/HarvesterDetail.js create mode 100644 frontend/src/HarvesterDetail.tsx diff --git a/README.md b/README.md index ff3a18dc..6103ca56 100644 --- a/README.md +++ b/README.md @@ -74,3 +74,22 @@ supported. An entity relationship diagram is shown below. +### Harvester permissions + +| Action | User status | +|------------------|---------------| +| View harvester | Users, Admins | +| View paths | Users, Admins | +| Add paths | Users, Admins | +| Edit harvester | Admins | +| Delete harvester | Admins | + +### Path permissions + +| Action | User status | +|-------------|---------------| +| View files | Users, Admins | +| Edit path | Admins | +| Delete path | Admins | + +All Harvester Admins are Admins on all paths on that Harvester. diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index a3b21537..15ff3d4c 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -57,7 +57,7 @@ def run(self): class MonitoredPath(models.Model): - harvester = models.ForeignKey(to=Harvester, on_delete=models.CASCADE) + harvester = models.ForeignKey(to=Harvester, related_name='monitored_paths', on_delete=models.CASCADE) path = models.TextField(unique=True) stable_time = models.PositiveSmallIntegerField(default=60) # seconds files must remain stable to be processed admin_group = models.ForeignKey( diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py index 44ce3c91..1ce1a3fc 100644 --- a/django/backend_django/galvanalyser/serializers.py +++ b/django/backend_django/galvanalyser/serializers.py @@ -16,66 +16,49 @@ class HarvesterSerializer(serializers.HyperlinkedModelSerializer): - links = serializers.SerializerMethodField() - - def get_links(self, harvester): - return {} - # 'monitored_paths': reverse_lazy( - # 'harvester-paths', - # request=self.context.get('request'), - # kwargs={'pk': harvester.id} - # ), - # 'users': reverse_lazy( - # 'harvester-users', - # request=self.context.get('request'), - # kwargs={'pk': harvester.id} - # ), - # 'admins': reverse_lazy( - # 'harvester-admins', - # request=self.context.get('request'), - # kwargs={'pk': harvester.id} - # ), - # } - class Meta: model = Harvester - fields = ['url', 'id', 'name', 'sleep_time', 'last_check_in', 'links'] + fields = ['url', 'id', 'name', 'sleep_time', 'last_check_in'] read_only_fields = ['url', 'id', 'last_check_in'] class HarvesterConfigSerializer(serializers.HyperlinkedModelSerializer): class Meta: model = Harvester - fields = ['url', 'id', 'api_key', 'name', 'last_check_in', 'sleep_time', 'paths'] - depth = 10 # max depth + fields = ['url', 'id', 'api_key', 'name', 'last_check_in', 'sleep_time', 'monitored_paths'] + depth = 1 # max depth class MonitoredPathSerializer(serializers.HyperlinkedModelSerializer): - links = serializers.SerializerMethodField() + users = serializers.SerializerMethodField() - def get_links(self, monitored_path): + def get_users(self, instance): + harvester_admins = instance.harvester.admin_group.user_set.all() + admins = instance.admin_group.user_set.all() + users = instance.user_group.user_set.all() return { - 'files': reverse_lazy( - 'monitored_path-files', - request=self.context.get('request'), - kwargs={'pk': monitored_path.id} - ), - 'users': reverse_lazy( - 'monitored_path-users', - request=self.context.get('request'), - kwargs={'pk': monitored_path.id} - ), - 'admins': reverse_lazy( - 'monitored_path-admins', - request=self.context.get('request'), - kwargs={'pk': monitored_path.id} - ), + 'harvester_admins': UserSerializer( + harvester_admins, + many=True, + context={'request': self.context['request']} + ).data, + 'admins': UserSerializer( + admins, + many=True, + context={'request': self.context['request']} + ).data, + 'users': UserSerializer( + users, + many=True, + context={'request': self.context['request']} + ).data, } class Meta: model = MonitoredPath - fields = '__all__' - read_only_fields = ['admin_group', 'user_group'] + fields = ['url', 'path', 'stable_time', 'harvester', 'users'] + read_only_fields = ['users'] + depth = 1 class ObservedFileSerializer(serializers.HyperlinkedModelSerializer): @@ -139,9 +122,15 @@ class Meta: class GroupSerializer(serializers.HyperlinkedModelSerializer): + users = serializers.SerializerMethodField() + + def get_users(self, instance): + return UserSerializer(instance.user_set.all(), many=True, context={'request': self.context['request']}).data + class Meta: model = Group - fields = '__all__' + fields = ['url', 'name', 'users'] + depth = 1 class UserSerializer(serializers.HyperlinkedModelSerializer): @@ -154,6 +143,4 @@ class Meta: 'last_name', 'is_staff', 'is_superuser', - 'groups', ] - depth = 1 diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 5e39752f..74994ced 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -42,6 +42,10 @@ from .tasks import get_env +def error_response(error: str, status: int = 400) -> Response: + return Response({'error': error}, status=status) + + class LoginView(KnoxLoginView): permission_classes = [AllowAny] authentication_classes = [BasicAuthentication] @@ -62,7 +66,7 @@ class HarvesterViewSet(viewsets.ModelViewSet): queryset = Harvester.objects.none().order_by('last_check_in', 'id') def get_queryset(self): - return Harvester.objects.complex_filter( + return Harvester.objects.filter( Q(user_group__in=self.request.user.groups.all()) | Q(admin_group__in=self.request.user.groups.all()) ).order_by('last_check_in', 'id') @@ -74,13 +78,13 @@ def create(self, request, *args, **kwargs): # Validate input if not request.data['name']: - return Response({'error': 'No name specified for Harvester.'}, status=400) + return error_response('No name specified for Harvester.') if not request.data['user']: - return Response({'error': 'No administrator id specified for Harvester.'}, status=400) + return error_response('No administrator id specified for Harvester.') if len(Harvester.objects.filter(name=request.data['name'])): - return Response({'error': 'Harvester with that name already exists'}, status=400) + return error_response('Harvester with that name already exists') if len(User.objects.filter(id=int(request.data['user']))) != 1: - return Response({'error': f'No user exists with id {request.data["user"]}'}, status=400) + return error_response('No user exists with id {request.data["user"]}') # Create Harvester harvester = Harvester.objects.create(name=request.data['name']) @@ -95,6 +99,32 @@ def create(self, request, *args, **kwargs): return Response(self.get_serializer(harvester).data) + def update(self, request, *args, **kwargs): + try: + harvester = Harvester.objects.get(id=kwargs.get('pk')) + except Harvester.DoesNotExist: + return error_response(f'Harvester with id {request.data["id"]} not found.') + if not request.user.groups.filter(id=harvester.admin_group_id).exists(): + return error_response(f'Access denied.') + + name = request.data.get('name') + if name != harvester.name: + if Harvester.objects.filter(name=name).exists(): + return error_response(f'Another Harvester already has the name {name}') + harvester.name = name + sleep_time = request.data.get('sleep_time', None) + if sleep_time is not None: + try: + sleep_time = int(sleep_time) + assert sleep_time > 0 + except (TypeError, ValueError, AssertionError): + return error_response('sleep_time must be an integer greater than 0') + if sleep_time != harvester.sleep_time: + harvester.sleep_time = sleep_time + + harvester.save() + return Response(self.get_serializer(harvester).data) + @action(detail=True, methods=['GET']) def env(self, request, pk: int = None): harvester = Harvester.objects.get(id=pk) @@ -111,39 +141,6 @@ def config(self, request, pk: int = None): harvester = get_object_or_404(Harvester, id=pk) return Response(HarvesterConfigSerializer(harvester, context={'request': request}).data) - @action(detail=True, methods=['GET']) - def paths(self, request, pk: int = None): - """ - MonitoredPaths for the Harvester. - """ - # TODO: Restrict access to Harvester or harvester user - harvester = get_object_or_404(Harvester, id=pk) - paths = MonitoredPath.objects.filter(harvester=harvester).order_by('id') - paths = self.paginate_queryset(paths) - return self.get_paginated_response(MonitoredPathSerializer(paths, many=True).data) - - @action(detail=True, methods=['GET']) - def users(self, request, pk: int = None): - """ - Users able to access the Harvester. Users can create MonitoredPaths. - """ - # TODO: Restrict access to Harvester or harvester user - harvester = get_object_or_404(Harvester, id=pk) - users = User.objects.filter(groups__in=[harvester.admin_group, harvester.user_group]) - users = self.paginate_queryset(users) - return self.get_paginated_response(UserSerializer(users, context={'request': request}, many=True).data) - - @action(detail=True, methods=['GET']) - def admins(self, request, pk: int = None): - """ - Users able to edit the Harvester. - """ - # TODO: Restrict access to Harvester or harvester user - harvester = get_object_or_404(Harvester, id=pk) - admins = User.objects.filter(groups__in=[harvester.admin_group]) - admins = self.paginate_queryset(admins) - return self.get_paginated_response(UserSerializer(admins, context={'request': request}, many=True).data) - @action(detail=True, methods=['POST']) def report(self, request, pk: int = None): """ @@ -206,8 +203,18 @@ class MonitoredPathViewSet(viewsets.ModelViewSet): TODO: document """ serializer_class = MonitoredPathSerializer + filterset_fields = ['path', 'harvester__id', 'harvester__name'] + search_fields = ['@path'] queryset = MonitoredPath.objects.all().order_by('id') + # Access restrictions + def get_queryset(self): + return MonitoredPath.objects.filter( + Q(user_group__in=self.request.user.groups.all()) | + Q(admin_group__in=self.request.user.groups.all()) | + Q(harvester__admin_group__in=self.request.user.groups.all()) + ).order_by('id') + def create(self, request, *args, **kwargs): """ Create a MonitoredPath for a Harvester and the user Groups required to control it. @@ -224,11 +231,16 @@ def create(self, request, *args, **kwargs): if len(MonitoredPath.objects.filter(path=path, harvester=harvester)): return Response({'error': 'Path already exists on Harvester.'}, status=400) # Check user is authorised to create paths on Harvester - if harvester.user_group not in request.user.groups and harvester.admin_group not in request.user.groups: + if not request.user.groups.filter(id=harvester.user_group_id).exists() and \ + not request.user.groups.filter(id=harvester.admin_group_id).exists(): return Response({'error': f'Permission denied to {request.user.username} for {harvester.name}'}) # Create Path - monitored_path = MonitoredPath.objects.create(path=path, harvester=harvester) + try: + stable_time = int(request.data['stable_time']) + monitored_path = MonitoredPath.objects.create(path=path, harvester=harvester, stable_time=stable_time) + except (TypeError, ValueError): + monitored_path = MonitoredPath.objects.create(path=path, harvester=harvester) # Create user/admin groups monitored_path.user_group = Group.objects.create(name=f"path_{harvester.id}_{monitored_path.id}_users") monitored_path.admin_group = Group.objects.create(name=f"path_{harvester.id}_{monitored_path.id}_admins") @@ -239,6 +251,33 @@ def create(self, request, *args, **kwargs): return Response(self.get_serializer(monitored_path).data) + def update(self, request, *args, **kwargs): + try: + path = MonitoredPath.objects.get(id=kwargs.get('pk')) + except MonitoredPath.DoesNotExist: + return error_response(f'Path with id {request.data["id"]} not found.') + if not request.user.groups.filter(id=path.admin_group_id).exists(): + if not request.user.groups.filter(id=path.harvester.admin_group_id).exists(): + return error_response(f'Access denied.') + + path_str = request.data.get('path') + if path_str != path.path: + if MonitoredPath.objects.filter(path=path_str, harvester=path.harvester).exists(): + return error_response(f'Path {path_str} already exists on {path.harvester.name}') + path.path = path_str + stable_time = request.data.get('stable_time', None) + if stable_time is not None: + try: + stable_time = int(stable_time) + assert stable_time > 0 + except (TypeError, ValueError, AssertionError): + return error_response('stable_time must be an integer greater than 0') + if stable_time != path.stable_time: + path.stable_time = stable_time + + path.save() + return Response(self.get_serializer(path).data) + @action(detail=True, methods=['GET']) def files(self, request, pk: int = None): """ diff --git a/frontend/src/APIConnection.ts b/frontend/src/APIConnection.ts index 099a509d..a7ca5b48 100644 --- a/frontend/src/APIConnection.ts +++ b/frontend/src/APIConnection.ts @@ -5,11 +5,11 @@ export type User = { last_name: string, is_staff: boolean, is_superuser: boolean, - groups: { - url: string, - name: string, - permissions: [] - }[], + // groups: { + // url: string, + // name: string, + // permissions: [] + // }[], token: string, } @@ -70,6 +70,7 @@ export class APIConnection { async fetch(url: string, options?: any): Promise { await this.get_is_logged_in(); console.info(`Fetch ${url} for ${this.user?.username}`) + console.debug('fetch options', options) const token = this.user?.token; let newOptions = {...options}; newOptions.credentials = 'same-origin'; diff --git a/frontend/src/HarvesterDetail.js b/frontend/src/HarvesterDetail.js deleted file mode 100644 index cf116801..00000000 --- a/frontend/src/HarvesterDetail.js +++ /dev/null @@ -1,307 +0,0 @@ -import React, { useEffect, useState, useCallback } from 'react'; -import TextField from '@mui/material/TextField'; -import Typography from '@mui/material/Typography'; -import Input from '@mui/material/Input'; -import InputAdornment from '@mui/material/InputAdornment'; -import { makeStyles } from '@mui/styles' -import Table from '@mui/material/Table'; -import TableBody from '@mui/material/TableBody'; -import Paper from '@mui/material/Paper'; -import Tooltip from '@mui/material/Tooltip'; -import AddIcon from '@mui/icons-material/Add'; -import IconButton from '@mui/material/IconButton'; -import TableCell from '@mui/material/TableCell'; -import MenuItem from '@mui/material/MenuItem'; -import Select from '@mui/material/Select'; -import Chip from '@mui/material/Chip'; -import SaveIcon from '@mui/icons-material/Save'; -import TableContainer from '@mui/material/TableContainer'; -import TableHead from '@mui/material/TableHead'; -import DeleteIcon from '@mui/icons-material/Delete'; -import TableRow from '@mui/material/TableRow'; -import Files from './Files' - -import { - monitored_paths, add_monitored_path, users, env_harvester, - update_monitored_path, delete_monitored_path, isAdmin, -} from './Api' - -const useStyles = makeStyles((theme) => ({ - paper: { - marginTop: theme.spacing(4), - }, - table: { - minWidth: 650, - }, - resize: { - fontSize: '11pt', - }, - input: { - marginLeft: theme.spacing(1), - flex: 1, - }, - inputAdornment: { - color: theme.palette.text.disabled, - }, - iconButton: { - padding: 10, - }, - chips: { - display: 'flex', - flexWrap: 'wrap', - }, - chip: { - margin: 2, - }, -})); - -function MyTableRow({env, userData, savedRow, onRowSave, selected, onSelectRow, disableSave, addIcon}) { - const classes = useStyles(); - const [row, setRow] = useState([]) - const [dirty, setDirty] = useState(false) - - const rowUnchanged = Object.keys(row).reduce((a, k) => { - return a && row[k] === savedRow[k]; - }, true); - - useEffect(() => { - if (!dirty) { - setRow(savedRow); - } - }, [dirty, savedRow]); - - - - let useRow = row; - if (useRow.id === undefined) { - useRow = savedRow; - } - - const setValue = (key) => (e) => { - setDirty(true); - setRow({...useRow, [key]: e.target.value}); - }; - - const ITEM_HEIGHT = 48; - const ITEM_PADDING_TOP = 8; - const MenuProps = { - PaperProps: { - style: { - maxHeight: ITEM_HEIGHT * 4.5 + ITEM_PADDING_TOP, - width: 250, - }, - }, - }; - - const idToName = (id) => { - const user = userData.find((x) => x.id === id); - return user ? user.username : 'Not Found'; - }; - - const Icon = addIcon ? : ; - - console.log('userData:', userData.results) - - return ( - - {onSelectRow(savedRow);}} - hover - selected={selected} - > - - {useRow.id} - - - - {env.GALVANALYSER_HARVESTER_BASE_PATH}/ - , - }} - value={useRow.path} - onChange={setValue('path')} /> - - - - - - - - { - setDirty(false); - onRowSave(row); - }} - > - {Icon} - - - - - - - ) -} - -export default function HarvesterDetail({harvester}) { - const classes = useStyles(); - - const [userData, setUserData] = useState({results: []}) - const [paths, setPaths] = useState([]) - const [selected, setSelected] = useState({id: null}) - const [envData, setEnvData] = useState([]) - - const userIsAdmin = isAdmin(); - - useEffect(() => { - env_harvester(harvester.id).then((response) => { - if (response.ok) { - return response.json().then(setEnvData); - } - }); - }, [harvester.id]); - - useEffect(() => { - users().then((response) => { - if (response.ok) { - response.json().then(setUserData); - } - }); - }, []); - - const refreshPaths = useCallback( - () => { - monitored_paths(harvester.id).then((response) => { - if (response.ok) { - return response.json().then((result) => { - const results = result.results; - console.log('Harvester details:', results) - setPaths(results.sort((arg1, arg2) => arg1.id - arg2.id)); - setSelected(oldSelected => { - const newSelected = results.find(x => x.id === oldSelected.id); - return newSelected || {id: null}; - }); - }); - } - }); - }, - [harvester.id], - ); - - useEffect(() => { - refreshPaths(); - }, [harvester, refreshPaths]); - - const addNewPath = (data) => { - add_monitored_path({harvester_id: harvester.id, path: data.path}).then(refreshPaths); - }; - const deletePath = () => { - delete_monitored_path(selected.id).then(refreshPaths); - }; - const updatePath = (value) => { - update_monitored_path(value.id, value).then(refreshPaths); - }; - - const isSelected = selected.id !== null; - - return ( - - - Harvester "{harvester.name}" monitored paths - - - - - - ID - Path - Users - - - - {paths.map((row) => ( - - ))} - {}} - disableSave={false} - addIcon={true} - placeholder={'Add Monitored Path'} - /> - -
- - - - - - - - - - - - - - {isSelected && - - } - - - ); -} diff --git a/frontend/src/HarvesterDetail.tsx b/frontend/src/HarvesterDetail.tsx new file mode 100644 index 00000000..d1ec9dbe --- /dev/null +++ b/frontend/src/HarvesterDetail.tsx @@ -0,0 +1,283 @@ +import React, {useEffect, useState, useCallback, ChangeEvent} from 'react'; +import TextField from '@mui/material/TextField'; +import Typography from '@mui/material/Typography'; +import Input from '@mui/material/Input'; +import InputAdornment from '@mui/material/InputAdornment'; +import { makeStyles } from '@mui/styles' +import Paper from '@mui/material/Paper'; +import Tooltip from '@mui/material/Tooltip'; +import AddIcon from '@mui/icons-material/Add'; +import IconButton from '@mui/material/IconButton'; +import TableCell from '@mui/material/TableCell'; +import MenuItem from '@mui/material/MenuItem'; +import Select from '@mui/material/Select'; +import Chip from '@mui/material/Chip'; +import SaveIcon from '@mui/icons-material/Save'; +import TableHead from '@mui/material/TableHead'; +import DeleteIcon from '@mui/icons-material/Delete'; +import TableRow from '@mui/material/TableRow'; +import PaginatedTable, {RowFunProps} from './PaginatedTable'; +import Connection, {User} from "./APIConnection"; +import Files from './Files' + +import { + monitored_paths, add_monitored_path, users, env_harvester, + update_monitored_path, delete_monitored_path, isAdmin, url, +} from './Api' +import {HarvesterFields} from "./Harvesters"; + +const useStyles = makeStyles((theme) => ({ + paper: { + marginTop: theme.spacing(4), + }, + table: { + minWidth: 650, + }, + resize: { + fontSize: '11pt', + }, + input: { + marginLeft: theme.spacing(1), + flex: 1, + }, + inputAdornment: { + color: theme.palette.text.disabled, + }, + iconButton: { + padding: 10, + }, + chips: { + display: 'flex', + flexWrap: 'wrap', + }, + chip: { + margin: 2, + }, +})); + +type MonitoredPathUserGroups = { + harvester_admins: User[]; + admins: User[]; + users: User[]; +} + +export type MonitoredPathFields = { + url: string; + harvester: number; + stable_time: number; + path: string; + users: MonitoredPathUserGroups; +} + +function MyTableRow(props: RowFunProps) { + const classes = useStyles(); + const [row, setRow] = useState({ + url: "", harvester: -1, stable_time: -1, path: '', users: {harvester_admins: [], admins: [], users: []} + }) + const [dirty, setDirty] = useState(false) + + const rowUnchanged = Object.keys(row).reduce((a, k) => { + //@ts-ignore + return a && row[k] === props.savedRow[k]; + }, true); + + useEffect(() => { + if (!dirty && props.savedRow) { + setRow(props.savedRow); + } + }, [dirty, props.savedRow]); + + let useRow = row; + if (row.harvester === -1 && props.savedRow) + useRow = props.savedRow; + + const setValue = (key: string) => (e: any) => { + setDirty(true); + setRow({...useRow, [key]: e.target?.value}); + }; + + const Icon = props.addIcon ? : ; + + return ( + + {props.onSelectRow(props.savedRow);}} + hover + selected={props.selected} + > + + + // {env.GALVANALYSER_HARVESTER_BASE_PATH}/ + // , + }} + value={useRow.path} + onChange={setValue('path')} /> + + + { + setDirty(true); + setRow({...row, stable_time: parseInt(e.target.value)}); + }} + > + + + + Harvester Admins:
+ {useRow.users.harvester_admins.map(u => ({u.username}))} + Admins:
+ {useRow.users.admins.map(u => ({u.username}))} + Users:
+ {useRow.users.users.map(u => ({u.username}))} + + + + + { + setDirty(false); + props.onRowSave(row); + }} + > + {Icon} + + + + + + + ) +} + +type HarvesterDetailProps = { + harvester: HarvesterFields, + [key: string]: any +} + +// TODO: Figure out why we get unique key errors +export default function HarvesterDetail(props: HarvesterDetailProps) { + const harvester = props.harvester + const classes = useStyles(); + + const [selected, setSelected] = useState(null) + + const [lastUpdated, setLastUpdated] = useState(new Date()) + + const addNewPath = (data: MonitoredPathFields) => { + const insert_data = {harvester: harvester.id, path: data.path, stable_time: data.stable_time} + Connection.fetch('monitored_paths/', {body: JSON.stringify(insert_data), method: 'POST'}) + .then(() => setLastUpdated(new Date())) + }; + const deletePath = () => { + if (isSelected) + Connection.fetch(selected.url, {method: 'DELETE'}) + .then(() => setLastUpdated(new Date())) + }; + const updatePath = (data: MonitoredPathFields) => { + const insert_data = {path: data.path, stable_time: data.stable_time} + Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) + .then(() => setLastUpdated(new Date())) + }; + + const isSelected = selected !== null; + + const column_headings = [ + {label: 'Path', help: 'Directory to watch'}, + {label: 'Stable Time (s)', help: 'Seconds files must remain unchanged to be considered stable and imported'}, + {label: 'Users', help: 'Users with access to this path\'s datasets'}, + {label: 'Save', help: 'Click to save edits to a row'}, + ] + + const table_head = column_headings.map(heading => ( + + + + {heading.label} + + + + )) + + return ( + + + Harvester "{harvester.name}" monitored paths + + {table_head})} + row_fun={(row: MonitoredPathFields) => ( + u.username).includes(Connection.user.username) || + row.users.admins.map((u: User) => u.username).includes(Connection.user.username) || + row.users.users.map((u: User) => u.username).includes(Connection.user.username) + ) + } + /> + )} + initial_url={`monitored_paths/?harvester__id=${harvester.id}`} + new_entry_row={( + { + }} + disableSave={false} + /> + )} + styles={classes} + last_updated={lastUpdated} + /> + + + u.username).includes(Connection.user.username) || + selected.users.admins.map((u: User) => u.username).includes(Connection.user.username) + ) + } + aria-label="delete" + onClick={deletePath} + > + + + + + {isSelected && + + } + + + ); +} diff --git a/frontend/src/Harvesters.tsx b/frontend/src/Harvesters.tsx index abad2d17..a59a5d0d 100644 --- a/frontend/src/Harvesters.tsx +++ b/frontend/src/Harvesters.tsx @@ -59,24 +59,30 @@ export default function Harvesters() { const [lastUpdated, setLastUpdated] = useState(new Date()) - const [selected, setSelected] = useState({id: null}) + const [selected, setSelected] = useState(null) const userIsAdmin = isAdmin() const addNewHarvester = (data: HarvesterFields) => { const insert_data: HarvesterWriteableFields = {name: data.name, sleep_time: data.sleep_time} - Connection.fetch('harvesters', {body: JSON.stringify(insert_data), method: 'POST'}) + Connection.fetch('harvesters/', {body: JSON.stringify(insert_data), method: 'POST'}) .then(() => setLastUpdated(new Date())) }; - const deleteHarvester= () => { - delete_harvester(selected.id); - }; - const updateHarvester= (value: any) => { - update_harvester(value.id, value); + const updateHarvester = (data: any) => { + const insert_data: HarvesterWriteableFields & {id: number} = { + id: data.id, + name: data.name, + sleep_time: data.sleep_time + } + Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) + .then(() => setLastUpdated(new Date())) }; - const runSelectedHarvester = () => { - run_harvester(selected.id); + const deleteHarvester = () => { + if (isSelected) + Connection.fetch(selected.url, {method: 'DELETE'}) + .then(() => setLastUpdated(new Date())) + .then(() => setSelected(null)) }; function table_row_generator(row: any) { @@ -84,7 +90,7 @@ export default function Harvesters() { key={row.id} savedRow={row} onRowSave={updateHarvester} - selected={selected.id === row.id} + selected={selected !== null && selected.id === row.id} onSelectRow={setSelected} disableSave={!userIsAdmin} />) @@ -150,6 +156,7 @@ export default function Harvesters() { {}} - disableSave={false} - addIcon={true} - /> - ) - const column_headings = [ {label: 'ID', help: 'Harvester id in database'}, {label: 'Name', help: 'Harvester name'}, @@ -212,13 +208,12 @@ export default function Harvesters() { )) - const isSelected = selected.id !== null; + const isSelected = selected !== null; const paginated_table = ({table_head})} row_fun= {table_row_generator} - initial_url={`${url}harvesters/`} - new_entry_row={new_row} + initial_url={`harvesters/`} styles={classes} last_updated={lastUpdated} />) @@ -238,20 +233,8 @@ export default function Harvesters() { - - - - - - - - {isSelected && - - } + {isSelected && } ); } diff --git a/frontend/src/PaginatedTable.tsx b/frontend/src/PaginatedTable.tsx index eeff5eeb..8efdcaab 100644 --- a/frontend/src/PaginatedTable.tsx +++ b/frontend/src/PaginatedTable.tsx @@ -19,7 +19,9 @@ export type RowFunProps = { [key: string]: any; } -type RowFun = (row: any) => ReactComponentElement +type RowFun = ((row: any, i: number, array: any[]) => ReactComponentElement) | + ((row: any, i: number) => ReactComponentElement) | + ((row: any) => ReactComponentElement) export type PaginatedTableProps = { header: ReactComponentElement, From 365ebd68eb3de513023fd67fad11fe6a0ccf27f1 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Mon, 9 Jan 2023 17:43:59 +0000 Subject: [PATCH 22/79] drop celery from backend --- django/backend_django/galvanalyser/models.py | 20 ++++----- django/backend_django/galvanalyser/tasks.py | 14 ------- django/backend_django/galvanalyser/views.py | 43 ++++++++++++++------ django/requirements.txt | 2 - django/server.sh | 17 ++++---- harvester/settings.py | 33 --------------- harvester/{init.py => start.py} | 2 +- 7 files changed, 49 insertions(+), 82 deletions(-) delete mode 100644 django/backend_django/galvanalyser/tasks.py delete mode 100644 harvester/settings.py rename harvester/{init.py => start.py} (98%) diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index 15ff3d4c..d3626dbd 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -8,13 +8,13 @@ import random -class FileState(models.IntegerChoices): - IMPORT_FAILED = -1 - UNSTABLE = 0 - GROWING = 1 - STABLE = 2 - IMPORTING = 3 - IMPORTED = 4 +class FileState(models.Choices): + IMPORT_FAILED = "IMPORT FAILED" + UNSTABLE = "UNSTABLE" + GROWING = "GROWING" + STABLE = "STABLE" + IMPORTING = "IMPORTING" + IMPORTED = "IMPORTED" class Harvester(models.Model): @@ -82,15 +82,15 @@ class HarvestError(models.Model): path = models.ForeignKey(to=MonitoredPath, on_delete=models.DO_NOTHING) file = models.TextField(null=True) error = models.TextField() - timestamp = models.DateTimeField(auto_created=True) + timestamp = models.DateTimeField(auto_now=True, null=True) class ObservedFile(models.Model): monitored_path = models.ForeignKey(to=MonitoredPath, related_name='files', on_delete=models.DO_NOTHING) relative_path = models.TextField() last_observed_size = models.PositiveBigIntegerField(null=False, default=0) - last_observed_time = models.DateTimeField() - state = models.SmallIntegerField(choices=FileState.choices, default=FileState.UNSTABLE, null=False) + last_observed_time = models.DateTimeField(null=True) + state = models.TextField(choices=FileState.choices, default=FileState.UNSTABLE, null=False) def inspect_size(self): path = Path(os.path.join(self.monitored_path.path, self.relative_path)) diff --git a/django/backend_django/galvanalyser/tasks.py b/django/backend_django/galvanalyser/tasks.py deleted file mode 100644 index f26cff73..00000000 --- a/django/backend_django/galvanalyser/tasks.py +++ /dev/null @@ -1,14 +0,0 @@ -from celery import shared_task -from .models import Harvester -import os - - -@shared_task -def get_env(): - env_var = 'GALVANALYSER_HARVESTER_BASE_PATH' - return {env_var: os.getenv(env_var)} - - -@shared_task -def run_harvester(harvester_id): - Harvester.objects.get(id=harvester_id).run() diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 74994ced..67afa417 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -39,7 +39,6 @@ from knox.views import LoginView as KnoxLoginView from rest_framework.authentication import BasicAuthentication import json -from .tasks import get_env def error_response(error: str, status: int = 400) -> Response: @@ -125,11 +124,11 @@ def update(self, request, *args, **kwargs): harvester.save() return Response(self.get_serializer(harvester).data) - @action(detail=True, methods=['GET']) - def env(self, request, pk: int = None): - harvester = Harvester.objects.get(id=pk) - result = get_env.apply_async(queue=harvester.name) - return Response(result.get()) + # @action(detail=True, methods=['GET']) + # def env(self, request, pk: int = None): + # harvester = Harvester.objects.get(id=pk) + # result = get_env.apply_async(queue=harvester.name) + # return Response(result.get()) @action(detail=True, methods=['GET']) def config(self, request, pk: int = None): @@ -169,33 +168,51 @@ def report(self, request, pk: int = None): path=path, error=str(error) ) + return Response({}) elif request.data['status'] == 'success': # Figure out what we succeeded in doing! content = request.data['content'] if content['task'] == 'file_size': # Harvester is reporting the size of a file # Update our database record and return a file status - file, _ = ObservedFile.objects.get_or_create(monitored_path=path) + file, _ = ObservedFile.objects.get_or_create(monitored_path=path, relative_path=request.data['file']) + size = content['size'] if size < file.last_observed_size: file.state = FileState.UNSTABLE elif size > file.last_observed_size: file.state = FileState.GROWING + + if size != file.last_observed_size: + file.last_observed_size = size + file.last_observed_time = timezone.now() else: # Recent changes if file.last_observed_time + timezone.timedelta(seconds=path.stable_time) > timezone.now(): file.state = FileState.UNSTABLE # Stable file -- already imported? elif file.state not in [FileState.IMPORTED, FileState.IMPORT_FAILED]: - file.state = FileState.UNSTABLE - file.last_observed_size = size - file.last_observed_time = timezone.now() + file.state = FileState.STABLE + + file.save() + return Response(ObservedFileSerializer(file, context={'request': self.request}).data) + elif content['task'] == 'import': + try: + file = ObservedFile.objects.get(monitored_path=path, relative_path=request.data['file']) + except ObservedFile.DoesNotExist: + return error_response("ObservedFile does not exist") + if content['status'] == 'begin': + file.state = FileState.IMPORTING + elif content['status'] == 'failed': + file.state = FileState.IMPORT_FAILED + elif content['status'] == 'complete': + file.state = FileState.IMPORTED file.save() - return Response(ObservedFileSerializer(file).data) + return Response(ObservedFileSerializer(file, context={'request': self.request})) else: - return Response({'error': 'Unrecognised task'}, status=400) + return error_response('Unrecognised task') else: - return Response({'error': 'Unrecognised status'}, status=400) + return error_response('Unrecognised status') class MonitoredPathViewSet(viewsets.ModelViewSet): diff --git a/django/requirements.txt b/django/requirements.txt index a85cb07c..617ee80b 100644 --- a/django/requirements.txt +++ b/django/requirements.txt @@ -1,6 +1,4 @@ -celery==5.2.7 Django==4.1.4 -django-celery-beat==2.4.0 django-cors-headers==3.13.0 django-filter==22.1 djangorestframework==3.14.0 diff --git a/django/server.sh b/django/server.sh index d00637d5..cb5da807 100644 --- a/django/server.sh +++ b/django/server.sh @@ -25,14 +25,13 @@ python manage.py loaddata galvanalyser/fixtures/Users.json || \ echo "admin:admin already exists; continuing" >&2 echo "Initialisation complete - starting server" -#exec "$@" -mkdir -p /var/run/celery /var/log/celery -chown -R nobody:nogroup /var/run/celery /var/log/celery +#mkdir -p /var/run/celery /var/log/celery +#chown -R nobody:nogroup /var/run/celery /var/log/celery -python manage.py runserver 0.0.0.0:5000 & \ -celery -A config.celery_settings beat \ - --loglevel=DEBUG \ - --logfile=/var/log/celery/scheduler.log \ - -s /var/run/celery/celerybeat-schedule \ - --uid=nobody --gid=nogroup +python manage.py runserver 0.0.0.0:5000 # & \ +#celery -A config.celery_settings beat \ +# --loglevel=DEBUG \ +# --logfile=/var/log/celery/scheduler.log \ +# -s django_celery_beat.schedulers:DatabaseScheduler \ +# --uid=nobody --gid=nogroup diff --git a/harvester/settings.py b/harvester/settings.py deleted file mode 100644 index 052d962e..00000000 --- a/harvester/settings.py +++ /dev/null @@ -1,33 +0,0 @@ -import json -import os -import pathlib - - -def get_settings_file() -> pathlib.Path: - return pathlib.Path(os.getenv('SETTINGS_FILE', "/harvester_files/.harvester.json")) - - -def get_logfile() -> pathlib.Path: - return pathlib.Path(os.getenv('LOG_FILE', "/harvester_files/harvester.log")) - - -def get_settings(): - with open(get_settings_file(), 'r') as f: - try: - return json.load(f) - except json.JSONDecodeError as e: - print(f"Error decoding json file {f.name}", e) - f.seek(0) - print(f.readlines()) - return None - - -def get_setting(*args): - settings = get_settings() - if not settings: - if len(args) == 1: - return None - return [None for _ in args] - if len(args) == 1: - return settings.get(args[0]) - return [settings.get(arg) for arg in args] diff --git a/harvester/init.py b/harvester/start.py similarity index 98% rename from harvester/init.py rename to harvester/start.py index 18845623..d6a4c09d 100644 --- a/harvester/init.py +++ b/harvester/start.py @@ -71,7 +71,7 @@ def register(url: str = None, name: str = None, user_id: int = None, run_foregro else: name_specified = True while True: - result = query(f"{url}harvesters/by_name/?name={name}") + result = query(f"{url}harvesters/?name={name}") if len(result['results']) > 0: click.echo(f"There is already a harvester called {name}.", err=True) From 0ecb0932233e49cdf4d9ec9eb26798ea33f7ebb3 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Mon, 9 Jan 2023 17:44:19 +0000 Subject: [PATCH 23/79] file import in progress --- docker-compose.override.yml | 14 +++--- docker-compose.yml | 17 ------- harvester/harvest.py | 88 ++++++++++++++++++++++++------------ harvester/parse/harvester.py | 86 ++++++++++++++++++++++++++--------- harvester/settings.py | 36 +++++++++++++++ 5 files changed, 165 insertions(+), 76 deletions(-) create mode 100644 harvester/settings.py diff --git a/docker-compose.override.yml b/docker-compose.override.yml index 3c9563f7..0c4a1894 100644 --- a/docker-compose.override.yml +++ b/docker-compose.override.yml @@ -6,16 +6,11 @@ services: dockerfile: Dockerfile context: ./django depends_on: - - redis - - rabbitmq - postgres ports: - "5001:5000" volumes: - ./django:/usr/app - - "${GALVANALYSER_HARVESTER_TEST_PATH}:/usr/test_data" - - "${GALVANALYSER_HARVESTER_BASE_PATH}:/usr/data" - - "${CELERY_LOG_DIR}:/var/log/celery" restart: unless-stopped working_dir: /usr/app command: ./server.sh @@ -23,19 +18,22 @@ services: env_file: - ./.env - ./django/.env.secret - worker: + + harvester: build: dockerfile: Dockerfile context: ./harvester - command: python init.py --name "Harvester03" --url http://app:5000/ --user_id 42 --run_foreground --restart + command: python start.py --name "harvey" --url http://app:5000/ --user_id 42 --run_foreground --restart # command: tail -F anything depends_on: - app volumes: - ./harvester:/usr/harvester - ./.harvester:/harvester_files - + - "${GALVANALYSER_HARVESTER_TEST_PATH}:/usr/test_data" + - "${GALVANALYSER_HARVESTER_BASE_PATH}:/usr/data" working_dir: /usr/harvester + frontend: image: frontend_dev build: diff --git a/docker-compose.yml b/docker-compose.yml index 44aeab80..752ba4d6 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -6,8 +6,6 @@ services: dockerfile: Dockerfile context: ./backend depends_on: - - redis - - rabbitmq - postgres ports: - "5001:5000" @@ -50,21 +48,6 @@ services: working_dir: /app env_file: - ./.env - rabbitmq: - image: "rabbitmq" - ports: - - "5672:5672" - env_file: - - ./.env - restart: unless-stopped - redis: - image: redis:5.0-alpine - restart: always - command: redis-server --requirepass ${REDIS_PASSWORD} - ports: - - "6379:6379" - volumes: - - "${REDIS_DATA_PATH}:/var/lib/redis" postgres: image: "postgres" stop_signal: SIGINT # Fast Shutdown mode diff --git a/harvester/harvest.py b/harvester/harvest.py index e2eb010e..4b51dc8e 100644 --- a/harvester/harvest.py +++ b/harvester/harvest.py @@ -8,15 +8,34 @@ from parse.harvester import import_file +logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__file__) -logger.addHandler(logging.StreamHandler(sys.stdout)) -logger.addHandler(logging.FileHandler(get_logfile())) - - -def report_harvest_result(path: str, content=None, file: str = None, error: BaseException = None): +# stream_handler = logging.StreamHandler(sys.stdout) +# stream_handler.setLevel(logging.INFO) +# logger.addHandler(stream_handler) +file_handler = logging.FileHandler(get_logfile()) +file_handler.setLevel(logging.INFO) +logger.addHandler(file_handler) + + +def split_path(core_path: os.PathLike|str, path: os.PathLike|str) -> (os.PathLike, os.PathLike): + """ + Split a path into the base path property and the rest + """ + path = os.path.abspath(path) + core_path_abs = os.path.abspath(core_path) + return core_path, os.path.relpath(path, core_path_abs) + + +def report_harvest_result( + path: os.PathLike|str, + content=None, + file: os.PathLike|str = None, + error: BaseException = None +): try: if error is not None: - data = {'status': 'error', 'error': error} + data = {'status': 'error', 'error': ";".join(error.args)} else: data = {'status': 'success', 'content': content} data['path'] = path @@ -25,8 +44,10 @@ def report_harvest_result(path: str, content=None, file: str = None, error: Base logger.debug(f"{get_setting('url')}report/; {json.dumps(data)}") return requests.post( f"{get_setting('url')}report/", - headers={'Authorization': f"Harvester {get_setting('api_key')}"}, - data=data + headers={ + 'Authorization': f"Harvester {get_setting('api_key')}" + }, + json=data ) except BaseException as e: logger.error(e) @@ -76,36 +97,45 @@ def update_config(): def harvest(): logger.info("Beginning harvest cycle") - paths = get_setting('watched_paths') + paths = get_setting('monitored_paths') if not paths: - logger.info("No paths are being watched.") + logger.info("No paths are being monitored.") return + logger.debug(paths) + for path in paths: - harvest_path(path) + harvest_path(path.get('path')) -def harvest_path(path: str): +def harvest_path(path: os.PathLike): logger.info(f"Harvesting from {path}") try: - for (dirpath, dirnames, filenames) in os.walk(path): + for (dir_path, dir_names, filenames) in os.walk(path): for filename in filenames: - logger.info(f"Reporting stats for {filename}") - result = report_harvest_result( - path=path, - file=filename, - content={ - 'task': 'file_size', - 'size': os.stat(filename).st_size - } - ) - if result is not None: - result = result.json() - status = result['status'] - logger.info(f"Server assigned status '{status}'") - if status == 'STABLE': - logger.info(f"Parsing STABLE file {filename}") - import_file(os.sep.join([dirpath, filename])) + try: + full_path = os.path.join(dir_path, filename) + core_path, file_path = split_path(path, full_path) + logger.info(f"Reporting stats for {file_path}") + result = report_harvest_result( + path=core_path, + file=file_path, + content={ + 'task': 'file_size', + 'size': os.stat(full_path).st_size + } + ) + if result is not None: + result = result.json() + status = result['state'] + logger.info(f"Server assigned status '{status}'") + if status == 'STABLE': + logger.info(f"Parsing STABLE file {file_path}") + result = import_file(core_path, file_path) + report_harvest_result(path=core_path, file=file_path, content=result) + except BaseException as e: + logger.error(e) + report_harvest_result(path=path, file=full_path, error=e) logger.info(f"Completed directory walking of {path}") except BaseException as e: logger.error(e) diff --git a/harvester/parse/harvester.py b/harvester/parse/harvester.py index f8908cec..3f96531e 100644 --- a/harvester/parse/harvester.py +++ b/harvester/parse/harvester.py @@ -3,6 +3,8 @@ # of Oxford, and the 'Galvanalyser' Developers. All rights reserved. import os + +import json import psutil from .database.util.battery_exceptions import UnsupportedFileTypeError @@ -16,6 +18,22 @@ MaccorExcelInputFile, MaccorRawInputFile, ) +import sys +import logging +import requests +sys.path.append(os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), '..'))) +from settings import get_setting, get_logfile + + +logging.basicConfig(level=logging.INFO) +logger = logging.getLogger(__file__) +# stream_handler = logging.StreamHandler(sys.stdout) +# stream_handler.setLevel(logging.INFO) +# logger.addHandler(stream_handler) +file_handler = logging.FileHandler(get_logfile()) +file_handler.setLevel(logging.INFO) +logger.addHandler(file_handler) + registered_input_files = [ BiologicMprInputFile, @@ -41,28 +59,55 @@ def has_handle(fpath): return False -def import_file(base_path, file_path_row, harvester_name, conn): +def report( + path: os.PathLike|str, + content=None, + file: os.PathLike|str = None, + error: BaseException = None +): + try: + if error is not None: + data = {'status': 'error', 'error': ";".join(error.args)} + else: + data = {'status': 'success', 'content': content} + data['path'] = path + if file is not None: + data['file'] = file + logger.debug(f"{get_setting('url')}report/; {json.dumps(data)}") + return requests.post( + f"{get_setting('url')}report/", + headers={ + 'Authorization': f"Harvester {get_setting('api_key')}" + }, + json=data + ) + except BaseException as e: + logger.error(e) + return None + + +def import_file(core_path: str, file_path: str): """ Attempts to import a given file """ - absolute_path = file_path_row.monitored_path - if not os.path.isabs(absolute_path) and base_path is not None: - absolute_path = os.path.join(base_path, absolute_path) - - fullpath = os.path.join( - absolute_path, file_path_row.observed_path - ) + full_file_path = os.sep.join([core_path, file_path]) print("") - if not os.path.isfile(fullpath): - print("Is not a file, skipping: " + fullpath) + if not os.path.isfile(full_file_path): + print("Is not a file, skipping: " + full_file_path) + report(path=core_path, file=file_path, error=FileNotFoundError()) return - print("Importing " + fullpath) - rows_updated = file_path_row.update_observed_file_state_if_state_is( - "IMPORTING", "STABLE", conn + print("Importing " + full_file_path) + report( + path=core_path, + file=file_path, + content={ + 'content': { + 'task': 'import', + 'status': 'begin' + } + } ) - if rows_updated == 0: - print("File was not stable as expected, skipping import") - return + try: # Attempt reading the file before updating the database to avoid # creating rows for a file we can't read. @@ -73,7 +118,7 @@ def import_file(base_path, file_path_row, harvester_name, conn): for input_file_cls in registered_input_files: try: print('Tried input reader {}'.format(input_file_cls)) - input_file = input_file_cls(fullpath) + input_file = input_file_cls(full_file_path) except Exception as e: print('...failed with: ', type(e), e) else: @@ -84,8 +129,5 @@ def import_file(base_path, file_path_row, harvester_name, conn): print("File successfully imported") except Exception as e: - file_path_row.update_observed_file_state("IMPORT_FAILED", conn) - print("Import failed for " + fullpath) - # perhaps the exception should be saved to the database - # print it for now during development - traceback.print_exc() + logger.error(e) + # report(path=core_path, file=file_path, error=e) diff --git a/harvester/settings.py b/harvester/settings.py new file mode 100644 index 00000000..7f68c20b --- /dev/null +++ b/harvester/settings.py @@ -0,0 +1,36 @@ +import json +import os +import pathlib + + +def get_settings_file() -> pathlib.Path: + return pathlib.Path(os.getenv('SETTINGS_FILE', "/harvester_files/.harvester.json")) + + +def get_logfile() -> pathlib.Path: + return pathlib.Path(os.getenv('LOG_FILE', "/harvester_files/harvester.log")) + + +def get_settings(): + try: + with open(get_settings_file(), 'r') as f: + try: + return json.load(f) + except json.JSONDecodeError as e: + print(f"Error decoding json file {f.name}", e) + f.seek(0) + print(f.readlines()) + except FileNotFoundError: + print(f'No config file at {get_settings_file()}') + return None + + +def get_setting(*args): + settings = get_settings() + if not settings: + if len(args) == 1: + return None + return [None for _ in args] + if len(args) == 1: + return settings.get(args[0]) + return [settings.get(arg) for arg in args] From 5f55f583607ad477731399501bcd32d0ba116208 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Tue, 10 Jan 2023 19:01:03 +0000 Subject: [PATCH 24/79] basic harvester upload --- .../galvanalyser/migrations/0001_initial.py | 170 -------------- django/backend_django/galvanalyser/models.py | 34 +-- .../galvanalyser/parsers/__init__.py | 9 - .../galvanalyser/parsers/classes.py | 32 --- .../galvanalyser/parsers/maccor.py | 210 ------------------ django/backend_django/galvanalyser/views.py | 60 ++++- harvester/harvest.py | 8 +- .../experiment/timeseries_data_row.py | 22 +- harvester/parse/harvester.py | 66 +++++- harvester/start.py | 2 +- 10 files changed, 140 insertions(+), 473 deletions(-) delete mode 100644 django/backend_django/galvanalyser/migrations/0001_initial.py delete mode 100644 django/backend_django/galvanalyser/parsers/__init__.py delete mode 100644 django/backend_django/galvanalyser/parsers/classes.py delete mode 100644 django/backend_django/galvanalyser/parsers/maccor.py diff --git a/django/backend_django/galvanalyser/migrations/0001_initial.py b/django/backend_django/galvanalyser/migrations/0001_initial.py deleted file mode 100644 index 9b579e54..00000000 --- a/django/backend_django/galvanalyser/migrations/0001_initial.py +++ /dev/null @@ -1,170 +0,0 @@ -# Generated by Django 4.1.4 on 2022-12-20 13:20 - -from django.conf import settings -from django.db import migrations, models -import django.db.models.deletion - - -class Migration(migrations.Migration): - - initial = True - - dependencies = [ - migrations.swappable_dependency(settings.AUTH_USER_MODEL), - ('auth', '0012_alter_user_first_name_max_length'), - ] - - operations = [ - migrations.CreateModel( - name='CellData', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField(unique=True)), - ('form_factor', models.TextField()), - ('link_to_datasheet', models.TextField()), - ('anode_chemistry', models.TextField()), - ('cathode_chemistry', models.TextField()), - ('nominal_capacity', models.FloatField()), - ('nominal_cell_weight', models.FloatField()), - ('manufacturer', models.TextField()), - ], - ), - migrations.CreateModel( - name='Dataset', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField()), - ('date', models.DateTimeField()), - ('type', models.TextField()), - ('purpose', models.TextField()), - ('json_data', models.JSONField()), - ('access_group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='auth.group')), - ('cell', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='galvanalyser.celldata')), - ('owner', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL)), - ], - options={ - 'unique_together': {('name', 'date')}, - }, - ), - migrations.CreateModel( - name='DataUnit', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField()), - ('symbol', models.TextField()), - ('description', models.TextField()), - ], - ), - migrations.CreateModel( - name='Equipment', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField(unique=True)), - ('type', models.TextField()), - ], - ), - migrations.CreateModel( - name='Harvester', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField(unique=True)), - ('api_key', models.TextField(null=True)), - ('last_check_in', models.DateTimeField(null=True)), - ('sleep_time', models.IntegerField(default=10)), - ('admin_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='harvester_admins', to='auth.group')), - ('user_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='harvester_users', to='auth.group')), - ], - ), - migrations.CreateModel( - name='MonitoredPath', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('path', models.TextField(unique=True)), - ('harvester', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.harvester')), - ], - options={ - 'unique_together': {('harvester', 'path')}, - }, - ), - migrations.CreateModel( - name='TimeseriesRangeLabel', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('label', models.TextField()), - ('range_start', models.PositiveBigIntegerField()), - ('range_end', models.PositiveBigIntegerField()), - ('info', models.TextField()), - ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.dataset')), - ], - ), - migrations.CreateModel( - name='MonitoredFor', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('path', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.monitoredpath')), - ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), - ], - ), - migrations.CreateModel( - name='DataColumnType', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField()), - ('description', models.TextField()), - ('is_default', models.BooleanField(default=False)), - ('unit', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='galvanalyser.dataunit')), - ], - options={ - 'unique_together': {('unit', 'name')}, - }, - ), - migrations.CreateModel( - name='DataColumn', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField()), - ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.dataset')), - ('type', models.ForeignKey(on_delete=django.db.models.deletion.RESTRICT, to='galvanalyser.datacolumntype')), - ], - options={ - 'unique_together': {('dataset', 'name')}, - }, - ), - migrations.CreateModel( - name='TimeseriesData', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sample', models.PositiveBigIntegerField()), - ('value', models.FloatField()), - ('column', models.ForeignKey(on_delete=django.db.models.deletion.RESTRICT, to='galvanalyser.datacolumn')), - ], - options={ - 'unique_together': {('sample', 'column')}, - }, - ), - migrations.CreateModel( - name='ObservedFile', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('relative_path', models.TextField()), - ('last_observed_size', models.PositiveBigIntegerField()), - ('last_observed_time', models.DateTimeField()), - ('state', models.SmallIntegerField(choices=[(-1, 'Import Failed'), (0, 'Unstable'), (1, 'Growing'), (2, 'Stable'), (3, 'Importing'), (4, 'Imported')], default=0)), - ('monitored_path', models.ForeignKey(on_delete=django.db.models.deletion.DO_NOTHING, to='galvanalyser.monitoredpath')), - ], - options={ - 'unique_together': {('monitored_path', 'relative_path')}, - }, - ), - migrations.CreateModel( - name='DatasetEquipment', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.dataset')), - ('equipment', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.equipment')), - ], - options={ - 'unique_together': {('dataset', 'equipment')}, - }, - ), - ] diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index d3626dbd..1f0764eb 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -2,9 +2,6 @@ from django.db import models from django.contrib.auth.models import User, Group -from .parsers import * -from pathlib import Path -import os import random @@ -92,20 +89,6 @@ class ObservedFile(models.Model): last_observed_time = models.DateTimeField(null=True) state = models.TextField(choices=FileState.choices, default=FileState.UNSTABLE, null=False) - def inspect_size(self): - path = Path(os.path.join(self.monitored_path.path, self.relative_path)) - last_observed_size = path.stat().st_size - if last_observed_size > self.last_observed_size: - self.last_observed_size = last_observed_size - self.state = FileState.GROWING - elif last_observed_size == self.last_observed_size: - if self.last_observed_time + timezone.timedelta(minutes=5) < timezone.now(): - self.state = FileState.STABLE - else: - self.state = FileState.UNSTABLE - - self.last_observed_time = timezone.now() - class Meta: unique_together = [['monitored_path', 'relative_path']] @@ -123,16 +106,15 @@ class CellData(models.Model): class Dataset(models.Model): cell = models.ForeignKey(to=CellData, on_delete=models.SET_NULL, null=True) - owner = models.ForeignKey(to=User, on_delete=models.SET_NULL, null=True) - access_group = models.ForeignKey(to=Group, on_delete=models.CASCADE) - name = models.TextField(null=False) + file = models.ForeignKey(to=ObservedFile, on_delete=models.DO_NOTHING, related_name='dataset') + name = models.TextField(null=True) date = models.DateTimeField(null=False) - type = models.TextField(null=False) + type = models.TextField(null=True) purpose = models.TextField() - json_data = models.JSONField() + json_data = models.JSONField(null=True) class Meta: - unique_together = [['name', 'date']] + unique_together = [['file', 'date']] class Equipment(models.Model): @@ -170,7 +152,7 @@ class Meta: class DataColumn(models.Model): - dataset = models.ForeignKey(to=Dataset, on_delete=models.CASCADE) + dataset = models.ForeignKey(to=Dataset, related_name='columns', on_delete=models.CASCADE) type = models.ForeignKey(to=DataColumnType, on_delete=models.RESTRICT) name = models.TextField(null=False) @@ -180,7 +162,7 @@ class Meta: class TimeseriesData(models.Model): sample = models.PositiveBigIntegerField(null=False) - column = models.ForeignKey(to=DataColumn, null=False, on_delete=models.RESTRICT) + column = models.ForeignKey(to=DataColumn, related_name='values', null=False, on_delete=models.RESTRICT) value = models.FloatField(null=False) class Meta: @@ -188,7 +170,7 @@ class Meta: class TimeseriesRangeLabel(models.Model): - dataset = models.ForeignKey(to=Dataset, null=False, on_delete=models.CASCADE) + dataset = models.ForeignKey(to=Dataset, related_name='range_labels', null=False, on_delete=models.CASCADE) label = models.TextField(null=False) range_start = models.PositiveBigIntegerField(null=False) range_end = models.PositiveBigIntegerField(null=False) diff --git a/django/backend_django/galvanalyser/parsers/__init__.py b/django/backend_django/galvanalyser/parsers/__init__.py deleted file mode 100644 index c0ff9887..00000000 --- a/django/backend_django/galvanalyser/parsers/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -from .classes import Parser -import pathlib - - -def parse(path: pathlib.Path, parser: Parser = None): - try: - pass - except BaseException: - pass diff --git a/django/backend_django/galvanalyser/parsers/classes.py b/django/backend_django/galvanalyser/parsers/classes.py deleted file mode 100644 index 161291a8..00000000 --- a/django/backend_django/galvanalyser/parsers/classes.py +++ /dev/null @@ -1,32 +0,0 @@ -import pathlib -from typing import List - - -class FileParseError(BaseException): - pass - - -class Parser: - """ - A Parser presents information from a dataset in a standardized format. - That format breaks data down into default columns and non-default columns. - Data are presented using Parser.read() which yields a row of data as key-value pairs. - Metadata can be accessed via the Parser.metadata object. - These are not guaranteed to conform to any particular structure. - """ - extensions: List[str] = [] - default_columns = [] - raw_data = None - metadata = {} - ready: bool = False - - def __init__(self, path: pathlib.Path = None, default_columns=None): - if default_columns is not None: - self.default_columns = [{'id': c.id, 'name': c.name} for c in default_columns] - self.path = path - - def read(self): - """ - Return a row of key-value pairs binding column names to cell values. - """ - return {} diff --git a/django/backend_django/galvanalyser/parsers/maccor.py b/django/backend_django/galvanalyser/parsers/maccor.py deleted file mode 100644 index 36dd03e6..00000000 --- a/django/backend_django/galvanalyser/parsers/maccor.py +++ /dev/null @@ -1,210 +0,0 @@ -import csv -import pathlib -import re -import os -import ntpath -import maya - -from .classes import Parser, FileParseError - - -def isfloat(value): - try: - float(value) - return True - except ValueError: - return False - - -def clean_key(key): - """ - Unescapes and removes trailing characters on strings - """ - return key.replace("''", "'").strip().rstrip(":") - - -def clean_value(value): - """ - Trims values - """ - return value.replace("''", "'").strip().rstrip("\0").strip() - - -def handle_recno(row, correct_number_of_columns, recno_col, row_idx): - """ - Ensure the record number is represented in the right place in the column - """ - if len(row) > correct_number_of_columns: - if recno_col >= 0: - row = ( - row[0:recno_col] - + [(row[recno_col] + row[recno_col + 1]).replace(",", "")] - + row[recno_col + 2:] - ) - else: - raise FileParseError(( - "There are more data columns than headers. " - f"Row {row_idx} has {len(row)} cols, expected {correct_number_of_columns}" - )) - elif recno_col >= 0: - row[recno_col] = row[recno_col].replace(",", "") - return row - - -def regularise_column_name(column_name: str) -> str: - if column_name == "Amp-hr": - return "Charge Capacity" - if column_name == "Amps": - return "Amps" - if column_name == "Watt-hr": - return "Energy Capacity" - if column_name == "StepTime": - return "Step Time" - if column_name == "Step (Sec)": - return "Step Time" - if column_name == "Volts": - return "Volts" - if column_name == "TestTime": - return "Time" - if column_name == "Test (Sec)": - return "Time" - if column_name == "Rec#": - return "Sample Number" - if column_name == "Temp 1": - return "Temperature" - return column_name - - -class MaccorTextFile(Parser): - extensions = ['csv', 'txt'] - header_row_count = 2 - delimiter = None - - def __init__(self, path: pathlib.Path): - super(MaccorTextFile, self).__init__(path) - self.path = "/usr/data/ocrsecio/TPG1+-+Cell+15+-+002.txt" - if not self.validate_file(): - raise FileParseError(f"File {path} is not a Maccor text file") - self.regularised_column_names = [] - with open(self.path, 'r') as f: - r = csv.reader(f, delimiter=self.delimiter) - first = next(r) - key = clean_key(first[0]) - self.metadata[key] = maya.parse(first[1]).datetime() - second = next(r) - key = clean_key(second[0]) - self.metadata[key] = maya.parse(second[1]).datetime() - self.metadata["Dataset Name"] = os.path.splitext( - ntpath.basename(self.path) - )[0] - self.metadata["Machine Type"] = "Maccor" - headers = [header for header in next(r) if header != ""] - correct_number_of_columns = len(headers) - try: - recno_col = headers.index("Rec#") - except ValueError: - recno_col = -1 - column_has_data = [False for column in headers] - row_idx = 1 - first_data = next(r) - first_data = handle_recno( - first_data, correct_number_of_columns, recno_col, row_idx - ) - column_is_numeric = [isfloat(column) for column in first_data] - numeric_columns = [] - for i in range(0, len(column_is_numeric)): - if column_is_numeric[i]: - numeric_columns.append(i) - else: - column_has_data[i] = True - for row_idx, row in enumerate(r, 1): - row = handle_recno(row, correct_number_of_columns, recno_col, row_idx) - for col in numeric_columns[:]: - is_float = True - try: - data_detected = float(row[col]) != 0.0 - except ValueError: - # Failed to cast a string to float so it is a value - column_is_numeric[col] = False - data_detected = True - is_float = False - if data_detected: - column_has_data[col] = True - numeric_columns.remove(col) - print( - "Found data in col {} ( {} ) : {}{} on row {}".format( - col, - headers[col], - row[col], - ( - (" as float: " + str(float(row[col]))) - if is_float - else "" - ), - row_idx, - ) - ) - - self.column_info = [ - { - "index": i, - "name": headers[i], - "regularised_name": regularise_column_name(headers[i]), - "has_data": column_has_data[i], - "is_numeric": column_is_numeric[i] - } - for i in range(0, len(headers)) - ] - self.metadata["num_rows"] = row_idx + 1 # account for 0-based indexing - if recno_col == -1: - # No Rec# , make up numbers - self.metadata["first_sample_no"] = 1 # Maccor count from 1 - self.metadata["last_sample_no"] = self.metadata["num_rows"] - else: - self.metadata["first_sample_no"] = int(first_data[recno_col]) - self.metadata["last_sample_no"] = int(row[recno_col]) - self.ready = True - - def read(self, populated_columns_only: bool = False): - if populated_columns_only: - columns = [c for c in self.column_info if c['has_data']] - else: - columns = self.column_info - with open(self.path, 'r') as f: - r = csv.reader(f, delimiter=self.delimiter) - for i, row in enumerate(r): - if i <= self.header_row_count: - continue - yield { - columns[i]['regularised_name']: - float(row[columns[i]['index']]) if columns[i]['is_numeric'] else row[columns[i]['index']] - for i in range(len(columns)) - } - - def validate_file(self) -> bool: - for delimiter in [',', '\t']: - with open(self.path, "r") as f: - line = f.readline() - line_start = "Today''s Date" + delimiter - date_regex = r"\d\d\/\d\d\/\d\d\d\d \d?\d:\d\d:\d\d [AP]M" - if not line.startswith(line_start): - continue - if not re.match((line_start + date_regex), line): - continue - line = f.readline() - line_start = "Date of Test:" + delimiter - if not line.startswith(line_start): - continue - if not re.match((line_start + date_regex), line): - continue - reader = csv.reader(f, delimiter=delimiter) - headers = next(reader) - if ( - "Amps" not in headers - or "Volts" not in headers - or "TestTime" not in headers - ): - continue - self.delimiter = delimiter - return True - return False diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 67afa417..43a07283 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -191,7 +191,7 @@ def report(self, request, pk: int = None): if file.last_observed_time + timezone.timedelta(seconds=path.stable_time) > timezone.now(): file.state = FileState.UNSTABLE # Stable file -- already imported? - elif file.state not in [FileState.IMPORTED, FileState.IMPORT_FAILED]: + elif file.state not in [FileState.IMPORTED.value, FileState.IMPORT_FAILED.value]: file.state = FileState.STABLE file.save() @@ -201,14 +201,60 @@ def report(self, request, pk: int = None): file = ObservedFile.objects.get(monitored_path=path, relative_path=request.data['file']) except ObservedFile.DoesNotExist: return error_response("ObservedFile does not exist") - if content['status'] == 'begin': - file.state = FileState.IMPORTING - elif content['status'] == 'failed': + if content['status'] in ['begin', 'in_progress', 'complete']: + try: + if content['status'] == 'begin': + file.state = FileState.IMPORTING + # TODO: process metadata under 'begin'? + dataset, _ = Dataset.objects.get_or_create( + defaults={'date': timezone.now()}, + file=file + ) + elif content['status'] == 'complete': + file.state = FileState.IMPORTED + else: + dataset = Dataset.objects.get(file=file) + for column_data in content['data']: + try: + column_type = DataColumnType.objects.get(id=column_data['column_id']) + column, _ = DataColumn.objects.get_or_create( + name=column_type.name, + type=column_type, + dataset=dataset + ) + except KeyError: + if 'unit_id' in column_data: + unit = DataUnit.objects.get(id=column_data['unit_id']) + else: + unit, _ = DataUnit.objects.get_or_create(symbol=column_data['unit_symbol']) + try: + column_type = DataColumnType.objects.get(unit=unit) + except DataColumnType.DoesNotExist: + column_type = DataColumnType.objects.create( + name=column_data['column_name'], + unit=unit + ) + column, _ = DataColumn.objects.get_or_create( + name=column_data['column_name'], + type=column_type, + dataset=dataset + ) + TimeseriesData.objects.bulk_create([ + TimeseriesData(sample=k, value=v, column_id=column.id) + for k, v in column_data['values'].items() + ]) + + except BaseException as e: + file.state = FileState.IMPORT_FAILED + HarvestError.objects.create(harvester=harvester, path=path, error=str(e)) + file.save() + return error_response(f"Error importing data: {e.args}") + if content['status'] == 'failed': file.state = FileState.IMPORT_FAILED - elif content['status'] == 'complete': - file.state = FileState.IMPORTED + file.save() - return Response(ObservedFileSerializer(file, context={'request': self.request})) + + return Response(ObservedFileSerializer(file, context={'request': self.request}).data) else: return error_response('Unrecognised task') else: diff --git a/harvester/harvest.py b/harvester/harvest.py index 4b51dc8e..506b324c 100644 --- a/harvester/harvest.py +++ b/harvester/harvest.py @@ -132,10 +132,14 @@ def harvest_path(path: os.PathLike): if status == 'STABLE': logger.info(f"Parsing STABLE file {file_path}") result = import_file(core_path, file_path) - report_harvest_result(path=core_path, file=file_path, content=result) + report_harvest_result( + path=core_path, + file=file_path, + content={'task': 'import', 'status': 'complete'} + ) except BaseException as e: logger.error(e) - report_harvest_result(path=path, file=full_path, error=e) + report_harvest_result(path=path, file=file_path, error=e) logger.info(f"Completed directory walking of {path}") except BaseException as e: logger.error(e) diff --git a/harvester/parse/database/experiment/timeseries_data_row.py b/harvester/parse/database/experiment/timeseries_data_row.py index 845a3b10..040e4452 100644 --- a/harvester/parse/database/experiment/timeseries_data_row.py +++ b/harvester/parse/database/experiment/timeseries_data_row.py @@ -17,17 +17,17 @@ IMPEDENCE_PHASE_COLUMN_ID = 9 FREQUENCY_COLUMN_ID = 10 -UNIT_UNITLESS = 0 -UNIT_SECONDS = 1 -UNIT_VOLTS = 2 -UNIT_AMPS = 3 -UNIT_WATT_HOURS = 4 -UNIT_AMP_HOURS = 5 -UNIT_CENTIGRADE = 6 -UNIT_WATTS = 7 -UNIT_OHMS = 8 -UNIT_DEGREES = 9 -UNIT_HERTZ = 10 +UNIT_UNITLESS = 1 +UNIT_SECONDS = 2 +UNIT_VOLTS = 3 +UNIT_AMPS = 4 +UNIT_WATT_HOURS = 5 +UNIT_AMP_HOURS = 6 +UNIT_CENTIGRADE = 7 +UNIT_WATTS = 8 +UNIT_OHMS = 9 +UNIT_DEGREES = 10 +UNIT_HERTZ = 11 class TimeseriesDataRow: def __init__(self, sample_no, column_id, value, column_type_id=None): diff --git a/harvester/parse/harvester.py b/harvester/parse/harvester.py index 3f96531e..e309726c 100644 --- a/harvester/parse/harvester.py +++ b/harvester/parse/harvester.py @@ -5,10 +5,12 @@ import os import json +import typing + import psutil from .database.util.battery_exceptions import UnsupportedFileTypeError - +from .database.util.iter_file import IteratorFile import traceback from .ivium_input_file import IviumInputFile @@ -24,6 +26,7 @@ sys.path.append(os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), '..'))) from settings import get_setting, get_logfile +from typing import TypedDict logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__file__) @@ -43,6 +46,9 @@ MaccorRawInputFile, ] +RECORD_NO_COLUMN_ID = 0 +UNIT_UNITLESS = 1 + def has_handle(fpath): """ @@ -101,10 +107,8 @@ def import_file(core_path: str, file_path: str): path=core_path, file=file_path, content={ - 'content': { - 'task': 'import', - 'status': 'begin' - } + 'task': 'import', + 'status': 'begin' } ) @@ -127,7 +131,59 @@ def import_file(core_path: str, file_path: str): if input_file is None: raise UnsupportedFileTypeError + # TODO: Query server payload size limit + query_max_size = 2 * 1_000_000 # approx 2MB + # Figure out column data + column_data = {} + mapping = input_file.get_file_column_to_standard_column_mapping() + record_number_column = [k for k, v in mapping.items() if v == RECORD_NO_COLUMN_ID] + record_number_column = record_number_column[0] if len(record_number_column) else None + generator = input_file.load_data(input_file.file_path, input_file.column_info.keys()) + for i, r in enumerate(generator): + record_number = int(r.get(record_number_column, i)) + for k, v in r.items(): + if k == record_number_column: + continue + if k in column_data: + column_data[k]['values'][record_number] = v + else: + column_data[k] = {} + if k in mapping: + column_data[k]['column_id'] = mapping[k] + else: + column_data[k]['column_name'] = k + if 'unit' in input_file.column_info[k]: + column_data[k]['unit_symbol'] = input_file.column_info[k].get('unit') + else: + column_data[k]['unit_id'] = UNIT_UNITLESS + column_data[k]['values'] = {} + + # TODO: Resume/append where record already exists + + # Send data + report(path=core_path, file=file_path, content={ + 'task': 'import', + 'status': 'in_progress', + 'data': [v for v in column_data.values()] + }) + + # Send metadata + print("File successfully imported") except Exception as e: logger.error(e) # report(path=core_path, file=file_path, error=e) + + +class DjangoColumn(TypedDict): + name: str + unit: typing.Optional[str | int] + values: list + + +def column_to_django_column(col) -> DjangoColumn: + return { + 'name': 'col', + 'unit': None, + 'values': [] + } diff --git a/harvester/start.py b/harvester/start.py index d6a4c09d..0b405d2e 100644 --- a/harvester/start.py +++ b/harvester/start.py @@ -181,7 +181,7 @@ def register(url: str = None, name: str = None, user_id: int = None, run_foregro help="Ignore other options and run harvester if config file already exists." ) def click_wrapper(url: str, name: str, user_id: int, run_foreground: bool, restart: bool): - if click.option('restart') and settings.get_setting('url'): + if restart and settings.get_setting('url'): harvest.run_cycle() else: register(url=url, name=name, user_id=user_id, run_foreground=run_foreground) From 4bc7b84172ad7ad2a7f6c5742690adab4e8f4d4f Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Wed, 11 Jan 2023 17:08:41 +0000 Subject: [PATCH 25/79] harvester import for files --- .../galvanalyser/fixtures/DataUnit.json | 33 +++-- django/backend_django/galvanalyser/models.py | 24 +++- .../galvanalyser/serializers.py | 14 ++- django/backend_django/galvanalyser/views.py | 74 +++++------ frontend/src/APIConnection.ts | 2 +- frontend/src/Files.js | 91 -------------- frontend/src/Files.tsx | 118 ++++++++++++++++++ frontend/src/HarvesterDetail.tsx | 14 +-- frontend/src/PaginatedTable.tsx | 2 +- harvester/harvest.py | 20 +-- harvester/parse/biologic_input_file.py | 20 +-- .../parse/database/experiment/input_file.py | 2 +- .../experiment/timeseries_data_row.py | 1 + harvester/parse/harvester.py | 90 +++++++++---- harvester/parse/ivium_input_file.py | 8 +- harvester/parse/maccor_input_file.py | 39 ++---- 16 files changed, 316 insertions(+), 236 deletions(-) delete mode 100644 frontend/src/Files.js create mode 100644 frontend/src/Files.tsx diff --git a/django/backend_django/galvanalyser/fixtures/DataUnit.json b/django/backend_django/galvanalyser/fixtures/DataUnit.json index 53b68f33..4cae6939 100644 --- a/django/backend_django/galvanalyser/fixtures/DataUnit.json +++ b/django/backend_django/galvanalyser/fixtures/DataUnit.json @@ -5,7 +5,8 @@ "fields": { "name": "Unitless", "symbol": "", - "description": "A value with no units" + "description": "A value with no units", + "is_default": true } }, { @@ -14,7 +15,8 @@ "fields": { "name": "Time", "symbol": "s", - "description": "Time in seconds" + "description": "Time in seconds", + "is_default": true } }, { @@ -23,7 +25,8 @@ "fields": { "name": "Volts", "symbol": "V", - "description": "Voltage" + "description": "Voltage", + "is_default": true } }, { @@ -32,7 +35,8 @@ "fields": { "name": "Amps", "symbol": "A", - "description": "Current" + "description": "Current", + "is_default": true } }, { @@ -41,7 +45,8 @@ "fields": { "name": "Energy", "symbol": "Wh", - "description": "Energy in Watt-Hours" + "description": "Energy in Watt-Hours", + "is_default": true } }, { @@ -50,7 +55,8 @@ "fields": { "name": "Charge", "symbol": "Ah", - "description": "Charge in Amp-Hours" + "description": "Charge in Amp-Hours", + "is_default": true } }, { @@ -59,7 +65,8 @@ "fields": { "name": "Temperature", "symbol": "°c", - "description": "Temperature in Centigrade" + "description": "Temperature in Centigrade", + "is_default": true } }, { @@ -68,7 +75,8 @@ "fields": { "name": "Power", "symbol": "W", - "description": "Power in Watts" + "description": "Power in Watts", + "is_default": true } }, { @@ -77,7 +85,8 @@ "fields": { "name": "Ohm", "symbol": "Ω", - "description": "Resistance or impediance in Ohms" + "description": "Resistance or impediance in Ohms", + "is_default": true } }, { @@ -86,7 +95,8 @@ "fields": { "name": "Degrees", "symbol": "°", - "description": "Angle in degrees" + "description": "Angle in degrees", + "is_default": true } }, { @@ -95,7 +105,8 @@ "fields": { "name": "Frequency", "symbol": "Hz", - "description": "Frequency in Hz" + "description": "Frequency in Hz", + "is_default": true } } ] \ No newline at end of file diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index 1f0764eb..605be37a 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -6,6 +6,7 @@ class FileState(models.Choices): + RETRY_IMPORT = "RETRY IMPORT" IMPORT_FAILED = "IMPORT FAILED" UNSTABLE = "UNSTABLE" GROWING = "GROWING" @@ -55,7 +56,7 @@ def run(self): class MonitoredPath(models.Model): harvester = models.ForeignKey(to=Harvester, related_name='monitored_paths', on_delete=models.CASCADE) - path = models.TextField(unique=True) + path = models.TextField() stable_time = models.PositiveSmallIntegerField(default=60) # seconds files must remain stable to be processed admin_group = models.ForeignKey( to=Group, @@ -106,7 +107,7 @@ class CellData(models.Model): class Dataset(models.Model): cell = models.ForeignKey(to=CellData, on_delete=models.SET_NULL, null=True) - file = models.ForeignKey(to=ObservedFile, on_delete=models.DO_NOTHING, related_name='dataset') + file = models.ForeignKey(to=ObservedFile, on_delete=models.DO_NOTHING, related_name='datasets') name = models.TextField(null=True) date = models.DateTimeField(null=False) type = models.TextField(null=True) @@ -134,6 +135,7 @@ class DataUnit(models.Model): name = models.TextField(null=False) symbol = models.TextField(null=False) description = models.TextField() + is_default = models.BooleanField(default=False) def __str__(self): if self.symbol: @@ -153,16 +155,30 @@ class Meta: class DataColumn(models.Model): dataset = models.ForeignKey(to=Dataset, related_name='columns', on_delete=models.CASCADE) - type = models.ForeignKey(to=DataColumnType, on_delete=models.RESTRICT) + type = models.ForeignKey(to=DataColumnType, on_delete=models.CASCADE) name = models.TextField(null=False) class Meta: unique_together = [['dataset', 'name']] +class DataColumnStringKeys(models.Model): + """ + String values are not allowed in TimeseriesData, + so instead we store integer keys whose string values + can be looked up in this table. + """ + column = models.ForeignKey(to=DataColumn, related_name='string_keys', on_delete=models.CASCADE) + key = models.PositiveBigIntegerField(null=False) + string = models.TextField(null=False) + + class Meta: + unique_together = [['column', 'key', 'string']] + + class TimeseriesData(models.Model): sample = models.PositiveBigIntegerField(null=False) - column = models.ForeignKey(to=DataColumn, related_name='values', null=False, on_delete=models.RESTRICT) + column = models.ForeignKey(to=DataColumn, related_name='values', null=False, on_delete=models.CASCADE) value = models.FloatField(null=False) class Meta: diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py index 1ce1a3fc..de148e11 100644 --- a/django/backend_django/galvanalyser/serializers.py +++ b/django/backend_django/galvanalyser/serializers.py @@ -12,7 +12,6 @@ TimeseriesRangeLabel from django.contrib.auth.models import User, Group from rest_framework import serializers -from rest_framework.reverse import reverse_lazy class HarvesterSerializer(serializers.HyperlinkedModelSerializer): @@ -56,7 +55,7 @@ def get_users(self, instance): class Meta: model = MonitoredPath - fields = ['url', 'path', 'stable_time', 'harvester', 'users'] + fields = ['url', 'id', 'path', 'stable_time', 'harvester', 'users'] read_only_fields = ['users'] depth = 1 @@ -64,7 +63,12 @@ class Meta: class ObservedFileSerializer(serializers.HyperlinkedModelSerializer): class Meta: model = ObservedFile - fields = '__all__' + fields = [ + 'url', 'id', + 'monitored_path', 'relative_path', + 'state', 'last_observed_time', 'last_observed_size', + 'datasets' + ] class CellDataSerializer(serializers.HyperlinkedModelSerializer): @@ -94,13 +98,13 @@ class Meta: class DataUnitSerializer(serializers.HyperlinkedModelSerializer): class Meta: model = DataUnit - fields = '__all__' + fields = ['url', 'id', 'name', 'symbol', 'description', 'is_default'] class DataColumnTypeSerializer(serializers.HyperlinkedModelSerializer): class Meta: model = DataColumnType - fields = '__all__' + fields = ['url', 'id', 'name', 'description', 'is_default', 'unit'] class DataColumnSerializer(serializers.HyperlinkedModelSerializer): diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 43a07283..236117f0 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -25,6 +25,7 @@ DatasetEquipment, \ DataUnit, \ DataColumnType, \ + DataColumnStringKeys, \ DataColumn, \ TimeseriesData, \ TimeseriesRangeLabel, \ @@ -239,8 +240,16 @@ def report(self, request, pk: int = None): type=column_type, dataset=dataset ) + # Create a value map for string data + if 'value_map' in column_data: + DataColumnStringKeys.objects.bulk_create( + DataColumnStringKeys(string=k, key=v, column=column) + for k, v in column_data['value_map'].items() + ) + + # Enter data en masse to avoid numerous expensive database calls TimeseriesData.objects.bulk_create([ - TimeseriesData(sample=k, value=v, column_id=column.id) + TimeseriesData(sample=k, value=v, column=column) for k, v in column_data['values'].items() ]) @@ -341,46 +350,33 @@ def update(self, request, *args, **kwargs): path.save() return Response(self.get_serializer(path).data) - @action(detail=True, methods=['GET']) - def files(self, request, pk: int = None): - """ - ObservedFiles for the MonitoredPath. - """ - # TODO: Restrict access to Harvester or harvester user - monitored_path = get_object_or_404(MonitoredPath, id=pk) - paths = ObservedFile.objects.filter(monitored_path=monitored_path).order_by('id') - paths = self.paginate_queryset(paths) - return self.get_paginated_response(ObservedFileSerializer(paths, many=True).data) - - @action(detail=True, methods=['GET']) - def users(self, request, pk: int = None): - """ - Users able to access the Harvester. Users can create MonitoredPaths. - """ - # TODO: Restrict access to Harvester or harvester user - monitored_path = get_object_or_404(Harvester, id=pk) - users = User.objects.filter(groups__in=[monitored_path.admin_group, monitored_path.user_group]) - users = self.paginate_queryset(users) - return self.get_paginated_response(UserSerializer(users, context={'request': request}, many=True).data) - - @action(detail=True, methods=['GET']) - def admins(self, request, pk: int = None): - """ - Users able to edit the Harvester. - """ - # TODO: Restrict access to Harvester or harvester user - monitored_path = get_object_or_404(Harvester, id=pk) - admins = User.objects.filter(groups__in=[monitored_path.admin_group]) - admins = self.paginate_queryset(admins) - return self.get_paginated_response(UserSerializer(admins, context={'request': request}, many=True).data) - class ObservedFileViewSet(viewsets.ModelViewSet): """ TODO: document """ serializer_class = ObservedFileSerializer - queryset = ObservedFile.objects.all() + filterset_fields = ['monitored_path__id', 'relative_path', 'state'] + search_fields = ['@monitored_path__path', '@relative_path', 'state'] + queryset = ObservedFile.objects.all().order_by('last_observed_time', 'id') + + # Access restrictions + def get_queryset(self): + return ObservedFile.objects.filter( + Q(monitored_path__user_group__in=self.request.user.groups.all()) | + Q(monitored_path__admin_group__in=self.request.user.groups.all()) | + Q(monitored_path__harvester__admin_group__in=self.request.user.groups.all()) + ).order_by('last_observed_time', 'id') + + @action(detail=True, methods=['GET']) + def reimport(self, request, pk: int = None): + try: + file = self.get_queryset().get(id=pk) + except ObservedFile.DoesNotExist: + return error_response('Requested file not found') + file.state = FileState.RETRY_IMPORT + file.save() + return Response(self.get_serializer(file, context={'request': request}).data) class CellDataViewSet(viewsets.ModelViewSet): @@ -420,7 +416,9 @@ class DataUnitViewSet(viewsets.ModelViewSet): TODO: document """ serializer_class = DataUnitSerializer - queryset = DataUnit.objects.all() + filterset_fields = ['name', 'symbol', 'is_default'] + search_fields = ['@name', '@symbol', '@description'] + queryset = DataUnit.objects.all().order_by('id') class DataColumnTypeViewSet(viewsets.ModelViewSet): @@ -428,7 +426,9 @@ class DataColumnTypeViewSet(viewsets.ModelViewSet): TODO: document """ serializer_class = DataColumnTypeSerializer - queryset = DataColumnType.objects.all() + filterset_fields = ['name', 'unit__symbol', 'unit__name', 'is_default'] + search_fields = ['@name', '@description'] + queryset = DataColumnType.objects.all().order_by('id') class DataColumnViewSet(viewsets.ModelViewSet): diff --git a/frontend/src/APIConnection.ts b/frontend/src/APIConnection.ts index a7ca5b48..08d18143 100644 --- a/frontend/src/APIConnection.ts +++ b/frontend/src/APIConnection.ts @@ -70,7 +70,7 @@ export class APIConnection { async fetch(url: string, options?: any): Promise { await this.get_is_logged_in(); console.info(`Fetch ${url} for ${this.user?.username}`) - console.debug('fetch options', options) + console.info('fetch options', options) const token = this.user?.token; let newOptions = {...options}; newOptions.credentials = 'same-origin'; diff --git a/frontend/src/Files.js b/frontend/src/Files.js deleted file mode 100644 index 1d4d182c..00000000 --- a/frontend/src/Files.js +++ /dev/null @@ -1,91 +0,0 @@ -import React, { useEffect, useState } from 'react'; -import { makeStyles } from '@mui/styles' -import Table from '@mui/material/Table'; -import TableBody from '@mui/material/TableBody'; -import Container from '@mui/material/Container'; -import TableCell from '@mui/material/TableCell'; -import TableContainer from '@mui/material/TableContainer'; -import TableHead from '@mui/material/TableHead'; -import TableRow from '@mui/material/TableRow'; -import Paper from '@mui/material/Paper'; -import { files } from './Api' - - -const useStyles = makeStyles((theme) => ({ - head: { - backgroundColor: theme.palette.primary.light, - }, - headCell: { - color: theme.palette.common.white, - }, - container: { - paddingTop: theme.spacing(4), - paddingBottom: theme.spacing(4), - }, - table: { - minWidth: 650, - }, -})); - -export default function Files({ path }) { - const classes = useStyles(); - - const [fileData, setFileData] = useState([]) - - useEffect(() => { - files(path.id).then((response) => { - if (response.ok) { - response.json().then((result) => { - const results = result.results; - setFileData(results.sort((arg1, arg2) => arg1.id - arg2.id)); - }); - } - }); - }, [path]); - - const datetimeOptions = { - year: 'numeric', month: 'numeric', day: 'numeric', - hour: 'numeric', minute: 'numeric', second: 'numeric', - }; - - return ( - - - - - - - Observed File - Last Observed Size - Last Observed Time - State - - - - {fileData.map((row) => ( - - - {row.path} - - - {row.last_observed_size} - - - { - Intl.DateTimeFormat('en-GB', datetimeOptions).format( - Date.parse(row.last_observed_time) - ) - } - - - {row.file_state} - - - ))} - -
- - - - ); -} diff --git a/frontend/src/Files.tsx b/frontend/src/Files.tsx new file mode 100644 index 00000000..1f54cbae --- /dev/null +++ b/frontend/src/Files.tsx @@ -0,0 +1,118 @@ +import React, { useState } from 'react'; +import { makeStyles } from '@mui/styles' +import Container from '@mui/material/Container'; +import TableCell from '@mui/material/TableCell'; +import TableHead from '@mui/material/TableHead'; +import TableRow from '@mui/material/TableRow'; +import Paper from '@mui/material/Paper'; +import PaginatedTable from './PaginatedTable'; +import Connection from "./APIConnection"; +import {MonitoredPathFields} from "./HarvesterDetail"; +import Tooltip from "@mui/material/Tooltip"; +import Typography from "@mui/material/Typography"; +import DatasetIcon from '@mui/icons-material/Dataset'; +import IconButton from "@mui/material/IconButton"; +import RefreshIcon from "@mui/icons-material/Refresh"; + + +const useStyles = makeStyles((theme) => ({ + head: { + backgroundColor: theme.palette.primary.light, + }, + headCell: { + color: theme.palette.common.black, + }, + container: { + paddingTop: theme.spacing(4), + paddingBottom: theme.spacing(4), + }, + table: { + minWidth: 650, + }, + paper: {} +})); + +export type FileFields = { + url: string, + id: number, + monitored_path: string, + relative_path: string, + state: string, + last_observed_time: string, + last_observed_size: number, + datasets: string[] +} + +export type FilesProps = { + path: MonitoredPathFields, + lastUpdated: Date +} + +export default function Files(props: FilesProps) { + const classes = useStyles(); + const [lastUpdated, setLastUpdated] = useState(props.lastUpdated) + + const forceReimport = (file: FileFields) => { + Connection.fetch(`${file.url}reimport/`) + .then(() => setLastUpdated(new Date())) + } + + const datetimeOptions: Intl.DateTimeFormatOptions = { + year: 'numeric', month: 'numeric', day: 'numeric', + hour: 'numeric', minute: 'numeric', second: 'numeric', + }; + + const column_headings = [ + {label: props.path.path, help: 'File path'}, + {label: 'Last Observed Size', help: 'Size of the file in bytes'}, + {label: 'Last Observed Time', help: 'Time file was last scanned'}, + {label: 'State', help: 'File state'}, + {label: 'Datasets', help: 'View datasets linked to this file'}, + {label: 'Force Re-import', help: 'Retry the import operation next time the file is scanned'} + ] + + const table_head = column_headings.map(heading => ( + + + + {heading.label} + + + + )) + + function row_fun(file: FileFields) { + return ( + + + {file.relative_path} + {file.last_observed_size} + + { + Intl.DateTimeFormat('en-GB', datetimeOptions).format( + Date.parse(file.last_observed_time) + ) + } + + {file.state} + {file.datasets.map(d => ())} + forceReimport(file)}> + + + ) + } + + return ( + + + {table_head})} + row_fun={row_fun} + initial_url={`files/?monitored_path__id=${props.path.id}`} + styles={classes} + last_updated={lastUpdated} + /> + + + ); +} diff --git a/frontend/src/HarvesterDetail.tsx b/frontend/src/HarvesterDetail.tsx index d1ec9dbe..2a63239f 100644 --- a/frontend/src/HarvesterDetail.tsx +++ b/frontend/src/HarvesterDetail.tsx @@ -19,11 +19,6 @@ import TableRow from '@mui/material/TableRow'; import PaginatedTable, {RowFunProps} from './PaginatedTable'; import Connection, {User} from "./APIConnection"; import Files from './Files' - -import { - monitored_paths, add_monitored_path, users, env_harvester, - update_monitored_path, delete_monitored_path, isAdmin, url, -} from './Api' import {HarvesterFields} from "./Harvesters"; const useStyles = makeStyles((theme) => ({ @@ -63,6 +58,7 @@ type MonitoredPathUserGroups = { export type MonitoredPathFields = { url: string; + id: number; harvester: number; stable_time: number; path: string; @@ -72,7 +68,7 @@ export type MonitoredPathFields = { function MyTableRow(props: RowFunProps) { const classes = useStyles(); const [row, setRow] = useState({ - url: "", harvester: -1, stable_time: -1, path: '', users: {harvester_admins: [], admins: [], users: []} + url: "", id: -1, harvester: -1, stable_time: -1, path: '', users: {harvester_admins: [], admins: [], users: []} }) const [dirty, setDirty] = useState(false) @@ -245,7 +241,7 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { - {isSelected && - - } + {isSelected && } ); diff --git a/frontend/src/PaginatedTable.tsx b/frontend/src/PaginatedTable.tsx index 8efdcaab..d459837c 100644 --- a/frontend/src/PaginatedTable.tsx +++ b/frontend/src/PaginatedTable.tsx @@ -138,7 +138,7 @@ export default class PaginatedTable extends Component { // @ts-ignore - +
{this.props.header} { // @ts-ignore diff --git a/harvester/harvest.py b/harvester/harvest.py index 506b324c..f59561e9 100644 --- a/harvester/harvest.py +++ b/harvester/harvest.py @@ -113,9 +113,9 @@ def harvest_path(path: os.PathLike): try: for (dir_path, dir_names, filenames) in os.walk(path): for filename in filenames: + full_path = os.path.join(dir_path, filename) + core_path, file_path = split_path(path, full_path) try: - full_path = os.path.join(dir_path, filename) - core_path, file_path = split_path(path, full_path) logger.info(f"Reporting stats for {file_path}") result = report_harvest_result( path=core_path, @@ -129,14 +129,14 @@ def harvest_path(path: os.PathLike): result = result.json() status = result['state'] logger.info(f"Server assigned status '{status}'") - if status == 'STABLE': - logger.info(f"Parsing STABLE file {file_path}") - result = import_file(core_path, file_path) - report_harvest_result( - path=core_path, - file=file_path, - content={'task': 'import', 'status': 'complete'} - ) + if status in ['STABLE', 'RETRY IMPORT']: + logger.info(f"Parsing file {file_path}") + if import_file(core_path, file_path): + report_harvest_result( + path=core_path, + file=file_path, + content={'task': 'import', 'status': 'complete'} + ) except BaseException as e: logger.error(e) report_harvest_result(path=path, file=file_path, error=e) diff --git a/harvester/parse/biologic_input_file.py b/harvester/parse/biologic_input_file.py index 83a7784e..a19b8f97 100644 --- a/harvester/parse/biologic_input_file.py +++ b/harvester/parse/biologic_input_file.py @@ -36,22 +36,22 @@ def __init__(self, file_path): self.mpr_file = BioLogic.MPRfile(file_path) super().__init__(file_path) - def get_file_column_to_standard_column_mapping(self): + def get_file_column_to_standard_column_mapping(self, default_columns: dict) -> dict: """ Return a dict with a key of the column name in the file that maps to the standard column name in the value. Only return values where a mapping exists """ return { - "I/mA": AMPS_COLUMN_ID, - "Ewe/V": VOLTAGE_COLUMN_ID, - "time/s": TEST_TIME_COLUMN_ID, - "Energy/W.h": ENERGY_CAPACITY_COLUMN_ID, - "Q charge/discharge/mA.h": CHARGE_CAPACITY_COLUMN_ID, - "Aux": TEMPERATURE_COLUMN_ID, - "|Z|/Ohm": IMPEDENCE_MAG_COLUMN_ID, - "Phase(Z)/deg": IMPEDENCE_PHASE_COLUMN_ID, - "freq/Hz": FREQUENCY_COLUMN_ID, + "I/mA": default_columns['Amps'], + "Ewe/V": default_columns['Volts'], + "time/s": default_columns['Time'], + "Energy/W.h": default_columns['Energy Capacity'], + "Q charge/discharge/mA.h": default_columns['Charge Capacity'], + "Aux": default_columns['Temperature'], + "|Z|/Ohm": default_columns['Impedence Magnitude'], + "Phase(Z)/deg": default_columns['Impedence Phase'], + "freq/Hz": default_columns['Frequency'], } def load_data(self, file_path, columns): diff --git a/harvester/parse/database/experiment/input_file.py b/harvester/parse/database/experiment/input_file.py index b68589a2..829ec5ec 100644 --- a/harvester/parse/database/experiment/input_file.py +++ b/harvester/parse/database/experiment/input_file.py @@ -137,7 +137,7 @@ def load_data(self, file_path, available_desired_columns): def get_data_labels(self): raise UnsupportedFileTypeError - def get_file_column_to_standard_column_mapping(self): + def get_file_column_to_standard_column_mapping(self, default_columns: dict): """ returns map of file column name strings to column id numbers """ diff --git a/harvester/parse/database/experiment/timeseries_data_row.py b/harvester/parse/database/experiment/timeseries_data_row.py index 040e4452..df38374a 100644 --- a/harvester/parse/database/experiment/timeseries_data_row.py +++ b/harvester/parse/database/experiment/timeseries_data_row.py @@ -29,6 +29,7 @@ UNIT_DEGREES = 10 UNIT_HERTZ = 11 + class TimeseriesDataRow: def __init__(self, sample_no, column_id, value, column_type_id=None): self.sample_no = sample_no diff --git a/harvester/parse/harvester.py b/harvester/parse/harvester.py index e309726c..924ee457 100644 --- a/harvester/parse/harvester.py +++ b/harvester/parse/harvester.py @@ -46,8 +46,37 @@ MaccorRawInputFile, ] -RECORD_NO_COLUMN_ID = 0 -UNIT_UNITLESS = 1 + +def get_api_ids(target: str) -> dict: + """ + Fetch standard ids from the server and return a name-id dictionary + """ + # TODO: abstract API URL (get_setting('url') returns Harvester not base URL) + url = f"http://app:5000/{target}/?default=True" + results = [] + entries = None + while True: + response = requests.get(url) + logger.debug(url) + data = response.json() + if entries is None: + entries = data['count'] + results = [*results, *data['results']] + if 'next' in data and data['next'] is not None: + url = data['next'] + else: + break + + assert entries is not None and len(results) == entries + return {r['name']: r['id'] for r in results} + + +def get_api_unit_ids() -> dict: + return get_api_ids('units') + + +def get_api_column_ids() -> dict: + return get_api_ids('columns') def has_handle(fpath): @@ -92,7 +121,7 @@ def report( return None -def import_file(core_path: str, file_path: str): +def import_file(core_path: str, file_path: str) -> bool: """ Attempts to import a given file """ @@ -101,7 +130,7 @@ def import_file(core_path: str, file_path: str): if not os.path.isfile(full_file_path): print("Is not a file, skipping: " + full_file_path) report(path=core_path, file=file_path, error=FileNotFoundError()) - return + return False print("Importing " + full_file_path) report( path=core_path, @@ -131,12 +160,21 @@ def import_file(core_path: str, file_path: str): if input_file is None: raise UnsupportedFileTypeError + # TODO Send metadata + + # TODO: Resume/append where record already exists + # TODO: Including getting existing string-int mapping + # TODO: Query server payload size limit query_max_size = 2 * 1_000_000 # approx 2MB # Figure out column data column_data = {} - mapping = input_file.get_file_column_to_standard_column_mapping() - record_number_column = [k for k, v in mapping.items() if v == RECORD_NO_COLUMN_ID] + default_column_ids = get_api_column_ids() + default_units = get_api_unit_ids() + mapping = input_file.get_file_column_to_standard_column_mapping(default_column_ids) + next_key = 0 + # Find out if there's a Sample number column, otherwise we use the row number + record_number_column = [k for k, v in mapping.items() if v == default_column_ids['Sample Number']] record_number_column = record_number_column[0] if len(record_number_column) else None generator = input_file.load_data(input_file.file_path, input_file.column_info.keys()) for i, r in enumerate(generator): @@ -145,7 +183,23 @@ def import_file(core_path: str, file_path: str): if k == record_number_column: continue if k in column_data: - column_data[k]['values'][record_number] = v + # Numeric data are stored directly + try: + column_data[k]['values'][record_number] = int(v) + except ValueError: + try: + column_data[k]['values'][record_number] = float(v) + # Strings are mapped to integer values using a value map which is also sent to the database + except ValueError: + if 'value_map' in column_data[k] and v in column_data[k]['value_map']: + column_data[k]['values'][record_number] = column_data[k]['value_map'][v] + else: + if 'value_map' in column_data[k]: + column_data[k]['value_map'][v] = next_key + else: + column_data[k]['value_map'] = {v: next_key} + column_data[k]['values'][record_number] = next_key + next_key += 1 else: column_data[k] = {} if k in mapping: @@ -155,11 +209,9 @@ def import_file(core_path: str, file_path: str): if 'unit' in input_file.column_info[k]: column_data[k]['unit_symbol'] = input_file.column_info[k].get('unit') else: - column_data[k]['unit_id'] = UNIT_UNITLESS + column_data[k]['unit_id'] = default_units['Unitless'] column_data[k]['values'] = {} - # TODO: Resume/append where record already exists - # Send data report(path=core_path, file=file_path, content={ 'task': 'import', @@ -167,23 +219,9 @@ def import_file(core_path: str, file_path: str): 'data': [v for v in column_data.values()] }) - # Send metadata - print("File successfully imported") except Exception as e: logger.error(e) # report(path=core_path, file=file_path, error=e) - - -class DjangoColumn(TypedDict): - name: str - unit: typing.Optional[str | int] - values: list - - -def column_to_django_column(col) -> DjangoColumn: - return { - 'name': 'col', - 'unit': None, - 'values': [] - } + return False + return True diff --git a/harvester/parse/ivium_input_file.py b/harvester/parse/ivium_input_file.py index b4672612..708bebb6 100644 --- a/harvester/parse/ivium_input_file.py +++ b/harvester/parse/ivium_input_file.py @@ -25,7 +25,7 @@ def __init__(self, file_path): self.validate_file(file_path) super().__init__(file_path) - def get_file_column_to_standard_column_mapping(self): + def get_file_column_to_standard_column_mapping(self, default_columns: dict) -> dict: print("Type is IVIUM") """ Return a dict with a key of the column name in the file that maps to @@ -33,7 +33,11 @@ def get_file_column_to_standard_column_mapping(self): mapping exists """ print("get_ivium_column_to_standard_column_mapping") - return {"amps": 3, "volts": 2, "test_time": 1} + return { + "amps": default_columns['Amps'], + "volts": default_columns['Volts'], + "test_time": default_columns['Time'] + } def load_data(self, file_path, columns): """ diff --git a/harvester/parse/maccor_input_file.py b/harvester/parse/maccor_input_file.py index dca71f0d..ed87747e 100644 --- a/harvester/parse/maccor_input_file.py +++ b/harvester/parse/maccor_input_file.py @@ -141,7 +141,7 @@ def load_metadata(self): print(metadata) return metadata, column_info - def get_file_column_to_standard_column_mapping(self): + def get_file_column_to_standard_column_mapping(self, default_columns: dict) -> dict: """ Return a dict with a key of the column name in the file that maps to the standard column name in the value. Only return values where a @@ -150,33 +150,18 @@ def get_file_column_to_standard_column_mapping(self): """ print("Type is MACCOR") print("get_maccor_column_to_standard_column_mapping") - all_values = { - "Amp-hr": 5, - "Amps": 3, - "Cyc#": None, - "DPt Time": None, - "Watt-hr": 4, - "State": None, - "Step": None, - "StepTime": 7, - "Step (Sec)": 7, - "Volts": 2, - "Capacity": None, - "Energy": None, - "Power": None, - "TestTime": 1, - "Test (Sec)": 1, - "Rec#": 0, - "Temp 1": 6, + return { + "Amp-hr": default_columns['Charge Capacity'], + "Amps": default_columns['Amps'], + "Watt-hr": default_columns['Energy Capacity'], + "StepTime": default_columns['Step Time'], + "Step (Sec)": default_columns['Step Time'], + "Volts": default_columns['Volts'], + "TestTime": default_columns['Time'], + "Test (Sec)": default_columns['Time'], + "Rec#": default_columns['Sample Number'], + "Temp 1": default_columns['Temperature'] } - print("all_values: " + str(all_values)) - filtered_values = { - file_col: std_col - for file_col, std_col in all_values.items() - if std_col is not None - } - print("filtered_values: " + str(filtered_values)) - return (filtered_values) def load_data(self, file_path, columns): """ From 6f9ab1928adf3fb5d7a287ee72843a10574cb102 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Thu, 12 Jan 2023 15:15:13 +0000 Subject: [PATCH 26/79] harvester cleanup, metadata --- .../galvanalyser/migrations/0001_initial.py | 191 +++++++++++++++ .../0002_alter_observedfile_state.py | 18 ++ .../0003_alter_observedfile_state.py | 18 ++ .../0004_alter_observedfile_state.py | 18 ++ .../0005_alter_observedfile_state.py | 18 ++ .../galvanalyser/serializers.py | 27 ++- django/backend_django/galvanalyser/views.py | 27 ++- harvester/harvest.py | 167 ------------- harvester/{parse => harvester}/__init__.py | 0 harvester/harvester/api.py | 74 ++++++ harvester/harvester/harvest.py | 174 ++++++++++++++ .../database => harvester/parse}/__init__.py | 0 .../parse/biologic_input_file.py | 46 ++-- .../parse/exceptions.py} | 16 -- .../parse}/input_file.py | 36 +-- .../{ => harvester}/parse/ivium_input_file.py | 17 +- .../parse/maccor_input_file.py | 31 +-- harvester/harvester/run.py | 88 +++++++ harvester/{ => harvester}/settings.py | 22 ++ .../parse/database/cell_data/__init__.py | 3 - harvester/parse/database/cell_data/cell.py | 39 --- .../parse/database/cell_data/cell_row.py | 213 ---------------- .../database/cell_data/manufacturer_row.py | 109 --------- .../parse/database/experiment/__init__.py | 6 - .../parse/database/experiment/access_row.py | 61 ----- .../parse/database/experiment/column_row.py | 91 ------- .../database/experiment/equipment_row.py | 135 ----------- .../experiment/timeseries_data_row.py | 194 --------------- harvester/parse/database/experiment/unit.py | 116 --------- harvester/parse/database/row.py | 15 -- harvester/parse/database/util/__init__.py | 0 harvester/parse/database/util/iter_file.py | 63 ----- harvester/parse/harvester.py | 227 ------------------ harvester/start.py | 14 +- 34 files changed, 729 insertions(+), 1545 deletions(-) create mode 100644 django/backend_django/galvanalyser/migrations/0001_initial.py create mode 100644 django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py create mode 100644 django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py create mode 100644 django/backend_django/galvanalyser/migrations/0004_alter_observedfile_state.py create mode 100644 django/backend_django/galvanalyser/migrations/0005_alter_observedfile_state.py delete mode 100644 harvester/harvest.py rename harvester/{parse => harvester}/__init__.py (100%) create mode 100644 harvester/harvester/api.py create mode 100644 harvester/harvester/harvest.py rename harvester/{parse/database => harvester/parse}/__init__.py (100%) rename harvester/{ => harvester}/parse/biologic_input_file.py (70%) rename harvester/{parse/database/util/battery_exceptions.py => harvester/parse/exceptions.py} (68%) rename harvester/{parse/database/experiment => harvester/parse}/input_file.py (82%) rename harvester/{ => harvester}/parse/ivium_input_file.py (96%) rename harvester/{ => harvester}/parse/maccor_input_file.py (96%) create mode 100644 harvester/harvester/run.py rename harvester/{ => harvester}/settings.py (61%) delete mode 100644 harvester/parse/database/cell_data/__init__.py delete mode 100644 harvester/parse/database/cell_data/cell.py delete mode 100644 harvester/parse/database/cell_data/cell_row.py delete mode 100644 harvester/parse/database/cell_data/manufacturer_row.py delete mode 100644 harvester/parse/database/experiment/__init__.py delete mode 100644 harvester/parse/database/experiment/access_row.py delete mode 100644 harvester/parse/database/experiment/column_row.py delete mode 100644 harvester/parse/database/experiment/equipment_row.py delete mode 100644 harvester/parse/database/experiment/timeseries_data_row.py delete mode 100644 harvester/parse/database/experiment/unit.py delete mode 100644 harvester/parse/database/row.py delete mode 100644 harvester/parse/database/util/__init__.py delete mode 100644 harvester/parse/database/util/iter_file.py delete mode 100644 harvester/parse/harvester.py diff --git a/django/backend_django/galvanalyser/migrations/0001_initial.py b/django/backend_django/galvanalyser/migrations/0001_initial.py new file mode 100644 index 00000000..869e8b79 --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0001_initial.py @@ -0,0 +1,191 @@ +# Generated by Django 4.1.4 on 2023-01-12 12:31 + +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + initial = True + + dependencies = [ + ('auth', '0012_alter_user_first_name_max_length'), + ] + + operations = [ + migrations.CreateModel( + name='CellData', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField(unique=True)), + ('form_factor', models.TextField()), + ('link_to_datasheet', models.TextField()), + ('anode_chemistry', models.TextField()), + ('cathode_chemistry', models.TextField()), + ('nominal_capacity', models.FloatField()), + ('nominal_cell_weight', models.FloatField()), + ('manufacturer', models.TextField()), + ], + ), + migrations.CreateModel( + name='Dataset', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField(null=True)), + ('date', models.DateTimeField()), + ('type', models.TextField(null=True)), + ('purpose', models.TextField()), + ('json_data', models.JSONField(null=True)), + ('cell', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='galvanalyser.celldata')), + ], + ), + migrations.CreateModel( + name='DataUnit', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField()), + ('symbol', models.TextField()), + ('description', models.TextField()), + ('is_default', models.BooleanField(default=False)), + ], + ), + migrations.CreateModel( + name='Equipment', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField(unique=True)), + ('type', models.TextField()), + ], + ), + migrations.CreateModel( + name='Harvester', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField(unique=True)), + ('api_key', models.TextField(null=True)), + ('last_check_in', models.DateTimeField(null=True)), + ('sleep_time', models.IntegerField(default=10)), + ('admin_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='editable_harvesters', to='auth.group')), + ('user_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='readable_harvesters', to='auth.group')), + ], + ), + migrations.CreateModel( + name='MonitoredPath', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('path', models.TextField()), + ('stable_time', models.PositiveSmallIntegerField(default=60)), + ('admin_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='editable_paths', to='auth.group')), + ('harvester', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='monitored_paths', to='galvanalyser.harvester')), + ('user_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='readable_paths', to='auth.group')), + ], + options={ + 'unique_together': {('harvester', 'path')}, + }, + ), + migrations.CreateModel( + name='TimeseriesRangeLabel', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('label', models.TextField()), + ('range_start', models.PositiveBigIntegerField()), + ('range_end', models.PositiveBigIntegerField()), + ('info', models.TextField()), + ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='range_labels', to='galvanalyser.dataset')), + ], + ), + migrations.CreateModel( + name='ObservedFile', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('relative_path', models.TextField()), + ('last_observed_size', models.PositiveBigIntegerField(default=0)), + ('last_observed_time', models.DateTimeField(null=True)), + ('state', models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE')), + ('monitored_path', models.ForeignKey(on_delete=django.db.models.deletion.DO_NOTHING, related_name='files', to='galvanalyser.monitoredpath')), + ], + options={ + 'unique_together': {('monitored_path', 'relative_path')}, + }, + ), + migrations.CreateModel( + name='HarvestError', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('file', models.TextField(null=True)), + ('error', models.TextField()), + ('timestamp', models.DateTimeField(auto_now=True, null=True)), + ('harvester', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='paths', to='galvanalyser.harvester')), + ('path', models.ForeignKey(on_delete=django.db.models.deletion.DO_NOTHING, to='galvanalyser.monitoredpath')), + ], + ), + migrations.AddField( + model_name='dataset', + name='file', + field=models.ForeignKey(on_delete=django.db.models.deletion.DO_NOTHING, related_name='datasets', to='galvanalyser.observedfile'), + ), + migrations.CreateModel( + name='DataColumnType', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField()), + ('description', models.TextField()), + ('is_default', models.BooleanField(default=False)), + ('unit', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='galvanalyser.dataunit')), + ], + options={ + 'unique_together': {('unit', 'name')}, + }, + ), + migrations.CreateModel( + name='DataColumn', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField()), + ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='columns', to='galvanalyser.dataset')), + ('type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.datacolumntype')), + ], + options={ + 'unique_together': {('dataset', 'name')}, + }, + ), + migrations.CreateModel( + name='TimeseriesData', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample', models.PositiveBigIntegerField()), + ('value', models.FloatField()), + ('column', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='values', to='galvanalyser.datacolumn')), + ], + options={ + 'unique_together': {('sample', 'column')}, + }, + ), + migrations.CreateModel( + name='DatasetEquipment', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.dataset')), + ('equipment', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.equipment')), + ], + options={ + 'unique_together': {('dataset', 'equipment')}, + }, + ), + migrations.AlterUniqueTogether( + name='dataset', + unique_together={('file', 'date')}, + ), + migrations.CreateModel( + name='DataColumnStringKeys', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('key', models.PositiveBigIntegerField()), + ('string', models.TextField()), + ('column', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='string_keys', to='galvanalyser.datacolumn')), + ], + options={ + 'unique_together': {('column', 'key', 'string')}, + }, + ), + ] diff --git a/django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py new file mode 100644 index 00000000..c8ff6eb3 --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-01-12 12:33 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0001_initial'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py new file mode 100644 index 00000000..426d6f48 --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-01-12 12:50 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0002_alter_observedfile_state'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/migrations/0004_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0004_alter_observedfile_state.py new file mode 100644 index 00000000..ec604a68 --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0004_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-01-12 13:00 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0003_alter_observedfile_state'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/migrations/0005_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0005_alter_observedfile_state.py new file mode 100644 index 00000000..2fd65bbf --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0005_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-01-12 13:03 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0004_alter_observedfile_state'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py index de148e11..932c6da9 100644 --- a/django/backend_django/galvanalyser/serializers.py +++ b/django/backend_django/galvanalyser/serializers.py @@ -11,6 +11,7 @@ TimeseriesData, \ TimeseriesRangeLabel from django.contrib.auth.models import User, Group +from django.conf.global_settings import DATA_UPLOAD_MAX_MEMORY_SIZE from rest_framework import serializers @@ -22,9 +23,33 @@ class Meta: class HarvesterConfigSerializer(serializers.HyperlinkedModelSerializer): + standard_units = serializers.SerializerMethodField() + standard_columns = serializers.SerializerMethodField() + max_upload_bytes = serializers.SerializerMethodField() + + def get_standard_units(self, instance): + return DataUnitSerializer( + DataUnit.objects.filter(is_default=True), + many=True, + context={'request': self.context['request']} + ).data + + def get_standard_columns(self, instance): + return DataColumnTypeSerializer( + DataColumnType.objects.filter(is_default=True), + many=True, + context={'request': self.context['request']} + ).data + + def get_max_upload_bytes(self, instance): + return DATA_UPLOAD_MAX_MEMORY_SIZE + class Meta: model = Harvester - fields = ['url', 'id', 'api_key', 'name', 'last_check_in', 'sleep_time', 'monitored_paths'] + fields = [ + 'url', 'id', 'api_key', 'name', 'last_check_in', 'sleep_time', 'monitored_paths', + 'standard_units', 'standard_columns', 'max_upload_bytes' + ] depth = 1 # max depth diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 236117f0..8e65be09 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -206,15 +206,34 @@ def report(self, request, pk: int = None): try: if content['status'] == 'begin': file.state = FileState.IMPORTING - # TODO: process metadata under 'begin'? + date = timezone.datetime.fromisoformat(content['test_date']).date() + # process metadata under 'begin' + core_metadata = content['core_metadata'] + extra_metadata = content['extra_metadata'] + defaults = {} + if 'Machine Type' in core_metadata: + defaults['type'] = core_metadata['Machine Type'] + if 'Dataset Name' in core_metadata: + defaults['name'] = core_metadata['Dataset Name'] + defaults['json_data'] = {} + if 'num_rows' in core_metadata: + defaults['json_data']['num_rows'] = core_metadata['num_rows'] + if 'first_sample_no' in core_metadata: + defaults['json_data']['first_sample_no'] = core_metadata['first_sample_no'] + if 'last_sample_no' in core_metadata: + defaults['json_data']['last_sample_no'] = core_metadata['last_sample_no'] + defaults['json_data'] = {**defaults['json_data'], **extra_metadata} + dataset, _ = Dataset.objects.get_or_create( - defaults={'date': timezone.now()}, - file=file + defaults=defaults, + file=file, + date=date ) elif content['status'] == 'complete': file.state = FileState.IMPORTED else: - dataset = Dataset.objects.get(file=file) + date = timezone.datetime.fromisoformat(content['test_date']).date() + dataset = Dataset.objects.get(file=file, date=date) for column_data in content['data']: try: column_type = DataColumnType.objects.get(id=column_data['column_id']) diff --git a/harvester/harvest.py b/harvester/harvest.py deleted file mode 100644 index f59561e9..00000000 --- a/harvester/harvest.py +++ /dev/null @@ -1,167 +0,0 @@ -import os.path -import sys -import time -import requests -import logging -import json -from settings import get_logfile, get_setting, get_settings, get_settings_file -from parse.harvester import import_file - - -logging.basicConfig(level=logging.INFO) -logger = logging.getLogger(__file__) -# stream_handler = logging.StreamHandler(sys.stdout) -# stream_handler.setLevel(logging.INFO) -# logger.addHandler(stream_handler) -file_handler = logging.FileHandler(get_logfile()) -file_handler.setLevel(logging.INFO) -logger.addHandler(file_handler) - - -def split_path(core_path: os.PathLike|str, path: os.PathLike|str) -> (os.PathLike, os.PathLike): - """ - Split a path into the base path property and the rest - """ - path = os.path.abspath(path) - core_path_abs = os.path.abspath(core_path) - return core_path, os.path.relpath(path, core_path_abs) - - -def report_harvest_result( - path: os.PathLike|str, - content=None, - file: os.PathLike|str = None, - error: BaseException = None -): - try: - if error is not None: - data = {'status': 'error', 'error': ";".join(error.args)} - else: - data = {'status': 'success', 'content': content} - data['path'] = path - if file is not None: - data['file'] = file - logger.debug(f"{get_setting('url')}report/; {json.dumps(data)}") - return requests.post( - f"{get_setting('url')}report/", - headers={ - 'Authorization': f"Harvester {get_setting('api_key')}" - }, - json=data - ) - except BaseException as e: - logger.error(e) - return None - - -def update_config(): - logger.info("Updating configuration from API") - try: - url = get_setting('url') - key = get_setting('api_key') - result = requests.get(f"{url}config/", headers={'Authorization': f"Harvester {key}"}) - if result.status_code == 200: - dirty = False - new = result.json() - old = get_settings() - if old is None: - old = {} - all_keys = [*new.keys(), *old.keys()] - for key in all_keys: - if key in old.keys() and key in new.keys(): - if json.dumps(old[key]) == json.dumps(new[key]): - continue - logger.info(f"Updating value for setting '{key}'") - logger.info(f"Old value: {json.dumps(old[key])}") - logger.info(f"New value: {json.dumps(new[key])}") - dirty = True - if key in old.keys(): - logger.info(f"Updating value for setting '{key}'") - logger.info(f"Old value: {json.dumps(old[key])}") - logger.info(f"New value: [not set]") - dirty = True - if key in new.keys(): - logger.info(f"Updating value for setting '{key}'") - logger.info(f"Old value: [not set]") - logger.info(f"New value: {json.dumps(new[key])}") - dirty = True - - if dirty: - with open(get_settings_file(), 'w') as f: - json.dump(result.json(), f) - else: - logger.error(f"Unable to fetch {url}config/ -- received HTTP {result.status_code}") - except BaseException as e: - logger.error(e) - - -def harvest(): - logger.info("Beginning harvest cycle") - paths = get_setting('monitored_paths') - if not paths: - logger.info("No paths are being monitored.") - return - - logger.debug(paths) - - for path in paths: - harvest_path(path.get('path')) - - -def harvest_path(path: os.PathLike): - logger.info(f"Harvesting from {path}") - try: - for (dir_path, dir_names, filenames) in os.walk(path): - for filename in filenames: - full_path = os.path.join(dir_path, filename) - core_path, file_path = split_path(path, full_path) - try: - logger.info(f"Reporting stats for {file_path}") - result = report_harvest_result( - path=core_path, - file=file_path, - content={ - 'task': 'file_size', - 'size': os.stat(full_path).st_size - } - ) - if result is not None: - result = result.json() - status = result['state'] - logger.info(f"Server assigned status '{status}'") - if status in ['STABLE', 'RETRY IMPORT']: - logger.info(f"Parsing file {file_path}") - if import_file(core_path, file_path): - report_harvest_result( - path=core_path, - file=file_path, - content={'task': 'import', 'status': 'complete'} - ) - except BaseException as e: - logger.error(e) - report_harvest_result(path=path, file=file_path, error=e) - logger.info(f"Completed directory walking of {path}") - except BaseException as e: - logger.error(e) - report_harvest_result(path=path, error=e) - - -def run(): - update_config() - harvest() - - -def run_cycle(): - while True: - try: - run() - sleep_time = get_setting('sleep_time') - if sleep_time is None: - sleep_time = 10 - time.sleep(sleep_time) - except BaseException as e: - logger.error(e) - - -if __name__ == "main": - run() diff --git a/harvester/parse/__init__.py b/harvester/harvester/__init__.py similarity index 100% rename from harvester/parse/__init__.py rename to harvester/harvester/__init__.py diff --git a/harvester/harvester/api.py b/harvester/harvester/api.py new file mode 100644 index 00000000..59f2d035 --- /dev/null +++ b/harvester/harvester/api.py @@ -0,0 +1,74 @@ +import os +import json +import requests +from .settings import get_setting, get_settings, get_settings_file, get_logger + +logger = get_logger(__file__) + + +def report_harvest_result( + path: os.PathLike|str, + content=None, + file: os.PathLike|str = None, + error: BaseException = None +): + try: + if error is not None: + data = {'status': 'error', 'error': ";".join(error.args)} + else: + data = {'status': 'success', 'content': content} + data['path'] = path + if file is not None: + data['file'] = file + logger.debug(f"{get_setting('url')}report/; {json.dumps(data)}") + return requests.post( + f"{get_setting('url')}report/", + headers={ + 'Authorization': f"Harvester {get_setting('api_key')}" + }, + json=data + ) + except BaseException as e: + logger.error(e) + return None + + +def update_config(): + logger.info("Updating configuration from API") + try: + url = get_setting('url') + key = get_setting('api_key') + result = requests.get(f"{url}config/", headers={'Authorization': f"Harvester {key}"}) + if result.status_code == 200: + dirty = False + new = result.json() + old = get_settings() + if old is None: + old = {} + all_keys = [*new.keys(), *old.keys()] + for key in all_keys: + if key in old.keys() and key in new.keys(): + if json.dumps(old[key]) == json.dumps(new[key]): + continue + logger.info(f"Updating value for setting '{key}'") + logger.info(f"Old value: {json.dumps(old[key])}") + logger.info(f"New value: {json.dumps(new[key])}") + dirty = True + if key in old.keys(): + logger.info(f"Updating value for setting '{key}'") + logger.info(f"Old value: {json.dumps(old[key])}") + logger.info(f"New value: [not set]") + dirty = True + if key in new.keys(): + logger.info(f"Updating value for setting '{key}'") + logger.info(f"Old value: [not set]") + logger.info(f"New value: {json.dumps(new[key])}") + dirty = True + + if dirty: + with open(get_settings_file(), 'w') as f: + json.dump(result.json(), f) + else: + logger.error(f"Unable to fetch {url}config/ -- received HTTP {result.status_code}") + except BaseException as e: + logger.error(e) diff --git a/harvester/harvester/harvest.py b/harvester/harvester/harvest.py new file mode 100644 index 00000000..c7e7a9d0 --- /dev/null +++ b/harvester/harvester/harvest.py @@ -0,0 +1,174 @@ +# SPDX-License-Identifier: BSD-2-Clause +# Copyright (c) 2020, The Chancellor, Masters and Scholars of the University +# of Oxford, and the 'Galvanalyser' Developers. All rights reserved. +import datetime +import os +import dateutil +import sys +from .parse.exceptions import UnsupportedFileTypeError + +from .parse.ivium_input_file import IviumInputFile +from .parse.biologic_input_file import BiologicMprInputFile +from .parse.maccor_input_file import ( + MaccorInputFile, + MaccorExcelInputFile, + MaccorRawInputFile, +) + +from .settings import get_logger, get_setting, get_standard_units, get_standard_columns +from .api import report_harvest_result + +logger = get_logger(__file__) + + +registered_input_files = [ + BiologicMprInputFile, + IviumInputFile, + MaccorInputFile, + MaccorExcelInputFile, + MaccorRawInputFile, +] + + +def serialize_datetime(v): + """ + Recursively search for date[time] classes and convert + dates to iso format strings and datetimes to timestamps + """ + if isinstance(v, datetime.datetime): + return v.timestamp() + if isinstance(v, datetime.date): + return v.isoformat() + if isinstance(v, dict): + return {k: serialize_datetime(x) for k, x in v.items()} + if isinstance(v, list): + return [serialize_datetime(x) for x in v] + return v + + +def import_file(core_path: str, file_path: str) -> bool: + """ + Attempts to import a given file + """ + default_column_ids = get_standard_columns() + default_units = get_standard_units() + max_upload_size = get_setting('max_upload_bytes') + full_file_path = os.sep.join([core_path, file_path]) + print("") + if not os.path.isfile(full_file_path): + print("Is not a file, skipping: " + full_file_path) + report_harvest_result(path=core_path, file=file_path, error=FileNotFoundError()) + return False + print("Importing " + full_file_path) + + try: + # Attempt reading the file before updating the database to avoid + # creating rows for a file we can't read. + # TODO handle rows in the dataset and access tables with no + # corresponding data since the import might fail while reading the data + # anyway + input_file = None + for input_file_cls in registered_input_files: + try: + print('Tried input reader {}'.format(input_file_cls)) + input_file = input_file_cls( + file_path=full_file_path, + standard_units=default_units, + standard_columns=default_column_ids + ) + except Exception as e: + print('...failed with: ', type(e), e) + else: + print('...succeeded...') + break + if input_file is None: + raise UnsupportedFileTypeError + + # Send metadata + core_metadata, extra_metadata = input_file.load_metadata() + report_harvest_result( + path=core_path, + file=file_path, + content={ + 'task': 'import', + 'status': 'begin', + 'core_metadata': serialize_datetime(core_metadata), + 'extra_metadata': serialize_datetime(extra_metadata), + 'test_date': serialize_datetime(core_metadata['Date of Test']) + } + ) + + # TODO: Resume/append where record already exists + # TODO: Including getting existing string-int mapping + + # Figure out column data + column_data = {} + mapping = input_file.get_file_column_to_standard_column_mapping() + next_key = 0 + # Find out if there's a Sample number column, otherwise we use the row number + record_number_column = [k for k, v in mapping.items() if v == default_column_ids['Sample Number']] + record_number_column = record_number_column[0] if len(record_number_column) else None + generator = input_file.load_data(input_file.file_path, input_file.column_info.keys()) + for i, r in enumerate(generator): + # limit size of requests. 100b/column is an arbitrary buffer size. + if sys.getsizeof(column_data) > max_upload_size - 100 * len(column_data): + report_harvest_result(path=core_path, file=file_path, content={ + 'task': 'import', + 'status': 'in_progress', + 'data': [v for v in column_data.values()] + }) + for k in column_data.keys(): + column_data[k]['values'] = {} + + record_number = int(r.get(record_number_column, i)) + for k, v in r.items(): + if k == record_number_column: + continue + if k in column_data: + # Numeric data are stored directly + try: + column_data[k]['values'][record_number] = int(v) + except ValueError: + try: + column_data[k]['values'][record_number] = float(v) + # Timestamps are stored using float conversion + except ValueError: + try: + column_data[k]['values'][record_number] = dateutil.parser.parse(v).timestamp() + # Strings are mapped to integer values using a value map which is also sent to the database + except ValueError: + if 'value_map' in column_data[k] and v in column_data[k]['value_map']: + column_data[k]['values'][record_number] = column_data[k]['value_map'][v] + else: + if 'value_map' in column_data[k]: + column_data[k]['value_map'][v] = next_key + else: + column_data[k]['value_map'] = {v: next_key} + column_data[k]['values'][record_number] = next_key + next_key += 1 + else: + column_data[k] = {} + if k in mapping: + column_data[k]['column_id'] = mapping[k] + else: + column_data[k]['column_name'] = k + if 'unit' in input_file.column_info[k]: + column_data[k]['unit_symbol'] = input_file.column_info[k].get('unit') + else: + column_data[k]['unit_id'] = default_units['Unitless'] + column_data[k]['values'] = {} + + # Send data + report_harvest_result(path=core_path, file=file_path, content={ + 'task': 'import', + 'status': 'in_progress', + 'data': [v for v in column_data.values()], + 'test_date': serialize_datetime(core_metadata['Date of Test']) + }) + + print("File successfully imported") + except Exception as e: + logger.error(e) + # report(path=core_path, file=file_path, error=e) + return False + return True diff --git a/harvester/parse/database/__init__.py b/harvester/harvester/parse/__init__.py similarity index 100% rename from harvester/parse/database/__init__.py rename to harvester/harvester/parse/__init__.py diff --git a/harvester/parse/biologic_input_file.py b/harvester/harvester/parse/biologic_input_file.py similarity index 70% rename from harvester/parse/biologic_input_file.py rename to harvester/harvester/parse/biologic_input_file.py index a19b8f97..47bf05fe 100644 --- a/harvester/parse/biologic_input_file.py +++ b/harvester/harvester/parse/biologic_input_file.py @@ -4,25 +4,9 @@ import os import ntpath -import copy from galvani import BioLogic -from galvani.BioLogic import VMPdata_colID_dtype_map, VMPdata_colID_flag_map -from .database.util.battery_exceptions import UnsupportedFileTypeError -from .database.experiment.input_file import InputFile -from .database.experiment.timeseries_data_row import ( - RECORD_NO_COLUMN_ID, - TEST_TIME_COLUMN_ID, - VOLTAGE_COLUMN_ID, - AMPS_COLUMN_ID, - ENERGY_CAPACITY_COLUMN_ID, - CHARGE_CAPACITY_COLUMN_ID, - TEMPERATURE_COLUMN_ID, - STEP_TIME_COLUMN_ID, - IMPEDENCE_MAG_COLUMN_ID, - IMPEDENCE_PHASE_COLUMN_ID, - FREQUENCY_COLUMN_ID, -) -from .database.experiment.unit import Unit +from .exceptions import UnsupportedFileTypeError +from .input_file import InputFile class BiologicMprInputFile(InputFile): @@ -30,28 +14,28 @@ class BiologicMprInputFile(InputFile): A class for handling input files """ - def __init__(self, file_path): + def __init__(self, file_path, **kwargs): if not file_path.endswith(".mpr"): raise UnsupportedFileTypeError self.mpr_file = BioLogic.MPRfile(file_path) - super().__init__(file_path) + super().__init__(file_path, **kwargs) - def get_file_column_to_standard_column_mapping(self, default_columns: dict) -> dict: + def get_file_column_to_standard_column_mapping(self) -> dict: """ Return a dict with a key of the column name in the file that maps to the standard column name in the value. Only return values where a mapping exists """ return { - "I/mA": default_columns['Amps'], - "Ewe/V": default_columns['Volts'], - "time/s": default_columns['Time'], - "Energy/W.h": default_columns['Energy Capacity'], - "Q charge/discharge/mA.h": default_columns['Charge Capacity'], - "Aux": default_columns['Temperature'], - "|Z|/Ohm": default_columns['Impedence Magnitude'], - "Phase(Z)/deg": default_columns['Impedence Phase'], - "freq/Hz": default_columns['Frequency'], + "I/mA": self.standard_columns['Amps'], + "Ewe/V": self.standard_columns['Volts'], + "time/s": self.standard_columns['Time'], + "Energy/W.h": self.standard_columns['Energy Capacity'], + "Q charge/discharge/mA.h": self.standard_columns['Charge Capacity'], + "Aux": self.standard_columns['Temperature'], + "|Z|/Ohm": self.standard_columns['Impedence Magnitude'], + "Phase(Z)/deg": self.standard_columns['Impedence Phase'], + "freq/Hz": self.standard_columns['Frequency'], } def load_data(self, file_path, columns): @@ -110,7 +94,7 @@ def load_metadata(self): for name in self.mpr_file.data.dtype.names } for name, data in columns_with_data.items(): - for unit in Unit.get_all_units(): + for unit in self.standard_units: if name[-len(unit):] == unit: data['unit'] = unit diff --git a/harvester/parse/database/util/battery_exceptions.py b/harvester/harvester/parse/exceptions.py similarity index 68% rename from harvester/parse/database/util/battery_exceptions.py rename to harvester/harvester/parse/exceptions.py index 421f2d9e..b801c256 100644 --- a/harvester/parse/database/util/battery_exceptions.py +++ b/harvester/harvester/parse/exceptions.py @@ -24,19 +24,3 @@ class EmptyFileError(Exception): """ pass - - -class DataGenerationError(Exception): - """ - Exception indicating the failure to generate some columns - """ - - pass - - -class InsertError(Exception): - """ - Exception indicating the failure to insert data - """ - - pass diff --git a/harvester/parse/database/experiment/input_file.py b/harvester/harvester/parse/input_file.py similarity index 82% rename from harvester/parse/database/experiment/input_file.py rename to harvester/harvester/parse/input_file.py index 829ec5ec..7b90164a 100644 --- a/harvester/parse/database/experiment/input_file.py +++ b/harvester/harvester/parse/input_file.py @@ -1,20 +1,5 @@ -from ..util.battery_exceptions import UnsupportedFileTypeError -from itertools import accumulate +from .exceptions import UnsupportedFileTypeError import traceback -from .timeseries_data_row import ( - RECORD_NO_COLUMN_ID, - TEST_TIME_COLUMN_ID, - VOLTAGE_COLUMN_ID, - AMPS_COLUMN_ID, - ENERGY_CAPACITY_COLUMN_ID, - CHARGE_CAPACITY_COLUMN_ID, - TEMPERATURE_COLUMN_ID, - STEP_TIME_COLUMN_ID, - IMPEDENCE_MAG_COLUMN_ID, - IMPEDENCE_PHASE_COLUMN_ID, - FREQUENCY_COLUMN_ID, -) -from .unit import Unit # see https://gist.github.com/jsheedy/ed81cdf18190183b3b7d # https://stackoverflow.com/a/30721460 @@ -24,9 +9,15 @@ class InputFile: """ A class for handling input files """ + unit_conversion_multipliers = { + 'mA': 1e-3, + 'mA.h': 1e-3 + } - def __init__(self, file_path): + def __init__(self, file_path, standard_columns: dict, standard_units: dict): self.file_path = file_path + self.standard_columns = standard_columns + self.standard_units = standard_units self.metadata, self.column_info = self.load_metadata() def get_columns(self): @@ -42,7 +33,7 @@ def get_columns(self): "file_column_to_standard_column is {}: {}\n" "column_info is {}\n" ).format(col, std, self.column_info[col])) - if self.column_info[col]['unit'] not in Unit.get_all_units(): + if self.column_info[col]['unit'] not in self.standard_units: raise RuntimeError( "Unknown unit {} provided for standard column mapping" .format(self.column_info[col]['unit']) @@ -60,9 +51,8 @@ def get_test_start_date(self): return self.metadata["Date of Test"] def convert_unit(self, name, value): - if 'unit' in self.column_info[name]: - unit = self.column_info[name]['unit'] - value = Unit.convert(unit, value) + if 'unit' in self.column_info[name] and self.column_info[name]['unit'] in self.unit_conversion_multipliers: + return value * self.unit_conversion_multipliers[self.column_info[name]['unit']] return value def get_data_row_generator( @@ -79,7 +69,7 @@ def get_data_row_generator( for name, col_id in column_name_to_id.items() } - sample_col_id = type_id_to_col_id.get(RECORD_NO_COLUMN_ID, None) + sample_col_id = type_id_to_col_id.get(self.standard_columns['Sample Number'], None) # reconstruct previous row mapping col ids to values if last_values is not None: @@ -137,7 +127,7 @@ def load_data(self, file_path, available_desired_columns): def get_data_labels(self): raise UnsupportedFileTypeError - def get_file_column_to_standard_column_mapping(self, default_columns: dict): + def get_file_column_to_standard_column_mapping(self): """ returns map of file column name strings to column id numbers """ diff --git a/harvester/parse/ivium_input_file.py b/harvester/harvester/parse/ivium_input_file.py similarity index 96% rename from harvester/parse/ivium_input_file.py rename to harvester/harvester/parse/ivium_input_file.py index 708bebb6..b150fcc5 100644 --- a/harvester/parse/ivium_input_file.py +++ b/harvester/harvester/parse/ivium_input_file.py @@ -3,12 +3,11 @@ # of Oxford, and the 'Galvanalyser' Developers. All rights reserved. import os -import csv import ntpath import re from datetime import datetime -from .database.experiment.input_file import InputFile -from .database.util.battery_exceptions import ( +from .input_file import InputFile +from .exceptions import ( UnsupportedFileTypeError, InvalidDataInFileError, ) @@ -21,11 +20,11 @@ class IviumInputFile(InputFile): A class for handling input files """ - def __init__(self, file_path): + def __init__(self, file_path, **kwargs): self.validate_file(file_path) - super().__init__(file_path) + super().__init__(file_path, **kwargs) - def get_file_column_to_standard_column_mapping(self, default_columns: dict) -> dict: + def get_file_column_to_standard_column_mapping(self) -> dict: print("Type is IVIUM") """ Return a dict with a key of the column name in the file that maps to @@ -34,9 +33,9 @@ def get_file_column_to_standard_column_mapping(self, default_columns: dict) -> d """ print("get_ivium_column_to_standard_column_mapping") return { - "amps": default_columns['Amps'], - "volts": default_columns['Volts'], - "test_time": default_columns['Time'] + "amps": self.standard_columns['Amps'], + "volts": self.standard_columns['Volts'], + "test_time": self.standard_columns['Time'] } def load_data(self, file_path, columns): diff --git a/harvester/parse/maccor_input_file.py b/harvester/harvester/parse/maccor_input_file.py similarity index 96% rename from harvester/parse/maccor_input_file.py rename to harvester/harvester/parse/maccor_input_file.py index ed87747e..240e6b85 100644 --- a/harvester/parse/maccor_input_file.py +++ b/harvester/harvester/parse/maccor_input_file.py @@ -9,10 +9,11 @@ from datetime import datetime import xlrd import maya -from .database.experiment.input_file import InputFile -from .database.util.battery_exceptions import ( +from .input_file import InputFile +from .exceptions import ( UnsupportedFileTypeError, EmptyFileError, + InvalidDataInFileError ) @@ -21,9 +22,9 @@ class MaccorInputFile(InputFile): A class for handling input files """ - def __init__(self, file_path): + def __init__(self, file_path, **kwargs): self.validate_file(file_path) - super().__init__(file_path) + super().__init__(file_path, **kwargs) def identify_columns(self, reader): """ @@ -141,7 +142,7 @@ def load_metadata(self): print(metadata) return metadata, column_info - def get_file_column_to_standard_column_mapping(self, default_columns: dict) -> dict: + def get_file_column_to_standard_column_mapping(self) -> dict: """ Return a dict with a key of the column name in the file that maps to the standard column name in the value. Only return values where a @@ -151,16 +152,16 @@ def get_file_column_to_standard_column_mapping(self, default_columns: dict) -> d print("Type is MACCOR") print("get_maccor_column_to_standard_column_mapping") return { - "Amp-hr": default_columns['Charge Capacity'], - "Amps": default_columns['Amps'], - "Watt-hr": default_columns['Energy Capacity'], - "StepTime": default_columns['Step Time'], - "Step (Sec)": default_columns['Step Time'], - "Volts": default_columns['Volts'], - "TestTime": default_columns['Time'], - "Test (Sec)": default_columns['Time'], - "Rec#": default_columns['Sample Number'], - "Temp 1": default_columns['Temperature'] + "Amp-hr": self.standard_columns['Charge Capacity'], + "Amps": self.standard_columns['Amps'], + "Watt-hr": self.standard_columns['Energy Capacity'], + "StepTime": self.standard_columns['Step Time'], + "Step (Sec)": self.standard_columns['Step Time'], + "Volts": self.standard_columns['Volts'], + "TestTime": self.standard_columns['Time'], + "Test (Sec)": self.standard_columns['Time'], + "Rec#": self.standard_columns['Sample Number'], + "Temp 1": self.standard_columns['Temperature'] } def load_data(self, file_path, columns): diff --git a/harvester/harvester/run.py b/harvester/harvester/run.py new file mode 100644 index 00000000..0ffd21b8 --- /dev/null +++ b/harvester/harvester/run.py @@ -0,0 +1,88 @@ +import os.path +import time +from .settings import get_logger, get_setting +from .api import report_harvest_result, update_config +from .harvest import import_file + +logger = get_logger(__file__) + + +def split_path(core_path: os.PathLike|str, path: os.PathLike|str) -> (os.PathLike, os.PathLike): + """ + Split a path into the base path property and the rest + """ + path = os.path.abspath(path) + core_path_abs = os.path.abspath(core_path) + return core_path, os.path.relpath(path, core_path_abs) + + +def harvest(): + logger.info("Beginning harvest cycle") + paths = get_setting('monitored_paths') + if not paths: + logger.info("No paths are being monitored.") + return + + logger.debug(paths) + + for path in paths: + harvest_path(path.get('path')) + + +def harvest_path(path: os.PathLike): + logger.info(f"Harvesting from {path}") + try: + for (dir_path, dir_names, filenames) in os.walk(path): + for filename in filenames: + full_path = os.path.join(dir_path, filename) + core_path, file_path = split_path(path, full_path) + try: + logger.info(f"Reporting stats for {file_path}") + result = report_harvest_result( + path=core_path, + file=file_path, + content={ + 'task': 'file_size', + 'size': os.stat(full_path).st_size + } + ) + if result is not None: + result = result.json() + status = result['state'] + logger.info(f"Server assigned status '{status}'") + if status in ['STABLE', 'RETRY IMPORT']: + logger.info(f"Parsing file {file_path}") + if import_file(core_path, file_path): + report_harvest_result( + path=core_path, + file=file_path, + content={'task': 'import', 'status': 'complete'} + ) + except BaseException as e: + logger.error(e) + report_harvest_result(path=path, file=file_path, error=e) + logger.info(f"Completed directory walking of {path}") + except BaseException as e: + logger.error(e) + report_harvest_result(path=path, error=e) + + +def run(): + update_config() + harvest() + + +def run_cycle(): + while True: + try: + run() + sleep_time = get_setting('sleep_time') + if sleep_time is None: + sleep_time = 10 + time.sleep(sleep_time) + except BaseException as e: + logger.error(e) + + +if __name__ == "main": + run() diff --git a/harvester/settings.py b/harvester/harvester/settings.py similarity index 61% rename from harvester/settings.py rename to harvester/harvester/settings.py index 7f68c20b..607d3816 100644 --- a/harvester/settings.py +++ b/harvester/harvester/settings.py @@ -1,6 +1,9 @@ import json import os import pathlib +import logging + +logging.basicConfig(level=logging.INFO) def get_settings_file() -> pathlib.Path: @@ -34,3 +37,22 @@ def get_setting(*args): if len(args) == 1: return settings.get(args[0]) return [settings.get(arg) for arg in args] + + +def get_standard_units(): + return {u['name']: u['id'] for u in get_setting('standard_units')} + + +def get_standard_columns(): + return {u['name']: u['id'] for u in get_setting('standard_columns')} + + +def get_logger(name): + logger = logging.getLogger(name) + # stream_handler = logging.StreamHandler(sys.stdout) + # stream_handler.setLevel(logging.INFO) + # logger.addHandler(stream_handler) + file_handler = logging.FileHandler(get_logfile()) + file_handler.setLevel(logging.INFO) + logger.addHandler(file_handler) + return logger diff --git a/harvester/parse/database/cell_data/__init__.py b/harvester/parse/database/cell_data/__init__.py deleted file mode 100644 index 3a8bde2e..00000000 --- a/harvester/parse/database/cell_data/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -from .cell_row import CellRow -from .cell import Cell -from .manufacturer_row import ManufacturerRow diff --git a/harvester/parse/database/cell_data/cell.py b/harvester/parse/database/cell_data/cell.py deleted file mode 100644 index f0ebb6fc..00000000 --- a/harvester/parse/database/cell_data/cell.py +++ /dev/null @@ -1,39 +0,0 @@ -from galvanalyser.database import Base -# from galvanalyser.database.experiment import Dataset -from sqlalchemy import ( - Column, ForeignKey, Integer, String, - DateTime, JSON, Table -) -from sqlalchemy.orm import relationship -from dataclasses import dataclass -from typing import List - - -@dataclass -class Cell(Base): - __tablename__ = 'cell' - __table_args__ = {'schema': 'cell_data'} - - id: int - # datasets: List[Dataset] - name: str - manufacturer: str - form_factor: str - link_to_datasheet: str - anode_chemistry: str - cathode_chemistry: str - nominal_capacity: str - nominal_cell_weight: str - - id = Column(Integer, primary_key=True) - datasets = relationship( - 'Dataset', backref='cell' - ) - name = Column(String) - manufacturer = Column(String) - form_factor = Column(String) - link_to_datasheet = Column(String) - anode_chemistry = Column(String) - cathode_chemistry = Column(String) - nominal_capacity = Column(String) - nominal_cell_weight = Column(String) diff --git a/harvester/parse/database/cell_data/cell_row.py b/harvester/parse/database/cell_data/cell_row.py deleted file mode 100644 index 3a04149f..00000000 --- a/harvester/parse/database/cell_data/cell_row.py +++ /dev/null @@ -1,213 +0,0 @@ -import psycopg2 -from galvanalyser.database import Row - - -class CellRow(Row): - def __init__( - self, - name, - id=None, - manufacturer=None, - form_factor=None, - link_to_datasheet=None, - anode_chemistry=None, - cathode_chemistry=None, - nominal_capacity=None, - nominal_cell_weight=None, - ): - self.id = id - self.name = name - self.manufacturer = manufacturer - self.form_factor = form_factor - self.link_to_datasheet = link_to_datasheet - self.anode_chemistry = anode_chemistry - self.cathode_chemistry = cathode_chemistry - self.nominal_capacity = nominal_capacity - self.nominal_cell_weight = nominal_cell_weight - - def to_dict(self): - obj = { - 'id': self.id, - 'name': self.name, - 'manufacturer': self.manufacturer, - 'form_factor': self.form_factor, - 'link_to_datasheet': self.link_to_datasheet, - 'anode_chemistry': self.anode_chemistry, - 'cathode_chemistry': self.cathode_chemistry, - 'nominal_capacity': self.nominal_capacity, - 'nominal_cell_weight': self.nominal_cell_weight, - } - return obj - - def __eq__(self, other): - if isinstance(other, CellRow): - return ( - self.id == other.id and - self.name == other.name and - self.manufacturer == other.manufacturer and - self.form_factor == other.form_factor and - self.link_to_datasheet == other.link_to_datasheet and - self.anode_chemistry == other.anode_chemistry and - self.cathode_chemistry == other.cathode_chemistry and - self.nominal_capacity == other.nominal_capacity and - self.nominal_cell_weight == other.nominal_cell_weight - ) - - return False - - def __repr__(self): - return ('CellRow({}, {}, {}, {}, {}, {}, {}, {})' - .format( - self.id, - self.name, - self.manufacturer, - self.form_factor, - self.link_to_datasheet, - self.anode_chemistry, - self.cathode_chemistry, - self.nominal_capacity, - self.nominal_cell_weight, - )) - - def insert(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "INSERT INTO cell_data.cell (" - "name, manufacturer, form_factor, " - "link_to_datasheet, anode_chemistry, " - "cathode_chemistry, nominal_capacity, " - "nominal_cell_weight) " - "VALUES (%s, %s, %s, %s, %s, %s, %s, %s) " - "RETURNING id" - ), - [ - self.name, - self.manufacturer, - self.form_factor, - self.link_to_datasheet, - self.anode_chemistry, - self.cathode_chemistry, - self.nominal_capacity, - self.nominal_cell_weight, - ], - ) - result = cursor.fetchone() - self.id = result[0] - - def update(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "UPDATE cell_data.cell SET " - "name = (%s), " - "manufacturer = (%s), form_factor = (%s), " - "link_to_datasheet = (%s), anode_chemistry = (%s), " - "cathode_chemistry = (%s), nominal_capacity = (%s), " - "nominal_cell_weight = (%s) " - "WHERE id=(%s)" - ), - [ - self.name, - self.manufacturer, self.form_factor, - self.link_to_datasheet, self.anode_chemistry, - self.cathode_chemistry, self.nominal_capacity, - self.nominal_cell_weight, self.id - ], - ) - - def delete(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "DELETE FROM cell_data.cell " - "WHERE id=(%s)" - ), - [self.id], - ) - - @staticmethod - def all(conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT id, name, manufacturer, form_factor, " - "link_to_datasheet, anode_chemistry, " - "cathode_chemistry, nominal_capacity, " - "nominal_cell_weight FROM " - "cell_data.cell" - ), - ) - records = cursor.fetchall() - return [ - CellRow( - id=result[0], - name=result[1], - manufacturer=result[2], - form_factor=result[3], - link_to_datasheet=result[4], - anode_chemistry=result[5], - cathode_chemistry=result[6], - nominal_capacity=result[7], - nominal_cell_weight=result[8], - ) - for result in records - ] - - @staticmethod - def select_from_id(id_, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT name, manufacturer, form_factor, " - "link_to_datasheet, anode_chemistry, " - "cathode_chemistry, nominal_capacity, " - "nominal_cell_weight FROM " - "cell_data.cell " - "WHERE id=(%s)" - ), - [id_], - ) - result = cursor.fetchone() - if result is None: - return None - return CellRow( - id=id_, - name=result[0], - manufacturer=result[1], - form_factor=result[2], - link_to_datasheet=result[3], - anode_chemistry=result[4], - cathode_chemistry=result[5], - nominal_capacity=result[6], - nominal_cell_weight=result[7], - ) - - @staticmethod - def select_from_name(name, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT id, manufacturer, form_factor, " - "link_to_datasheet, anode_chemistry, " - "cathode_chemistry, nominal_capacity, " - "nominal_cell_weight FROM " - "cell_data.cell " - "WHERE name=(%s)" - ), - [name], - ) - result = cursor.fetchone() - if result is None: - return None - return CellRow( - id=result[0], - name=name, - manufacturer=result[1], - form_factor=result[2], - link_to_datasheet=result[3], - anode_chemistry=result[4], - cathode_chemistry=result[5], - nominal_capacity=result[6], - nominal_cell_weight=result[7], - ) diff --git a/harvester/parse/database/cell_data/manufacturer_row.py b/harvester/parse/database/cell_data/manufacturer_row.py deleted file mode 100644 index 1318b4bc..00000000 --- a/harvester/parse/database/cell_data/manufacturer_row.py +++ /dev/null @@ -1,109 +0,0 @@ -import psycopg2 -from galvanalyser.database import Row - -class ManufacturerRow(Row): - def __init__( - self, - name, - id=None, - ): - self.id = id - self.name = name - - - def to_dict(self): - obj = { - 'id': self.id, - 'name': self.name, - } - return obj - - def __eq__(self, other): - if isinstance(other, ManufacturerRow): - return ( - self.id == other.id and - self.name == other.name - ) - - return False - - def __repr__(self): - return ('ManufacturerRow({}, {})' - .format( - self.id, - self.name, - )) - - def insert(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "INSERT INTO cell_data.manufacturer (name) " - "VALUES (%s)" - "RETURNING id" - ), - [ - self.name, - ], - ) - self.id = cursor.fetchone()[0] - - def update(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "UPDATE cell_data.manufacturer SET " - "name = (%s) " - "WHERE id=(%s)" - ), - [ - self.name, self.id - ], - ) - - def delete(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "DELETE FROM cell_data.manufacturer " - "WHERE id=(%s)" - ), - [self.id], - ) - - @staticmethod - def all(conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT id, name FROM " - "cell_data.manufacturer" - ), - ) - records = cursor.fetchall() - return [ - ManufacturerRow( - id=result[0], - name=result[1], - ) - for result in records - ] - - @staticmethod - def select_from_id(_id, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT name FROM " - "cell_data.manufacturer " - "WHERE id=(%s)" - ), - [_id], - ) - result = cursor.fetchone() - if result is None: - return None - return ManufacturerRow( - id=_id, - name=result[0], - ) diff --git a/harvester/parse/database/experiment/__init__.py b/harvester/parse/database/experiment/__init__.py deleted file mode 100644 index 6d6bc40f..00000000 --- a/harvester/parse/database/experiment/__init__.py +++ /dev/null @@ -1,6 +0,0 @@ -from .access_row import AccessRow -from .equipment_row import EquipmentRow -from .column_row import ColumnRow -from .unit import Unit -from .input_file import InputFile -from .timeseries_data_row import TimeseriesDataRow diff --git a/harvester/parse/database/experiment/access_row.py b/harvester/parse/database/experiment/access_row.py deleted file mode 100644 index 32432c4c..00000000 --- a/harvester/parse/database/experiment/access_row.py +++ /dev/null @@ -1,61 +0,0 @@ - -class AccessRow: - def __init__(self, dataset_id, user_id): - self.dataset_id = dataset_id - self.user_id = user_id - - def insert(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "INSERT INTO experiment.access (dataset_id, user_id) " - "VALUES (%s, %s) ON CONFLICT DO NOTHING" - ), - [self.dataset_id, self.user_id], - ) - - @staticmethod - def exists(dataset_id, user_id, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT COUNT(1) " - "FROM experiment.access " - "WHERE dataset_id=(%s) AND user_id=(%s)" - ), - [dataset_id, user_id], - ) - result = cursor.fetchone() - return bool(result) - - @staticmethod - def select_from_dataset_id(dataset_id, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT user_id FROM experiment.access " - "WHERE dataset_id=(%s)" - ), - [dataset_id], - ) - records = cursor.fetchall() - return [ - AccessRow(dataset_id=dataset_id, user_id=result[0]) - for result in records - ] - - @staticmethod - def select_from_user_id(user_id, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT dataset_id FROM experiment.access " - "WHERE user_id=(%s)" - ), - [user_id], - ) - records = cursor.fetchall() - return [ - AccessRow(dataset_id=result[0], user_id=user_id) - for result in records - ] diff --git a/harvester/parse/database/experiment/column_row.py b/harvester/parse/database/experiment/column_row.py deleted file mode 100644 index 1d34d02c..00000000 --- a/harvester/parse/database/experiment/column_row.py +++ /dev/null @@ -1,91 +0,0 @@ -from ..row import Row - - -class ColumnRow(Row): - def __init__(self, type_id, name, dataset_id, id_=None): - self.id = id_ - self.type_id = type_id - self.dataset_id = dataset_id - self.name = name - - def to_dict(self): - obj = { - 'id': self.id, - 'name': self.name, - 'type_id': self.type_id, - 'dataset_id': self.dataset_id, - } - return obj - - def insert(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - 'INSERT INTO experiment."column" (type_id, name, dataset_id) ' - "VALUES (%s, %s, %s) RETURNING id" - ), - [self.type_id, self.name, self.dataset_id], - ) - self.id = cursor.fetchone()[0] - - @staticmethod - def select_from_id(id_, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - 'SELECT type_id, dataset_id, name FROM experiment."column" ' - "WHERE id=(%s)" - ), - [id_], - ) - result = cursor.fetchone() - if result is None: - return None - return ColumnRow( - id_=id_, - type_id=result[0], - dataset_id=result[1], - name=result[2] - ) - - @staticmethod - def select_from_dataset_with_name(dataset_id, name, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - 'SELECT id, type_id FROM experiment."column" ' - "WHERE dataset_id=(%s) AND name=(%s)" - ), - [dataset_id, name], - ) - result = cursor.fetchone() - if result is None: - return None - return ColumnRow( - id_=result[0], - type_id=result[1], - dataset_id=dataset_id, - name=name, - ) - - - @staticmethod - def select_from_type_id(type_id, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - 'SELECT id, name, dataset_id FROM experiment."column" ' - "WHERE type_id=(%s)" - ), - [type_id], - ) - records = cursor.fetchall() - return [ - ColumnRow( - id_=result[0], - type_id=type_id, - name=result[1], - dataset_id=result[2], - ) - for result in records - ] diff --git a/harvester/parse/database/experiment/equipment_row.py b/harvester/parse/database/experiment/equipment_row.py deleted file mode 100644 index d5943678..00000000 --- a/harvester/parse/database/experiment/equipment_row.py +++ /dev/null @@ -1,135 +0,0 @@ -from ..row import Row - - -class EquipmentRow(Row): - def __init__( - self, - name, - id=None, - type=None, - ): - self.id = id - self.name = name - self.type = type - - def to_dict(self): - obj = { - 'id': self.id, - 'name': self.name, - 'type': self.type, - } - return obj - - def __eq__(self, other): - if isinstance(other, EquipmentRow): - return ( - self.id == other.id and - self.name == other.name and - self.type == other.type - ) - - return False - - def insert(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "INSERT INTO experiment.equipment (" - "name, type) " - "VALUES (%s, %s) " - "RETURNING id" - ), - [ - self.name, - self.type, - ], - ) - result = cursor.fetchone() - self.id = result[0] - - def update(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "UPDATE experiment.equipment SET " - "name = (%s), " - "type = (%s) " - "WHERE id=(%s)" - ), - [ - self.name, - self.type, self.id, - ], - ) - - def delete(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "DELETE FROM experiment.equipment " - "WHERE id=(%s)" - ), - [self.id], - ) - - @staticmethod - def all(conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT id, name, type " - "FROM " - "experiment.equipment" - ), - ) - records = cursor.fetchall() - return [ - EquipmentRow( - id=result[0], - name=result[1], - type=result[2], - ) - for result in records - ] - - @staticmethod - def select_from_id(id_, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT name, type " - "FROM " - "experiment.equipment " - "WHERE id=(%s)" - ), - [id_], - ) - result = cursor.fetchone() - if result is None: - return None - return EquipmentRow( - id=id_, - name=result[0], - type=result[1], - ) - - @staticmethod - def select_from_name(name, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT id, type " - "FROM " - "experiment.equipment " - "WHERE name=(%s)" - ), - [name], - ) - result = cursor.fetchone() - if result is None: - return None - return EquipmentRow( - id=result[0], - name=name, - type=result[1], - ) diff --git a/harvester/parse/database/experiment/timeseries_data_row.py b/harvester/parse/database/experiment/timeseries_data_row.py deleted file mode 100644 index df38374a..00000000 --- a/harvester/parse/database/experiment/timeseries_data_row.py +++ /dev/null @@ -1,194 +0,0 @@ -from ..util.iter_file import IteratorFile -from timeit import default_timer as timer - -from .column_row import ColumnRow - -from ..util import battery_exceptions - -RECORD_NO_COLUMN_ID = 0 -TEST_TIME_COLUMN_ID = 1 -VOLTAGE_COLUMN_ID = 2 -AMPS_COLUMN_ID = 3 -ENERGY_CAPACITY_COLUMN_ID = 4 -CHARGE_CAPACITY_COLUMN_ID = 5 -TEMPERATURE_COLUMN_ID = 6 -STEP_TIME_COLUMN_ID = 7 -IMPEDENCE_MAG_COLUMN_ID = 8 -IMPEDENCE_PHASE_COLUMN_ID = 9 -FREQUENCY_COLUMN_ID = 10 - -UNIT_UNITLESS = 1 -UNIT_SECONDS = 2 -UNIT_VOLTS = 3 -UNIT_AMPS = 4 -UNIT_WATT_HOURS = 5 -UNIT_AMP_HOURS = 6 -UNIT_CENTIGRADE = 7 -UNIT_WATTS = 8 -UNIT_OHMS = 9 -UNIT_DEGREES = 10 -UNIT_HERTZ = 11 - - -class TimeseriesDataRow: - def __init__(self, sample_no, column_id, value, column_type_id=None): - self.sample_no = sample_no - self.column_id = column_id - self.column_type_id = column_type_id - self.value = value - - def __str__(self): - return ( - 'TimeseriesDataRow(sample_no={} ' - 'column_id={}, value={})' - ).format( - self.sample_no, - self.column_id, - self.value - ) - - def __repr__(self): - return self.__str__() - - def insert(self, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "INSERT INTO experiment.timeseries_data " - "(sample_no, column_id, value) " - "VALUES (, %s, %s, %s)" - ), - [self.sample_no, self.column_id, self.value], - ) - - @staticmethod - def insert_input_file( - input_file, - dataset_id, - conn, - last_values=None, - ): - column_name_to_id = {} - # create mapping from col id to col name, creating new columns as - # appropriate - columns = input_file.get_columns() - has_record_column = False - for name, type_id in columns: - # don't want to create a column for sample number - if type_id == RECORD_NO_COLUMN_ID: - has_record_column = True - column_name_to_id[name] = -2 - continue - - col = ColumnRow.select_from_dataset_with_name( - dataset_id, name, conn - ) - if col is None: - col = ColumnRow( - dataset_id=dataset_id, - type_id=type_id, - name=name - ) - col.insert(conn) - column_name_to_id[name] = col.id - - print("Getting data") - row_generator = input_file.get_data_row_generator( - column_name_to_id, - last_values, - ) - iter_file = IteratorFile(row_generator) - num_value_columns = len(columns) - if has_record_column: - num_value_columns -= 1 - start_row = 0 if last_values is None else last_values[0].sample_no - num_rows_to_insert = input_file.metadata["num_rows"] - start_row - expected_insert_count = num_rows_to_insert * num_value_columns - with conn.cursor() as cursor: - print("Copying data to table") - start = timer() - cursor.copy_expert( - 'COPY experiment.timeseries_data FROM STDIN', iter_file - ) - end = timer() - if cursor.rowcount != expected_insert_count: - raise battery_exceptions.InsertError( - "Insert failed. Inserted {} of {} values ({} rows * {} columns) before failure".format( - cursor.rowcount, - expected_insert_count, - num_rows_to_insert, - num_value_columns, - ) - ) - print("Done copying data to table") - print( - "Inserted {} rows ({} sample sets) in {:.2f} seconds".format( - cursor.rowcount, num_rows_to_insert, end - start - ) - ) - - @staticmethod - def select_one_from_dataset_id_and_sample_no(dataset_id, sample_no, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "SELECT column_id, value " - "FROM experiment.timeseries_data " - "WHERE dataset_id=(%s) AND sample_no=(%s) " - "LIMIT 1" - ), - [dataset_id, sample_no], - ) - result = cursor.fetchone() - if result is None: - return None - return TimeseriesDataRow( - dataset_id=dataset_id, - sample_no=sample_no, - column_id=result[0], - value=result[1], - ) - - @staticmethod - def get_column_type_id(col_id, cursor): - cursor.execute( - ( - "SELECT type_id " - 'FROM experiment."column" ' - "WHERE id=(%s)" - "" - ), - [col_id], - ) - return cursor.fetchone()[0] - - @staticmethod - def select_latest_by_dataset_id(dataset_id, conn): - with conn.cursor() as cursor: - cursor.execute( - ( - "WITH dataset_columns as (" - 'SELECT id FROM experiment."column" WHERE ' - "dataset_id=(%s)) " - "SELECT sample_no, column_id, value " - "FROM experiment.timeseries_data " - "WHERE column_id IN (SELECT id FROM dataset_columns) " - "AND sample_no IN ( " - "SELECT sample_no from experiment.timeseries_data " - "WHERE column_id IN (SELECT id FROM dataset_columns) " - "ORDER BY sample_no DESC LIMIT 1) " - ), - [dataset_id], - ) - records = cursor.fetchall() - return [ - TimeseriesDataRow( - sample_no=result[0], - column_id=result[1], - column_type_id=TimeseriesDataRow.get_column_type_id( - result[1], cursor - ), - value=result[2], - ) - for result in records - ] diff --git a/harvester/parse/database/experiment/unit.py b/harvester/parse/database/experiment/unit.py deleted file mode 100644 index 86beb0ec..00000000 --- a/harvester/parse/database/experiment/unit.py +++ /dev/null @@ -1,116 +0,0 @@ -from dataclasses import dataclass - -from .timeseries_data_row import ( - UNIT_UNITLESS, - UNIT_SECONDS, - UNIT_VOLTS, - UNIT_AMPS, - UNIT_WATT_HOURS, - UNIT_AMP_HOURS, - UNIT_CENTIGRADE, - UNIT_WATTS, - UNIT_OHMS, - UNIT_DEGREES, - UNIT_HERTZ, -) - - -class Base: - pass - -class Type: - def __init__(self, *args, **kwargs): - pass - -class Column(Type): - pass - -class Integer(Type): - pass - -class String(Type): - pass - - -@dataclass -class Unit(Base): - __tablename__ = 'unit' - __table_args__ = {'schema': 'experiment'} - - id: int - name: str - symbol: str - description: str - - id = Column(Integer, primary_key=True) - name = Column(String) - symbol = Column(String) - description = Column(String) - - conversions = { - 'V': { - 'multiplier': 1, - 'standard_unit': UNIT_VOLTS, - }, - 'Volts': { - 'multiplier': 1, - 'standard_unit': UNIT_VOLTS, - }, - 's': { - 'multiplier': 1, - 'standard_unit': UNIT_SECONDS, - }, - 'W.h': { - 'multiplier': 1, - 'standard_unit': UNIT_WATT_HOURS, - }, - 'Watt-hr': { - 'multiplier': 1, - 'standard_unit': UNIT_WATT_HOURS, - }, - 'A.h': { - 'multiplier': 1, - 'standard_unit': UNIT_AMP_HOURS, - }, - 'Amp-hr': { - 'multiplier': 1, - 'standard_unit': UNIT_AMP_HOURS, - }, - 'Amps': { - 'multiplier': 1, - 'standard_unit': UNIT_AMPS, - }, - 'A': { - 'multiplier': 1, - 'standard_unit': UNIT_AMPS, - }, - 'mA': { - 'multiplier': 1e-3, - 'standard_unit': UNIT_VOLTS, - }, - 'mA.h': { - 'multiplier': 1e-3, - 'standard_unit': UNIT_AMP_HOURS, - }, - '': { - 'multiplier': 1, - 'standard_unit': UNIT_UNITLESS, - }, - 'celsius': { - 'multiplier': 1, - 'standard_unit': UNIT_CENTIGRADE, - } - } - @classmethod - def get_all_units(cls): - return cls.conversions.keys() - - @classmethod - def convert(cls, symbol, value): - if symbol not in cls.conversions: - raise RuntimeError('Unknown Unit {}'.format(symbol)) - return cls.conversions[symbol]['multiplier'] * value - - - - diff --git a/harvester/parse/database/row.py b/harvester/parse/database/row.py deleted file mode 100644 index d94e14eb..00000000 --- a/harvester/parse/database/row.py +++ /dev/null @@ -1,15 +0,0 @@ -import json - -class Row: - def to_dict(self, arg): - raise NotImplementedError - - @classmethod - def to_json(cls, arg): - if isinstance(arg, list): - list_obj = [x.to_dict() for x in arg] - return json.dumps(list_obj) - elif isinstance(arg, cls): - return json.dumps(arg.to_dict()) - - diff --git a/harvester/parse/database/util/__init__.py b/harvester/parse/database/util/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/harvester/parse/database/util/iter_file.py b/harvester/parse/database/util/iter_file.py deleted file mode 100644 index 1fc39a44..00000000 --- a/harvester/parse/database/util/iter_file.py +++ /dev/null @@ -1,63 +0,0 @@ -import io -import sys - - -class IteratorFile(io.TextIOBase): - """ given an iterator which yields strings, - return a file like object for reading those strings """ - - def __init__(self, it): - self._it = it - self._f = io.StringIO() - self.buffered_chars = 0 - - def read(self, length=sys.maxsize): - - try: - while self.buffered_chars < length: - self.buffered_chars += self._f.write(next(self._it) + "\n") - - except StopIteration as e: - # soak up StopIteration. this block is not necessary because - # of finally, but just to be explicit - pass - - except: # Exception as e: - raise - # print("uncaught exception: {}".format(e)) - - finally: - self._f.seek(0) - data = self._f.read(length) - - # save the remainder for next read - remainder = self._f.read() - self._f.seek(0) - self._f.truncate(0) - self.buffered_chars = self._f.write(remainder) - return data - - def readline(self): - try: - # load up a line to make sure that there is one to read - self._f.write(next(self._it) + "\n") - except StopIteration as e: - # soak up StopIteration. this block is not necessary because - # of finally, but just to be explicit - pass - - except: # Exception as e: - raise - # print("uncaught exception: {}".format(e)) - - finally: - self._f.seek(0) - data = self._f.readline() - - # save the remainder for next read - remainder = self._f.read() - self._f.seek(0) - self._f.truncate(0) - # store size of data in buffer for the read method - self.buffered_chars = self._f.write(remainder) - return data diff --git a/harvester/parse/harvester.py b/harvester/parse/harvester.py deleted file mode 100644 index 924ee457..00000000 --- a/harvester/parse/harvester.py +++ /dev/null @@ -1,227 +0,0 @@ -# SPDX-License-Identifier: BSD-2-Clause -# Copyright (c) 2020, The Chancellor, Masters and Scholars of the University -# of Oxford, and the 'Galvanalyser' Developers. All rights reserved. - -import os - -import json -import typing - -import psutil - -from .database.util.battery_exceptions import UnsupportedFileTypeError -from .database.util.iter_file import IteratorFile -import traceback - -from .ivium_input_file import IviumInputFile -from .biologic_input_file import BiologicMprInputFile -from .maccor_input_file import ( - MaccorInputFile, - MaccorExcelInputFile, - MaccorRawInputFile, -) -import sys -import logging -import requests -sys.path.append(os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), '..'))) -from settings import get_setting, get_logfile - -from typing import TypedDict - -logging.basicConfig(level=logging.INFO) -logger = logging.getLogger(__file__) -# stream_handler = logging.StreamHandler(sys.stdout) -# stream_handler.setLevel(logging.INFO) -# logger.addHandler(stream_handler) -file_handler = logging.FileHandler(get_logfile()) -file_handler.setLevel(logging.INFO) -logger.addHandler(file_handler) - - -registered_input_files = [ - BiologicMprInputFile, - IviumInputFile, - MaccorInputFile, - MaccorExcelInputFile, - MaccorRawInputFile, -] - - -def get_api_ids(target: str) -> dict: - """ - Fetch standard ids from the server and return a name-id dictionary - """ - # TODO: abstract API URL (get_setting('url') returns Harvester not base URL) - url = f"http://app:5000/{target}/?default=True" - results = [] - entries = None - while True: - response = requests.get(url) - logger.debug(url) - data = response.json() - if entries is None: - entries = data['count'] - results = [*results, *data['results']] - if 'next' in data and data['next'] is not None: - url = data['next'] - else: - break - - assert entries is not None and len(results) == entries - return {r['name']: r['id'] for r in results} - - -def get_api_unit_ids() -> dict: - return get_api_ids('units') - - -def get_api_column_ids() -> dict: - return get_api_ids('columns') - - -def has_handle(fpath): - """ - Returns true if the file is in use by a process - """ - for proc in psutil.process_iter(): - try: - for item in proc.open_files(): - if fpath == item.path: - return True - except Exception: - pass - - return False - - -def report( - path: os.PathLike|str, - content=None, - file: os.PathLike|str = None, - error: BaseException = None -): - try: - if error is not None: - data = {'status': 'error', 'error': ";".join(error.args)} - else: - data = {'status': 'success', 'content': content} - data['path'] = path - if file is not None: - data['file'] = file - logger.debug(f"{get_setting('url')}report/; {json.dumps(data)}") - return requests.post( - f"{get_setting('url')}report/", - headers={ - 'Authorization': f"Harvester {get_setting('api_key')}" - }, - json=data - ) - except BaseException as e: - logger.error(e) - return None - - -def import_file(core_path: str, file_path: str) -> bool: - """ - Attempts to import a given file - """ - full_file_path = os.sep.join([core_path, file_path]) - print("") - if not os.path.isfile(full_file_path): - print("Is not a file, skipping: " + full_file_path) - report(path=core_path, file=file_path, error=FileNotFoundError()) - return False - print("Importing " + full_file_path) - report( - path=core_path, - file=file_path, - content={ - 'task': 'import', - 'status': 'begin' - } - ) - - try: - # Attempt reading the file before updating the database to avoid - # creating rows for a file we can't read. - # TODO handle rows in the dataset and access tables with no - # corresponding data since the import might fail while reading the data - # anyway - input_file = None - for input_file_cls in registered_input_files: - try: - print('Tried input reader {}'.format(input_file_cls)) - input_file = input_file_cls(full_file_path) - except Exception as e: - print('...failed with: ', type(e), e) - else: - print('...succeeded...') - break - if input_file is None: - raise UnsupportedFileTypeError - - # TODO Send metadata - - # TODO: Resume/append where record already exists - # TODO: Including getting existing string-int mapping - - # TODO: Query server payload size limit - query_max_size = 2 * 1_000_000 # approx 2MB - # Figure out column data - column_data = {} - default_column_ids = get_api_column_ids() - default_units = get_api_unit_ids() - mapping = input_file.get_file_column_to_standard_column_mapping(default_column_ids) - next_key = 0 - # Find out if there's a Sample number column, otherwise we use the row number - record_number_column = [k for k, v in mapping.items() if v == default_column_ids['Sample Number']] - record_number_column = record_number_column[0] if len(record_number_column) else None - generator = input_file.load_data(input_file.file_path, input_file.column_info.keys()) - for i, r in enumerate(generator): - record_number = int(r.get(record_number_column, i)) - for k, v in r.items(): - if k == record_number_column: - continue - if k in column_data: - # Numeric data are stored directly - try: - column_data[k]['values'][record_number] = int(v) - except ValueError: - try: - column_data[k]['values'][record_number] = float(v) - # Strings are mapped to integer values using a value map which is also sent to the database - except ValueError: - if 'value_map' in column_data[k] and v in column_data[k]['value_map']: - column_data[k]['values'][record_number] = column_data[k]['value_map'][v] - else: - if 'value_map' in column_data[k]: - column_data[k]['value_map'][v] = next_key - else: - column_data[k]['value_map'] = {v: next_key} - column_data[k]['values'][record_number] = next_key - next_key += 1 - else: - column_data[k] = {} - if k in mapping: - column_data[k]['column_id'] = mapping[k] - else: - column_data[k]['column_name'] = k - if 'unit' in input_file.column_info[k]: - column_data[k]['unit_symbol'] = input_file.column_info[k].get('unit') - else: - column_data[k]['unit_id'] = default_units['Unitless'] - column_data[k]['values'] = {} - - # Send data - report(path=core_path, file=file_path, content={ - 'task': 'import', - 'status': 'in_progress', - 'data': [v for v in column_data.values()] - }) - - print("File successfully imported") - except Exception as e: - logger.error(e) - # report(path=core_path, file=file_path, error=e) - return False - return True diff --git a/harvester/start.py b/harvester/start.py index 0b405d2e..56d2a745 100644 --- a/harvester/start.py +++ b/harvester/start.py @@ -3,8 +3,8 @@ import json import requests import subprocess -import harvest -import settings +import harvester.run +import harvester.settings def query(url: str, data: object = None) -> object: @@ -140,7 +140,7 @@ def register(url: str = None, name: str = None, user_id: int = None, run_foregro result = query(f"{url}harvesters/", {'user': uid, 'name': name}) # Save credentials - file_name = settings.get_settings_file() + file_name = harvester.settings.get_settings_file() with open(file_name, 'w+') as f: json.dump(result, f) click.echo("Details:") @@ -157,10 +157,10 @@ def register(url: str = None, name: str = None, user_id: int = None, run_foregro click.echo("The harvester will check for updates frequently until you change its polling rate when you update it.") click.echo("Launching harvester...") if run_foreground: - harvest.run_cycle() + harvester.run.run_cycle() else: subprocess.Popen(["python", "harvest.py"]) - click.echo(f"Complete. Harvester is running and logging to {settings.get_logfile()}") + click.echo(f"Complete. Harvester is running and logging to {harvester.settings.get_logfile()}") @click.command() @@ -181,8 +181,8 @@ def register(url: str = None, name: str = None, user_id: int = None, run_foregro help="Ignore other options and run harvester if config file already exists." ) def click_wrapper(url: str, name: str, user_id: int, run_foreground: bool, restart: bool): - if restart and settings.get_setting('url'): - harvest.run_cycle() + if restart and harvester.settings.get_setting('url'): + harvester.run.run_cycle() else: register(url=url, name=name, user_id=user_id, run_foreground=run_foreground) From e0155a1f564f08b6330dfe31d5a223ed90ee422d Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Fri, 13 Jan 2023 15:29:32 +0000 Subject: [PATCH 27/79] harvester handle existing data --- .../0006_alter_observedfile_state.py | 18 +++++++ .../0007_alter_observedfile_state.py | 18 +++++++ .../0008_alter_observedfile_state.py | 18 +++++++ .../0009_alter_observedfile_state.py | 18 +++++++ .../0010_alter_observedfile_state.py | 18 +++++++ .../0011_alter_observedfile_state.py | 18 +++++++ .../galvanalyser/serializers.py | 4 +- django/backend_django/galvanalyser/views.py | 41 +++++++++----- harvester/harvester/harvest.py | 38 ++++++++----- .../harvester/parse/biologic_input_file.py | 3 +- harvester/harvester/parse/input_file.py | 2 + harvester/harvester/parse/ivium_input_file.py | 8 +-- .../harvester/parse/maccor_input_file.py | 53 ++++++++++--------- harvester/harvester/run.py | 3 ++ harvester/harvester/settings.py | 9 +++- 15 files changed, 211 insertions(+), 58 deletions(-) create mode 100644 django/backend_django/galvanalyser/migrations/0006_alter_observedfile_state.py create mode 100644 django/backend_django/galvanalyser/migrations/0007_alter_observedfile_state.py create mode 100644 django/backend_django/galvanalyser/migrations/0008_alter_observedfile_state.py create mode 100644 django/backend_django/galvanalyser/migrations/0009_alter_observedfile_state.py create mode 100644 django/backend_django/galvanalyser/migrations/0010_alter_observedfile_state.py create mode 100644 django/backend_django/galvanalyser/migrations/0011_alter_observedfile_state.py diff --git a/django/backend_django/galvanalyser/migrations/0006_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0006_alter_observedfile_state.py new file mode 100644 index 00000000..08025df4 --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0006_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-01-13 07:19 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0005_alter_observedfile_state'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/migrations/0007_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0007_alter_observedfile_state.py new file mode 100644 index 00000000..260577c8 --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0007_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-01-13 07:58 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0006_alter_observedfile_state'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/migrations/0008_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0008_alter_observedfile_state.py new file mode 100644 index 00000000..d02ee693 --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0008_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-01-13 09:27 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0007_alter_observedfile_state'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/migrations/0009_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0009_alter_observedfile_state.py new file mode 100644 index 00000000..8b085d42 --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0009_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-01-13 09:41 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0008_alter_observedfile_state'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/migrations/0010_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0010_alter_observedfile_state.py new file mode 100644 index 00000000..1c04df2e --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0010_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-01-13 10:36 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0009_alter_observedfile_state'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/migrations/0011_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0011_alter_observedfile_state.py new file mode 100644 index 00000000..5e165ba9 --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0011_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-01-13 15:13 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0010_alter_observedfile_state'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py index 932c6da9..cc22b3dd 100644 --- a/django/backend_django/galvanalyser/serializers.py +++ b/django/backend_django/galvanalyser/serializers.py @@ -94,6 +94,7 @@ class Meta: 'state', 'last_observed_time', 'last_observed_size', 'datasets' ] + depth = 1 class CellDataSerializer(serializers.HyperlinkedModelSerializer): @@ -103,9 +104,10 @@ class Meta: class DatasetSerializer(serializers.HyperlinkedModelSerializer): + class Meta: model = Dataset - fields = '__all__' + fields = ['url', 'id', 'name', 'date', 'type', 'purpose', 'cell', 'file'] class EquipmentSerializer(serializers.HyperlinkedModelSerializer): diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 8e65be09..d8390578 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -46,6 +46,14 @@ def error_response(error: str, status: int = 400) -> Response: return Response({'error': error}, status=status) +def deserialize_datetime(serialized_value: str | float) -> timezone.datetime: + if isinstance(serialized_value, str): + return timezone.make_aware(timezone.datetime.fromisoformat(serialized_value)) + if isinstance(serialized_value, float): + return timezone.make_aware(timezone.datetime.fromtimestamp(serialized_value)) + raise TypeError + + class LoginView(KnoxLoginView): permission_classes = [AllowAny] authentication_classes = [BasicAuthentication] @@ -164,11 +172,18 @@ def report(self, request, pk: int = None): error = json.dumps(error) except json.JSONDecodeError: error = str(error) - HarvestError.objects.create( + err = HarvestError.objects.create( harvester=harvester, path=path, error=str(error) ) + if request.data.get('file'): + try: + file = ObservedFile.objects.get(monitored_path=path, relative_path=request.data['file']) + err.file = file + err.save() + except ObservedFile.DoesNotExist: + pass return Response({}) elif request.data['status'] == 'success': # Figure out what we succeeded in doing! @@ -206,7 +221,7 @@ def report(self, request, pk: int = None): try: if content['status'] == 'begin': file.state = FileState.IMPORTING - date = timezone.datetime.fromisoformat(content['test_date']).date() + date = deserialize_datetime(content['test_date']) # process metadata under 'begin' core_metadata = content['core_metadata'] extra_metadata = content['extra_metadata'] @@ -230,9 +245,10 @@ def report(self, request, pk: int = None): date=date ) elif content['status'] == 'complete': - file.state = FileState.IMPORTED + if file.state == FileState.IMPORTING.value: + file.state = FileState.IMPORTED else: - date = timezone.datetime.fromisoformat(content['test_date']).date() + date = deserialize_datetime(content['test_date']) dataset = Dataset.objects.get(file=file, date=date) for column_data in content['data']: try: @@ -261,20 +277,22 @@ def report(self, request, pk: int = None): ) # Create a value map for string data if 'value_map' in column_data: + DataColumnStringKeys.objects.filter(column=column).delete() DataColumnStringKeys.objects.bulk_create( - DataColumnStringKeys(string=k, key=v, column=column) - for k, v in column_data['value_map'].items() + [DataColumnStringKeys(string=k, key=v, column=column) + for k, v in column_data['value_map'].items()] ) # Enter data en masse to avoid numerous expensive database calls - TimeseriesData.objects.bulk_create([ - TimeseriesData(sample=k, value=v, column=column) - for k, v in column_data['values'].items() - ]) + TimeseriesData.objects.filter(column=column).delete() + TimeseriesData.objects.bulk_create( + [TimeseriesData(sample=k, value=v, column=column) + for k, v in column_data['values'].items()] + ) except BaseException as e: file.state = FileState.IMPORT_FAILED - HarvestError.objects.create(harvester=harvester, path=path, error=str(e)) + HarvestError.objects.create(harvester=harvester, path=path, file=file, error=str(e)) file.save() return error_response(f"Error importing data: {e.args}") if content['status'] == 'failed': @@ -488,4 +506,3 @@ class GroupViewSet(viewsets.ModelViewSet): """ serializer_class = GroupSerializer queryset = Group.objects.all() - diff --git a/harvester/harvester/harvest.py b/harvester/harvester/harvest.py index c7e7a9d0..1dfbe5e5 100644 --- a/harvester/harvester/harvest.py +++ b/harvester/harvester/harvest.py @@ -54,12 +54,11 @@ def import_file(core_path: str, file_path: str) -> bool: default_units = get_standard_units() max_upload_size = get_setting('max_upload_bytes') full_file_path = os.sep.join([core_path, file_path]) - print("") if not os.path.isfile(full_file_path): - print("Is not a file, skipping: " + full_file_path) + logger.warn(f"{full_file_path} is not a file, skipping") report_harvest_result(path=core_path, file=file_path, error=FileNotFoundError()) return False - print("Importing " + full_file_path) + logger.info("Importing " + full_file_path) try: # Attempt reading the file before updating the database to avoid @@ -70,23 +69,23 @@ def import_file(core_path: str, file_path: str) -> bool: input_file = None for input_file_cls in registered_input_files: try: - print('Tried input reader {}'.format(input_file_cls)) + logger.debug('Tried input reader {}'.format(input_file_cls)) input_file = input_file_cls( file_path=full_file_path, standard_units=default_units, standard_columns=default_column_ids ) except Exception as e: - print('...failed with: ', type(e), e) + logger.debug('...failed with: ', type(e), e) else: - print('...succeeded...') + logger.debug('...succeeded...') break if input_file is None: raise UnsupportedFileTypeError # Send metadata core_metadata, extra_metadata = input_file.load_metadata() - report_harvest_result( + report = report_harvest_result( path=core_path, file=file_path, content={ @@ -97,9 +96,14 @@ def import_file(core_path: str, file_path: str) -> bool: 'test_date': serialize_datetime(core_metadata['Date of Test']) } ) - - # TODO: Resume/append where record already exists - # TODO: Including getting existing string-int mapping + if report is None: + return False + if not report.ok: + try: + logger.error(f"API responded with Error: {report.json()['error']}") + except BaseException: + logger.error(f"API Error: {report.status_code}") + return False # Figure out column data column_data = {} @@ -159,16 +163,24 @@ def import_file(core_path: str, file_path: str) -> bool: column_data[k]['values'] = {} # Send data - report_harvest_result(path=core_path, file=file_path, content={ + report = report_harvest_result(path=core_path, file=file_path, content={ 'task': 'import', 'status': 'in_progress', 'data': [v for v in column_data.values()], 'test_date': serialize_datetime(core_metadata['Date of Test']) }) + if report is None: + return False + if not report.ok: + try: + logger.error(f"API responded with Error: {report.json()['error']}") + except BaseException: + logger.error(f"API Error: {report.status_code}") + return False - print("File successfully imported") + logger.info("File successfully imported") except Exception as e: logger.error(e) - # report(path=core_path, file=file_path, error=e) + report_harvest_result(path=core_path, file=file_path, error=e) return False return True diff --git a/harvester/harvester/parse/biologic_input_file.py b/harvester/harvester/parse/biologic_input_file.py index 47bf05fe..57aebea7 100644 --- a/harvester/harvester/parse/biologic_input_file.py +++ b/harvester/harvester/parse/biologic_input_file.py @@ -19,6 +19,7 @@ def __init__(self, file_path, **kwargs): raise UnsupportedFileTypeError self.mpr_file = BioLogic.MPRfile(file_path) super().__init__(file_path, **kwargs) + self.logger.info("Type is BioLogic") def get_file_column_to_standard_column_mapping(self) -> dict: """ @@ -102,5 +103,5 @@ def load_metadata(self): # if sample number not provided by file then we count from 0 metadata["first_sample_no"] = 0 metadata["last_sample_no"] = metadata["num_rows"] - 1 - print(metadata, columns_with_data) + self.logger.debug(metadata, columns_with_data) return metadata, columns_with_data diff --git a/harvester/harvester/parse/input_file.py b/harvester/harvester/parse/input_file.py index 7b90164a..5dba5fa6 100644 --- a/harvester/harvester/parse/input_file.py +++ b/harvester/harvester/parse/input_file.py @@ -1,5 +1,6 @@ from .exceptions import UnsupportedFileTypeError import traceback +from ..settings import get_logger # see https://gist.github.com/jsheedy/ed81cdf18190183b3b7d # https://stackoverflow.com/a/30721460 @@ -18,6 +19,7 @@ def __init__(self, file_path, standard_columns: dict, standard_units: dict): self.file_path = file_path self.standard_columns = standard_columns self.standard_units = standard_units + self.logger = get_logger(f"InputFile({self.file_path})") self.metadata, self.column_info = self.load_metadata() def get_columns(self): diff --git a/harvester/harvester/parse/ivium_input_file.py b/harvester/harvester/parse/ivium_input_file.py index b150fcc5..33331f5a 100644 --- a/harvester/harvester/parse/ivium_input_file.py +++ b/harvester/harvester/parse/ivium_input_file.py @@ -23,15 +23,15 @@ class IviumInputFile(InputFile): def __init__(self, file_path, **kwargs): self.validate_file(file_path) super().__init__(file_path, **kwargs) + self.logger.info("Type is IVIUM") def get_file_column_to_standard_column_mapping(self) -> dict: - print("Type is IVIUM") """ Return a dict with a key of the column name in the file that maps to the standard column name in the value. Only return values where a mapping exists """ - print("get_ivium_column_to_standard_column_mapping") + self.logger.debug("get_ivium_column_to_standard_column_mapping") return { "amps": self.standard_columns['Amps'], "volts": self.standard_columns['Volts'], @@ -60,7 +60,7 @@ def load_data(self, file_path, columns): line = line.decode('ascii') if len(line) != 40: - print(line) + self.logger.debug(line) raise InvalidDataInFileError( ( "Incorrect line length on line {} was {} expected {}" @@ -286,7 +286,7 @@ def load_metadata(self): metadata["first_sample_no"] = 1 # if sample number not provided by file then we count from 0 metadata["last_sample_no"] = len(self._sample_rows) - 1 - print(metadata) + self.logger.debug(metadata) # put in all the ivium metadata metadata["misc_file_data"] = dict(self._file_metadata) return metadata, columns_with_data diff --git a/harvester/harvester/parse/maccor_input_file.py b/harvester/harvester/parse/maccor_input_file.py index 240e6b85..975bf5ae 100644 --- a/harvester/harvester/parse/maccor_input_file.py +++ b/harvester/harvester/parse/maccor_input_file.py @@ -25,6 +25,7 @@ class MaccorInputFile(InputFile): def __init__(self, file_path, **kwargs): self.validate_file(file_path) super().__init__(file_path, **kwargs) + self.logger.info("Type is MACCOR") def identify_columns(self, reader): """ @@ -43,7 +44,7 @@ def identify_columns(self, reader): first_data, correct_number_of_columns, recno_col, row_idx ) column_is_numeric = [isfloat(column) for column in first_data] - print(column_is_numeric) + self.logger.debug(column_is_numeric) numeric_columns = [] for i in range(0, len(column_is_numeric)): if column_is_numeric[i]: @@ -64,7 +65,7 @@ def identify_columns(self, reader): if data_detected: column_has_data[col] = True numeric_columns.remove(col) - print( + self.logger.debug( "Found data in col {} ( {} ) : {}{} on row {}".format( col, headers[col], @@ -112,8 +113,8 @@ def identify_columns(self, reader): else: first_rec = int(first_data[recno_col]) last_rec = int(row[recno_col]) - print(column_info) - print("Num rows {}".format(total_rows)) + self.logger.debug(column_info) + self.logger.debug("Num rows {}".format(total_rows)) return column_info, total_rows, first_rec, last_rec def load_metadata(self): @@ -139,7 +140,7 @@ def load_metadata(self): metadata["num_rows"] = total_rows metadata["first_sample_no"] = first_rec metadata["last_sample_no"] = last_rec - print(metadata) + self.logger.debug(metadata) return metadata, column_info def get_file_column_to_standard_column_mapping(self) -> dict: @@ -149,8 +150,7 @@ def get_file_column_to_standard_column_mapping(self) -> dict: mapping exists """ - print("Type is MACCOR") - print("get_maccor_column_to_standard_column_mapping") + self.logger.debug("get_maccor_column_to_standard_column_mapping") return { "Amp-hr": self.standard_columns['Charge Capacity'], "Amps": self.standard_columns['Amps'], @@ -396,8 +396,8 @@ def identify_columns(self, wbook): numeric_columns.append(col) else: column_has_data[col] = True - print("headers: {}".format(headers)) - print("numeric_columns: {}".format(numeric_columns)) + self.logger.debug("headers: {}".format(headers)) + self.logger.debug("numeric_columns: {}".format(numeric_columns)) try: recno_col = headers.index("Rec#") first_rec = sheet.cell_value(headers_row+1, recno_col) @@ -406,7 +406,7 @@ def identify_columns(self, wbook): first_rec = 1 total_rows = 0 for sheet_id in range(0, wbook.nsheets): - print("Loading sheet... " + str(sheet_id)) + self.logger.debug("Loading sheet... " + str(sheet_id)) sheet = wbook.sheet_by_index(sheet_id) total_rows += sheet.nrows - 1 - int(self._has_metadata_row) for row in range(headers_row+1, sheet.nrows): @@ -414,7 +414,7 @@ def identify_columns(self, wbook): if float(sheet.cell_value(row, column)) != 0.0: column_has_data[column] = True numeric_columns.remove(column) - print( + self.logger.debug( "Found data in col {} ( {} ) : {}".format( column, headers[column], @@ -430,7 +430,7 @@ def identify_columns(self, wbook): except ValueError: # Don't have record numbers, make them up last_rec = total_rows - print("Unloading sheet " + str(sheet_id)) + self.logger.debug("Unloading sheet " + str(sheet_id)) wbook.unload_sheet(sheet_id) column_info = { @@ -440,8 +440,8 @@ def identify_columns(self, wbook): } for i in range(0, len(headers)) } - print(column_info) - print("Num rows {}".format(total_rows)) + self.logger.debug(column_info) + self.logger.debug("Num rows {}".format(total_rows)) return column_info, total_rows, first_rec, last_rec def load_data(self, file_path, @@ -455,7 +455,7 @@ def load_data(self, file_path, headers_row = 0 with xlrd.open_workbook( - file_path, on_demand=True, logfile=LogFilter() + file_path, on_demand=True, logfile=LogFilter(self.logger) ) as wbook: sheet = wbook.sheet_by_index(0) columns_of_interest = [] @@ -471,7 +471,7 @@ def load_data(self, file_path, column_name = column_renames[column_name] column_names.append(column_name) for sheet_id in range(0, wbook.nsheets): - print("Loading sheet..." + str(sheet_id)) + self.logger.debug("Loading sheet..." + str(sheet_id)) sheet = wbook.sheet_by_index(sheet_id) for row in range(headers_row+1, sheet.nrows): yield { @@ -482,7 +482,7 @@ def load_data(self, file_path, ) for col_idx in columns_of_interest } - print("Unloading sheet " + str(sheet_id)) + self.logger.debug("Unloading sheet " + str(sheet_id)) wbook.unload_sheet(sheet_id) def load_metadata(self): @@ -492,7 +492,7 @@ def load_metadata(self): metadata = {} metadata['Filename'] = self.file_path with xlrd.open_workbook( - self.file_path, on_demand=True, logfile=LogFilter() + self.file_path, on_demand=True, logfile=LogFilter(self.logger) ) as wbook: sheet = wbook.sheet_by_index(0) col = 0 @@ -511,7 +511,7 @@ def load_metadata(self): metadata[key] = xlrd.xldate.xldate_as_datetime( sheet.cell_value(0, col + 1), wbook.datemode ) - print( + self.logger.debug( "key " + key + " value: " @@ -546,7 +546,7 @@ def load_metadata(self): metadata["num_rows"] = total_rows metadata["first_sample_no"] = first_rec metadata["last_sample_no"] = last_rec - print(metadata) + self.logger.debug(metadata) return metadata, column_info def validate_file(self, file_path): @@ -598,16 +598,16 @@ def load_metadata(self): metadata["num_rows"] = total_rows metadata["first_sample_no"] = first_rec metadata["last_sample_no"] = last_rec - print(metadata) + self.logger.debug(metadata) return metadata, column_info def validate_file(self, file_path): - print('is_maccor_raw_file') + self.logger.debug('is_maccor_raw_file') with open(file_path, "r") as f: - print('got line') + self.logger.debug('got line') line = f.readline() - print('got line', line) + self.logger.debug('got line', line) line_start = "Today's Date" if not line.startswith(line_start): raise UnsupportedFileTypeError @@ -634,13 +634,16 @@ def validate_file(self, file_path): class LogFilter(object): + def __init__(self, logger): + self.logger = logger + def write(self, *args): if len(args) != 1 or not ( args[0] == "\n" or args[0] == "WARNING *** OLE2 inconsistency: SSCS size is 0 but SSAT size is non-zero" ): - print("".join(args)) + self.logger.debug("".join(args)) def writelines(self, *args): pass diff --git a/harvester/harvester/run.py b/harvester/harvester/run.py index 0ffd21b8..067d93f3 100644 --- a/harvester/harvester/run.py +++ b/harvester/harvester/run.py @@ -58,6 +58,9 @@ def harvest_path(path: os.PathLike): file=file_path, content={'task': 'import', 'status': 'complete'} ) + logger.info(f"Successfully parsed file {file_path}") + else: + logger.warn(f"FAILED parsing file {file_path}") except BaseException as e: logger.error(e) report_harvest_result(path=path, file=file_path, error=e) diff --git a/harvester/harvester/settings.py b/harvester/harvester/settings.py index 607d3816..6131a2f6 100644 --- a/harvester/harvester/settings.py +++ b/harvester/harvester/settings.py @@ -2,8 +2,13 @@ import os import pathlib import logging +import logging.handlers -logging.basicConfig(level=logging.INFO) +logging.basicConfig( + format='%(asctime)s %(levelname)s %(message)s [%(name)s]', + level=logging.INFO, + datefmt='%Y-%m-%d %H:%M:%S' +) def get_settings_file() -> pathlib.Path: @@ -52,7 +57,7 @@ def get_logger(name): # stream_handler = logging.StreamHandler(sys.stdout) # stream_handler.setLevel(logging.INFO) # logger.addHandler(stream_handler) - file_handler = logging.FileHandler(get_logfile()) + file_handler = logging.handlers.RotatingFileHandler(get_logfile(), maxBytes=5_000_000, backupCount=5) file_handler.setLevel(logging.INFO) logger.addHandler(file_handler) return logger From 37d4d99ba77ccac3183972c11c5cf72753f41447 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Wed, 18 Jan 2023 16:25:55 +0000 Subject: [PATCH 28/79] user management --- .../backend_django/galvanalyser/pagination.py | 9 + .../galvanalyser/serializers.py | 156 ++++++++-- django/backend_django/galvanalyser/views.py | 129 +++++++- frontend/src/APIConnection.ts | 1 + frontend/src/App.css | 2 +- frontend/src/Cells.js | 272 ----------------- frontend/src/Cells.tsx | 262 ++++++++++++++++ frontend/src/Datasets.js | 208 ------------- frontend/src/Datasets.tsx | 287 ++++++++++++++++++ frontend/src/Equipment.js | 201 ------------ frontend/src/Equipment.tsx | 212 +++++++++++++ frontend/src/HarvesterDetail.tsx | 227 +++++++------- frontend/src/Harvesters.tsx | 23 +- frontend/src/PaginatedTable.tsx | 11 +- frontend/src/UserRoleSet.tsx | 198 ++++++++++++ frontend/src/index.css | 5 + 16 files changed, 1343 insertions(+), 860 deletions(-) create mode 100644 django/backend_django/galvanalyser/pagination.py delete mode 100644 frontend/src/Cells.js create mode 100644 frontend/src/Cells.tsx delete mode 100644 frontend/src/Datasets.js create mode 100644 frontend/src/Datasets.tsx delete mode 100644 frontend/src/Equipment.js create mode 100644 frontend/src/Equipment.tsx create mode 100644 frontend/src/UserRoleSet.tsx diff --git a/django/backend_django/galvanalyser/pagination.py b/django/backend_django/galvanalyser/pagination.py new file mode 100644 index 00000000..018f59cc --- /dev/null +++ b/django/backend_django/galvanalyser/pagination.py @@ -0,0 +1,9 @@ +from rest_framework.pagination import PageNumberPagination, BasePagination + + +class Unpaginatable(PageNumberPagination): + def paginate_queryset(self, queryset, request, view=None): + if request.query_params.get('all', False) == 'true': + return None + + return super(Unpaginatable, self).paginate_queryset(queryset, request, view=view) diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py index cc22b3dd..2aa1fc46 100644 --- a/django/backend_django/galvanalyser/serializers.py +++ b/django/backend_django/galvanalyser/serializers.py @@ -16,10 +16,40 @@ class HarvesterSerializer(serializers.HyperlinkedModelSerializer): + user_sets = serializers.SerializerMethodField() + + def get_user_sets(self, instance): + return [ + UserSetSerializer( + instance.admin_group, + context={ + 'request': self.context.get('request'), + 'name': 'Admins', + 'description': ( + 'Administrators can change harvester properties, ' + 'as well as any of the harvester\'s paths or datasets.' + ), + 'is_admin': True + } + ).data, + UserSetSerializer( + instance.user_group, + context={ + 'request': self.context.get('request'), + 'name': 'Users', + 'description': ( + 'Users can view harvester properties. ' + 'They can also add monitored paths.' + ) + } + ).data, + ] + class Meta: model = Harvester - fields = ['url', 'id', 'name', 'sleep_time', 'last_check_in'] - read_only_fields = ['url', 'id', 'last_check_in'] + fields = ['url', 'id', 'name', 'sleep_time', 'last_check_in', 'user_sets'] + read_only_fields = ['url', 'id', 'last_check_in', 'user_sets'] + depth = 1 class HarvesterConfigSerializer(serializers.HyperlinkedModelSerializer): @@ -50,38 +80,53 @@ class Meta: 'url', 'id', 'api_key', 'name', 'last_check_in', 'sleep_time', 'monitored_paths', 'standard_units', 'standard_columns', 'max_upload_bytes' ] + read_only_fields = fields depth = 1 # max depth class MonitoredPathSerializer(serializers.HyperlinkedModelSerializer): - users = serializers.SerializerMethodField() - - def get_users(self, instance): - harvester_admins = instance.harvester.admin_group.user_set.all() - admins = instance.admin_group.user_set.all() - users = instance.user_group.user_set.all() - return { - 'harvester_admins': UserSerializer( - harvester_admins, - many=True, - context={'request': self.context['request']} + user_sets = serializers.SerializerMethodField() + + def get_user_sets(self, instance): + return [ + UserSetSerializer( + instance.harvester.admin_group, + context={ + 'request': self.context.get('request'), + 'name': 'Harvester admins', + 'description': ( + 'Harvester administrators can alter any of the harvester\'s paths or datasets.' + ), + 'is_admin': True + } ).data, - 'admins': UserSerializer( - admins, - many=True, - context={'request': self.context['request']} + UserSetSerializer( + instance.admin_group, + context={ + 'request': self.context.get('request'), + 'name': 'Admins', + 'description': ( + 'Administrators can change paths and their datasets.' + ), + 'is_admin': True + } ).data, - 'users': UserSerializer( - users, - many=True, - context={'request': self.context['request']} + UserSetSerializer( + instance.user_group, + context={ + 'request': self.context.get('request'), + 'name': 'Users', + 'description': ( + 'Users can monitored paths and their datasets.' + ) + } ).data, - } + ] class Meta: model = MonitoredPath - fields = ['url', 'id', 'path', 'stable_time', 'harvester', 'users'] - read_only_fields = ['users'] + fields = ['url', 'id', 'path', 'stable_time', 'harvester', 'user_sets'] + read_only_fields = ['url', 'id', 'harvester', 'user_sets'] depth = 1 @@ -94,26 +139,50 @@ class Meta: 'state', 'last_observed_time', 'last_observed_size', 'datasets' ] + read_only_fields = [ + 'url', 'id', 'monitored_path', 'relative_path', + 'last_observed_time', 'last_observed_size', 'datasets' + ] depth = 1 class CellDataSerializer(serializers.HyperlinkedModelSerializer): + in_use = serializers.SerializerMethodField() + + def get_in_use(self, instance): + return Dataset.objects.filter(cell=instance).exists() + class Meta: model = CellData - fields = '__all__' + fields = [ + 'url', 'id', 'name', + 'form_factor', 'link_to_datasheet', + 'anode_chemistry', 'cathode_chemistry', + 'nominal_capacity', 'nominal_cell_weight', 'manufacturer', + 'in_use' + ] + read_only_fields = ['id', 'url', 'in_use'] class DatasetSerializer(serializers.HyperlinkedModelSerializer): + user_sets = serializers.SerializerMethodField() + + def get_user_sets(self, instance): + return MonitoredPathSerializer( + instance.file.monitored_path, context={'request': self.context.get('request')} + ).data.get('user_sets') class Meta: model = Dataset - fields = ['url', 'id', 'name', 'date', 'type', 'purpose', 'cell', 'file'] + fields = ['url', 'id', 'name', 'date', 'type', 'purpose', 'cell', 'file', 'user_sets'] + read_only_fields = ['date', 'file', 'id', 'url', 'user_sets'] class EquipmentSerializer(serializers.HyperlinkedModelSerializer): class Meta: model = Equipment - fields = '__all__' + fields = ['url', 'id', 'name', 'type', 'datasets'] + depth = 1 class DatasetEquipmentSerializer(serializers.HyperlinkedModelSerializer): @@ -160,15 +229,46 @@ def get_users(self, instance): class Meta: model = Group - fields = ['url', 'name', 'users'] + fields = [ + 'url', 'name', 'users', + 'readable_paths', 'editable_paths', 'readable_harvesters', 'editable_harvesters' + ] depth = 1 +class UserSetSerializer(serializers.HyperlinkedModelSerializer): + description = serializers.SerializerMethodField() + users = serializers.SerializerMethodField() + name = serializers.SerializerMethodField() + is_admin = serializers.SerializerMethodField() + + def get_description(self, instance): + return self.context.get('description') + + def get_users(self, instance): + return UserSerializer(instance.user_set.all(), many=True, context={'request': self.context['request']}).data + + def get_name(self, instance): + return self.context.get('name', instance.name) + + def get_is_admin(self, instance): + """ + Admin groups can control their own members, as well as members in groups + lower down the list of UserSets[] + """ + return self.context.get('is_admin', False) + + class Meta: + model = Group + fields = ['url', 'id', 'name', 'description', 'is_admin', 'users'] + + class UserSerializer(serializers.HyperlinkedModelSerializer): class Meta: model = User fields = [ 'url', + 'id', 'username', 'first_name', 'last_name', diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index d8390578..5b6ba2b5 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -416,20 +416,30 @@ def reimport(self, request, pk: int = None): return Response(self.get_serializer(file, context={'request': request}).data) -class CellDataViewSet(viewsets.ModelViewSet): +class DatasetViewSet(viewsets.ModelViewSet): """ TODO: document """ - serializer_class = CellDataSerializer - queryset = CellData.objects.all() + serializer_class = DatasetSerializer + filterset_fields = ['name', 'type', 'cell__name'] + search_fields = ['@name', 'type'] + queryset = Dataset.objects.none().order_by('-date', '-id') + # Access restrictions + def get_queryset(self): + return Dataset.objects.filter( + Q(file__monitored_path__user_group__in=self.request.user.groups.all()) | + Q(file__monitored_path__admin_group__in=self.request.user.groups.all()) | + Q(file__monitored_path__harvester__admin_group__in=self.request.user.groups.all()) + ).order_by('-date', '-id') -class DatasetViewSet(viewsets.ModelViewSet): + +class CellDataViewSet(viewsets.ModelViewSet): """ TODO: document """ - serializer_class = DatasetSerializer - queryset = Dataset.objects.all() + serializer_class = CellDataSerializer + queryset = CellData.objects.all() class EquipmentViewSet(viewsets.ModelViewSet): @@ -505,4 +515,109 @@ class GroupViewSet(viewsets.ModelViewSet): TODO: document """ serializer_class = GroupSerializer - queryset = Group.objects.all() + queryset = Group.objects.none().order_by('-id') + + def get_queryset(self): + return self.request.user.groups.all().order_by('-id') + + @action(detail=True, methods=['POST']) + def remove(self, request, pk: int = None): + # A user can be removed from a group if: + # 1. The user removing them is an admin on that group or a senior group, AND + # 2. The harvester's admin group will not be left without any members + + # Determine what kind of group we're in + try: + group = Group.objects.get(id=pk) + except Group.DoesNotExist: + return error_response(f"Group {pk} not found") + + def drop_user(target_group: Group, request): + try: + user = User.objects.get(id=request.data.get('user')) + except User.DoesNotExist: + return error_response(f"Could not find user {request.data.get('user')}") + if not target_group.user_set.contains(user): + return error_response(f"That user is not in that group") + target_group.user_set.remove(user) + target_group.save() + return Response(GroupSerializer(target_group, context={'request': request}).data) + + if group.editable_harvesters.first() is not None: + if not group.user_set.contains(self.request.user).exists(): + return error_response(f"You are not authorised to edit this group") + if len(group.user_set.all()) <= 1: + return error_response(f"Removing that user would leave the group empty") + return drop_user(group, self.request) + + if group.readable_harvesters.first() is not None: + harvester = group.readable_harvesters.first() + if not group.user_set.contains(self.request.user) \ + and not harvester.admin_group.user_set.contains(self.request.user): + return error_response(f"You are not authorised to edit this group") + return drop_user(group, self.request) + + if group.editable_paths.first() is not None: + path = group.editable_paths.first() + if not group.user_set.contains(self.request.user) \ + and not path.harvester.admin_group.user_set.contains(self.request.user): + return error_response(f"You are not authorised to edit this group") + return drop_user(group, self.request) + + if group.readable_paths.first() is not None: + path = group.readable_paths.first() + if not group.user_set.contains(self.request.user) \ + and not path.admin_group.user_set.contains(self.request.user) \ + and not path.harvester.admin_group.user_set.contains(self.request.user): + return error_response(f"You are not authorised to edit this group") + return drop_user(group, self.request) + + return error_response(f"Not a valid group for editing") + + @action(detail=True, methods=['POST']) + def add(self, request, pk: int = None): + # Determine what kind of group we're in + try: + group = Group.objects.get(id=pk) + except Group.DoesNotExist: + return error_response(f"Group {pk} not found") + + def add_user(target_group: Group, request): + try: + user = User.objects.get(id=request.data.get('user')) + except User.DoesNotExist: + return error_response(f"Could not find user {request.data.get('user')}") + if target_group.user_set.contains(user): + return error_response(f"That user is already in that group") + target_group.user_set.add(user) + target_group.save() + return Response(GroupSerializer(target_group, context={'request': request}).data) + + if group.editable_harvesters.first() is not None: + if not group.user_set.contains(self.request.user).exists(): + return error_response(f"You are not authorised to edit this group") + return add_user(group, self.request) + + if group.readable_harvesters.first() is not None: + harvester = group.readable_harvesters.first() + if not group.user_set.contains(self.request.user) \ + and not harvester.admin_group.user_set.contains(self.request.user): + return error_response(f"You are not authorised to edit this group") + return add_user(group, self.request) + + if group.editable_paths.first() is not None: + path = group.editable_paths.first() + if not group.user_set.contains(self.request.user) \ + and not path.harvester.admin_group.user_set.contains(self.request.user): + return error_response(f"You are not authorised to edit this group") + return add_user(group, self.request) + + if group.readable_paths.first() is not None: + path = group.readable_paths.first() + if not group.user_set.contains(self.request.user) \ + and not path.admin_group.user_set.contains(self.request.user) \ + and not path.harvester.admin_group.user_set.contains(self.request.user): + return error_response(f"You are not authorised to edit this group") + return add_user(group, self.request) + + return error_response(f"Not a valid group for editing") diff --git a/frontend/src/APIConnection.ts b/frontend/src/APIConnection.ts index 08d18143..d5028612 100644 --- a/frontend/src/APIConnection.ts +++ b/frontend/src/APIConnection.ts @@ -1,5 +1,6 @@ export type User = { url: string, + id: number, username: string, first_name: string, last_name: string, diff --git a/frontend/src/App.css b/frontend/src/App.css index 74b5e053..e70a402e 100644 --- a/frontend/src/App.css +++ b/frontend/src/App.css @@ -35,4 +35,4 @@ to { transform: rotate(360deg); } -} +} \ No newline at end of file diff --git a/frontend/src/Cells.js b/frontend/src/Cells.js deleted file mode 100644 index bca1317d..00000000 --- a/frontend/src/Cells.js +++ /dev/null @@ -1,272 +0,0 @@ -import React, { useEffect, useState } from 'react'; -import Typography from '@mui/material/Typography'; -import TextField from '@mui/material/TextField'; -import { makeStyles } from '@mui/styles' -import Table from '@mui/material/Table'; -import TableBody from '@mui/material/TableBody'; -import Paper from '@mui/material/Paper'; -import Tooltip from '@mui/material/Tooltip'; -import AddIcon from '@mui/icons-material/Add'; -import IconButton from '@mui/material/IconButton'; -import TableCell from '@mui/material/TableCell'; -import Container from '@mui/material/Container'; -import SaveIcon from '@mui/icons-material/Save'; -import TableContainer from '@mui/material/TableContainer'; -import TableHead from '@mui/material/TableHead'; -import DeleteIcon from '@mui/icons-material/Delete'; -import TableRow from '@mui/material/TableRow'; -import { - cells, add_cell, - update_cell, delete_cell -} from './Api' - -const useStyles = makeStyles((theme) => ({ - container: { - paddingTop: theme.spacing(4), - paddingBottom: theme.spacing(4), - }, - table: { - minWidth: 650, - }, - resize: { - fontSize: '10pt', - }, - input: { - marginLeft: theme.spacing(1), - flex: 1, - }, - iconButton: { - padding: 10, - }, -})); - -function MyTableRow({savedRow, onRowSave, selected, onSelectRow}) { - const classes = useStyles(); - const [row, setRow] = useState([]) - - useEffect(() => { - setRow(savedRow); - }, [savedRow]); - - const rowUnchanged = Object.keys(row).reduce((a, k) => { - return a && row[k] === savedRow[k]; - }, true); - - let useRow = row; - if (useRow.id === undefined) { - useRow = savedRow; - } - Object.keys(useRow).map((k) => { - useRow[k] = useRow[k] === null ? '' : useRow[k]; - return null - }); - - const setValue = (key) => (e) => { - setRow({...useRow, [key]: e.target.value}); - }; - - return ( - - {onSelectRow(savedRow);}} - hover - selected={selected} - > - - - - - - - - - - - - - - - - - - - - - - - - - - - - {onRowSave(row);}} - > - - - - - - - - ) -} - -export default function Cells() { - const classes = useStyles(); - - const [cellData, setCellData] = useState([]) - const [selected, setSelected] = useState({id: null}) - - - useEffect(() => { - refreshCells(); - }, []); - - const refreshCells = () => { - cells().then((response) => { - if (response.ok) { - return response.json().then((result) => { - const results = result.results; - setCellData(results.sort((arg1, arg2) => arg1.id - arg2.id)); - }); - } - }); - }; - - const addNewCell = () => { - add_cell({name: 'Edit me'}).then(refreshCells); - }; - const deleteCell = () => { - delete_cell(selected.id).then(refreshCells); - }; - const updateCell = (value) => { - Object.keys(value).map((k) => { - value[k] = value[k] === '' ? null : value[k]; - return null - }); - update_cell(value.id, value).then(refreshCells); - }; - - -const column_headings = [ - {label: 'Name', help: 'Cell Name'}, - {label: 'Manufacturer', help: 'Cell Manufacturer'}, - {label: 'Form Factor', help: 'Form Factor'}, - {label: 'Datasheet', help: 'URL to datasheet'}, - {label: 'Anode Chemistry', help: 'Anode Chemistry'}, - {label: 'Cathode Chemistry', help: 'Cathode Chemistry'}, - {label: 'Nominal Capacity', help: 'Nominal Capacity'}, - {label: 'Nominal Cell Weight', help: 'Nominal Cell Weight'}, - {label: 'Save', help: 'Click to save edits to a row'}, - ] - - return ( - - - -
- - - {column_headings.map(heading => ( - - - - {heading.label} - - - - )) - } - - - - {cellData.map((row) => ( - - ))} - -
- - - - - - - - - - - - - - - - ); -} diff --git a/frontend/src/Cells.tsx b/frontend/src/Cells.tsx new file mode 100644 index 00000000..b9fcd729 --- /dev/null +++ b/frontend/src/Cells.tsx @@ -0,0 +1,262 @@ +import React, { useEffect, useState } from 'react'; +import Typography from '@mui/material/Typography'; +import TextField from '@mui/material/TextField'; +import { makeStyles } from '@mui/styles' +import Paper from '@mui/material/Paper'; +import Tooltip from '@mui/material/Tooltip'; +import AddIcon from '@mui/icons-material/Add'; +import IconButton from '@mui/material/IconButton'; +import TableCell from '@mui/material/TableCell'; +import Container from '@mui/material/Container'; +import SaveIcon from '@mui/icons-material/Save'; +import TableHead from '@mui/material/TableHead'; +import DeleteIcon from '@mui/icons-material/Delete'; +import TableRow from '@mui/material/TableRow'; +import PaginatedTable, {RowFunProps} from './PaginatedTable'; +import Connection from "./APIConnection"; + +export type CellFields = { + url: string; + id: number; + name: string; + form_factor: string; + link_to_datasheet: string; + anode_chemistry: string; + cathode_chemistry: string; + nominal_capacity: number; + nominal_cell_weight: number; + manufacturer: string; + in_use: boolean; +} + +const useStyles = makeStyles((theme) => ({ + container: { + paddingTop: theme.spacing(4), + paddingBottom: theme.spacing(4), + }, + table: { + minWidth: 650, + }, + resize: { + fontSize: '10pt', + }, + input: { + marginLeft: theme.spacing(1), + flex: 1, + }, + iconButton: { + padding: 10, + }, + paper: {} +})); + +const column_headings = [ + // {label: 'ID', help: 'Id in database'}, + {label: 'Name', help: ''}, + {label: 'Form Factor', help: 'Form factor of the cell'}, + {label: 'Datasheet', help: 'Link to the cell\'s datasheet'}, + {label: 'Anode Chemistry', help: 'Chemistry of the cell\'s anode'}, + {label: 'Cathode Chemistry', help: 'Chemistry of the cell\'s cathode'}, + {label: 'Nominal Capacity', help: 'Nominal cell capacity'}, + {label: 'Nominal Weight', help: 'Nominal cell weight'}, + {label: 'Manufacturer', help: 'Manufacturer of the cell'}, + {label: 'Save', help: 'Click to save edits to a row. Edits are disabled for cells that are in use'}, + {label: 'Delete', help: 'Delete a cell that is not in use'}, +] + +const table_head = column_headings.map(heading => ( + + + + {heading.label} + + + +)) + +export default function Cells() { + const classes = useStyles(); + const [lastUpdated, setLastUpdated] = useState(new Date()) + + const [selected, setSelected] = useState(null) + + const get_write_data: (data: CellFields) => Partial = (data) => { + return { + name: data.name, + form_factor: data.form_factor, + link_to_datasheet: data.link_to_datasheet, + manufacturer: data.manufacturer, + anode_chemistry: data.anode_chemistry, + cathode_chemistry: data.cathode_chemistry, + nominal_capacity: data.nominal_capacity, + nominal_cell_weight: data.nominal_cell_weight + } + } + + const addNewCell = (data: CellFields) => { + const insert_data = get_write_data(data) + Connection.fetch('cells/', {body: JSON.stringify(insert_data), method: 'POST'}) + .then(() => setLastUpdated(new Date())) + }; + + const updateCell = (data: CellFields) => { + const insert_data = get_write_data(data) + Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) + .then(() => setLastUpdated(new Date())) + }; + + const deleteCell = (data: CellFields) => { + Connection.fetch(data.url, {method: 'DELETE'}) + .then(() => setLastUpdated(new Date())) + .then(() => { + if (selected?.id === data.id) + setSelected(null) + }) + }; + + function MyTableRow(props: RowFunProps) { + const classes = useStyles(); + const [row, setRow] = useState({ + url: "", + id: -1, + name: "", + form_factor: "", + link_to_datasheet: "", + anode_chemistry: "", + cathode_chemistry: "", + nominal_capacity: 0, + nominal_cell_weight: 0, + manufacturer: "", + in_use: false, + }) + const [dirty, setDirty] = useState(false) + + useEffect(() => { + if (!dirty && props.savedRow) { + setRow(props.savedRow); + } + }, [dirty, props.savedRow]); + + let useRow = row; + if (row.id === -1 && props.savedRow) + useRow = props.savedRow; + + const setValue = (key: string) => (e: any) => { + setDirty(true); + setRow({...useRow, [key]: e.target?.value}); + }; + + const Icon = props.addIcon ? : ; + + const string_fields: (keyof CellFields)[] = [ + 'name', 'manufacturer', 'form_factor', 'link_to_datasheet', 'anode_chemistry', 'cathode_chemistry' + ] + const number_fields: (keyof CellFields)[] = ['nominal_capacity', 'nominal_cell_weight'] + + return ( + + {props.onSelectRow(props.savedRow);}} + hover + selected={props.selected} + > + { + string_fields.map(n => ( + { + useRow.in_use ? useRow[n] : () + } + )) + } + { + number_fields.map(n => ( + { + useRow.in_use ? useRow[n] : () + } + )) + } + + + + {props.onRowSave(row);}} + > + {Icon} + + + + + + + + deleteCell(useRow)} + > + + + + + + + + ) + } + + function table_row_generator(row: any) { + return () + } + + const paginated_table = ({table_head})} + row_fun= {table_row_generator} + new_entry_row={( + { + }} + disableSave={false} + /> + )} + initial_url={`cells/`} + styles={classes} + last_updated={lastUpdated} + />) + + return ( + + + {paginated_table} + + + ); +} diff --git a/frontend/src/Datasets.js b/frontend/src/Datasets.js deleted file mode 100644 index d9cd9d63..00000000 --- a/frontend/src/Datasets.js +++ /dev/null @@ -1,208 +0,0 @@ - -import React, {useEffect, useState} from "react"; -import { DataGrid, GridRowsProp, GridColDef } from '@mui/x-data-grid/'; -import Container from '@mui/material/Container'; -import { datasets } from './Api'; -import { makeStyles } from '@mui/styles' -import Button from '@mui/material/Button'; -import { useNavigate } from "react-router-dom"; -import GetDatasetPython from "./GetDatasetPython" -import GetDatasetMatlab from "./GetDatasetMatlab" -import Dialog from '@mui/material/Dialog'; -import DialogActions from '@mui/material/DialogActions'; -import DialogContent from '@mui/material/DialogContent'; -import DialogTitle from '@mui/material/DialogTitle'; - - -const useStyles = makeStyles((theme) => ({ - container: { - paddingTop: theme.spacing(4), - paddingBottom: theme.spacing(4), - height: '100%', - }, - button: { - margin: theme.spacing(1), - } -})); - - - -export default function Datasets() { - const [data, setData] = useState(null) - const classes = useStyles(); - const navigate = useNavigate(); - - const [select, setSelect] = useState(null) - - // TODO: use controlled selectionModel, cause this api is changin... - const handleSelectionChange = (e) => { - if (e.selectionModel) { - if (e.selectionModel.length > 0) { - setSelect(e.selectionModel[0]); - } - } else { - if (e.length > 0) { - setSelect(e[0]); - } - } - }; - - useEffect(() => { - datasets().then((response) => { - if (response.ok) { - return response.json().then(data => { - const results = data.results; - setData(data.sort((a, b) => { - if (a.date > b.date) { - return -1; - } - if (a.date < b.date) { - return 1; - } - return 0; - })); - }); - } - }); - }, []) - - const [codeOpen, setCodeOpen] = React.useState(false); - - const handleCodeOpen = () => { - setCodeOpen(true); - }; - - const handleCodeClose = () => { - setCodeOpen(false); - }; - - const [codeMatlabOpen, setMatlabCodeOpen] = React.useState(false); - - const handleMatlabCodeOpen = () => { - setMatlabCodeOpen(true); - }; - - const handleMatlabCodeClose = () => { - setMatlabCodeOpen(false); - }; - - - - const columns: GridColDef[] = [ - { field: 'dataset_id', headerName: 'ID', width: 70}, - { field: 'name', headerName: 'Name', flex: true}, - { - field: 'date', headerName: 'Date', width: 110, - valueFormatter: (params: GridValueFormatterParams) => { - return Intl.DateTimeFormat('en-GB').format(params.value); - } - }, - { field: 'type', headerName: 'Type', width: 90 }, - { field: 'cell', headerName: 'Cell', width: 100 }, - { field: 'owner', headerName: 'Owner', width: 120 }, - { field: 'purpose', headerName: 'Purpose', width: 250 }, - { field: 'metadata', headerName: 'Metadata', type: 'boolean', width: 120 }, - ]; - - let rows: GridRowsProp = [] - if ( data ) { - rows = data.map((d, i) => { - return { - id: i, - dataset_id: d.id, - name: d.name, - type: d.type, - date: Date.parse(d.date), - cell: d.cell ? d.cell.name : '', - owner: d.owner ? d.owner.username : '', - purpose: d.purpose, - metadata: !(!d.cell || !d.owner || !d.purpose || d.equipment.length === 0) - }; - }); - } - - - let autoHeight = true; - let divStyle = { width: '100%' }; - console.log('datasets', rows) - - - return ( - -
- -
- {data && data[select] && - - } - {data && data[select] && - - - - - {`API Code (Python) for dataset "${data[select].name}"`} - - - - - - - - - - } - {data && data[select] && - - - - - {`API Code (MATLAB) for dataset "${data[select].name}"`} - - - - - - - - - - } - - ); -} diff --git a/frontend/src/Datasets.tsx b/frontend/src/Datasets.tsx new file mode 100644 index 00000000..8dd16ec6 --- /dev/null +++ b/frontend/src/Datasets.tsx @@ -0,0 +1,287 @@ + +import React, {useEffect, useState} from "react"; +import Container from '@mui/material/Container'; +import { makeStyles } from '@mui/styles' +import Button from '@mui/material/Button'; +import { useNavigate } from "react-router-dom"; +import GetDatasetPython from "./GetDatasetPython" +import GetDatasetMatlab from "./GetDatasetMatlab" +import Dialog from '@mui/material/Dialog'; +import DialogActions from '@mui/material/DialogActions'; +import DialogContent from '@mui/material/DialogContent'; +import DialogTitle from '@mui/material/DialogTitle'; +import Connection from "./APIConnection" +import PaginatedTable, {RowFunProps} from "./PaginatedTable" +import TableCell from "@mui/material/TableCell"; +import Tooltip from "@mui/material/Tooltip"; +import Typography from "@mui/material/Typography"; +import TableHead from "@mui/material/TableHead"; +import { Paper } from "@mui/material"; +import SaveIcon from "@mui/icons-material/Save"; +import TableRow from "@mui/material/TableRow"; +import TextField from "@mui/material/TextField"; +import IconButton from "@mui/material/IconButton"; +import {UserSet} from "./UserRoleSet"; + +export type DatasetFields = { + url: string; + id: number; + name: string; + type: string; + date: string; + cell: string; + purpose: string; + user_sets: UserSet[]; +} + +const useStyles = makeStyles((theme) => ({ + button: { + margin: theme.spacing(1), + }, + container: { + paddingTop: theme.spacing(4), + paddingBottom: theme.spacing(4), + }, + table: { + minWidth: 650, + }, + resize: { + fontSize: '11pt', + }, + input: { + marginLeft: theme.spacing(1), + flex: 1, + }, + iconButton: { + padding: 10, + }, + paper: {} +})); + +function MyTableRow(props: RowFunProps) { + const classes = useStyles(); + const [row, setRow] = useState({ + url: "", id: -1, name: '', type: '', date: '', cell: '', purpose: '', user_sets: [] + }) + const [dirty, setDirty] = useState(false) + + const rowUnchanged = Object.keys(row).reduce((a, k) => { + //@ts-ignore + return a && row[k] === props.savedRow[k]; + }, true); + + useEffect(() => { + if (!dirty && props.savedRow) { + setRow(props.savedRow); + } + }, [dirty, props.savedRow]); + + let useRow = row; + if (row.id === -1 && props.savedRow) + useRow = props.savedRow; + + const setValue = (key: string) => (e: any) => { + setDirty(true); + setRow({...useRow, [key]: e.target?.value}); + }; + + const Icon = ; + + return ( + + {props.onSelectRow(props.savedRow);}} + hover + selected={props.selected} + > + {useRow.id} + {useRow.date} + + + + + + + + + + {useRow.cell} + + + + { + setDirty(false); + props.onRowSave(row); + }} + > + {Icon} + + + + + + + ) +} + +export default function Datasets() { + const classes = useStyles(); + const [selected, setSelected] = useState(null) + const [lastUpdated, setLastUpdated] = useState(new Date()) + + const updateRow = (data: DatasetFields) => { + const insert_data = {name: data.name, type: data.type, purpose: data.purpose} + Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) + .then(() => setLastUpdated(new Date())) + }; + + const column_headings = [ + {label: 'ID', help: 'Unique ID in database'}, + {label: 'Date', help: 'Date of Test'}, + {label: 'Name', help: ''}, + {label: 'Type', help: 'File type determined by Harvester'}, + {label: 'Purpose', help: 'Short description of dataset purpose'}, + {label: 'Cell', help: 'Cell that generated the dataset'}, + {label: 'Save', help: 'Save changes'}, + ] + + const table_head = column_headings.map(heading => ( + + + + {heading.label} + + + + )) + const navigate = useNavigate(); + + const [codeOpen, setCodeOpen] = React.useState(false); + + const handleCodeOpen = () => { + setCodeOpen(true); + }; + + const handleCodeClose = () => { + setCodeOpen(false); + }; + + const [codeMatlabOpen, setMatlabCodeOpen] = React.useState(false); + + const handleMatlabCodeOpen = () => { + setMatlabCodeOpen(true); + }; + + const handleMatlabCodeClose = () => { + setMatlabCodeOpen(false); + }; + + return ( + + + {table_head})} + row_fun={(row: DatasetFields) => ( + + )} + initial_url={`datasets/`} + styles={classes} + last_updated={lastUpdated} + /> + + {selected !== null && + + } + {selected !== null && + + + + + {`API Code (Python) for dataset "${selected.name}"`} + + + + + + + + + + } + {selected !== null && + + + + + {`API Code (MATLAB) for dataset "${selected.name}"`} + + + + + + + + + + } + + ); +} diff --git a/frontend/src/Equipment.js b/frontend/src/Equipment.js deleted file mode 100644 index a923bff6..00000000 --- a/frontend/src/Equipment.js +++ /dev/null @@ -1,201 +0,0 @@ -import React, { useEffect, useState } from 'react'; -import Typography from '@mui/material/Typography'; -import TextField from '@mui/material/TextField'; -import { makeStyles } from '@mui/styles' -import Table from '@mui/material/Table'; -import TableBody from '@mui/material/TableBody'; -import Paper from '@mui/material/Paper'; -import Tooltip from '@mui/material/Tooltip'; -import AddIcon from '@mui/icons-material/Add'; -import IconButton from '@mui/material/IconButton'; -import TableCell from '@mui/material/TableCell'; -import Container from '@mui/material/Container'; -import SaveIcon from '@mui/icons-material/Save'; -import TableContainer from '@mui/material/TableContainer'; -import TableHead from '@mui/material/TableHead'; -import DeleteIcon from '@mui/icons-material/Delete'; -import TableRow from '@mui/material/TableRow'; -import { - equipment, add_equipment, - update_equipment, delete_equipment -} from './Api' - -const useStyles = makeStyles((theme) => ({ - container: { - paddingTop: theme.spacing(4), - paddingBottom: theme.spacing(4), - }, - table: { - minWidth: 650, - }, - resize: { - fontSize: '10pt', - }, - input: { - marginLeft: theme.spacing(1), - flex: 1, - }, - iconButton: { - padding: 10, - }, -})); - -function MyTableRow({savedRow, onRowSave, selected, onSelectRow}) { - const classes = useStyles(); - const [row, setRow] = useState([]) - - useEffect(() => { - setRow(savedRow); - }, [savedRow]); - - const rowUnchanged = Object.keys(row).reduce((a, k) => { - return a && row[k] === savedRow[k]; - }, true); - - let useRow = row; - if (useRow.id === undefined) { - useRow = savedRow; - } - Object.keys(useRow).map((k) => { - useRow[k] = useRow[k] === null ? '' : useRow[k]; - return null - }); - - const setValue = (key) => (e) => { - setRow({...useRow, [key]: e.target.value}); - }; - - return ( - - {onSelectRow(savedRow);}} - hover - selected={selected} - > - - - - - - - - - - {onRowSave(row);}} - > - - - - - - - - ) -} - -export default function Equipment() { - const classes = useStyles(); - - const [equipData, setEquipData] = useState([]) - const [selected, setSelected] = useState({id: null}) - - - useEffect(() => { - refreshEquip(); - }, []); - - const refreshEquip = () => { - equipment().then((response) => { - if (response.ok) { - return response.json().then((result) => { - const results = result.results; - setEquipData(results.sort((arg1, arg2) => arg1.id - arg2.id)); - }); - } - }); - }; - - const addNewEquip = () => { - add_equipment({name: 'Edit me'}).then(refreshEquip); - }; - const deleteEquip = () => { - delete_equipment(selected.id).then(refreshEquip); - }; - const updateEquip = (value) => { - Object.keys(value).map((k) => { - value[k] = value[k] === '' ? null : value[k]; - return null - }); - update_equipment(value.id, value).then(refreshEquip); - }; - - const column_headings = [ - {label: 'Name', help: 'Equipment Name'}, - {label: 'Type', help: 'Equipment Type'}, - {label: 'Save', help: 'Click to save edits to a row'}, - ] - - return ( - - - - - - - {column_headings.map(heading => ( - - - - {heading.label} - - - - )) - } - - - - {equipData.map((row) => ( - - ))} - -
- - - - - - - - - - - - - - - - ); -} diff --git a/frontend/src/Equipment.tsx b/frontend/src/Equipment.tsx new file mode 100644 index 00000000..18a49419 --- /dev/null +++ b/frontend/src/Equipment.tsx @@ -0,0 +1,212 @@ +import React, { useEffect, useState } from 'react'; +import Typography from '@mui/material/Typography'; +import TextField from '@mui/material/TextField'; +import { makeStyles } from '@mui/styles' +import Paper from '@mui/material/Paper'; +import Tooltip from '@mui/material/Tooltip'; +import AddIcon from '@mui/icons-material/Add'; +import IconButton from '@mui/material/IconButton'; +import TableCell from '@mui/material/TableCell'; +import Container from '@mui/material/Container'; +import SaveIcon from '@mui/icons-material/Save'; +import TableHead from '@mui/material/TableHead'; +import DeleteIcon from '@mui/icons-material/Delete'; +import TableRow from '@mui/material/TableRow'; +import PaginatedTable, {RowFunProps} from './PaginatedTable'; +import Connection from "./APIConnection"; + +export type EquipmentFields = { + url: string; + id: number; + name: string; + type: string; + in_use: boolean; +} + +const useStyles = makeStyles((theme) => ({ + container: { + paddingTop: theme.spacing(4), + paddingBottom: theme.spacing(4), + }, + table: { + minWidth: 650, + }, + resize: { + fontSize: '10pt', + }, + input: { + marginLeft: theme.spacing(1), + flex: 1, + }, + iconButton: { + padding: 10, + }, + paper: {} +})); + +const column_headings = [ + {label: 'Name', help: 'Equipment Name'}, + {label: 'Type', help: 'Equipment Type'}, + {label: 'Save', help: 'Click to save edits to a row'}, +] + +const table_head = column_headings.map(heading => ( + + + + {heading.label} + + + +)) + +export default function Equipment() { + const classes = useStyles(); + const [lastUpdated, setLastUpdated] = useState(new Date()) + + const [selected, setSelected] = useState(null) + + const get_write_data: (data: EquipmentFields) => Partial = (data) => { + return { name: data.name, type: data.type } + } + + const addNewEquipment = (data: EquipmentFields) => { + const insert_data = get_write_data(data) + Connection.fetch('equipment/', {body: JSON.stringify(insert_data), method: 'POST'}) + .then(() => setLastUpdated(new Date())) + }; + + const updateEquipment = (data: EquipmentFields) => { + const insert_data = get_write_data(data) + Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) + .then(() => setLastUpdated(new Date())) + }; + + const deleteEquipment = (data: EquipmentFields) => { + Connection.fetch(data.url, {method: 'DELETE'}) + .then(() => setLastUpdated(new Date())) + .then(() => { + if (selected?.id === data.id) + setSelected(null) + }) + }; + + function MyTableRow(props: RowFunProps) { + const classes = useStyles(); + const [row, setRow] = useState({ + url: "", + id: -1, + name: "", + type: "", + in_use: false, + }) + const [dirty, setDirty] = useState(false) + + useEffect(() => { + if (!dirty && props.savedRow) { + setRow(props.savedRow); + } + }, [dirty, props.savedRow]); + + let useRow = row; + if (row.id === -1 && props.savedRow) + useRow = props.savedRow; + + const setValue = (key: string) => (e: any) => { + setDirty(true); + setRow({...useRow, [key]: e.target?.value}); + }; + + const Icon = props.addIcon ? : ; + + const string_fields: (keyof EquipmentFields)[] = ['name', 'type'] + + return ( + + {props.onSelectRow(props.savedRow);}} + hover + selected={props.selected} + > + { + string_fields.map(n => ( + { + useRow.in_use ? useRow[n] : () + } + )) + } + + + + {props.onRowSave(row);}} + > + {Icon} + + + + + + + + deleteEquipment(useRow)} + > + + + + + + + + ) + } + + function table_row_generator(row: any) { + return () + } + + const paginated_table = ({table_head})} + row_fun= {table_row_generator} + new_entry_row={( + { + }} + disableSave={false} + /> + )} + initial_url={`equipment/`} + styles={classes} + last_updated={lastUpdated} + />) + + return ( + + + {paginated_table} + + + ); +} diff --git a/frontend/src/HarvesterDetail.tsx b/frontend/src/HarvesterDetail.tsx index 2a63239f..d3fca129 100644 --- a/frontend/src/HarvesterDetail.tsx +++ b/frontend/src/HarvesterDetail.tsx @@ -1,17 +1,12 @@ -import React, {useEffect, useState, useCallback, ChangeEvent} from 'react'; +import React, {useEffect, useState} from 'react'; import TextField from '@mui/material/TextField'; import Typography from '@mui/material/Typography'; -import Input from '@mui/material/Input'; -import InputAdornment from '@mui/material/InputAdornment'; import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; import Tooltip from '@mui/material/Tooltip'; import AddIcon from '@mui/icons-material/Add'; import IconButton from '@mui/material/IconButton'; import TableCell from '@mui/material/TableCell'; -import MenuItem from '@mui/material/MenuItem'; -import Select from '@mui/material/Select'; -import Chip from '@mui/material/Chip'; import SaveIcon from '@mui/icons-material/Save'; import TableHead from '@mui/material/TableHead'; import DeleteIcon from '@mui/icons-material/Delete'; @@ -20,6 +15,7 @@ import PaginatedTable, {RowFunProps} from './PaginatedTable'; import Connection, {User} from "./APIConnection"; import Files from './Files' import {HarvesterFields} from "./Harvesters"; +import UserRoleSet, {UserSet} from "./UserRoleSet"; const useStyles = makeStyles((theme) => ({ paper: { @@ -50,101 +46,108 @@ const useStyles = makeStyles((theme) => ({ }, })); -type MonitoredPathUserGroups = { - harvester_admins: User[]; - admins: User[]; - users: User[]; -} - export type MonitoredPathFields = { url: string; id: number; harvester: number; stable_time: number; path: string; - users: MonitoredPathUserGroups; + user_sets: UserSet[]; +} +type HarvesterDetailProps = { + harvester: HarvesterFields, + [key: string]: any } -function MyTableRow(props: RowFunProps) { +// TODO: Figure out why we get unique key errors +export default function HarvesterDetail(props: HarvesterDetailProps) { + const harvester = props.harvester const classes = useStyles(); - const [row, setRow] = useState({ - url: "", id: -1, harvester: -1, stable_time: -1, path: '', users: {harvester_admins: [], admins: [], users: []} - }) - const [dirty, setDirty] = useState(false) - const rowUnchanged = Object.keys(row).reduce((a, k) => { - //@ts-ignore - return a && row[k] === props.savedRow[k]; - }, true); + const [selected, setSelected] = useState(null) - useEffect(() => { - if (!dirty && props.savedRow) { - setRow(props.savedRow); - } - }, [dirty, props.savedRow]); + const [lastUpdated, setLastUpdated] = useState(new Date()) - let useRow = row; - if (row.harvester === -1 && props.savedRow) - useRow = props.savedRow; + function MyTableRow(props: RowFunProps) { + const classes = useStyles(); + const [row, setRow] = useState({ + url: "", id: -1, harvester: -1, stable_time: -1, path: '', user_sets: [] + }) + const [dirty, setDirty] = useState(false) - const setValue = (key: string) => (e: any) => { - setDirty(true); - setRow({...useRow, [key]: e.target?.value}); - }; + const rowUnchanged = Object.keys(row).reduce((a, k) => { + //@ts-ignore + return a && row[k] === props.savedRow[k]; + }, true); - const Icon = props.addIcon ? : ; + useEffect(() => { + if (!dirty && props.savedRow) { + setRow(props.savedRow); + } + }, [dirty, props.savedRow]); - return ( - - {props.onSelectRow(props.savedRow);}} - hover - selected={props.selected} - > - - - // {env.GALVANALYSER_HARVESTER_BASE_PATH}/ - // , - }} - value={useRow.path} - onChange={setValue('path')} /> - - - { - setDirty(true); - setRow({...row, stable_time: parseInt(e.target.value)}); - }} - > - - - - Harvester Admins:
- {useRow.users.harvester_admins.map(u => ({u.username}))} - Admins:
- {useRow.users.admins.map(u => ({u.username}))} - Users:
- {useRow.users.users.map(u => ({u.username}))} - - - + let useRow = row; + if (row.harvester === -1 && props.savedRow) + useRow = props.savedRow; + + const setValue = (key: string) => (e: any) => { + setDirty(true); + setRow({...useRow, [key]: e.target?.value}); + }; + + const Icon = props.addIcon ? : ; + + return ( + + {props.onSelectRow(props.savedRow);}} + hover + selected={props.selected} + > + + + // {env.GALVANALYSER_HARVESTER_BASE_PATH}/ + // , + }} + value={useRow.path} + onChange={setValue('path')} /> + + + { + setDirty(true); + setRow({...row, stable_time: parseInt(e.target.value)}); + }} + > + + + + + + + ) { {Icon} - - - - - ) -} - -type HarvesterDetailProps = { - harvester: HarvesterFields, - [key: string]: any -} - -// TODO: Figure out why we get unique key errors -export default function HarvesterDetail(props: HarvesterDetailProps) { - const harvester = props.harvester - const classes = useStyles(); + + + + + ) + } - const [selected, setSelected] = useState(null) - - const [lastUpdated, setLastUpdated] = useState(new Date()) const addNewPath = (data: MonitoredPathFields) => { const insert_data = {harvester: harvester.id, path: data.path, stable_time: data.stable_time} @@ -183,7 +173,7 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { .then(() => setLastUpdated(new Date())) }; const deletePath = () => { - if (isSelected) + if (selected !== null) Connection.fetch(selected.url, {method: 'DELETE'}) .then(() => setLastUpdated(new Date())) }; @@ -193,8 +183,6 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { .then(() => setLastUpdated(new Date())) }; - const isSelected = selected !== null; - const column_headings = [ {label: 'Path', help: 'Directory to watch'}, {label: 'Stable Time (s)', help: 'Seconds files must remain unchanged to be considered stable and imported'}, @@ -225,14 +213,12 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { key={row.path} savedRow={row} onRowSave={updatePath} - selected={isSelected && selected.path === row.path} + selected={selected !== null && selected.path === row.path} onSelectRow={setSelected} disableSave={ - Connection.user === null || !( - row.users.harvester_admins.map((u: User) => u.username).includes(Connection.user.username) || - row.users.admins.map((u: User) => u.username).includes(Connection.user.username) || - row.users.users.map((u: User) => u.username).includes(Connection.user.username) - ) + Connection.user === null || !row.user_sets.reduce((prev, u) => { + return prev || (Connection.user !== null && u.users.map(usr => usr.id).includes(Connection.user.id)) + }, false) } /> )} @@ -240,10 +226,7 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { new_entry_row={( { @@ -258,9 +241,9 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { u.username).includes(Connection.user.username) || - selected.users.admins.map((u: User) => u.username).includes(Connection.user.username) + selected === null || Connection.user === null || !( + selected.user_sets.find(u => u.name.toLowerCase() === "harvester admins")?.users.map((u: User) => u.username).includes(Connection.user.username) || + selected.user_sets.find(u => u.name.toLowerCase() === "admins")?.users.map((u: User) => u.username).includes(Connection.user.username) ) } aria-label="delete" @@ -270,7 +253,7 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { - {isSelected && } + {selected !== null && } ); diff --git a/frontend/src/Harvesters.tsx b/frontend/src/Harvesters.tsx index a59a5d0d..a6a2a6cf 100644 --- a/frontend/src/Harvesters.tsx +++ b/frontend/src/Harvesters.tsx @@ -3,7 +3,6 @@ import TextField from '@mui/material/TextField'; import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; import Typography from '@mui/material/Typography'; -import PlayArrowIcon from '@mui/icons-material/PlayArrow'; import Tooltip from '@mui/material/Tooltip'; import AddIcon from '@mui/icons-material/Add'; import IconButton from '@mui/material/IconButton'; @@ -16,11 +15,8 @@ import TableRow from '@mui/material/TableRow'; import PaginatedTable, {RowFunProps} from './PaginatedTable'; import HarvesterDetail from './HarvesterDetail'; -import { url, - run_harvester, harvesters, add_harvester, - update_harvester, delete_harvester, isAdmin -} from './Api' import Connection from "./APIConnection"; +import {isAdmin} from "./Api"; export type HarvesterWriteableFields = { name: string; @@ -62,15 +58,8 @@ export default function Harvesters() { const [selected, setSelected] = useState(null) const userIsAdmin = isAdmin() - const addNewHarvester = (data: HarvesterFields) => { - const insert_data: HarvesterWriteableFields = {name: data.name, sleep_time: data.sleep_time} - Connection.fetch('harvesters/', {body: JSON.stringify(insert_data), method: 'POST'}) - .then(() => setLastUpdated(new Date())) - }; - const updateHarvester = (data: any) => { - const insert_data: HarvesterWriteableFields & {id: number} = { - id: data.id, + const insert_data: HarvesterWriteableFields = { name: data.name, sleep_time: data.sleep_time } @@ -79,7 +68,7 @@ export default function Harvesters() { }; const deleteHarvester = () => { - if (isSelected) + if (selected !== null) Connection.fetch(selected.url, {method: 'DELETE'}) .then(() => setLastUpdated(new Date())) .then(() => setSelected(null)) @@ -208,8 +197,6 @@ export default function Harvesters() { )) - const isSelected = selected !== null; - const paginated_table = ({table_head})} row_fun= {table_row_generator} @@ -225,7 +212,7 @@ export default function Harvesters() { @@ -234,7 +221,7 @@ export default function Harvesters() { - {isSelected && } + {selected !== null && } ); } diff --git a/frontend/src/PaginatedTable.tsx b/frontend/src/PaginatedTable.tsx index d459837c..ad159c31 100644 --- a/frontend/src/PaginatedTable.tsx +++ b/frontend/src/PaginatedTable.tsx @@ -36,6 +36,7 @@ type PaginatedTableState = { row_data: any[]; links: PaginationLinks; last_updated: Date; + loading: boolean; } export type PaginationLinks = { @@ -87,7 +88,8 @@ export default class PaginatedTable extends Component { + this.setState({loading: true}) if (!url) return; this.current_url = url; await Connection.fetch(url) @@ -118,11 +121,13 @@ export default class PaginatedTable extends Component { console.error('Paginated Table error', e) + this.setState({loading: false}) }) } @@ -138,7 +143,7 @@ export default class PaginatedTable extends Component { // @ts-ignore - +
{this.props.header} { // @ts-ignore diff --git a/frontend/src/UserRoleSet.tsx b/frontend/src/UserRoleSet.tsx new file mode 100644 index 00000000..1bb2b6bd --- /dev/null +++ b/frontend/src/UserRoleSet.tsx @@ -0,0 +1,198 @@ +import Connection, {User} from './APIConnection' +import React, {Component} from "react"; +import IconButton from "@mui/material/IconButton"; +import Autocomplete from "@mui/material/Autocomplete"; +import TextField from "@mui/material/TextField"; +import AddIcon from '@mui/icons-material/Add'; +import Typography from "@mui/material/Typography"; +import Tooltip from "@mui/material/Tooltip"; +import Divider from "@mui/material/Divider"; +import Avatar from "@mui/material/Avatar"; +import Popover from "@mui/material/Popover"; +import Chip from "@mui/material/Chip"; + +export type UserSet = { + id: number; + url: string; + name: string; + description?: string; + is_admin?: boolean; + users: User[] +} + +export type UserSetProps = { + user_sets: UserSet[]; + last_updated: Date; + set_last_updated: (date: Date) => void; + editable?: boolean; +} + +type UserSetState = { + all_users: User[] +} + +type AddUserButtonProps = { + user_set: UserSet; + all_users: User[]; + set_last_updated: (date: Date) => void; + [key: string]: any +} + +function AddUserButton(props: AddUserButtonProps) { + const [anchorEl, setAnchorEl] = React.useState(null); + + const handleClick = (event: React.MouseEvent) => { + event.preventDefault() + setAnchorEl(event.currentTarget); + }; + + const handleClose = () => { + setAnchorEl(null); + }; + + const handleChange = (event: React.SyntheticEvent, value: any) => { + handleClose() + console.log(value) + const user_id = value.id; + Connection.fetch( + `${props.user_set.url}add/`, + {method: 'POST', body: JSON.stringify({user: user_id})} + ) + .then(() => props.set_last_updated(new Date())) + } + + const open = Boolean(anchorEl); + const id = open ? `add-user-button-${props.user_set.id}` : undefined; + + const exclude_user_ids = props.user_set.users.map(u => u.id) + const users_to_include = props.all_users.filter(u => !exclude_user_ids.includes(u.id)) + + return ( +
+ + + + + ({label: u.username, id: u.id}))} + sx={{ width: 300 }} + onChange={handleChange} + isOptionEqualToValue={((option, value) => option.id === value.id)} + renderInput={(params) => } + /> + +
+ ); +} + +/** + * Return lists of user roles that we can assign users to/delete users from. + */ +export default class UserRoleSet extends Component { + + constructor(props: UserSetProps) { + super(props); + this.state = {all_users: []} + } + + async componentDidMount() { + Connection.fetch('users/?all=true') + .then(r => this.setState({all_users: r})) + } + + handleDelete(user_id: number, group_url: string) { + Connection.fetch( + `${group_url}remove/`, + {method: 'POST', body: JSON.stringify({user: user_id})} + ).then(() => this.props.set_last_updated(new Date())) + } + + editable: boolean = this.props.editable !== false + _parent_group: UserSet|null = null + _subsequent_editable: boolean = this.editable + + // Work out permissions for each group + is_set_editable = this.props.user_sets.map(u => { + const editable = this._subsequent_editable || + (this.editable && Connection.user && u.users.map(usr => usr.id).includes(Connection.user.id)) + if (editable && u.is_admin) + this._subsequent_editable = true + const out = {id: u.id, editable: this.editable && editable, parent: this._parent_group} + this._parent_group = u + return out + }) + + get user_sets() { + return this.props.user_sets.map(u =>
+ + + {u.name} + + + {u.users.map(usr => { + const editability = this.is_set_editable.find(s => s.id === u.id) + const editable = editability?.editable + || (Connection.user && usr.id === Connection.user.id) + const undeleteable = u.is_admin && u.users.length + (editability?.parent?.users.length || 0) <= 1 + if (editable && undeleteable) + return + } + label={{usr.username}} + size={'small'} + /> + + else if (editable) + return this.handleDelete(usr.id, u.url)} + avatar={} + label={{usr.username}} + size={'small'} + /> + else + return } + label={{usr.username}} + size={'small'} + /> + })} + { + this.is_set_editable.find(s => s.id === u.id)?.editable && + + } +
) + } + + render() { + return this.user_sets; + } +} \ No newline at end of file diff --git a/frontend/src/index.css b/frontend/src/index.css index ec2585e8..2310b8c5 100644 --- a/frontend/src/index.css +++ b/frontend/src/index.css @@ -11,3 +11,8 @@ code { font-family: source-code-pro, Menlo, Monaco, Consolas, 'Courier New', monospace; } + +/* Override .MuiPopover-paper because we can't do it inside the UserRoleSet component */ +.MuiPopover-paper { + overflow: visible; +} \ No newline at end of file From d7b7d1cf51dde47c9e7d88f1da149b279c29f1b4 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Wed, 18 Jan 2023 16:26:31 +0000 Subject: [PATCH 29/79] slow harvester harvesting Slow due to fragmenting large files into ~2MB chunks for sending to Django --- django/backend_django/galvanalyser/models.py | 4 +- django/backend_django/galvanalyser/views.py | 17 ++++--- harvester/harvester/api.py | 3 +- harvester/harvester/harvest.py | 47 ++++++++++++++++---- harvester/harvester/run.py | 5 +++ 5 files changed, 57 insertions(+), 19 deletions(-) diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index 605be37a..1f01e87a 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -124,8 +124,8 @@ class Equipment(models.Model): class DatasetEquipment(models.Model): - dataset = models.ForeignKey(to=Dataset, on_delete=models.CASCADE) - equipment = models.ForeignKey(to=Equipment, on_delete=models.CASCADE) + dataset = models.ForeignKey(to=Dataset, related_name='equipment', on_delete=models.CASCADE) + equipment = models.ForeignKey(to=Equipment, related_name='datasets', on_delete=models.CASCADE) class Meta: unique_together = [['dataset', 'equipment']] diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 5b6ba2b5..167c40f1 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -71,13 +71,13 @@ class HarvesterViewSet(viewsets.ModelViewSet): serializer_class = HarvesterSerializer filterset_fields = ['name'] search_fields = ['@name'] - queryset = Harvester.objects.none().order_by('last_check_in', 'id') + queryset = Harvester.objects.none().order_by('-last_check_in', '-id') def get_queryset(self): return Harvester.objects.filter( Q(user_group__in=self.request.user.groups.all()) | Q(admin_group__in=self.request.user.groups.all()) - ).order_by('last_check_in', 'id') + ).order_by('-last_check_in', '-id') def create(self, request, *args, **kwargs): """ @@ -284,7 +284,10 @@ def report(self, request, pk: int = None): ) # Enter data en masse to avoid numerous expensive database calls - TimeseriesData.objects.filter(column=column).delete() + TimeseriesData.objects.filter( + column=column, + sample__in=column_data['values'].keys() + ).delete() TimeseriesData.objects.bulk_create( [TimeseriesData(sample=k, value=v, column=column) for k, v in column_data['values'].items()] @@ -314,7 +317,7 @@ class MonitoredPathViewSet(viewsets.ModelViewSet): serializer_class = MonitoredPathSerializer filterset_fields = ['path', 'harvester__id', 'harvester__name'] search_fields = ['@path'] - queryset = MonitoredPath.objects.all().order_by('id') + queryset = MonitoredPath.objects.none().order_by('-id') # Access restrictions def get_queryset(self): @@ -322,7 +325,7 @@ def get_queryset(self): Q(user_group__in=self.request.user.groups.all()) | Q(admin_group__in=self.request.user.groups.all()) | Q(harvester__admin_group__in=self.request.user.groups.all()) - ).order_by('id') + ).order_by('-id') def create(self, request, *args, **kwargs): """ @@ -395,7 +398,7 @@ class ObservedFileViewSet(viewsets.ModelViewSet): serializer_class = ObservedFileSerializer filterset_fields = ['monitored_path__id', 'relative_path', 'state'] search_fields = ['@monitored_path__path', '@relative_path', 'state'] - queryset = ObservedFile.objects.all().order_by('last_observed_time', 'id') + queryset = ObservedFile.objects.none().order_by('-last_observed_time', '-id') # Access restrictions def get_queryset(self): @@ -403,7 +406,7 @@ def get_queryset(self): Q(monitored_path__user_group__in=self.request.user.groups.all()) | Q(monitored_path__admin_group__in=self.request.user.groups.all()) | Q(monitored_path__harvester__admin_group__in=self.request.user.groups.all()) - ).order_by('last_observed_time', 'id') + ).order_by('-last_observed_time', '-id') @action(detail=True, methods=['GET']) def reimport(self, request, pk: int = None): diff --git a/harvester/harvester/api.py b/harvester/harvester/api.py index 59f2d035..385bf652 100644 --- a/harvester/harvester/api.py +++ b/harvester/harvester/api.py @@ -26,7 +26,8 @@ def report_harvest_result( headers={ 'Authorization': f"Harvester {get_setting('api_key')}" }, - json=data + json=data, + timeout=120 ) except BaseException as e: logger.error(e) diff --git a/harvester/harvester/harvest.py b/harvester/harvester/harvest.py index 1dfbe5e5..82a40124 100644 --- a/harvester/harvester/harvest.py +++ b/harvester/harvester/harvest.py @@ -2,6 +2,7 @@ # Copyright (c) 2020, The Chancellor, Masters and Scholars of the University # of Oxford, and the 'Galvanalyser' Developers. All rights reserved. import datetime +import json import os import dateutil import sys @@ -109,46 +110,74 @@ def import_file(core_path: str, file_path: str) -> bool: column_data = {} mapping = input_file.get_file_column_to_standard_column_mapping() next_key = 0 + # limit size of requests. 1kb/column is an arbitrary buffer size. + size = 0 + max_size = (max_upload_size / 1) - (1000 * len(extra_metadata)) + nth_part = 0 + start_row = 0 # Find out if there's a Sample number column, otherwise we use the row number record_number_column = [k for k, v in mapping.items() if v == default_column_ids['Sample Number']] record_number_column = record_number_column[0] if len(record_number_column) else None generator = input_file.load_data(input_file.file_path, input_file.column_info.keys()) for i, r in enumerate(generator): - # limit size of requests. 100b/column is an arbitrary buffer size. - if sys.getsizeof(column_data) > max_upload_size - 100 * len(column_data): - report_harvest_result(path=core_path, file=file_path, content={ + # Data are stored up in rows and shipped out when + # adding the current row would exceed the server data + # size limit. + # If sent, sent data are wiped from column_data. + # New row data are added to column_data below. + size = sys.getsizeof(json.dumps(column_data)) + if size > max_size: + logger.info(f"Upload part {nth_part} (rows {start_row}-{i - 1}; {size}bytes)") + nth_part += 1 + start_row = i + report = report_harvest_result(path=core_path, file=file_path, content={ 'task': 'import', 'status': 'in_progress', - 'data': [v for v in column_data.values()] + 'data': [v for v in column_data.values()], + 'test_date': serialize_datetime(core_metadata['Date of Test']) }) + if report is None: + return False + if not report.ok: + try: + logger.error(f"API responded with Error: {report.json()['error']}") + except BaseException: + logger.error(f"API Error: {report.status_code}") + return False for k in column_data.keys(): column_data[k]['values'] = {} + if i > 0: + for k, v in new_row.items(): + column_data[k]['values'][record_number] = v + record_number = int(r.get(record_number_column, i)) + new_row = {} + for k, v in r.items(): if k == record_number_column: continue if k in column_data: # Numeric data are stored directly try: - column_data[k]['values'][record_number] = int(v) + new_row[k] = int(v) except ValueError: try: - column_data[k]['values'][record_number] = float(v) + new_row[k] = float(v) # Timestamps are stored using float conversion except ValueError: try: - column_data[k]['values'][record_number] = dateutil.parser.parse(v).timestamp() + new_row[k] = dateutil.parser.parse(v).timestamp() # Strings are mapped to integer values using a value map which is also sent to the database except ValueError: if 'value_map' in column_data[k] and v in column_data[k]['value_map']: - column_data[k]['values'][record_number] = column_data[k]['value_map'][v] + new_row[k] = column_data[k]['value_map'][v] else: if 'value_map' in column_data[k]: column_data[k]['value_map'][v] = next_key else: column_data[k]['value_map'] = {v: next_key} - column_data[k]['values'][record_number] = next_key + new_row[k] = next_key next_key += 1 else: column_data[k] = {} diff --git a/harvester/harvester/run.py b/harvester/harvester/run.py index 067d93f3..71be675e 100644 --- a/harvester/harvester/run.py +++ b/harvester/harvester/run.py @@ -61,6 +61,11 @@ def harvest_path(path: os.PathLike): logger.info(f"Successfully parsed file {file_path}") else: logger.warn(f"FAILED parsing file {file_path}") + report_harvest_result( + path=path, + file=file_path, + content={'task': 'import', 'status': 'failed'} + ) except BaseException as e: logger.error(e) report_harvest_result(path=path, file=file_path, error=e) From a542f217ce61adbabc0932697b56e897302a48dd Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Thu, 19 Jan 2023 17:34:24 +0000 Subject: [PATCH 30/79] frontend fixes --- frontend/src/Cells.tsx | 20 ++++----- frontend/src/Equipment.tsx | 22 +++++----- frontend/src/UserRoleSet.tsx | 80 +++++++++++++++++++----------------- 3 files changed, 63 insertions(+), 59 deletions(-) diff --git a/frontend/src/Cells.tsx b/frontend/src/Cells.tsx index b9fcd729..5963cbe4 100644 --- a/frontend/src/Cells.tsx +++ b/frontend/src/Cells.tsx @@ -41,7 +41,7 @@ const useStyles = makeStyles((theme) => ({ fontSize: '10pt', }, input: { - marginLeft: theme.spacing(1), + marginLeft: theme.spacing(0), flex: 1, }, iconButton: { @@ -163,8 +163,8 @@ export default function Cells() { { string_fields.map(n => ( { - useRow.in_use ? useRow[n] : ( ( { - useRow.in_use ? useRow[n] : ( {props.onRowSave(row);}} > {Icon} @@ -206,8 +206,8 @@ export default function Cells() { deleteCell(useRow)} + disabled={row.in_use} + onClick={() => deleteCell(row)} > @@ -242,9 +242,9 @@ export default function Cells() { }} onRowSave={addNewCell} selected={false} - onSelectRow={() => { - }} + onSelectRow={() => {}} disableSave={false} + addIcon={true} /> )} initial_url={`cells/`} diff --git a/frontend/src/Equipment.tsx b/frontend/src/Equipment.tsx index 18a49419..723ce098 100644 --- a/frontend/src/Equipment.tsx +++ b/frontend/src/Equipment.tsx @@ -47,7 +47,8 @@ const useStyles = makeStyles((theme) => ({ const column_headings = [ {label: 'Name', help: 'Equipment Name'}, {label: 'Type', help: 'Equipment Type'}, - {label: 'Save', help: 'Click to save edits to a row'}, + {label: 'Save', help: 'Click to save edits to a row. Edits are disabled for equipment that is in use'}, + {label: 'Delete', help: 'Delete equipment that is not in use'}, ] const table_head = column_headings.map(heading => ( @@ -131,14 +132,15 @@ export default function Equipment() { { string_fields.map(n => ( { - useRow.in_use ? useRow[n] : () + onChange={setValue(n)} + /> } )) } @@ -146,7 +148,7 @@ export default function Equipment() { {props.onRowSave(row);}} > {Icon} @@ -158,7 +160,7 @@ export default function Equipment() { deleteEquipment(useRow)} > @@ -187,14 +189,12 @@ export default function Equipment() { new_entry_row={( { - }} + onSelectRow={() => {}} disableSave={false} + addIcon={true} /> )} initial_url={`equipment/`} diff --git a/frontend/src/UserRoleSet.tsx b/frontend/src/UserRoleSet.tsx index 1bb2b6bd..c2d2b9d9 100644 --- a/frontend/src/UserRoleSet.tsx +++ b/frontend/src/UserRoleSet.tsx @@ -10,6 +10,7 @@ import Divider from "@mui/material/Divider"; import Avatar from "@mui/material/Avatar"; import Popover from "@mui/material/Popover"; import Chip from "@mui/material/Chip"; +import Stack from "@mui/material/Stack"; export type UserSet = { id: number; @@ -143,52 +144,55 @@ export default class UserRoleSet extends Component { get user_sets() { return this.props.user_sets.map(u =>
- + {u.name} - {u.users.map(usr => { - const editability = this.is_set_editable.find(s => s.id === u.id) - const editable = editability?.editable - || (Connection.user && usr.id === Connection.user.id) - const undeleteable = u.is_admin && u.users.length + (editability?.parent?.users.length || 0) <= 1 - if (editable && undeleteable) - return - + {u.users.map(usr => { + const editability = this.is_set_editable.find(s => s.id === u.id) + const editable = editability?.editable + || (Connection.user && usr.id === Connection.user.id) + const undeleteable = u.is_admin && u.users.length + (editability?.parent?.users.length || 0) <= 1 + if (editable && undeleteable) + return + } + label={{usr.username}} + size={'small'} + /> + + else if (editable) + return this.handleDelete(usr.id, u.url)} avatar={} label={{usr.username}} size={'small'} /> - - else if (editable) - return this.handleDelete(usr.id, u.url)} - avatar={} - label={{usr.username}} - size={'small'} - /> - else - return } - label={{usr.username}} - size={'small'} - /> - })} - { - this.is_set_editable.find(s => s.id === u.id)?.editable && - - } + else + return } + label={{usr.username}} + size={'small'} + /> + })} + { + this.is_set_editable.find(s => s.id === u.id)?.editable && + + } +
) } From 38f11c978c17aef806126f0872f4d848dbdecddc Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Wed, 25 Jan 2023 18:06:52 +0000 Subject: [PATCH 31/79] AsyncTable frontend --- .../galvanalyser/migrations/0001_initial.py | 191 ------------ .../0002_alter_observedfile_state.py | 18 -- .../0003_alter_observedfile_state.py | 18 -- .../0004_alter_observedfile_state.py | 18 -- .../0005_alter_observedfile_state.py | 18 -- .../0006_alter_observedfile_state.py | 18 -- .../0007_alter_observedfile_state.py | 18 -- .../0008_alter_observedfile_state.py | 18 -- .../0009_alter_observedfile_state.py | 18 -- .../0010_alter_observedfile_state.py | 18 -- .../0011_alter_observedfile_state.py | 18 -- django/backend_django/galvanalyser/models.py | 33 +- .../galvanalyser/serializers.py | 25 +- django/backend_django/galvanalyser/views.py | 204 +++++++++++-- django/worker.sh | 12 - frontend/src/APIConnection.ts | 27 +- frontend/src/Api.js | 10 +- frontend/src/AsyncTable.tsx | 273 +++++++++++++++++ frontend/src/Cells.tsx | 267 +++++++--------- frontend/src/Core.js | 2 +- frontend/src/Datasets.tsx | 166 +++------- frontend/src/Equipment.tsx | 192 ++++-------- frontend/src/Files.tsx | 112 +++---- frontend/src/GetDatasetMatlab.js | 2 +- frontend/src/GetDatasetPython.js | 2 +- frontend/src/HarvesterDetail.tsx | 285 +++++++----------- frontend/src/Harvesters.tsx | 246 ++++++--------- frontend/src/PaginatedTable.tsx | 190 ++++++++---- frontend/src/UserRoleSet.tsx | 7 +- 29 files changed, 1108 insertions(+), 1318 deletions(-) delete mode 100644 django/backend_django/galvanalyser/migrations/0001_initial.py delete mode 100644 django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py delete mode 100644 django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py delete mode 100644 django/backend_django/galvanalyser/migrations/0004_alter_observedfile_state.py delete mode 100644 django/backend_django/galvanalyser/migrations/0005_alter_observedfile_state.py delete mode 100644 django/backend_django/galvanalyser/migrations/0006_alter_observedfile_state.py delete mode 100644 django/backend_django/galvanalyser/migrations/0007_alter_observedfile_state.py delete mode 100644 django/backend_django/galvanalyser/migrations/0008_alter_observedfile_state.py delete mode 100644 django/backend_django/galvanalyser/migrations/0009_alter_observedfile_state.py delete mode 100644 django/backend_django/galvanalyser/migrations/0010_alter_observedfile_state.py delete mode 100644 django/backend_django/galvanalyser/migrations/0011_alter_observedfile_state.py delete mode 100644 django/worker.sh create mode 100644 frontend/src/AsyncTable.tsx diff --git a/django/backend_django/galvanalyser/migrations/0001_initial.py b/django/backend_django/galvanalyser/migrations/0001_initial.py deleted file mode 100644 index 869e8b79..00000000 --- a/django/backend_django/galvanalyser/migrations/0001_initial.py +++ /dev/null @@ -1,191 +0,0 @@ -# Generated by Django 4.1.4 on 2023-01-12 12:31 - -from django.db import migrations, models -import django.db.models.deletion - - -class Migration(migrations.Migration): - - initial = True - - dependencies = [ - ('auth', '0012_alter_user_first_name_max_length'), - ] - - operations = [ - migrations.CreateModel( - name='CellData', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField(unique=True)), - ('form_factor', models.TextField()), - ('link_to_datasheet', models.TextField()), - ('anode_chemistry', models.TextField()), - ('cathode_chemistry', models.TextField()), - ('nominal_capacity', models.FloatField()), - ('nominal_cell_weight', models.FloatField()), - ('manufacturer', models.TextField()), - ], - ), - migrations.CreateModel( - name='Dataset', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField(null=True)), - ('date', models.DateTimeField()), - ('type', models.TextField(null=True)), - ('purpose', models.TextField()), - ('json_data', models.JSONField(null=True)), - ('cell', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='galvanalyser.celldata')), - ], - ), - migrations.CreateModel( - name='DataUnit', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField()), - ('symbol', models.TextField()), - ('description', models.TextField()), - ('is_default', models.BooleanField(default=False)), - ], - ), - migrations.CreateModel( - name='Equipment', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField(unique=True)), - ('type', models.TextField()), - ], - ), - migrations.CreateModel( - name='Harvester', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField(unique=True)), - ('api_key', models.TextField(null=True)), - ('last_check_in', models.DateTimeField(null=True)), - ('sleep_time', models.IntegerField(default=10)), - ('admin_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='editable_harvesters', to='auth.group')), - ('user_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='readable_harvesters', to='auth.group')), - ], - ), - migrations.CreateModel( - name='MonitoredPath', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('path', models.TextField()), - ('stable_time', models.PositiveSmallIntegerField(default=60)), - ('admin_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='editable_paths', to='auth.group')), - ('harvester', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='monitored_paths', to='galvanalyser.harvester')), - ('user_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='readable_paths', to='auth.group')), - ], - options={ - 'unique_together': {('harvester', 'path')}, - }, - ), - migrations.CreateModel( - name='TimeseriesRangeLabel', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('label', models.TextField()), - ('range_start', models.PositiveBigIntegerField()), - ('range_end', models.PositiveBigIntegerField()), - ('info', models.TextField()), - ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='range_labels', to='galvanalyser.dataset')), - ], - ), - migrations.CreateModel( - name='ObservedFile', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('relative_path', models.TextField()), - ('last_observed_size', models.PositiveBigIntegerField(default=0)), - ('last_observed_time', models.DateTimeField(null=True)), - ('state', models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE')), - ('monitored_path', models.ForeignKey(on_delete=django.db.models.deletion.DO_NOTHING, related_name='files', to='galvanalyser.monitoredpath')), - ], - options={ - 'unique_together': {('monitored_path', 'relative_path')}, - }, - ), - migrations.CreateModel( - name='HarvestError', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('file', models.TextField(null=True)), - ('error', models.TextField()), - ('timestamp', models.DateTimeField(auto_now=True, null=True)), - ('harvester', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='paths', to='galvanalyser.harvester')), - ('path', models.ForeignKey(on_delete=django.db.models.deletion.DO_NOTHING, to='galvanalyser.monitoredpath')), - ], - ), - migrations.AddField( - model_name='dataset', - name='file', - field=models.ForeignKey(on_delete=django.db.models.deletion.DO_NOTHING, related_name='datasets', to='galvanalyser.observedfile'), - ), - migrations.CreateModel( - name='DataColumnType', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField()), - ('description', models.TextField()), - ('is_default', models.BooleanField(default=False)), - ('unit', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='galvanalyser.dataunit')), - ], - options={ - 'unique_together': {('unit', 'name')}, - }, - ), - migrations.CreateModel( - name='DataColumn', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.TextField()), - ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='columns', to='galvanalyser.dataset')), - ('type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.datacolumntype')), - ], - options={ - 'unique_together': {('dataset', 'name')}, - }, - ), - migrations.CreateModel( - name='TimeseriesData', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sample', models.PositiveBigIntegerField()), - ('value', models.FloatField()), - ('column', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='values', to='galvanalyser.datacolumn')), - ], - options={ - 'unique_together': {('sample', 'column')}, - }, - ), - migrations.CreateModel( - name='DatasetEquipment', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.dataset')), - ('equipment', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.equipment')), - ], - options={ - 'unique_together': {('dataset', 'equipment')}, - }, - ), - migrations.AlterUniqueTogether( - name='dataset', - unique_together={('file', 'date')}, - ), - migrations.CreateModel( - name='DataColumnStringKeys', - fields=[ - ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('key', models.PositiveBigIntegerField()), - ('string', models.TextField()), - ('column', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='string_keys', to='galvanalyser.datacolumn')), - ], - options={ - 'unique_together': {('column', 'key', 'string')}, - }, - ), - ] diff --git a/django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py deleted file mode 100644 index c8ff6eb3..00000000 --- a/django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.1.4 on 2023-01-12 12:33 - -from django.db import migrations, models - - -class Migration(migrations.Migration): - - dependencies = [ - ('galvanalyser', '0001_initial'), - ] - - operations = [ - migrations.AlterField( - model_name='observedfile', - name='state', - field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), - ), - ] diff --git a/django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py deleted file mode 100644 index 426d6f48..00000000 --- a/django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.1.4 on 2023-01-12 12:50 - -from django.db import migrations, models - - -class Migration(migrations.Migration): - - dependencies = [ - ('galvanalyser', '0002_alter_observedfile_state'), - ] - - operations = [ - migrations.AlterField( - model_name='observedfile', - name='state', - field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), - ), - ] diff --git a/django/backend_django/galvanalyser/migrations/0004_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0004_alter_observedfile_state.py deleted file mode 100644 index ec604a68..00000000 --- a/django/backend_django/galvanalyser/migrations/0004_alter_observedfile_state.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.1.4 on 2023-01-12 13:00 - -from django.db import migrations, models - - -class Migration(migrations.Migration): - - dependencies = [ - ('galvanalyser', '0003_alter_observedfile_state'), - ] - - operations = [ - migrations.AlterField( - model_name='observedfile', - name='state', - field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), - ), - ] diff --git a/django/backend_django/galvanalyser/migrations/0005_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0005_alter_observedfile_state.py deleted file mode 100644 index 2fd65bbf..00000000 --- a/django/backend_django/galvanalyser/migrations/0005_alter_observedfile_state.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.1.4 on 2023-01-12 13:03 - -from django.db import migrations, models - - -class Migration(migrations.Migration): - - dependencies = [ - ('galvanalyser', '0004_alter_observedfile_state'), - ] - - operations = [ - migrations.AlterField( - model_name='observedfile', - name='state', - field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), - ), - ] diff --git a/django/backend_django/galvanalyser/migrations/0006_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0006_alter_observedfile_state.py deleted file mode 100644 index 08025df4..00000000 --- a/django/backend_django/galvanalyser/migrations/0006_alter_observedfile_state.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.1.4 on 2023-01-13 07:19 - -from django.db import migrations, models - - -class Migration(migrations.Migration): - - dependencies = [ - ('galvanalyser', '0005_alter_observedfile_state'), - ] - - operations = [ - migrations.AlterField( - model_name='observedfile', - name='state', - field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), - ), - ] diff --git a/django/backend_django/galvanalyser/migrations/0007_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0007_alter_observedfile_state.py deleted file mode 100644 index 260577c8..00000000 --- a/django/backend_django/galvanalyser/migrations/0007_alter_observedfile_state.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.1.4 on 2023-01-13 07:58 - -from django.db import migrations, models - - -class Migration(migrations.Migration): - - dependencies = [ - ('galvanalyser', '0006_alter_observedfile_state'), - ] - - operations = [ - migrations.AlterField( - model_name='observedfile', - name='state', - field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), - ), - ] diff --git a/django/backend_django/galvanalyser/migrations/0008_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0008_alter_observedfile_state.py deleted file mode 100644 index d02ee693..00000000 --- a/django/backend_django/galvanalyser/migrations/0008_alter_observedfile_state.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.1.4 on 2023-01-13 09:27 - -from django.db import migrations, models - - -class Migration(migrations.Migration): - - dependencies = [ - ('galvanalyser', '0007_alter_observedfile_state'), - ] - - operations = [ - migrations.AlterField( - model_name='observedfile', - name='state', - field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), - ), - ] diff --git a/django/backend_django/galvanalyser/migrations/0009_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0009_alter_observedfile_state.py deleted file mode 100644 index 8b085d42..00000000 --- a/django/backend_django/galvanalyser/migrations/0009_alter_observedfile_state.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.1.4 on 2023-01-13 09:41 - -from django.db import migrations, models - - -class Migration(migrations.Migration): - - dependencies = [ - ('galvanalyser', '0008_alter_observedfile_state'), - ] - - operations = [ - migrations.AlterField( - model_name='observedfile', - name='state', - field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), - ), - ] diff --git a/django/backend_django/galvanalyser/migrations/0010_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0010_alter_observedfile_state.py deleted file mode 100644 index 1c04df2e..00000000 --- a/django/backend_django/galvanalyser/migrations/0010_alter_observedfile_state.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.1.4 on 2023-01-13 10:36 - -from django.db import migrations, models - - -class Migration(migrations.Migration): - - dependencies = [ - ('galvanalyser', '0009_alter_observedfile_state'), - ] - - operations = [ - migrations.AlterField( - model_name='observedfile', - name='state', - field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), - ), - ] diff --git a/django/backend_django/galvanalyser/migrations/0011_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0011_alter_observedfile_state.py deleted file mode 100644 index 5e165ba9..00000000 --- a/django/backend_django/galvanalyser/migrations/0011_alter_observedfile_state.py +++ /dev/null @@ -1,18 +0,0 @@ -# Generated by Django 4.1.4 on 2023-01-13 15:13 - -from django.db import migrations, models - - -class Migration(migrations.Migration): - - dependencies = [ - ('galvanalyser', '0010_alter_observedfile_state'), - ] - - operations = [ - migrations.AlterField( - model_name='observedfile', - name='state', - field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), - ), - ] diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index 1f01e87a..4890ae33 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -1,3 +1,4 @@ +from django.db.models import F from django.utils import timezone from django.db import models from django.contrib.auth.models import User, Group @@ -55,7 +56,7 @@ def run(self): class MonitoredPath(models.Model): - harvester = models.ForeignKey(to=Harvester, related_name='monitored_paths', on_delete=models.CASCADE) + harvester = models.ForeignKey(to=Harvester, related_name='monitored_paths', on_delete=models.DO_NOTHING) path = models.TextField() stable_time = models.PositiveSmallIntegerField(default=60) # seconds files must remain stable to be processed admin_group = models.ForeignKey( @@ -75,16 +76,8 @@ class Meta: unique_together = [['harvester', 'path']] -class HarvestError(models.Model): - harvester = models.ForeignKey(to=Harvester, related_name='paths', on_delete=models.CASCADE) - path = models.ForeignKey(to=MonitoredPath, on_delete=models.DO_NOTHING) - file = models.TextField(null=True) - error = models.TextField() - timestamp = models.DateTimeField(auto_now=True, null=True) - - class ObservedFile(models.Model): - monitored_path = models.ForeignKey(to=MonitoredPath, related_name='files', on_delete=models.DO_NOTHING) + monitored_path = models.ForeignKey(to=MonitoredPath, related_name='files', on_delete=models.CASCADE) relative_path = models.TextField() last_observed_size = models.PositiveBigIntegerField(null=False, default=0) last_observed_time = models.DateTimeField(null=True) @@ -94,6 +87,14 @@ class Meta: unique_together = [['monitored_path', 'relative_path']] +class HarvestError(models.Model): + harvester = models.ForeignKey(to=Harvester, related_name='paths', on_delete=models.CASCADE) + path = models.ForeignKey(to=MonitoredPath, on_delete=models.DO_NOTHING) + file = models.ForeignKey(to=ObservedFile, related_name='errors', on_delete=models.DO_NOTHING) + error = models.TextField() + timestamp = models.DateTimeField(auto_now=True, null=True) + + class CellData(models.Model): name = models.TextField(null=False, unique=True) form_factor = models.TextField() @@ -121,14 +122,7 @@ class Meta: class Equipment(models.Model): name = models.TextField(null=False, unique=True) type = models.TextField() - - -class DatasetEquipment(models.Model): - dataset = models.ForeignKey(to=Dataset, related_name='equipment', on_delete=models.CASCADE) - equipment = models.ForeignKey(to=Equipment, related_name='datasets', on_delete=models.CASCADE) - - class Meta: - unique_together = [['dataset', 'equipment']] + datasets = models.ManyToManyField(to=Dataset, related_name='equipment') class DataUnit(models.Model): @@ -182,6 +176,9 @@ class TimeseriesData(models.Model): value = models.FloatField(null=False) class Meta: + indexes = [ + models.Index('sample', 'column_id', name='sc_ref') + ] unique_together = [['sample', 'column']] diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py index 2aa1fc46..0428738d 100644 --- a/django/backend_django/galvanalyser/serializers.py +++ b/django/backend_django/galvanalyser/serializers.py @@ -1,15 +1,16 @@ from .models import Harvester, \ + HarvestError, \ MonitoredPath, \ ObservedFile, \ CellData, \ Dataset, \ Equipment, \ - DatasetEquipment, \ DataUnit, \ DataColumnType, \ DataColumn, \ TimeseriesData, \ - TimeseriesRangeLabel + TimeseriesRangeLabel, \ + FileState from django.contrib.auth.models import User, Group from django.conf.global_settings import DATA_UPLOAD_MAX_MEMORY_SIZE from rest_framework import serializers @@ -136,16 +137,23 @@ class Meta: fields = [ 'url', 'id', 'monitored_path', 'relative_path', - 'state', 'last_observed_time', 'last_observed_size', + 'state', 'last_observed_time', 'last_observed_size', 'errors', 'datasets' ] read_only_fields = [ 'url', 'id', 'monitored_path', 'relative_path', - 'last_observed_time', 'last_observed_size', 'datasets' + 'last_observed_time', 'last_observed_size', 'datasets', + 'errors' ] depth = 1 +class HarvestErrorSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = HarvestError + fields = ['url', 'id', 'harvester', 'path', 'file', 'error', 'timestamp'] + + class CellDataSerializer(serializers.HyperlinkedModelSerializer): in_use = serializers.SerializerMethodField() @@ -174,8 +182,9 @@ def get_user_sets(self, instance): class Meta: model = Dataset - fields = ['url', 'id', 'name', 'date', 'type', 'purpose', 'cell', 'file', 'user_sets'] + fields = ['url', 'id', 'name', 'date', 'type', 'purpose', 'cell', 'equipment', 'file', 'user_sets'] read_only_fields = ['date', 'file', 'id', 'url', 'user_sets'] + depth = 1 class EquipmentSerializer(serializers.HyperlinkedModelSerializer): @@ -185,12 +194,6 @@ class Meta: depth = 1 -class DatasetEquipmentSerializer(serializers.HyperlinkedModelSerializer): - class Meta: - model = DatasetEquipment - fields = '__all__' - - class DataUnitSerializer(serializers.HyperlinkedModelSerializer): class Meta: model = DataUnit diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 167c40f1..0a9d66fd 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -1,3 +1,6 @@ +import io +import sys + from django.db.models import Q from .serializers import HarvesterSerializer, \ @@ -7,14 +10,14 @@ CellDataSerializer, \ DatasetSerializer, \ EquipmentSerializer, \ - DatasetEquipmentSerializer, \ DataUnitSerializer, \ DataColumnTypeSerializer, \ DataColumnSerializer, \ TimeseriesDataSerializer, \ TimeseriesRangeLabelSerializer, \ UserSerializer, \ - GroupSerializer + GroupSerializer, \ + HarvestErrorSerializer from .models import Harvester, \ HarvestError, \ MonitoredPath, \ @@ -22,7 +25,6 @@ CellData, \ Dataset, \ Equipment, \ - DatasetEquipment, \ DataUnit, \ DataColumnType, \ DataColumnStringKeys, \ @@ -40,6 +42,17 @@ from knox.views import LoginView as KnoxLoginView from rest_framework.authentication import BasicAuthentication import json +import time +import logging + +logger = logging.getLogger(__name__) +logger.addHandler(logging.StreamHandler()) + + +def checkpoint(msg: str, t: float, log_fun=logger.warning) -> float: + t2 = time.time() + log_fun(f"{msg} (in {round(t2 - t, 2)}s)") + return t2 def error_response(error: str, status: int = 400) -> Response: @@ -159,6 +172,8 @@ def report(self, request, pk: int = None): """ # TODO access class Harvester harvester = Harvester.objects.get(id=pk) + harvester.last_check_in = timezone.now() + harvester.save() if request.data.get('status') is None: return Response({'error': 'Badly formatted request'}, status=400) try: @@ -172,11 +187,24 @@ def report(self, request, pk: int = None): error = json.dumps(error) except json.JSONDecodeError: error = str(error) - err = HarvestError.objects.create( - harvester=harvester, - path=path, - error=str(error) - ) + file_rel_path = request.data.get('file') + if file_rel_path: + err = HarvestError.objects.create( + harvester=harvester, + path=path, + file=ObservedFile.objects.get_or_create( + monitored_path=path, + relative_path=file_rel_path, + defaults={'state': FileState.IMPORT_FAILED} + ), + error=str(error) + ) + else: + err = HarvestError.objects.create( + harvester=harvester, + path=path, + error=str(error) + ) if request.data.get('file'): try: file = ObservedFile.objects.get(monitored_path=path, relative_path=request.data['file']) @@ -248,9 +276,12 @@ def report(self, request, pk: int = None): if file.state == FileState.IMPORTING.value: file.state = FileState.IMPORTED else: + time_start = time.time() date = deserialize_datetime(content['test_date']) dataset = Dataset.objects.get(file=file, date=date) for column_data in content['data']: + time_col_start = time.time() + logger.warning(f"Column {column_data.get('column_name', column_data.get('column_id'))}") try: column_type = DataColumnType.objects.get(id=column_data['column_id']) column, _ = DataColumn.objects.get_or_create( @@ -277,22 +308,136 @@ def report(self, request, pk: int = None): ) # Create a value map for string data if 'value_map' in column_data: + time_value_rm = time.time() DataColumnStringKeys.objects.filter(column=column).delete() + time_value_add = checkpoint('deleted existing value map', time_value_rm) DataColumnStringKeys.objects.bulk_create( [DataColumnStringKeys(string=k, key=v, column=column) for k, v in column_data['value_map'].items()] ) - - # Enter data en masse to avoid numerous expensive database calls + checkpoint('created value map', time_value_add) + + # # Enter data en masse to avoid numerous expensive database calls + # time_ts_rm = time.time() + # TimeseriesData.objects.filter( + # column=column, + # sample__in=column_data['values'].keys() + # ).delete() + # time_ts_prep = checkpoint('deleted existing timeseries data', time_ts_rm) + # ts = [ + # TimeseriesData(sample=k, value=v, column=column) + # for k, v in column_data['values'].items() + # ] + # time_ts_add = checkpoint('prepared ts objects', time_ts_prep) + # TimeseriesData.objects.bulk_create( + # [TimeseriesData(sample=k, value=v, column=column) + # for k, v in column_data['values'].items()] + # ) + # checkpoint('created timeseries data', time_ts_add) + # checkpoint('column complete', time_col_start) + + # time_ts_rm = time.time() + # TimeseriesData.objects.filter( + # column=column, + # sample__in=column_data['values'].keys() + # ).delete() + # time_ts_prep = checkpoint('deleted existing timeseries data', time_ts_rm) + # rows = [] + # for s, v in column_data['values'].items(): + # rows.append((int(s), int(v), column.id)) + # time_ts_add = checkpoint('prepared ts objects', time_ts_prep) + # from django.db import connection + # with connection.cursor() as cursor: + # query = cursor.executemany( + # "INSERT INTO galvanalyser_timeseriesdata (sample, value, column_id) VALUES(%s, %s, %s)", + # rows) + # checkpoint('created timeseries data', time_ts_add) + # checkpoint('column complete', time_col_start) + + time_ts_rm = time.time() TimeseriesData.objects.filter( column=column, sample__in=column_data['values'].keys() ).delete() - TimeseriesData.objects.bulk_create( - [TimeseriesData(sample=k, value=v, column=column) - for k, v in column_data['values'].items()] - ) + time_ts_prep = checkpoint('deleted existing timeseries data', time_ts_rm) + + class IteratorFile(io.TextIOBase): + """ given an iterator which yields strings, + return a file like object for reading those strings """ + + def __init__(self, it): + self._it = it + self._f = io.StringIO() + self.buffered_chars = 0 + + def read(self, length=sys.maxsize): + + try: + while self.buffered_chars < length: + self.buffered_chars += self._f.write(next(self._it) + "\n") + + except StopIteration as e: + # soak up StopIteration. this block is not necessary because + # of finally, but just to be explicit + pass + + except: # Exception as e: + raise + # print("uncaught exception: {}".format(e)) + + finally: + self._f.seek(0) + data = self._f.read(length) + + # save the remainder for next read + remainder = self._f.read() + self._f.seek(0) + self._f.truncate(0) + self.buffered_chars = self._f.write(remainder) + return data + + def readline(self): + try: + # load up a line to make sure that there is one to read + self._f.write(next(self._it) + "\n") + except StopIteration as e: + # soak up StopIteration. this block is not necessary because + # of finally, but just to be explicit + pass + + except: # Exception as e: + raise + # print("uncaught exception: {}".format(e)) + + finally: + self._f.seek(0) + data = self._f.readline() + + # save the remainder for next read + remainder = self._f.read() + self._f.seek(0) + self._f.truncate(0) + # store size of data in buffer for the read method + self.buffered_chars = self._f.write(remainder) + return data + rows = [] + i = TimeseriesData.objects.last().id + for s, v in column_data['values'].items(): + i += 1 + rows.append(f"{i}\t{int(s)}\t{int(v)}\t{column.id}") + + iter_file = IteratorFile(rows.__iter__()) + time_ts_add = checkpoint('prepared ts objects', time_ts_prep) + from django.db import connection + with connection.cursor() as cursor: + cursor.copy_expert( + 'COPY galvanalyser_timeseriesdata FROM STDIN', + iter_file + ) + checkpoint('created timeseries data', time_ts_add) + checkpoint('column complete', time_col_start) + checkpoint('complete', time_start) except BaseException as e: file.state = FileState.IMPORT_FAILED HarvestError.objects.create(harvester=harvester, path=path, file=file, error=str(e)) @@ -359,7 +504,6 @@ def create(self, request, *args, **kwargs): monitored_path.save() # Add user as admin request.user.groups.add(monitored_path.admin_group) - request.user.save() return Response(self.get_serializer(monitored_path).data) @@ -437,28 +581,38 @@ def get_queryset(self): ).order_by('-date', '-id') -class CellDataViewSet(viewsets.ModelViewSet): +class HarvestErrorViewSet(viewsets.ModelViewSet): """ TODO: document """ - serializer_class = CellDataSerializer - queryset = CellData.objects.all() + serializer_class = HarvestErrorSerializer + filterset_fields = ['file', 'path', 'harvester'] + search_fields = ['@error'] + queryset = HarvestError.objects.none().order_by('-timestamp') + + # Access restrictions + def get_queryset(self): + return HarvestError.objects.filter( + Q(path__user_group__in=self.request.user.groups.all()) | + Q(path__admin_group__in=self.request.user.groups.all()) | + Q(harvester__admin_group__in=self.request.user.groups.all()) + ).order_by('-timestamp') -class EquipmentViewSet(viewsets.ModelViewSet): +class CellDataViewSet(viewsets.ModelViewSet): """ TODO: document """ - serializer_class = EquipmentSerializer - queryset = Equipment.objects.all() + serializer_class = CellDataSerializer + queryset = CellData.objects.all().order_by('-id') -class DatasetEquipmentViewSet(viewsets.ModelViewSet): +class EquipmentViewSet(viewsets.ModelViewSet): """ TODO: document """ - serializer_class = DatasetEquipmentSerializer - queryset = DatasetEquipment.objects.all() + serializer_class = EquipmentSerializer + queryset = Equipment.objects.all() class DataUnitViewSet(viewsets.ModelViewSet): @@ -543,7 +697,6 @@ def drop_user(target_group: Group, request): if not target_group.user_set.contains(user): return error_response(f"That user is not in that group") target_group.user_set.remove(user) - target_group.save() return Response(GroupSerializer(target_group, context={'request': request}).data) if group.editable_harvesters.first() is not None: @@ -593,7 +746,6 @@ def add_user(target_group: Group, request): if target_group.user_set.contains(user): return error_response(f"That user is already in that group") target_group.user_set.add(user) - target_group.save() return Response(GroupSerializer(target_group, context={'request': request}).data) if group.editable_harvesters.first() is not None: diff --git a/django/worker.sh b/django/worker.sh deleted file mode 100644 index 81e1ffd4..00000000 --- a/django/worker.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env bash - -mkdir -p /var/run/celery /var/log/celery -chown -R nobody:nogroup /var/run/celery /var/log/celery - -cd backend_django || exit 1 -exec celery -A config.celery_settings worker \ - --loglevel=INFO \ - --logfile=/var/log/celery/worker.log \ - -O fair \ - -Q $HARVESTER_USERNAME \ - --uid=nobody --gid=nogroup diff --git a/frontend/src/APIConnection.ts b/frontend/src/APIConnection.ts index d5028612..f11ad3be 100644 --- a/frontend/src/APIConnection.ts +++ b/frontend/src/APIConnection.ts @@ -15,20 +15,26 @@ export type User = { } export type SingleAPIResponse = any +export type MultipleAPIResponse = SingleAPIResponse[] export type PaginatedAPIResponse = { count: number, previous?: string, next?: string, results: SingleAPIResponse[] } +export type ErrorCode = number -export type APIResponse = SingleAPIResponse | PaginatedAPIResponse - +export type APIResponse = SingleAPIResponse | + MultipleAPIResponse | + PaginatedAPIResponse | + ErrorCode export class APIConnection { - url: string = 'http://localhost:5001/'.toLowerCase() + url: string = 'http://localhost:5000/'.toLowerCase() user: User | null = null + results: { [result_name: string]: APIResponse } constructor() { console.info("Spawn API connection") this.login('admin', 'admin'); + this.results = {} } login(username: string, password: string) { @@ -68,7 +74,7 @@ export class APIConnection { return cookie !== undefined && this.user !== null; } - async fetch(url: string, options?: any): Promise { + async fetch(url: string, options?: any, cache_name: string = ""): Promise { await this.get_is_logged_in(); console.info(`Fetch ${url} for ${this.user?.username}`) console.info('fetch options', options) @@ -91,8 +97,11 @@ export class APIConnection { // return response; // }); } + if (response.status === 404) + return 404; return response.json(); - }).catch(e => { + }) + .catch(e => { console.error(e); return { count: 0, @@ -103,6 +112,14 @@ export class APIConnection { }; }); } + + static get_result_array: (r: APIResponse) => MultipleAPIResponse = r => { + if (r instanceof Array) + return r; + if (r.results !== undefined) + return r.results; + return r; + } } const Connection = new APIConnection(); diff --git a/frontend/src/Api.js b/frontend/src/Api.js index 975b6761..0fe3d5bd 100644 --- a/frontend/src/Api.js +++ b/frontend/src/Api.js @@ -1,5 +1,5 @@ -export const url = 'http://localhost:5001/'; +export const url = 'http://localhost:5000/'; const headers = { 'Accept': 'application/json', 'Content-Type': 'application/json' @@ -15,10 +15,10 @@ export function getUser() {return user;} export function isAdmin() { return user !== null; - if (!user) { - return false; - } - return user.groups.find(g => g.groupname === 'admin') + // if (!user) { + // return false; + // } + // return user.groups.find(g => g.groupname === 'admin') } export async function login(username, password) { diff --git a/frontend/src/AsyncTable.tsx b/frontend/src/AsyncTable.tsx new file mode 100644 index 00000000..4c76aef2 --- /dev/null +++ b/frontend/src/AsyncTable.tsx @@ -0,0 +1,273 @@ +import React, {Component, ReactElement, Fragment, BaseSyntheticEvent, ReactEventHandler} from "react"; +import TableContainer from "@mui/material/TableContainer"; +import Table from "@mui/material/Table"; +import TableBody from "@mui/material/TableBody"; +import Connection, {APIConnection, APIResponse, SingleAPIResponse} from "./APIConnection"; +import TableRow from "@mui/material/TableRow"; +import TableCell, {TableCellProps} from "@mui/material/TableCell"; +import CircularProgress from "@mui/material/CircularProgress"; +import Tooltip, {TooltipProps} from "@mui/material/Tooltip"; +import Typography, {TypographyProps} from "@mui/material/Typography"; +import TableHead from "@mui/material/TableHead"; + +export type Column = { + label: string; + help?: string; + headerTableCellProps?: Partial; + headerTooltipProps?: Partial; + headerTypographyProps?: Partial; + contentTableCellProps?: Partial; +} + +export type CellContext = { + column_properties: Column; + update: ReactEventHandler; + refresh: () => void; + refresh_all_rows: () => void; +} + +export type Cell = ReactElement | + ((row_data: any) => ReactElement) | + ((row_data: any, context: CellContext) => ReactElement) + +type CompleteHeading = { + label: string; + help: string; + tableCellProps: Partial; + tooltipProps: Partial; + typographyProps: Partial; +} + +export type AsyncTableProps = { + columns: Column[]; + rows: Cell[]; + initial_url: string; + new_entry_row?: Cell[]; + new_row_values?: any; + styles?: any; + [key: string]: any; +} + +type AsyncTableState = { + row_data: any[]; + new_row: any; + last_updated: Date; + loading: boolean; + loading_rows: number[]; +} + +/** + * AsyncTable is designed to present data fetched from an API and allow + * individual entries (rows) to be updated in isolation. + * + * AsyncTable takes an array of columns that define the headers and the + * common row properties, and an array of elements or functions that + * resolve into the contents of the TableCell elements in each TableRow + * in the body. + * + * The functions that generate cell contents are passed the row data + * and the context. `context` is a CellContext object that exposes + * the column properties, and functions for updating local content + * and for refreshing local content from the remote API. + * + * Data fetching is the responsibility of the AsyncTable via the + * APIConnection class. It determines where to fetch data from + * using the `initial_url` parameter. + * - Updates to individual rows are the responsibility of the calling + * code. + * - Refreshing a row uses the row's `url` property to know where to look + * + * This class abstracts away a lot of repetitive table-building code. + */ +export default class AsyncTable extends Component { + current_url: string = ""; + + state: AsyncTableState = { + row_data: [], + new_row: null, + last_updated: new Date(0), + loading: true, + loading_rows: [] + } + + constructor(props: AsyncTableProps) { + if (props.columns.length !== props.rows.length) + throw new Error(`Length of rows (${props.rows.length}) must match number of columns (${props.columns.length})`) + if (props.new_entry_row !== undefined && props.columns.length !== props.new_entry_row?.length) + throw new Error(`Length of new_entry_row (${props.new_entry_row.length}) must match number of columns (${props.columns.length})`) + super(props) + if (!this.current_url) this.current_url = props.initial_url + if (props.new_entry_row?.length) + this.state.new_row = this.new_row_template + } + + get new_row_template() { + return {id: -1, url: "", ...this.props.new_row_values} + } + + componentDidMount() { + this.get_data(this.props.initial_url) + console.log("Mounted AsyncTable", this) + } + + componentDidUpdate(prevProps: AsyncTableProps) { + console.log("Updated AsyncTable", this, prevProps) + // Typical usage (don't forget to compare props): + if (this.props.initial_url !== prevProps.initial_url) + this.setState({row_data: []}) + if (this.props.initial_url !== prevProps.initial_url || this.props.last_updated !== prevProps.last_updated) + this.get_data(this.props.initial_url) + } + + reset_new_row = () => this.setState({new_row: this.props.new_row_values? this.new_row_template : null}) + + get_data: (url: string) => void = async (url) => { + this.setState({loading: true}) + if (!url) return; + this.current_url = url; + await Connection.fetch(url) + .then(res => APIConnection.get_result_array(res)) + .then((res) => { + console.log(res) + this.setState({ + row_data: res.map(r => ({...r, _changed: false})), + loading: false, + loading_rows: [] + }) + }) + .catch(e => { + console.error('Async Table error', e) + this.setState({loading: false, loading_rows: []}) + }) + } + + refresh_row = async (row: {id: number, url: string, [key: string]: any}) => { + const loading_rows = this.state.loading_rows.filter(i => i !== row.id) + loading_rows.push(row.id) + this.setState({loading_rows: loading_rows}) + await Connection.fetch(row.url) + .then((res: SingleAPIResponse) => { + // If we deleted the row, delete it in state + if (res === 404) + this.setState({row_data: this.state.row_data.filter(r => r.id !== row.id)}) + // otherwise, update + else + this.setState({row_data: this.state.row_data.map(r => r.id === row.id ? {...res, _changed: false} : r)}) + }) + .catch(e => console.error('AsyncTable.update_single_row error', e, row)) + .finally( + () => this.setState({loading_rows: this.state.loading_rows.filter(i => i !== row.id)}) + ) + } + + update_all = async () => { + this.reset_new_row() + return this.get_data(this.current_url) + } + + get header_row() { + const column_headings: CompleteHeading[] = this.props.columns.map( + (heading: Column) => ({ + label: heading.label, + help: heading.help || "", + tableCellProps: heading.headerTableCellProps || {}, + tooltipProps: heading.headerTooltipProps || {}, + typographyProps: heading.headerTypographyProps || {}, + }) + ) + + return ( + + + {column_headings.map((heading, i) => + + { + + + {heading.label} + + + } + + )} + + ) + } + + loading_row(id: number) { + return + + + + + } + + row_conversion_context = (row: any, i: number) => ({ + column: this.props.columns[i], + update: (event: BaseSyntheticEvent) => this.setState({ + // Amend row_data to include new value for [name] + row_data: this.state.row_data.map( + r => r.id === row.id ? + {...row, [event.target.name]: event.target.value, _changed: true} : r + ) + }), + refresh: () => this.refresh_row(row), + refresh_all_rows: this.update_all + }) + + wrap_cells_in_row = (contents: any, row_index: number) => { + const cells = contents.map((cell: any, i: number) => + {cell} + ) + return {cells} + } + + row_data_to_tablerow = (row: any, row_index: number) => { + if (this.state.loading_rows.includes(row.id)) + return this.loading_row(row.id) + + const row_contents = this.props.rows.map((cell: any, i: number) => { + if (typeof cell === 'function') + return cell(row, this.row_conversion_context(row, i)) + return cell + }) + return this.wrap_cells_in_row(row_contents, row_index) + } + + new_row_to_tablerow = () => { + if (!this.props.new_entry_row?.length) + return + const row_contents = this.props.new_entry_row.map((cell: any, i: number) => { + if (typeof cell === 'function') + return cell(this.state.new_row, { + ...this.row_conversion_context(this.state.new_row, i), + update: (event: BaseSyntheticEvent) => this.setState({ + new_row: {...this.state.new_row, [event.target.name]: event.target.value, _changed: true} + }) + }) + return cell + }) + return this.wrap_cells_in_row(row_contents, -1) + } + + render() { + return ( + +
+ {this.header_row} + { + + {this.state.loading && this.loading_row(-2)} + {!this.state.loading && this.state.row_data.map(this.row_data_to_tablerow)} + { + !this.state.loading && + this.props.new_entry_row?.length && + this.new_row_to_tablerow() + } + + } +
+ + ) + } +} \ No newline at end of file diff --git a/frontend/src/Cells.tsx b/frontend/src/Cells.tsx index 5963cbe4..1359b95d 100644 --- a/frontend/src/Cells.tsx +++ b/frontend/src/Cells.tsx @@ -1,19 +1,15 @@ -import React, { useEffect, useState } from 'react'; -import Typography from '@mui/material/Typography'; +import React, { Fragment } from 'react'; import TextField from '@mui/material/TextField'; import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; import Tooltip from '@mui/material/Tooltip'; import AddIcon from '@mui/icons-material/Add'; import IconButton from '@mui/material/IconButton'; -import TableCell from '@mui/material/TableCell'; import Container from '@mui/material/Container'; import SaveIcon from '@mui/icons-material/Save'; -import TableHead from '@mui/material/TableHead'; import DeleteIcon from '@mui/icons-material/Delete'; -import TableRow from '@mui/material/TableRow'; -import PaginatedTable, {RowFunProps} from './PaginatedTable'; import Connection from "./APIConnection"; +import AsyncTable, {CellContext} from "./AsyncTable"; export type CellFields = { url: string; @@ -50,35 +46,27 @@ const useStyles = makeStyles((theme) => ({ paper: {} })); -const column_headings = [ +const columns = [ // {label: 'ID', help: 'Id in database'}, {label: 'Name', help: ''}, + {label: 'Manufacturer', help: 'Manufacturer of the cell'}, {label: 'Form Factor', help: 'Form factor of the cell'}, {label: 'Datasheet', help: 'Link to the cell\'s datasheet'}, {label: 'Anode Chemistry', help: 'Chemistry of the cell\'s anode'}, {label: 'Cathode Chemistry', help: 'Chemistry of the cell\'s cathode'}, {label: 'Nominal Capacity', help: 'Nominal cell capacity'}, {label: 'Nominal Weight', help: 'Nominal cell weight'}, - {label: 'Manufacturer', help: 'Manufacturer of the cell'}, {label: 'Save', help: 'Click to save edits to a row. Edits are disabled for cells that are in use'}, {label: 'Delete', help: 'Delete a cell that is not in use'}, ] -const table_head = column_headings.map(heading => ( - - - - {heading.label} - - - -)) +const string_fields: (keyof CellFields)[] = [ + 'name', 'manufacturer', 'form_factor', 'link_to_datasheet', 'anode_chemistry', 'cathode_chemistry' +] +const number_fields: (keyof CellFields)[] = ['nominal_capacity', 'nominal_cell_weight'] export default function Cells() { const classes = useStyles(); - const [lastUpdated, setLastUpdated] = useState(new Date()) - - const [selected, setSelected] = useState(null) const get_write_data: (data: CellFields) => Partial = (data) => { return { @@ -95,167 +83,120 @@ export default function Cells() { const addNewCell = (data: CellFields) => { const insert_data = get_write_data(data) - Connection.fetch('cells/', {body: JSON.stringify(insert_data), method: 'POST'}) - .then(() => setLastUpdated(new Date())) + return Connection.fetch('cells/', {body: JSON.stringify(insert_data), method: 'POST'}) }; const updateCell = (data: CellFields) => { const insert_data = get_write_data(data) - Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) - .then(() => setLastUpdated(new Date())) + return Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) }; - const deleteCell = (data: CellFields) => { - Connection.fetch(data.url, {method: 'DELETE'}) - .then(() => setLastUpdated(new Date())) - .then(() => { - if (selected?.id === data.id) - setSelected(null) - }) - }; - - function MyTableRow(props: RowFunProps) { - const classes = useStyles(); - const [row, setRow] = useState({ - url: "", - id: -1, - name: "", - form_factor: "", - link_to_datasheet: "", - anode_chemistry: "", - cathode_chemistry: "", - nominal_capacity: 0, - nominal_cell_weight: 0, - manufacturer: "", - in_use: false, - }) - const [dirty, setDirty] = useState(false) - - useEffect(() => { - if (!dirty && props.savedRow) { - setRow(props.savedRow); - } - }, [dirty, props.savedRow]); + const deleteCell = (data: CellFields) => Connection.fetch(data.url, {method: 'DELETE'}) - let useRow = row; - if (row.id === -1 && props.savedRow) - useRow = props.savedRow; - - const setValue = (key: string) => (e: any) => { - setDirty(true); - setRow({...useRow, [key]: e.target?.value}); - }; - - const Icon = props.addIcon ? : ; - - const string_fields: (keyof CellFields)[] = [ - 'name', 'manufacturer', 'form_factor', 'link_to_datasheet', 'anode_chemistry', 'cathode_chemistry' - ] - const number_fields: (keyof CellFields)[] = ['nominal_capacity', 'nominal_cell_weight'] - - return ( - - {props.onSelectRow(props.savedRow);}} - hover - selected={props.selected} - > - { - string_fields.map(n => ( - { - row.in_use ? row[n] : () - } - )) - } - { - number_fields.map(n => ( - { - row.in_use ? row[n] : () - } - )) - } - - + return ( + + + (cell: CellFields, context: CellContext) => + + ), + ...number_fields.map(n => (cell: CellFields, context: CellContext) => + + ), + (cell, context) => + {props.onRowSave(row);}} + disabled={!cell._changed || cell.in_use} + onClick={() => updateCell(cell).then(context.refresh)} > - {Icon} + - - - - + + , + (cell, context) => + deleteCell(row)} + disabled={cell.in_use} + onClick={() => deleteCell(cell).then(context.refresh)} > - - - - - ) - } - - function table_row_generator(row: any) { - return () - } - - const paginated_table = ({table_head})} - row_fun= {table_row_generator} - new_entry_row={( - {}} - disableSave={false} - addIcon={true} - /> - )} - initial_url={`cells/`} - styles={classes} - last_updated={lastUpdated} - />) - - return ( - - - {paginated_table} + + + ]} + new_entry_row={[ + ...string_fields.map(n => (cell: CellFields, context: CellContext) => + + ), + ...number_fields.map(n => (cell: CellFields, context: CellContext) => + + ), + (cell, context) => + + + addNewCell(cell).then(context.refresh_all_rows)} + > + + + + + , + + ]} + new_row_values={{ + name: '', manufacturer: '', form_factor: '', link_to_datasheet: '', anode_chemistry: '', cathode_chemistry: '', + nominal_capacity: 0, nominal_cell_weight: 0 + }} + initial_url="cells/?all=true" + /> ); diff --git a/frontend/src/Core.js b/frontend/src/Core.js index 8ddcbe1c..2fae4af6 100644 --- a/frontend/src/Core.js +++ b/frontend/src/Core.js @@ -1,4 +1,4 @@ -import React, {useEffect} from "react"; +import React from "react"; import { Routes, Route, diff --git a/frontend/src/Datasets.tsx b/frontend/src/Datasets.tsx index 8dd16ec6..fdd446b1 100644 --- a/frontend/src/Datasets.tsx +++ b/frontend/src/Datasets.tsx @@ -1,5 +1,5 @@ -import React, {useEffect, useState} from "react"; +import React, {useEffect, useState, Fragment} from "react"; import Container from '@mui/material/Container'; import { makeStyles } from '@mui/styles' import Button from '@mui/material/Button'; @@ -11,17 +11,13 @@ import DialogActions from '@mui/material/DialogActions'; import DialogContent from '@mui/material/DialogContent'; import DialogTitle from '@mui/material/DialogTitle'; import Connection from "./APIConnection" -import PaginatedTable, {RowFunProps} from "./PaginatedTable" -import TableCell from "@mui/material/TableCell"; -import Tooltip from "@mui/material/Tooltip"; -import Typography from "@mui/material/Typography"; -import TableHead from "@mui/material/TableHead"; +import AsyncTable, {CellContext} from "./AsyncTable" import { Paper } from "@mui/material"; import SaveIcon from "@mui/icons-material/Save"; -import TableRow from "@mui/material/TableRow"; import TextField from "@mui/material/TextField"; import IconButton from "@mui/material/IconButton"; import {UserSet} from "./UserRoleSet"; +import SettingsIcon from "@mui/icons-material/Settings"; export type DatasetFields = { url: string; @@ -58,125 +54,26 @@ const useStyles = makeStyles((theme) => ({ paper: {} })); -function MyTableRow(props: RowFunProps) { - const classes = useStyles(); - const [row, setRow] = useState({ - url: "", id: -1, name: '', type: '', date: '', cell: '', purpose: '', user_sets: [] - }) - const [dirty, setDirty] = useState(false) - - const rowUnchanged = Object.keys(row).reduce((a, k) => { - //@ts-ignore - return a && row[k] === props.savedRow[k]; - }, true); - - useEffect(() => { - if (!dirty && props.savedRow) { - setRow(props.savedRow); - } - }, [dirty, props.savedRow]); - - let useRow = row; - if (row.id === -1 && props.savedRow) - useRow = props.savedRow; - - const setValue = (key: string) => (e: any) => { - setDirty(true); - setRow({...useRow, [key]: e.target?.value}); - }; - - const Icon = ; - - return ( - - {props.onSelectRow(props.savedRow);}} - hover - selected={props.selected} - > - {useRow.id} - {useRow.date} - - - - - - - - - - {useRow.cell} - - - - { - setDirty(false); - props.onRowSave(row); - }} - > - {Icon} - - - - - - - ) -} - export default function Datasets() { const classes = useStyles(); const [selected, setSelected] = useState(null) - const [lastUpdated, setLastUpdated] = useState(new Date()) const updateRow = (data: DatasetFields) => { const insert_data = {name: data.name, type: data.type, purpose: data.purpose} - Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) - .then(() => setLastUpdated(new Date())) - }; + return Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) + } - const column_headings = [ + const columns = [ {label: 'ID', help: 'Unique ID in database'}, {label: 'Date', help: 'Date of Test'}, {label: 'Name', help: ''}, {label: 'Type', help: 'File type determined by Harvester'}, {label: 'Purpose', help: 'Short description of dataset purpose'}, {label: 'Cell', help: 'Cell that generated the dataset'}, + {label: 'Details', help: 'Advanced dataset properties'}, {label: 'Save', help: 'Save changes'}, ] - const table_head = column_headings.map(heading => ( - - - - {heading.label} - - - - )) const navigate = useNavigate(); const [codeOpen, setCodeOpen] = React.useState(false); @@ -202,20 +99,43 @@ export default function Datasets() { return ( - {table_head})} - row_fun={(row: DatasetFields) => ( - - )} - initial_url={`datasets/`} + {dataset.id}, + (dataset: DatasetFields) => {dataset.date}, + // these fields have the same shape, so condense the code. + // as const stops TypeScript from complaining about strings assigned to keyof DatasetFields + ...(['name', 'type', 'purpose'] as const).map( + (n) => ((dataset: DatasetFields, context: CellContext) => + + ) + ), + (dataset: DatasetFields) => {dataset.cell}, + (dataset: any) => + selected?.id === dataset.id? setSelected(null) : setSelected(dataset)}> + + + , + (dataset: any, context) => + updateRow(dataset).then(context.refresh)} + > + + + + ]} + initial_url={`datasets/?all=true`} styles={classes} - last_updated={lastUpdated} /> {selected !== null && diff --git a/frontend/src/Equipment.tsx b/frontend/src/Equipment.tsx index 723ce098..9f6934d3 100644 --- a/frontend/src/Equipment.tsx +++ b/frontend/src/Equipment.tsx @@ -1,18 +1,14 @@ -import React, { useEffect, useState } from 'react'; -import Typography from '@mui/material/Typography'; +import React, { Fragment } from 'react'; import TextField from '@mui/material/TextField'; import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; import Tooltip from '@mui/material/Tooltip'; import AddIcon from '@mui/icons-material/Add'; import IconButton from '@mui/material/IconButton'; -import TableCell from '@mui/material/TableCell'; import Container from '@mui/material/Container'; import SaveIcon from '@mui/icons-material/Save'; -import TableHead from '@mui/material/TableHead'; import DeleteIcon from '@mui/icons-material/Delete'; -import TableRow from '@mui/material/TableRow'; -import PaginatedTable, {RowFunProps} from './PaginatedTable'; +import AsyncTable, {CellContext} from './AsyncTable'; import Connection from "./APIConnection"; export type EquipmentFields = { @@ -44,28 +40,17 @@ const useStyles = makeStyles((theme) => ({ paper: {} })); -const column_headings = [ +const columns = [ {label: 'Name', help: 'Equipment Name'}, {label: 'Type', help: 'Equipment Type'}, {label: 'Save', help: 'Click to save edits to a row. Edits are disabled for equipment that is in use'}, {label: 'Delete', help: 'Delete equipment that is not in use'}, ] -const table_head = column_headings.map(heading => ( - - - - {heading.label} - - - -)) +const string_fields: (keyof EquipmentFields)[] = ['name', 'type'] export default function Equipment() { const classes = useStyles(); - const [lastUpdated, setLastUpdated] = useState(new Date()) - - const [selected, setSelected] = useState(null) const get_write_data: (data: EquipmentFields) => Partial = (data) => { return { name: data.name, type: data.type } @@ -73,139 +58,94 @@ export default function Equipment() { const addNewEquipment = (data: EquipmentFields) => { const insert_data = get_write_data(data) - Connection.fetch('equipment/', {body: JSON.stringify(insert_data), method: 'POST'}) - .then(() => setLastUpdated(new Date())) + return Connection.fetch('equipment/', {body: JSON.stringify(insert_data), method: 'POST'}) }; const updateEquipment = (data: EquipmentFields) => { const insert_data = get_write_data(data) - Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) - .then(() => setLastUpdated(new Date())) - }; - - const deleteEquipment = (data: EquipmentFields) => { - Connection.fetch(data.url, {method: 'DELETE'}) - .then(() => setLastUpdated(new Date())) - .then(() => { - if (selected?.id === data.id) - setSelected(null) - }) + return Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) }; - function MyTableRow(props: RowFunProps) { - const classes = useStyles(); - const [row, setRow] = useState({ - url: "", - id: -1, - name: "", - type: "", - in_use: false, - }) - const [dirty, setDirty] = useState(false) - - useEffect(() => { - if (!dirty && props.savedRow) { - setRow(props.savedRow); - } - }, [dirty, props.savedRow]); - - let useRow = row; - if (row.id === -1 && props.savedRow) - useRow = props.savedRow; - - const setValue = (key: string) => (e: any) => { - setDirty(true); - setRow({...useRow, [key]: e.target?.value}); - }; - - const Icon = props.addIcon ? : ; - - const string_fields: (keyof EquipmentFields)[] = ['name', 'type'] + const deleteEquipment = (data: EquipmentFields) => Connection.fetch(data.url, {method: 'DELETE'}) - return ( - - {props.onSelectRow(props.savedRow);}} - hover - selected={props.selected} - > - { - string_fields.map(n => ( + return ( + + + (equipment: EquipmentFields, context: CellContext) => { - row.in_use ? row[n] : } - )) - } - - + ), + (equipment, context) => + {props.onRowSave(row);}} + disabled={!equipment._changed || equipment.in_use} + onClick={() => updateEquipment(equipment).then(context.refresh)} > - {Icon} + - - - - + + , + (equipment, context) => + deleteEquipment(useRow)} + disabled={equipment.in_use} + onClick={() => deleteEquipment(equipment).then(context.refresh)} > - - - - - ) - } - - function table_row_generator(row: any) { - return () - } - - const paginated_table = ({table_head})} - row_fun= {table_row_generator} - new_entry_row={( - {}} - disableSave={false} - addIcon={true} - /> - )} - initial_url={`equipment/`} - styles={classes} - last_updated={lastUpdated} - />) - - return ( - - - {paginated_table} + + + ]} + new_entry_row={[ + ...string_fields.map(n => (equipment: EquipmentFields, context: CellContext) => + { + equipment.in_use ? equipment[n] : + } + ), + (equipment, context) => + + + addNewEquipment(equipment).then(context.refresh_all_rows)} + > + + + + + , + + ]} + new_row_values={{name: '', type: ''}} + initial_url={`equipment/?all=true`} + styles={classes} + /> ); diff --git a/frontend/src/Files.tsx b/frontend/src/Files.tsx index 1f54cbae..5c657b95 100644 --- a/frontend/src/Files.tsx +++ b/frontend/src/Files.tsx @@ -1,16 +1,12 @@ -import React, { useState } from 'react'; +import React, { Fragment } from 'react'; import { makeStyles } from '@mui/styles' import Container from '@mui/material/Container'; -import TableCell from '@mui/material/TableCell'; -import TableHead from '@mui/material/TableHead'; -import TableRow from '@mui/material/TableRow'; +import Tooltip from "@mui/material/Tooltip"; +import Typography from "@mui/material/Typography"; import Paper from '@mui/material/Paper'; -import PaginatedTable from './PaginatedTable'; +import AsyncTable from './AsyncTable'; import Connection from "./APIConnection"; import {MonitoredPathFields} from "./HarvesterDetail"; -import Tooltip from "@mui/material/Tooltip"; -import Typography from "@mui/material/Typography"; -import DatasetIcon from '@mui/icons-material/Dataset'; import IconButton from "@mui/material/IconButton"; import RefreshIcon from "@mui/icons-material/Refresh"; @@ -33,36 +29,34 @@ const useStyles = makeStyles((theme) => ({ })); export type FileFields = { - url: string, - id: number, - monitored_path: string, - relative_path: string, - state: string, - last_observed_time: string, - last_observed_size: number, - datasets: string[] + url: string; + id: number; + monitored_path: string; + relative_path: string; + state: string; + last_observed_time: string; + last_observed_size: number; + errors: { + error: string; + timestamp: string; + [key: string]: any; + } + datasets: string[]; } -export type FilesProps = { - path: MonitoredPathFields, - lastUpdated: Date -} +export type FilesProps = { path: MonitoredPathFields } export default function Files(props: FilesProps) { const classes = useStyles(); - const [lastUpdated, setLastUpdated] = useState(props.lastUpdated) - const forceReimport = (file: FileFields) => { - Connection.fetch(`${file.url}reimport/`) - .then(() => setLastUpdated(new Date())) - } + const forceReimport = (file: FileFields) => Connection.fetch(`${file.url}reimport/`) const datetimeOptions: Intl.DateTimeFormatOptions = { year: 'numeric', month: 'numeric', day: 'numeric', hour: 'numeric', minute: 'numeric', second: 'numeric', }; - const column_headings = [ + const columns = [ {label: props.path.path, help: 'File path'}, {label: 'Last Observed Size', help: 'Size of the file in bytes'}, {label: 'Last Observed Time', help: 'Time file was last scanned'}, @@ -71,48 +65,38 @@ export default function Files(props: FilesProps) { {label: 'Force Re-import', help: 'Retry the import operation next time the file is scanned'} ] - const table_head = column_headings.map(heading => ( - - - - {heading.label} - - - - )) - - function row_fun(file: FileFields) { - return ( - - - {file.relative_path} - {file.last_observed_size} - - { - Intl.DateTimeFormat('en-GB', datetimeOptions).format( - Date.parse(file.last_observed_time) - ) - } - - {file.state} - {file.datasets.map(d => ())} - forceReimport(file)}> - - - ) + const file_state = (file: FileFields) => { + let state = file.state === 'IMPORT FAILED' ? + {file.state} : {file.state} + if (file.errors.length) + state = {state} + return state } return ( - - {table_head})} - row_fun={row_fun} - initial_url={`files/?monitored_path__id=${props.path.id}`} - styles={classes} - last_updated={lastUpdated} - /> - + + {file.relative_path}, + (file: any) => {file.last_observed_size}, + (file: any) => { + Intl.DateTimeFormat('en-GB', datetimeOptions).format( + Date.parse(file.last_observed_time) + )} + , + (file: any) => {file_state(file)}, + (file: any) => {file.datasets.length}, + (file: any, context) => + forceReimport(file).then(context.refresh)}> + + ]} + initial_url={`files/?monitored_path__id=${props.path.id}&all=true`} + styles={classes} + /> + ); } diff --git a/frontend/src/GetDatasetMatlab.js b/frontend/src/GetDatasetMatlab.js index 3793e500..b38d58c1 100644 --- a/frontend/src/GetDatasetMatlab.js +++ b/frontend/src/GetDatasetMatlab.js @@ -17,7 +17,7 @@ export default function GetDatasetMatlab({dataset}) { let domain = window.location.href.split('/')[2]; domain = domain.split(':')[0] - const host = `http://${domain}:5001` + const host = `http://${domain}:5000` const codeString = `%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % galvanalyser REST API access diff --git a/frontend/src/GetDatasetPython.js b/frontend/src/GetDatasetPython.js index 2d1ea40d..9b9eb9c0 100644 --- a/frontend/src/GetDatasetPython.js +++ b/frontend/src/GetDatasetPython.js @@ -17,7 +17,7 @@ export default function GetDatasetPython({dataset}) { let domain = window.location.href.split('/')[2]; domain = domain.split(':')[0] - const host = `http://${domain}:5001` + const host = `http://${domain}:5000` const column_ids = dataset.columns.map(column => { return ` '${column.name}': ${column.id},` }) diff --git a/frontend/src/HarvesterDetail.tsx b/frontend/src/HarvesterDetail.tsx index d3fca129..b79e4b0b 100644 --- a/frontend/src/HarvesterDetail.tsx +++ b/frontend/src/HarvesterDetail.tsx @@ -1,21 +1,18 @@ -import React, {useEffect, useState} from 'react'; +import React, {useState, Fragment} from 'react'; import TextField from '@mui/material/TextField'; import Typography from '@mui/material/Typography'; import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; -import Tooltip from '@mui/material/Tooltip'; import AddIcon from '@mui/icons-material/Add'; import IconButton from '@mui/material/IconButton'; -import TableCell from '@mui/material/TableCell'; import SaveIcon from '@mui/icons-material/Save'; -import TableHead from '@mui/material/TableHead'; import DeleteIcon from '@mui/icons-material/Delete'; -import TableRow from '@mui/material/TableRow'; -import PaginatedTable, {RowFunProps} from './PaginatedTable'; -import Connection, {User} from "./APIConnection"; +import Connection from "./APIConnection"; import Files from './Files' import {HarvesterFields} from "./Harvesters"; import UserRoleSet, {UserSet} from "./UserRoleSet"; +import AsyncTable from "./AsyncTable"; +import SearchIcon from "@mui/icons-material/Search"; const useStyles = makeStyles((theme) => ({ paper: { @@ -68,193 +65,137 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { const [lastUpdated, setLastUpdated] = useState(new Date()) - function MyTableRow(props: RowFunProps) { - const classes = useStyles(); - const [row, setRow] = useState({ - url: "", id: -1, harvester: -1, stable_time: -1, path: '', user_sets: [] - }) - const [dirty, setDirty] = useState(false) - - const rowUnchanged = Object.keys(row).reduce((a, k) => { - //@ts-ignore - return a && row[k] === props.savedRow[k]; - }, true); - - useEffect(() => { - if (!dirty && props.savedRow) { - setRow(props.savedRow); - } - }, [dirty, props.savedRow]); - - let useRow = row; - if (row.harvester === -1 && props.savedRow) - useRow = props.savedRow; + const addNewPath = (data: MonitoredPathFields) => { + const insert_data = {harvester: harvester.id, path: data.path, stable_time: data.stable_time} + return Connection.fetch('monitored_paths/', {body: JSON.stringify(insert_data), method: 'POST'}) + }; + const deletePath = (data: MonitoredPathFields) => Connection.fetch(data.url, {method: 'DELETE'}) - const setValue = (key: string) => (e: any) => { - setDirty(true); - setRow({...useRow, [key]: e.target?.value}); - }; + const updatePath = (data: MonitoredPathFields) => { + const insert_data = {path: data.path, stable_time: data.stable_time} + return Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) + }; - const Icon = props.addIcon ? : ; + const columns = [ + {label: 'Path', help: 'Directory to watch'}, + {label: 'Stable Time (s)', help: 'Seconds files must remain unchanged to be considered stable and imported'}, + {label: 'Users', help: 'Users with access to this path\'s datasets'}, + {label: 'Files', help: 'View files in this directory'}, + {label: 'Save', help: 'Save changes'}, + {label: 'Delete', help: 'Delete monitored path (imported datasets will remain)'}, + ] - return ( - - {props.onSelectRow(props.savedRow);}} - hover - selected={props.selected} - > - + return ( + + + {harvester.name} - monitored paths + + - // {env.GALVANALYSER_HARVESTER_BASE_PATH}/ - // , + } }} - value={useRow.path} - onChange={setValue('path')} /> - - + value={row.path} + name="path" + onChange={context.update} + /> + , + (row: any, context) => { - setDirty(true); - setRow({...row, stable_time: parseInt(e.target.value)}); - }} + value={row.stable_time ? row.stable_time : ''} + name="stable_time" + onChange={context.update} > - - + , + (row: any, context) => - - - - - { - setDirty(false); - props.onRowSave(row); - }} - > - {Icon} - - - - - - - ) - } - - - const addNewPath = (data: MonitoredPathFields) => { - const insert_data = {harvester: harvester.id, path: data.path, stable_time: data.stable_time} - Connection.fetch('monitored_paths/', {body: JSON.stringify(insert_data), method: 'POST'}) - .then(() => setLastUpdated(new Date())) - }; - const deletePath = () => { - if (selected !== null) - Connection.fetch(selected.url, {method: 'DELETE'}) - .then(() => setLastUpdated(new Date())) - }; - const updatePath = (data: MonitoredPathFields) => { - const insert_data = {path: data.path, stable_time: data.stable_time} - Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) - .then(() => setLastUpdated(new Date())) - }; - - const column_headings = [ - {label: 'Path', help: 'Directory to watch'}, - {label: 'Stable Time (s)', help: 'Seconds files must remain unchanged to be considered stable and imported'}, - {label: 'Users', help: 'Users with access to this path\'s datasets'}, - {label: 'Save', help: 'Click to save edits to a row'}, - ] - - const table_head = column_headings.map(heading => ( - - - - {heading.label} - - - - )) - - return ( - - - Harvester "{harvester.name}" monitored paths - - {table_head})} - row_fun={(row: MonitoredPathFields) => ( - { - return prev || (Connection.user !== null && u.users.map(usr => usr.id).includes(Connection.user.id)) - }, false) - } - /> - )} - initial_url={`monitored_paths/?harvester__id=${harvester.id}`} - new_entry_row={( - { - }} - disableSave={false} - /> - )} + , + (row: any) => + selected?.id === row.id? setSelected(null) : setSelected(row)}> + + + , + (row: any, context) => + updatePath(row).then(context.refresh)} + > + + + , + (row: any, context) => + deletePath(row).then(context.refresh)} + > + + + , + ]} + initial_url={`monitored_paths/?harvester__id=${harvester.id}&all=true`} + new_entry_row={[ + (new_row: any, context) => + + , + (new_row: any, context) => + + + , + , + , + (new_row: any, context) => + addNewPath(new_row).then(context.refresh_all_rows)} + > + + + , + , + ]} + new_row_values={{path: "", stable_time: 60}} styles={classes} last_updated={lastUpdated} /> - - - u.name.toLowerCase() === "harvester admins")?.users.map((u: User) => u.username).includes(Connection.user.username) || - selected.user_sets.find(u => u.name.toLowerCase() === "admins")?.users.map((u: User) => u.username).includes(Connection.user.username) - ) - } - aria-label="delete" - onClick={deletePath} - > - - - - - {selected !== null && } + {selected !== null && } - ); } diff --git a/frontend/src/Harvesters.tsx b/frontend/src/Harvesters.tsx index a6a2a6cf..e9abc3ec 100644 --- a/frontend/src/Harvesters.tsx +++ b/frontend/src/Harvesters.tsx @@ -1,22 +1,18 @@ -import React, { useEffect, useState } from 'react'; +import React, { useState, Fragment } from 'react'; import TextField from '@mui/material/TextField'; import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; import Typography from '@mui/material/Typography'; -import Tooltip from '@mui/material/Tooltip'; -import AddIcon from '@mui/icons-material/Add'; import IconButton from '@mui/material/IconButton'; -import TableCell from '@mui/material/TableCell'; import Container from '@mui/material/Container'; import SaveIcon from '@mui/icons-material/Save'; -import TableHead from '@mui/material/TableHead'; +import SearchIcon from '@mui/icons-material/Search'; import DeleteIcon from '@mui/icons-material/Delete'; -import TableRow from '@mui/material/TableRow'; -import PaginatedTable, {RowFunProps} from './PaginatedTable'; import HarvesterDetail from './HarvesterDetail'; import Connection from "./APIConnection"; -import {isAdmin} from "./Api"; +import {UserSet} from "./UserRoleSet"; +import AsyncTable, {Column} from "./AsyncTable"; export type HarvesterWriteableFields = { name: string; @@ -27,6 +23,7 @@ export type HarvesterFields = HarvesterWriteableFields & { url: string; id: number; last_check_in: string | null; + user_sets: UserSet[]; } const useStyles = makeStyles((theme) => ({ @@ -53,175 +50,102 @@ const useStyles = makeStyles((theme) => ({ export default function Harvesters() { const classes = useStyles(); - const [lastUpdated, setLastUpdated] = useState(new Date()) - const [selected, setSelected] = useState(null) - const userIsAdmin = isAdmin() - - const updateHarvester = (data: any) => { + const userIsAdmin = (harvester: HarvesterFields) => + Connection.user !== null && + harvester?.user_sets?.find(u => u.name.toLowerCase() === 'admins')?.users + .map(usr => usr.username) + .includes(Connection.user.username) + + const updateHarvester = (data: HarvesterFields) => { + console.log('updateHarvester', data) const insert_data: HarvesterWriteableFields = { name: data.name, sleep_time: data.sleep_time } - Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) - .then(() => setLastUpdated(new Date())) - }; - - const deleteHarvester = () => { - if (selected !== null) - Connection.fetch(selected.url, {method: 'DELETE'}) - .then(() => setLastUpdated(new Date())) - .then(() => setSelected(null)) + return Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) }; - function table_row_generator(row: any) { - return () - } - - function MyTableRow(props: RowFunProps) { - const classes = useStyles(); - const [row, setRow] = useState({ - id: -1, - url: "", - name: "", - last_check_in: null, - sleep_time: 3600 - }) - const [dirty, setDirty] = useState(false) - - useEffect(() => { - if (!dirty && props.savedRow) { - setRow(props.savedRow); - } - }, [dirty, props.savedRow]); - - let useRow = row; - if (row.id === -1 && props.savedRow) - useRow = props.savedRow; - - const Icon = props.addIcon ? : ; - - return ( - - {props.onSelectRow(props.savedRow);}} - hover - selected={props.selected} - > - - {props.savedRow?.id || ""} - - - - { - setDirty(true); - setRow({...row, name: e.target.value}); - }} - > - - - - {(props.savedRow?.last_check_in && - Intl.DateTimeFormat('en-GB', - { dateStyle: 'long', timeStyle: 'long' }).format( - Date.parse(props.savedRow.last_check_in) - )) || (None)} - - - { - setDirty(true); - setRow({...row, sleep_time: parseInt(e.target.value)}); - }} - > - - - - - - { - props.onRowSave(row); - setDirty(false); - }} - > - { Icon } - - - - - - - ) - } + const deleteHarvester = (harvester: HarvesterFields) => Connection.fetch(harvester.url, {method: 'DELETE'}) - const column_headings = [ + const columns: Column[] = [ {label: 'ID', help: 'Harvester id in database'}, {label: 'Name', help: 'Harvester name'}, {label: 'Last Check In', help: 'Datetime of last harvester run that successfully contacted the database'}, - {label: 'Sleep Time (s)', help: 'If set, harvester is run every day on this hour'}, + {label: 'Sleep Time (s)', help: 'Time harvester waits after completing a cycle before beginning the next'}, + {label: 'Details', help: 'View harvester path information'}, {label: 'Save', help: 'Click to save edits to a row'}, + {label: 'Delete', help: 'Delete a harvester'}, ] - const table_head = column_headings.map(heading => ( - - - - {heading.label} - - - - )) - - const paginated_table = ({table_head})} - row_fun= {table_row_generator} - initial_url={`harvesters/`} - styles={classes} - last_updated={lastUpdated} - />) - return ( - - {paginated_table} - - - - - - - - - {selected !== null && } + + { {row.id}, + (row: any, context) => + + + , + (row: any) => + { + (row.last_check_in && + Intl.DateTimeFormat( + 'en-GB', + { dateStyle: 'long', timeStyle: 'long' }) + .format(Date.parse(row.last_check_in)) + ) || (None) + } + , + (row: any, context) => + + + , + (row: any) => + selected?.id === row.id? setSelected(null) : setSelected(row)}> + + + , + (row: any, context) => + updateHarvester(row).then(context.refresh)} + > + + + , + (row: any, context) => + deleteHarvester(row).then(context.refresh)} + > + + + , + ]} + initial_url="harvesters/?all=true" + />} + + {selected !== null && } ); } diff --git a/frontend/src/PaginatedTable.tsx b/frontend/src/PaginatedTable.tsx index ad159c31..85475f49 100644 --- a/frontend/src/PaginatedTable.tsx +++ b/frontend/src/PaginatedTable.tsx @@ -2,12 +2,34 @@ * Offer a table with previous/next links. */ import classNames from 'classnames' -import {Component, ReactComponentElement} from "react"; +import React, {Component, ReactComponentElement} from "react"; import TableContainer from "@mui/material/TableContainer"; import Table from "@mui/material/Table"; import TableBody from "@mui/material/TableBody"; import Button from '@mui/material/Button'; -import Connection, {APIResponse} from "./APIConnection"; +import Connection, {APIResponse, SingleAPIResponse} from "./APIConnection"; +import TableRow from "@mui/material/TableRow"; +import TableCell, {TableCellProps} from "@mui/material/TableCell"; +import LoadingButton from "@mui/lab/LoadingButton"; +import Tooltip, {TooltipProps} from "@mui/material/Tooltip"; +import Typography, {TypographyProps} from "@mui/material/Typography"; +import TableHead from "@mui/material/TableHead"; + +export type Heading = { + label: string; + help?: string; + tableCellProps?: Partial; + tooltipProps?: Partial; + typographyProps?: Partial; +} + +type CompleteHeading = { + label: string; + help: string; + tableCellProps: Partial; + tooltipProps: Partial; + typographyProps: Partial; +} export type RowFunProps = { savedRow?: T; @@ -24,12 +46,12 @@ type RowFun = ((row: any, i: number, array: any[]) => ReactComponentElement ((row: any) => ReactComponentElement) export type PaginatedTableProps = { - header: ReactComponentElement, - row_fun: RowFun, - initial_url: string, - new_entry_row?: ReactComponentElement, - styles?: any, - [key: string]: any + column_headings: Heading[]; + row_fun: RowFun; + initial_url: string; + new_entry_row?: ReactComponentElement; + styles?: any; + [key: string]: any; } type PaginatedTableState = { @@ -37,6 +59,7 @@ type PaginatedTableState = { links: PaginationLinks; last_updated: Date; loading: boolean; + loading_rows: number[]; } export type PaginationLinks = { @@ -55,29 +78,31 @@ type PaginationProps = PaginationLinks & { class Pagination extends Component { render() { return ( -
- - -
+
+ + +
) } } @@ -85,11 +110,12 @@ class Pagination extends Component { export default class PaginatedTable extends Component { current_url: string = ""; - state = { + state: PaginatedTableState = { row_data: [], links: {previous: null, next: null}, last_updated: new Date(0), - loading: true + loading: true, + loading_rows: [] } constructor(props: PaginatedTableProps) { @@ -99,13 +125,16 @@ export default class PaginatedTable extends Component { @@ -113,7 +142,6 @@ export default class PaginatedTable extends Component { console.log(res); this.setState({ @@ -122,40 +150,94 @@ export default class PaginatedTable extends Component { console.error('Paginated Table error', e) - this.setState({loading: false}) + this.setState({loading: false, loading_rows: []}) + }) + } + + update_single_row = async (row: {id: number, [key: string]: any}) => { + const loading_rows = this.state.loading_rows.filter(i => i !== row.id) + loading_rows.push(row.id) + this.setState({loading_rows: loading_rows}) + await Connection.fetch(row.url) + .then((res: SingleAPIResponse) => { + console.log(res) + this.setState({row_data: this.state.row_data.map(r => r.id === row.id ? res : r)}) + }) + .catch(e => console.error('PaginatedTable.update_single_row error', e)) + .finally( + () => this.setState({loading_rows: this.state.loading_rows.filter(i => i !== row.id)}) + ) + } + + get header_row() { + const column_headings: CompleteHeading[] = this.props.column_headings.map( + (heading: Heading) => ({ + label: heading.label, + help: heading.help || "", + tableCellProps: heading.tableCellProps || {}, + tooltipProps: heading.tooltipProps || {}, + typographyProps: heading.typographyProps || {}, }) + ) + + return ( + + + {column_headings.map((heading, i) => + + { + + + {heading.label} + + + } + + )} + + ) + } + + get loading_row() { + return + + + + } render() { return ( -
+
- - { - // @ts-ignore - - {this.props.header} - { - // @ts-ignore - - {this.state.row_data.map(this.props.row_fun)} - {this.props.new_entry_row} - - } -
- } + + + {this.header_row} + { + + { + this.state.loading && this.loading_row + } + {!this.state.loading && this.state.row_data.map(this.props.row_fun)} + {!this.state.loading && this.props.new_entry_row} + + } +
{ }) get user_sets() { - return this.props.user_sets.map(u =>
+ return this.props.user_sets.map(u =>
{u.name} - + {u.users.map(usr => { const editability = this.is_set_editable.find(s => s.id === u.id) const editable = editability?.editable - || (Connection.user && usr.id === Connection.user.id) const undeleteable = u.is_admin && u.users.length + (editability?.parent?.users.length || 0) <= 1 if (editable && undeleteable) return Date: Fri, 27 Jan 2023 17:03:45 +0000 Subject: [PATCH 32/79] frontend depth fetch --- frontend/src/APIConnection.ts | 45 +++- frontend/src/AsyncTable.tsx | 155 +++++++------ frontend/src/Cells.tsx | 70 ++---- frontend/src/Datasets.tsx | 86 ++++++-- frontend/src/Equipment.tsx | 53 ++--- frontend/src/Files.tsx | 16 +- frontend/src/HarvesterDetail.tsx | 70 ++---- frontend/src/Harvesters.tsx | 20 +- frontend/src/PaginatedTable.tsx | 361 ++++++++++--------------------- frontend/src/UserRoleSet.tsx | 10 +- 10 files changed, 379 insertions(+), 507 deletions(-) diff --git a/frontend/src/APIConnection.ts b/frontend/src/APIConnection.ts index f11ad3be..84ddbcd0 100644 --- a/frontend/src/APIConnection.ts +++ b/frontend/src/APIConnection.ts @@ -14,7 +14,11 @@ export type User = { token: string, } -export type SingleAPIResponse = any +export interface APIObject { + id: number; + url: string; +} +export type SingleAPIResponse = APIObject & {[prop: string]: any} export type MultipleAPIResponse = SingleAPIResponse[] export type PaginatedAPIResponse = { count: number, previous?: string, next?: string, results: SingleAPIResponse[] @@ -74,7 +78,7 @@ export class APIConnection { return cookie !== undefined && this.user !== null; } - async fetch(url: string, options?: any, cache_name: string = ""): Promise { + async fetch(url: string, options?: any, depth: number = 1): Promise { await this.get_is_logged_in(); console.info(`Fetch ${url} for ${this.user?.username}`) console.info('fetch options', options) @@ -101,6 +105,24 @@ export class APIConnection { return 404; return response.json(); }) + .then(async json => { + if (typeof json === 'number' || !depth) + return json + // Recursively fetch objects by links + if (json instanceof Array) + return await Promise.all( + json.map(r => this.fetch_children(r, options, depth - 1)) + ) + if (json.results !== undefined) { + json.results = await Promise.all( + json.results.map(async (r: SingleAPIResponse) => await this.fetch_children(r, options, depth - 1)) + ) + return json + } + }) + .then(r => { + console.log(url, options, depth, r); return r + }) .catch(e => { console.error(e); return { @@ -113,12 +135,27 @@ export class APIConnection { }); } - static get_result_array: (r: APIResponse) => MultipleAPIResponse = r => { + fetch_children: (r: SingleAPIResponse, options: any, depth: number) => Promise = + async (r: SingleAPIResponse, options: any, depth: number) => { + for (const k in r) { + if (k === 'url') + continue + if (typeof r[k] === "string" && r[k].startsWith(this.url)) { + r[k] = await this.fetch(r[k], options, depth) + console.log(r, k, r[k]) + } + } + return r + } + + static get_result_array: ((r: APIResponse) => MultipleAPIResponse|ErrorCode) = r => { if (r instanceof Array) return r; + if (typeof r === 'number') + return r; if (r.results !== undefined) return r.results; - return r; + return [r]; } } diff --git a/frontend/src/AsyncTable.tsx b/frontend/src/AsyncTable.tsx index 4c76aef2..b7633505 100644 --- a/frontend/src/AsyncTable.tsx +++ b/frontend/src/AsyncTable.tsx @@ -1,8 +1,8 @@ -import React, {Component, ReactElement, Fragment, BaseSyntheticEvent, ReactEventHandler} from "react"; +import React, {Component, ReactElement, BaseSyntheticEvent, ReactEventHandler} from "react"; import TableContainer from "@mui/material/TableContainer"; import Table from "@mui/material/Table"; import TableBody from "@mui/material/TableBody"; -import Connection, {APIConnection, APIResponse, SingleAPIResponse} from "./APIConnection"; +import Connection, {APIConnection, APIObject} from "./APIConnection"; import TableRow from "@mui/material/TableRow"; import TableCell, {TableCellProps} from "@mui/material/TableCell"; import CircularProgress from "@mui/material/CircularProgress"; @@ -19,16 +19,19 @@ export type Column = { contentTableCellProps?: Partial; } -export type CellContext = { - column_properties: Column; +export type RowGeneratorContext = { + columns: Column[]; update: ReactEventHandler; + update_direct: (field_name: K, new_value: T[K]) => void; refresh: () => void; refresh_all_rows: () => void; + is_new_row: boolean; + value_changed: boolean; } -export type Cell = ReactElement | - ((row_data: any) => ReactElement) | - ((row_data: any, context: CellContext) => ReactElement) +export type RowGenerator = + ((row_data: T) => ReactElement[]) | + ((row_data: T, context: RowGeneratorContext) => ReactElement[]) type CompleteHeading = { label: string; @@ -38,38 +41,40 @@ type CompleteHeading = { typographyProps: Partial; } -export type AsyncTableProps = { +export type AsyncTableProps = { columns: Column[]; - rows: Cell[]; + row_generator: RowGenerator; initial_url: string; - new_entry_row?: Cell[]; - new_row_values?: any; + new_row_values?: Partial; styles?: any; - [key: string]: any; } type AsyncTableState = { row_data: any[]; new_row: any; - last_updated: Date; loading: boolean; loading_rows: number[]; + changed_rows: number[]; } +export const NEW_ROW_ID = -1 + /** * AsyncTable is designed to present data fetched from an API and allow * individual entries (rows) to be updated in isolation. * * AsyncTable takes an array of columns that define the headers and the - * common row properties, and an array of elements or functions that - * resolve into the contents of the TableCell elements in each TableRow - * in the body. + * common row properties, and a functions that resolve into the an array of + * contents of the TableCell elements in each TableRow in the body. * - * The functions that generate cell contents are passed the row data + * The function that generates cell contents is passed the row data * and the context. `context` is a CellContext object that exposes * the column properties, and functions for updating local content * and for refreshing local content from the remote API. * + * If `new_row_values` is specified, the row generator will be called + * with those values to generate an extra row for adding new items. + * * Data fetching is the responsibility of the AsyncTable via the * APIConnection class. It determines where to fetch data from * using the `initial_url` parameter. @@ -79,25 +84,21 @@ type AsyncTableState = { * * This class abstracts away a lot of repetitive table-building code. */ -export default class AsyncTable extends Component { +export default class AsyncTable extends Component, AsyncTableState> { current_url: string = ""; state: AsyncTableState = { row_data: [], new_row: null, - last_updated: new Date(0), loading: true, - loading_rows: [] + loading_rows: [], + changed_rows: [] } - constructor(props: AsyncTableProps) { - if (props.columns.length !== props.rows.length) - throw new Error(`Length of rows (${props.rows.length}) must match number of columns (${props.columns.length})`) - if (props.new_entry_row !== undefined && props.columns.length !== props.new_entry_row?.length) - throw new Error(`Length of new_entry_row (${props.new_entry_row.length}) must match number of columns (${props.columns.length})`) + constructor(props: AsyncTableProps) { super(props) if (!this.current_url) this.current_url = props.initial_url - if (props.new_entry_row?.length) + if (props.new_row_values !== undefined) this.state.new_row = this.new_row_template } @@ -110,13 +111,13 @@ export default class AsyncTable extends Component) { console.log("Updated AsyncTable", this, prevProps) // Typical usage (don't forget to compare props): - if (this.props.initial_url !== prevProps.initial_url) + if (this.props.initial_url !== prevProps.initial_url) { this.setState({row_data: []}) - if (this.props.initial_url !== prevProps.initial_url || this.props.last_updated !== prevProps.last_updated) this.get_data(this.props.initial_url) + } } reset_new_row = () => this.setState({new_row: this.props.new_row_values? this.new_row_template : null}) @@ -126,13 +127,16 @@ export default class AsyncTable extends Component APIConnection.get_result_array(res)) + .then(APIConnection.get_result_array) .then((res) => { + if (typeof(res) === 'number') + throw new Error(res.toString()) console.log(res) this.setState({ - row_data: res.map(r => ({...r, _changed: false})), + row_data: res, loading: false, - loading_rows: [] + loading_rows: [], + changed_rows: [] }) }) .catch(e => { @@ -146,13 +150,24 @@ export default class AsyncTable extends Component { + .then(APIConnection.get_result_array) + .then((res) => { // If we deleted the row, delete it in state - if (res === 404) + if (typeof res === 'number') { + console.info(`${row.url} -> ${res}`) this.setState({row_data: this.state.row_data.filter(r => r.id !== row.id)}) - // otherwise, update - else - this.setState({row_data: this.state.row_data.map(r => r.id === row.id ? {...res, _changed: false} : r)}) + } else { + // otherwise, update + const row_data = res.pop() + if (row_data === undefined) { + console.error(res) + throw new Error(`refresh_row expected 1 API result, got ${res.length}`) + } + this.setState({ + row_data: this.state.row_data.map(r => r.id === row.id ? row_data : r), + changed_rows: this.state.changed_rows.filter(i => i !== row_data.id) + }) + } }) .catch(e => console.error('AsyncTable.update_single_row error', e, row)) .finally( @@ -202,54 +217,50 @@ export default class AsyncTable extends Component } - row_conversion_context = (row: any, i: number) => ({ - column: this.props.columns[i], - update: (event: BaseSyntheticEvent) => this.setState({ + row_conversion_context = (row: any, is_new_row: boolean) => { + let update_fun: RowGeneratorContext["update_direct"] = (name, value) => this.setState({ // Amend row_data to include new value for [name] row_data: this.state.row_data.map( - r => r.id === row.id ? - {...row, [event.target.name]: event.target.value, _changed: true} : r - ) - }), - refresh: () => this.refresh_row(row), - refresh_all_rows: this.update_all - }) + r => r.id === row.id ? {...row, [name]: value} : r + ), + changed_rows: [...this.state.changed_rows, row.id] + }) + if (is_new_row) + update_fun = (name, value) => this.setState({ + new_row: {...this.state.new_row, [name]: value, _changed: true}, + changed_rows: [...this.state.changed_rows, row.id] + }) - wrap_cells_in_row = (contents: any, row_index: number) => { + return { + columns: this.props.columns, + update: (event: BaseSyntheticEvent) => update_fun(event.target.name, event.target.value), + update_direct: update_fun, + refresh: () => this.refresh_row(row), + refresh_all_rows: this.update_all, + is_new_row, + value_changed: this.state.changed_rows.includes(row.id) + } + } + + wrap_cells_in_row = (contents: ReactElement[], row_index: number) => { const cells = contents.map((cell: any, i: number) => {cell} ) return {cells} } - row_data_to_tablerow = (row: any, row_index: number) => { + row_data_to_tablerow = (row: T, row_index: number) => { + const is_new_row = row_index === NEW_ROW_ID + if (is_new_row) + row_index = -1 + if (this.state.loading_rows.includes(row.id)) return this.loading_row(row.id) - const row_contents = this.props.rows.map((cell: any, i: number) => { - if (typeof cell === 'function') - return cell(row, this.row_conversion_context(row, i)) - return cell - }) + const row_contents = this.props.row_generator(row, this.row_conversion_context(row, is_new_row)) return this.wrap_cells_in_row(row_contents, row_index) } - new_row_to_tablerow = () => { - if (!this.props.new_entry_row?.length) - return - const row_contents = this.props.new_entry_row.map((cell: any, i: number) => { - if (typeof cell === 'function') - return cell(this.state.new_row, { - ...this.row_conversion_context(this.state.new_row, i), - update: (event: BaseSyntheticEvent) => this.setState({ - new_row: {...this.state.new_row, [event.target.name]: event.target.value, _changed: true} - }) - }) - return cell - }) - return this.wrap_cells_in_row(row_contents, -1) - } - render() { return ( @@ -261,8 +272,8 @@ export default class AsyncTable extends Component } diff --git a/frontend/src/Cells.tsx b/frontend/src/Cells.tsx index 1359b95d..6304e2f3 100644 --- a/frontend/src/Cells.tsx +++ b/frontend/src/Cells.tsx @@ -9,7 +9,7 @@ import Container from '@mui/material/Container'; import SaveIcon from '@mui/icons-material/Save'; import DeleteIcon from '@mui/icons-material/Delete'; import Connection from "./APIConnection"; -import AsyncTable, {CellContext} from "./AsyncTable"; +import AsyncTable from "./AsyncTable"; export type CellFields = { url: string; @@ -60,10 +60,10 @@ const columns = [ {label: 'Delete', help: 'Delete a cell that is not in use'}, ] -const string_fields: (keyof CellFields)[] = [ +const string_fields = [ 'name', 'manufacturer', 'form_factor', 'link_to_datasheet', 'anode_chemistry', 'cathode_chemistry' -] -const number_fields: (keyof CellFields)[] = ['nominal_capacity', 'nominal_cell_weight'] +] as const +const number_fields = ['nominal_capacity', 'nominal_cell_weight'] as const export default function Cells() { const classes = useStyles(); @@ -96,10 +96,10 @@ export default function Cells() { return ( - columns={columns} - rows={[ - ...string_fields.map(n => (cell: CellFields, context: CellContext) => + row_generator={(cell, context) => [ + ...string_fields.map(n => ), - ...number_fields.map(n => (cell: CellFields, context: CellContext) => + ...number_fields.map(n => ), - (cell, context) => + updateCell(cell).then(context.refresh)} + disabled={!context.value_changed || cell.in_use} + onClick={ + context.is_new_row? + () => addNewCell(cell).then(context.refresh_all_rows) : + () => updateCell(cell).then(context.refresh)} > - + {context.is_new_row? : } , - (cell, context) => + context.is_new_row? : ]} - new_entry_row={[ - ...string_fields.map(n => (cell: CellFields, context: CellContext) => - - ), - ...number_fields.map(n => (cell: CellFields, context: CellContext) => - - ), - (cell, context) => - - - addNewCell(cell).then(context.refresh_all_rows)} - > - - - - - , - - ]} new_row_values={{ name: '', manufacturer: '', form_factor: '', link_to_datasheet: '', anode_chemistry: '', cathode_chemistry: '', nominal_capacity: 0, nominal_cell_weight: 0 diff --git a/frontend/src/Datasets.tsx b/frontend/src/Datasets.tsx index fdd446b1..b749ae8b 100644 --- a/frontend/src/Datasets.tsx +++ b/frontend/src/Datasets.tsx @@ -1,5 +1,5 @@ -import React, {useEffect, useState, Fragment} from "react"; +import React, {useEffect, useState, Fragment, ReactElement} from "react"; import Container from '@mui/material/Container'; import { makeStyles } from '@mui/styles' import Button from '@mui/material/Button'; @@ -10,14 +10,19 @@ import Dialog from '@mui/material/Dialog'; import DialogActions from '@mui/material/DialogActions'; import DialogContent from '@mui/material/DialogContent'; import DialogTitle from '@mui/material/DialogTitle'; -import Connection from "./APIConnection" -import AsyncTable, {CellContext} from "./AsyncTable" -import { Paper } from "@mui/material"; +import Connection, {APIConnection} from "./APIConnection" +import AsyncTable from "./AsyncTable" +import Paper from "@mui/material/Paper"; +import Select from "@mui/material/Select"; import SaveIcon from "@mui/icons-material/Save"; import TextField from "@mui/material/TextField"; import IconButton from "@mui/material/IconButton"; import {UserSet} from "./UserRoleSet"; import SettingsIcon from "@mui/icons-material/Settings"; +import {CellFields} from "./Cells"; +import MenuItem from "@mui/material/MenuItem"; +import CircularProgress from "@mui/material/CircularProgress"; +import {EquipmentFields} from "./Equipment"; export type DatasetFields = { url: string; @@ -25,7 +30,8 @@ export type DatasetFields = { name: string; type: string; date: string; - cell: string; + cell: CellFields | null; + equipment: EquipmentFields[]; purpose: string; user_sets: UserSet[]; } @@ -57,9 +63,29 @@ const useStyles = makeStyles((theme) => ({ export default function Datasets() { const classes = useStyles(); const [selected, setSelected] = useState(null) + const [cellListLoading, setCellListLoading] = useState(true) + const [cellList, setCellList] = useState([]) + + useEffect(() => { + Connection.fetch('cells/?all=true') + .then(APIConnection.get_result_array) + .then(r => { + if (typeof r === 'number') + throw new Error(`cells/?all=true -> ${r}`) + // @ts-ignore + setCellList(r) + setCellListLoading(false) + }) + }, []) const updateRow = (data: DatasetFields) => { - const insert_data = {name: data.name, type: data.type, purpose: data.purpose} + const insert_data = { + name: data.name, + type: data.type, + purpose: data.purpose, + cell: data.cell || null, + equipment: data.equipment.map(e => e.id) + } return Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) } @@ -96,18 +122,35 @@ export default function Datasets() { setMatlabCodeOpen(false); }; + const get_items = (dataset: DatasetFields) => { + const menuItem = (cell: CellFields) => {cell.name} + const items: ReactElement[] = [] + if (dataset?.cell) { + items.push(menuItem(dataset.cell)) + if (!cellListLoading) + items.push(None) + } + if (cellListLoading) + items.push() + if (cellList.length) + items.push(...cellList.filter(c => c.id !== dataset.cell?.id).map(menuItem)) + if (!items.length) + items.push(No cells defined) + return items + } + return ( - columns={columns} - rows={[ - (dataset: DatasetFields) => {dataset.id}, - (dataset: DatasetFields) => {dataset.date}, + row_generator={(dataset, context) => [ + {dataset.id}, + {dataset.date}, // these fields have the same shape, so condense the code. // as const stops TypeScript from complaining about strings assigned to keyof DatasetFields ...(['name', 'type', 'purpose'] as const).map( - (n) => ((dataset: DatasetFields, context: CellContext) => + (n) => - ) + ), - (dataset: DatasetFields) => {dataset.cell}, - (dataset: any) => + + + , + selected?.id === dataset.id? setSelected(null) : setSelected(dataset)}> , - (dataset: any, context) => + updateRow(dataset).then(context.refresh)} > diff --git a/frontend/src/Equipment.tsx b/frontend/src/Equipment.tsx index 9f6934d3..8c4132b6 100644 --- a/frontend/src/Equipment.tsx +++ b/frontend/src/Equipment.tsx @@ -8,7 +8,7 @@ import IconButton from '@mui/material/IconButton'; import Container from '@mui/material/Container'; import SaveIcon from '@mui/icons-material/Save'; import DeleteIcon from '@mui/icons-material/Delete'; -import AsyncTable, {CellContext} from './AsyncTable'; +import AsyncTable from './AsyncTable'; import Connection from "./APIConnection"; export type EquipmentFields = { @@ -47,7 +47,7 @@ const columns = [ {label: 'Delete', help: 'Delete equipment that is not in use'}, ] -const string_fields: (keyof EquipmentFields)[] = ['name', 'type'] +const string_fields = ['name', 'type'] as const export default function Equipment() { const classes = useStyles(); @@ -71,10 +71,10 @@ export default function Equipment() { return ( - columns={columns} - rows={[ - ...string_fields.map(n => (equipment: EquipmentFields, context: CellContext) => + row_generator={(equipment, context) => [ + ...string_fields.map(n => { equipment.in_use ? equipment[n] : } ), - (equipment, context) => + updateEquipment(equipment).then(context.refresh)} + disabled={!context.value_changed || equipment.in_use} + onClick={ + context.is_new_row? + () => addNewEquipment(equipment).then(context.refresh_all_rows) : + () => updateEquipment(equipment).then(context.refresh) + } > - + {context.is_new_row? : } , - (equipment, context) => + context.is_new_row? : ]} - new_entry_row={[ - ...string_fields.map(n => (equipment: EquipmentFields, context: CellContext) => - { - equipment.in_use ? equipment[n] : - } - ), - (equipment, context) => - - - addNewEquipment(equipment).then(context.refresh_all_rows)} - > - - - - - , - - ]} new_row_values={{name: '', type: ''}} initial_url={`equipment/?all=true`} styles={classes} diff --git a/frontend/src/Files.tsx b/frontend/src/Files.tsx index 5c657b95..18ff734c 100644 --- a/frontend/src/Files.tsx +++ b/frontend/src/Files.tsx @@ -76,20 +76,20 @@ export default function Files(props: FilesProps) { return ( - key="files" columns={columns} - rows={[ - (file: any) => {file.relative_path}, - (file: any) => {file.last_observed_size}, - (file: any) => { + row_generator={(file, context) => [ + {file.relative_path}, + {file.last_observed_size}, + { Intl.DateTimeFormat('en-GB', datetimeOptions).format( Date.parse(file.last_observed_time) )} , - (file: any) => {file_state(file)}, - (file: any) => {file.datasets.length}, - (file: any, context) => + {file_state(file)}, + {file.datasets.length}, + forceReimport(file).then(context.refresh)}> ]} diff --git a/frontend/src/HarvesterDetail.tsx b/frontend/src/HarvesterDetail.tsx index b79e4b0b..80a518a1 100644 --- a/frontend/src/HarvesterDetail.tsx +++ b/frontend/src/HarvesterDetail.tsx @@ -63,8 +63,6 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { const [selected, setSelected] = useState(null) - const [lastUpdated, setLastUpdated] = useState(new Date()) - const addNewPath = (data: MonitoredPathFields) => { const insert_data = {harvester: harvester.id, path: data.path, stable_time: data.stable_time} return Connection.fetch('monitored_paths/', {body: JSON.stringify(insert_data), method: 'POST'}) @@ -90,23 +88,24 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { {harvester.name} - monitored paths - key={`${harvester.id}_paths`} columns={columns} - rows={[ - (row: any, context) => + row_generator={(row, context) => [ + , - (row: any, context) => + , - (row: any, context) => + context.is_new_row? : , - (row: any) => + context.is_new_row? : selected?.id === row.id? setSelected(null) : setSelected(row)}> , - (row: any, context) => + updatePath(row).then(context.refresh)} + disabled={!context.value_changed} + onClick={ + context.is_new_row? + () => addNewPath(row).then(context.refresh_all_rows) : + () => updatePath(row).then(context.refresh) + } > - + {context.is_new_row? : } , - (row: any, context) => + context.is_new_row? : deletePath(row).then(context.refresh)} @@ -151,49 +154,8 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { , ]} initial_url={`monitored_paths/?harvester__id=${harvester.id}&all=true`} - new_entry_row={[ - (new_row: any, context) => - - , - (new_row: any, context) => - - - , - , - , - (new_row: any, context) => - addNewPath(new_row).then(context.refresh_all_rows)} - > - - - , - , - ]} new_row_values={{path: "", stable_time: 60}} styles={classes} - last_updated={lastUpdated} /> {selected !== null && } diff --git a/frontend/src/Harvesters.tsx b/frontend/src/Harvesters.tsx index e9abc3ec..040cb880 100644 --- a/frontend/src/Harvesters.tsx +++ b/frontend/src/Harvesters.tsx @@ -81,11 +81,11 @@ export default function Harvesters() { return ( - { columns={columns} - rows={[ - (row: any) => {row.id}, - (row: any, context) => + row_generator={(row, context) => [ + {row.id}, + , - (row: any) => + { (row.last_check_in && Intl.DateTimeFormat( @@ -104,7 +104,7 @@ export default function Harvesters() { ) || (None) } , - (row: any, context) => + , - (row: any) => + selected?.id === row.id? setSelected(null) : setSelected(row)}> , - (row: any, context) => + updateHarvester(row).then(context.refresh)} > , - (row: any, context) => + ; - tooltipProps?: Partial; - typographyProps?: Partial; -} - -type CompleteHeading = { - label: string; - help: string; - tableCellProps: Partial; - tooltipProps: Partial; - typographyProps: Partial; -} - -export type RowFunProps = { - savedRow?: T; - onRowSave: (row: any) => void; - selected: boolean; - onSelectRow: (id: any) => void; - disabledSave?: boolean; - addIcon?: boolean; - [key: string]: any; -} - -type RowFun = ((row: any, i: number, array: any[]) => ReactComponentElement) | - ((row: any, i: number) => ReactComponentElement) | - ((row: any) => ReactComponentElement) - -export type PaginatedTableProps = { - column_headings: Heading[]; - row_fun: RowFun; - initial_url: string; - new_entry_row?: ReactComponentElement; - styles?: any; - [key: string]: any; -} - -type PaginatedTableState = { - row_data: any[]; - links: PaginationLinks; - last_updated: Date; - loading: boolean; - loading_rows: number[]; -} - -export type PaginationLinks = { - previous?: string | null, - next?: string | null, -} - -type PaginationDataFun = (url?: string | null) => APIResponse - -type PaginationProps = PaginationLinks & { - get_data_fun: PaginationDataFun; - position: string; -} - - -class Pagination extends Component { - render() { - return ( -
- - -
- ) - } -} - -export default class PaginatedTable extends Component { - current_url: string = ""; - - state: PaginatedTableState = { - row_data: [], - links: {previous: null, next: null}, - last_updated: new Date(0), - loading: true, - loading_rows: [] - } - - constructor(props: PaginatedTableProps) { - super(props) - if (!this.current_url) this.current_url = props.initial_url - } - - componentDidMount() { - this.get_data(this.props.initial_url) - console.log("Mounted PaginatedTable", this) - } - - componentDidUpdate(prevProps: PaginatedTableProps) { - console.log("Updated PaginatedTable", this, prevProps) - // Typical usage (don't forget to compare props): - if (this.props.initial_url !== prevProps.initial_url) - this.setState({row_data: []}) - if (this.props.initial_url !== prevProps.initial_url || this.props.last_updated !== prevProps.last_updated) - this.get_data(this.props.initial_url) - } - - get_data: PaginationDataFun = async (url) => { - this.setState({loading: true}) - if (!url) return; - this.current_url = url; - await Connection.fetch(url) - .then((res: APIResponse) => { - console.log(res); - this.setState({ - row_data: res.results, - links: { - next: res.next, - previous: res.previous - }, - loading: false, - loading_rows: [] - }) - }) - .catch(e => { - console.error('Paginated Table error', e) - this.setState({loading: false, loading_rows: []}) - }) - } - - update_single_row = async (row: {id: number, [key: string]: any}) => { - const loading_rows = this.state.loading_rows.filter(i => i !== row.id) - loading_rows.push(row.id) - this.setState({loading_rows: loading_rows}) - await Connection.fetch(row.url) - .then((res: SingleAPIResponse) => { - console.log(res) - this.setState({row_data: this.state.row_data.map(r => r.id === row.id ? res : r)}) - }) - .catch(e => console.error('PaginatedTable.update_single_row error', e)) - .finally( - () => this.setState({loading_rows: this.state.loading_rows.filter(i => i !== row.id)}) - ) - } - - get header_row() { - const column_headings: CompleteHeading[] = this.props.column_headings.map( - (heading: Heading) => ({ - label: heading.label, - help: heading.help || "", - tableCellProps: heading.tableCellProps || {}, - tooltipProps: heading.tooltipProps || {}, - typographyProps: heading.typographyProps || {}, - }) - ) - - return ( - - - {column_headings.map((heading, i) => - - { - - - {heading.label} - - - } - - )} - - ) - } - - get loading_row() { - return - - - - - } - - render() { - return ( -
- - - - {this.header_row} - { - - { - this.state.loading && this.loading_row - } - {!this.state.loading && this.state.row_data.map(this.props.row_fun)} - {!this.state.loading && this.props.new_entry_row} - - } -
- - -
- ) - } -} \ No newline at end of file +export type unused = any +// /** +// * Offer a table with previous/next links. +// */ +// import classNames from 'classnames' +// import React, {Component, ReactComponentElement} from "react"; +// import TableContainer from "@mui/material/TableContainer"; +// import Table from "@mui/material/Table"; +// import TableBody from "@mui/material/TableBody"; +// import Button from '@mui/material/Button'; +// import Connection, {APIResponse, APIObject, SingleAPIResponse} from "./APIConnection"; +// import TableRow from "@mui/material/TableRow"; +// import TableCell, {TableCellProps} from "@mui/material/TableCell"; +// import LoadingButton from "@mui/lab/LoadingButton"; +// import Tooltip, {TooltipProps} from "@mui/material/Tooltip"; +// import Typography, {TypographyProps} from "@mui/material/Typography"; +// import TableHead from "@mui/material/TableHead"; +// import AsyncTable from "./AsyncTable"; +// +// type PaginatedTableProps = { +// initial_url: string; +// } +// +// type PaginatedTableState = { +// links: PaginationLinks; +// current_url: string; +// } +// +// export type PaginationLinks = { +// previous?: string | null, +// next?: string | null, +// } +// +// type PaginationDataFun = (url?: string | null) => APIResponse +// +// type PaginationProps = PaginationLinks & { +// get_data_fun: PaginationDataFun; +// position: string; +// } +// +// +// class Pagination extends AsyncTable { +// render() { +// return ( +//
+// +// +//
+// ) +// } +// } +// +// export default class PaginatedTable extends Component { +// +// state: PaginatedTableState = { +// links: {previous: null, next: null}, +// current_url: "" +// } +// +// constructor(props: PaginatedTableProps) { +// super(props) +// if (!this.state.current_url) this.state.current_url = props.initial_url +// } +// +// componentDidMount() { +// this.get_data(this.props.initial_url) +// console.log("Mounted PaginatedTable", this) +// } +// +// render() { +// return ( +//
+// +// +// +//
+// ) +// } +// } \ No newline at end of file diff --git a/frontend/src/UserRoleSet.tsx b/frontend/src/UserRoleSet.tsx index d46d3e85..7da6dceb 100644 --- a/frontend/src/UserRoleSet.tsx +++ b/frontend/src/UserRoleSet.tsx @@ -1,4 +1,4 @@ -import Connection, {User} from './APIConnection' +import Connection, {APIConnection, User} from './APIConnection' import React, {Component} from "react"; import IconButton from "@mui/material/IconButton"; import Autocomplete from "@mui/material/Autocomplete"; @@ -117,6 +117,14 @@ export default class UserRoleSet extends Component { async componentDidMount() { Connection.fetch('users/?all=true') + .then(r => { + r = APIConnection.get_result_array(r) + if (typeof r === 'number') { + throw new Error(`users/?all=true -> ${r}`) + } + return r + }) + // @ts-ignore .then(r => this.setState({all_users: r})) } From a6cebb108877cf9394911ffb6c1369bba2ad88e3 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Fri, 27 Jan 2023 17:04:24 +0000 Subject: [PATCH 33/79] unmanaged timeseriesdata table --- .../galvanalyser/management/__init__.py | 0 .../management/commands/__init__.py | 0 .../management/commands/init_db.py | 23 ++++++++ django/backend_django/galvanalyser/models.py | 11 ++-- .../galvanalyser/serializers.py | 9 ++-- django/backend_django/galvanalyser/views.py | 52 ++----------------- django/server.sh | 1 + 7 files changed, 38 insertions(+), 58 deletions(-) create mode 100644 django/backend_django/galvanalyser/management/__init__.py create mode 100644 django/backend_django/galvanalyser/management/commands/__init__.py create mode 100644 django/backend_django/galvanalyser/management/commands/init_db.py diff --git a/django/backend_django/galvanalyser/management/__init__.py b/django/backend_django/galvanalyser/management/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/django/backend_django/galvanalyser/management/commands/__init__.py b/django/backend_django/galvanalyser/management/commands/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/django/backend_django/galvanalyser/management/commands/init_db.py b/django/backend_django/galvanalyser/management/commands/init_db.py new file mode 100644 index 00000000..d1394a73 --- /dev/null +++ b/django/backend_django/galvanalyser/management/commands/init_db.py @@ -0,0 +1,23 @@ +from django.core.management.base import BaseCommand +from django.db import connection + + +class Command(BaseCommand): + help = "Create timeseries_data table in database." + + def handle(self, *args, **options): + self.stdout.write("Creating timeseries_data table... ") + with connection.cursor() as curs: + curs.execute(""" + CREATE TABLE IF NOT EXISTS timeseries_data ( + sample bigint NOT NULL, + column_id bigint NOT NULL, + value double precision NOT NULL, + PRIMARY KEY (sample, column_id), + FOREIGN KEY (column_id) + REFERENCES "galvanalyser_datacolumn" (id) MATCH SIMPLE + ON UPDATE CASCADE + ON DELETE RESTRICT + ) WITH (OIDS = FALSE) + """) + self.stdout.write(self.style.SUCCESS('Complete.')) diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index 4890ae33..38e7686c 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -172,14 +172,15 @@ class Meta: class TimeseriesData(models.Model): sample = models.PositiveBigIntegerField(null=False) - column = models.ForeignKey(to=DataColumn, related_name='values', null=False, on_delete=models.CASCADE) + column_id = models.PositiveIntegerField(null=False) value = models.FloatField(null=False) class Meta: - indexes = [ - models.Index('sample', 'column_id', name='sc_ref') - ] - unique_together = [['sample', 'column']] + managed = False + db_table = "timeseriesdata" + + def __str__(self): + return f"{self.column_id}[{self.sample}]: {self.value}" class TimeseriesRangeLabel(models.Model): diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py index 0428738d..aa7be247 100644 --- a/django/backend_django/galvanalyser/serializers.py +++ b/django/backend_django/galvanalyser/serializers.py @@ -50,7 +50,6 @@ class Meta: model = Harvester fields = ['url', 'id', 'name', 'sleep_time', 'last_check_in', 'user_sets'] read_only_fields = ['url', 'id', 'last_check_in', 'user_sets'] - depth = 1 class HarvesterConfigSerializer(serializers.HyperlinkedModelSerializer): @@ -82,7 +81,6 @@ class Meta: 'standard_units', 'standard_columns', 'max_upload_bytes' ] read_only_fields = fields - depth = 1 # max depth class MonitoredPathSerializer(serializers.HyperlinkedModelSerializer): @@ -145,7 +143,6 @@ class Meta: 'last_observed_time', 'last_observed_size', 'datasets', 'errors' ] - depth = 1 class HarvestErrorSerializer(serializers.HyperlinkedModelSerializer): @@ -180,18 +177,19 @@ def get_user_sets(self, instance): instance.file.monitored_path, context={'request': self.context.get('request')} ).data.get('user_sets') + def update(self, instance, validated_data): + pass + class Meta: model = Dataset fields = ['url', 'id', 'name', 'date', 'type', 'purpose', 'cell', 'equipment', 'file', 'user_sets'] read_only_fields = ['date', 'file', 'id', 'url', 'user_sets'] - depth = 1 class EquipmentSerializer(serializers.HyperlinkedModelSerializer): class Meta: model = Equipment fields = ['url', 'id', 'name', 'type', 'datasets'] - depth = 1 class DataUnitSerializer(serializers.HyperlinkedModelSerializer): @@ -236,7 +234,6 @@ class Meta: 'url', 'name', 'users', 'readable_paths', 'editable_paths', 'readable_harvesters', 'editable_harvesters' ] - depth = 1 class UserSetSerializer(serializers.HyperlinkedModelSerializer): diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 0a9d66fd..27726094 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -2,7 +2,6 @@ import sys from django.db.models import Q - from .serializers import HarvesterSerializer, \ HarvesterConfigSerializer, \ MonitoredPathSerializer, \ @@ -317,48 +316,10 @@ def report(self, request, pk: int = None): ) checkpoint('created value map', time_value_add) - # # Enter data en masse to avoid numerous expensive database calls - # time_ts_rm = time.time() - # TimeseriesData.objects.filter( - # column=column, - # sample__in=column_data['values'].keys() - # ).delete() - # time_ts_prep = checkpoint('deleted existing timeseries data', time_ts_rm) - # ts = [ - # TimeseriesData(sample=k, value=v, column=column) - # for k, v in column_data['values'].items() - # ] - # time_ts_add = checkpoint('prepared ts objects', time_ts_prep) - # TimeseriesData.objects.bulk_create( - # [TimeseriesData(sample=k, value=v, column=column) - # for k, v in column_data['values'].items()] - # ) - # checkpoint('created timeseries data', time_ts_add) - # checkpoint('column complete', time_col_start) - - # time_ts_rm = time.time() - # TimeseriesData.objects.filter( - # column=column, - # sample__in=column_data['values'].keys() - # ).delete() - # time_ts_prep = checkpoint('deleted existing timeseries data', time_ts_rm) - # rows = [] - # for s, v in column_data['values'].items(): - # rows.append((int(s), int(v), column.id)) - # time_ts_add = checkpoint('prepared ts objects', time_ts_prep) - # from django.db import connection - # with connection.cursor() as cursor: - # query = cursor.executemany( - # "INSERT INTO galvanalyser_timeseriesdata (sample, value, column_id) VALUES(%s, %s, %s)", - # rows) - # checkpoint('created timeseries data', time_ts_add) - # checkpoint('column complete', time_col_start) - time_ts_rm = time.time() - TimeseriesData.objects.filter( - column=column, - sample__in=column_data['values'].keys() - ).delete() + from django.db import connection + with connection.cursor() as cursor: + cursor.execute(f"DELETE FROM timeseries_data WHERE column_id='{column.id}' AND sample IN ({','.join(column_data['values'].keys())})") time_ts_prep = checkpoint('deleted existing timeseries data', time_ts_rm) class IteratorFile(io.TextIOBase): @@ -421,17 +382,14 @@ def readline(self): self.buffered_chars = self._f.write(remainder) return data rows = [] - i = TimeseriesData.objects.last().id for s, v in column_data['values'].items(): - i += 1 - rows.append(f"{i}\t{int(s)}\t{int(v)}\t{column.id}") + rows.append(f"{int(s)}\t{column.id}\t{int(v)}") iter_file = IteratorFile(rows.__iter__()) time_ts_add = checkpoint('prepared ts objects', time_ts_prep) - from django.db import connection with connection.cursor() as cursor: cursor.copy_expert( - 'COPY galvanalyser_timeseriesdata FROM STDIN', + 'COPY timeseries_data FROM STDIN', iter_file ) checkpoint('created timeseries data', time_ts_add) diff --git a/django/server.sh b/django/server.sh index cb5da807..31f57b1a 100644 --- a/django/server.sh +++ b/django/server.sh @@ -17,6 +17,7 @@ done cd backend_django || exit 1 python manage.py makemigrations python manage.py migrate +python manage.py init_db >&2 echo "... populating database" python manage.py loaddata galvanalyser/fixtures/DataUnit.json From 31243f74a3711a8c07d4d5855c1e10a71afeb517 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Fri, 27 Jan 2023 17:04:55 +0000 Subject: [PATCH 34/79] testing old backend for comparison --- .env | 4 ++-- .../experiment/timeseries_data_row.py | 19 ++++++++++++++++--- backend/setup.py | 4 ++-- backend/test/test_harvester.py | 1 + docker-compose.override.yml | 18 +++++++++++++++++- docker-compose.yml | 2 +- 6 files changed, 39 insertions(+), 9 deletions(-) diff --git a/.env b/.env index bc17149a..18bc874f 100644 --- a/.env +++ b/.env @@ -18,8 +18,8 @@ GALVANALYSER_HARVESTER_TEST_PATH=./.run/test_datafiles GALVANALYSER_HARVESTER_BASE_PATH=./.run/datafiles # username and password for default harvester account -HARVESTER_USERNAME=harv -HARVESTER_PASSWORD=harv +HARVESTER_USERNAME=postgres +HARVESTER_PASSWORD=postgres # secret used to encrypt JWT for galvanalyser web app and api GALVANALYSER_SECRET_KEY=secret_key diff --git a/backend/galvanalyser/database/experiment/timeseries_data_row.py b/backend/galvanalyser/database/experiment/timeseries_data_row.py index 78f22910..65646fa9 100644 --- a/backend/galvanalyser/database/experiment/timeseries_data_row.py +++ b/backend/galvanalyser/database/experiment/timeseries_data_row.py @@ -1,6 +1,7 @@ import psycopg2 from galvanalyser.database.util.iter_file import IteratorFile from timeit import default_timer as timer +import time from galvanalyser.database.experiment import ColumnRow @@ -71,6 +72,8 @@ def insert_input_file( column_name_to_id = {} # create mapping from col id to col name, creating new columns as # appropriate + print(f"Getting column data") + start = time.time() columns = input_file.get_columns() has_record_column = False for name, type_id in columns: @@ -91,12 +94,20 @@ def insert_input_file( ) col.insert(conn) column_name_to_id[name] = col.id + print(f"Got column data ({time.time() - start})") + checkpoint = time.time() print("Getting data") row_generator = input_file.get_data_row_generator( column_name_to_id, last_values, ) + print(f"Got data ({time.time() - checkpoint})") + checkpoint = time.time() + print(f"Creating iter_file") + iter_file = IteratorFile(row_generator) + with open(f"/usr/data/{input_file.metadata['Machine Type']}.itr", "w+") as f: + f.writelines(iter_file) iter_file = IteratorFile(row_generator) num_value_columns = len(columns) if has_record_column: @@ -104,13 +115,15 @@ def insert_input_file( start_row = 0 if last_values is None else last_values[0].sample_no num_rows_to_insert = input_file.metadata["num_rows"] - start_row expected_insert_count = num_rows_to_insert * num_value_columns + print(f"Created iter_file ({time.time() - checkpoint})") + checkpoint = time.time() with conn.cursor() as cursor: print("Copying data to table") - start = timer() cursor.copy_expert( 'COPY experiment.timeseries_data FROM STDIN', iter_file ) - end = timer() + print(f"Copied data ({time.time() - checkpoint})") + checkpoint = time.time() if cursor.rowcount != expected_insert_count: raise battery_exceptions.InsertError( "Insert failed. Inserted {} of {} values ({} rows * {} columns) before failure".format( @@ -123,7 +136,7 @@ def insert_input_file( print("Done copying data to table") print( "Inserted {} rows ({} sample sets) in {:.2f} seconds".format( - cursor.rowcount, num_rows_to_insert, end - start + cursor.rowcount, num_rows_to_insert, time.time() - start ) ) diff --git a/backend/setup.py b/backend/setup.py index d48f3aae..cdcda32e 100644 --- a/backend/setup.py +++ b/backend/setup.py @@ -19,7 +19,7 @@ ], python_requires='>=3.5', install_requires=[ - 'sqlalchemy', + 'sqlalchemy==1.4.46', 'sqlalchemy_utils', 'marshmallow', 'intervals', @@ -33,6 +33,6 @@ 'psutil', 'maya', 'xlrd==1.2.0', - 'openpyxl', + 'openpyxl' ] ) diff --git a/backend/test/test_harvester.py b/backend/test/test_harvester.py index 654bc077..10580700 100644 --- a/backend/test/test_harvester.py +++ b/backend/test/test_harvester.py @@ -11,6 +11,7 @@ import os import json from datetime import datetime, timezone, timedelta +import unittest diff --git a/docker-compose.override.yml b/docker-compose.override.yml index 0c4a1894..d3705b2c 100644 --- a/docker-compose.override.yml +++ b/docker-compose.override.yml @@ -8,7 +8,7 @@ services: depends_on: - postgres ports: - - "5001:5000" + - "5000:5000" volumes: - ./django:/usr/app restart: unless-stopped @@ -42,3 +42,19 @@ services: ports: - "3000:3000" command: yarn start + +# old_worker: +# build: +# dockerfile: Dockerfile +# context: ./backend +# command: python manage.py test +# depends_on: +# - postgres +# volumes: +# - ./backend:/usr/app +# - "${GALVANALYSER_HARVESTER_BASE_PATH}:/usr/data" +# - "${GALVANALYSER_HARVESTER_TEST_PATH}:/usr/test_data" +# - "${CELERY_LOG_DIR}:/var/log/celery" +# working_dir: /usr/app +# env_file: +# - ./.env diff --git a/docker-compose.yml b/docker-compose.yml index 752ba4d6..936a606c 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -8,7 +8,7 @@ services: depends_on: - postgres ports: - - "5001:5000" + - "5000:5000" volumes: - ./backend:/usr/app - "${GALVANALYSER_HARVESTER_TEST_PATH}:/usr/test_data" From 9edab3bee51de19b558e0f14dd3d33b402a2064f Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Thu, 2 Feb 2023 17:34:35 +0000 Subject: [PATCH 35/79] harvester screens for data; async responsive frontend --- django/backend_django/galvanalyser/models.py | 5 +- .../galvanalyser/serializers.py | 50 +++-- django/backend_django/galvanalyser/views.py | 12 +- frontend/src/APIConnection.ts | 29 ++- frontend/src/AsyncTable.tsx | 96 +++++---- frontend/src/Cells.tsx | 36 ++-- frontend/src/Datasets.tsx | 89 +++++++-- frontend/src/Equipment.tsx | 2 +- frontend/src/Files.tsx | 2 +- frontend/src/HarvesterDetail.tsx | 2 +- frontend/src/Harvesters.tsx | 2 +- harvester/harvester/api.py | 10 +- harvester/harvester/harvest.py | 186 +++++++++++++++++- harvester/harvester/run.py | 2 +- harvester/harvester/settings.py | 2 + 15 files changed, 425 insertions(+), 100 deletions(-) diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index 38e7686c..3c18b21c 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -177,11 +177,14 @@ class TimeseriesData(models.Model): class Meta: managed = False - db_table = "timeseriesdata" + db_table = "timeseries_data" def __str__(self): return f"{self.column_id}[{self.sample}]: {self.value}" + def __repr__(self): + return str(self) + class TimeseriesRangeLabel(models.Model): dataset = models.ForeignKey(to=Dataset, related_name='range_labels', null=False, on_delete=models.CASCADE) diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py index aa7be247..3c355943 100644 --- a/django/backend_django/galvanalyser/serializers.py +++ b/django/backend_django/galvanalyser/serializers.py @@ -10,7 +10,8 @@ DataColumn, \ TimeseriesData, \ TimeseriesRangeLabel, \ - FileState + FileState, DataColumnStringKeys +from django.db import connection from django.contrib.auth.models import User, Group from django.conf.global_settings import DATA_UPLOAD_MAX_MEMORY_SIZE from rest_framework import serializers @@ -77,10 +78,11 @@ def get_max_upload_bytes(self, instance): class Meta: model = Harvester fields = [ - 'url', 'id', 'api_key', 'name', 'last_check_in', 'sleep_time', 'monitored_paths', + 'url', 'id', 'api_key', 'name', 'sleep_time', 'monitored_paths', 'standard_units', 'standard_columns', 'max_upload_bytes' ] read_only_fields = fields + depth = 1 class MonitoredPathSerializer(serializers.HyperlinkedModelSerializer): @@ -126,17 +128,41 @@ class Meta: model = MonitoredPath fields = ['url', 'id', 'path', 'stable_time', 'harvester', 'user_sets'] read_only_fields = ['url', 'id', 'harvester', 'user_sets'] - depth = 1 class ObservedFileSerializer(serializers.HyperlinkedModelSerializer): + upload_info = serializers.SerializerMethodField() + + def get_upload_info(self, instance): + if not self.context.get('with_upload_info'): + return None + try: + columns = DataColumn.objects.filter(dataset__file=instance) + column_data = [] + for c in columns: + keys = DataColumnStringKeys.objects.filter(column=c).order_by('key') + column_data.append({ + 'name': c.name, + 'id': c.id, + 'keymap': [{'key': k.key, 'value': k.string} for k in keys] + }) + with connection.cursor() as cur: + cur.execute(f"SELECT sample FROM timeseries_data WHERE column_id={columns.first().id} ORDER BY sample DESC LIMIT 1") + last_record = cur.fetchone()[0] + return { + 'columns': column_data, + 'last_record_number': last_record + } + except BaseException as e: + return {'columns': [], 'last_record_number': None, 'error': str(e)} + class Meta: model = ObservedFile fields = [ 'url', 'id', 'monitored_path', 'relative_path', 'state', 'last_observed_time', 'last_observed_size', 'errors', - 'datasets' + 'datasets', 'upload_info' ] read_only_fields = [ 'url', 'id', 'monitored_path', 'relative_path', @@ -169,6 +195,13 @@ class Meta: read_only_fields = ['id', 'url', 'in_use'] +class EquipmentSerializer(serializers.HyperlinkedModelSerializer): + class Meta: + model = Equipment + fields = ['url', 'id', 'name', 'type', 'datasets'] + read_only_fields = ['url', 'id', 'datasets'] + + class DatasetSerializer(serializers.HyperlinkedModelSerializer): user_sets = serializers.SerializerMethodField() @@ -177,21 +210,12 @@ def get_user_sets(self, instance): instance.file.monitored_path, context={'request': self.context.get('request')} ).data.get('user_sets') - def update(self, instance, validated_data): - pass - class Meta: model = Dataset fields = ['url', 'id', 'name', 'date', 'type', 'purpose', 'cell', 'equipment', 'file', 'user_sets'] read_only_fields = ['date', 'file', 'id', 'url', 'user_sets'] -class EquipmentSerializer(serializers.HyperlinkedModelSerializer): - class Meta: - model = Equipment - fields = ['url', 'id', 'name', 'type', 'datasets'] - - class DataUnitSerializer(serializers.HyperlinkedModelSerializer): class Meta: model = DataUnit diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 27726094..7a7cc725 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -195,7 +195,7 @@ def report(self, request, pk: int = None): monitored_path=path, relative_path=file_rel_path, defaults={'state': FileState.IMPORT_FAILED} - ), + )[0], error=str(error) ) else: @@ -316,11 +316,8 @@ def report(self, request, pk: int = None): ) checkpoint('created value map', time_value_add) - time_ts_rm = time.time() + time_ts_prep = time.time() from django.db import connection - with connection.cursor() as cursor: - cursor.execute(f"DELETE FROM timeseries_data WHERE column_id='{column.id}' AND sample IN ({','.join(column_data['values'].keys())})") - time_ts_prep = checkpoint('deleted existing timeseries data', time_ts_rm) class IteratorFile(io.TextIOBase): """ given an iterator which yields strings, @@ -406,7 +403,10 @@ def readline(self): file.save() - return Response(ObservedFileSerializer(file, context={'request': self.request}).data) + return Response(ObservedFileSerializer(file, context={ + 'request': self.request, + 'with_upload_info': content['status'] == 'begin' + }).data) else: return error_response('Unrecognised task') else: diff --git a/frontend/src/APIConnection.ts b/frontend/src/APIConnection.ts index 84ddbcd0..e56ea90d 100644 --- a/frontend/src/APIConnection.ts +++ b/frontend/src/APIConnection.ts @@ -117,8 +117,8 @@ export class APIConnection { json.results = await Promise.all( json.results.map(async (r: SingleAPIResponse) => await this.fetch_children(r, options, depth - 1)) ) - return json } + return await this.fetch_children(json, options, depth - 1) }) .then(r => { console.log(url, options, depth, r); return r @@ -137,12 +137,27 @@ export class APIConnection { fetch_children: (r: SingleAPIResponse, options: any, depth: number) => Promise = async (r: SingleAPIResponse, options: any, depth: number) => { - for (const k in r) { - if (k === 'url') - continue - if (typeof r[k] === "string" && r[k].startsWith(this.url)) { - r[k] = await this.fetch(r[k], options, depth) - console.log(r, k, r[k]) + if (depth >= 0) { + // Children are always GET requests because we don't want to PATCH/etc them + const _fetch = async (x: any) => { + if (typeof x === "string" && x.startsWith(this.url)) { + console.log("fetch child for", r.url, x) + return await this.fetch(x, options, depth) + } + return x + } + + if (options?.method) { + options.method = "GET" + delete options.body + } + for (const k in r) { + if (k === 'url') + continue + if (r[k] instanceof Array) + r[k] = await Promise.all(r[k].map((x: any) => _fetch(x))) + else + r[k] = await _fetch(r[k]) } } return r diff --git a/frontend/src/AsyncTable.tsx b/frontend/src/AsyncTable.tsx index b7633505..310237a6 100644 --- a/frontend/src/AsyncTable.tsx +++ b/frontend/src/AsyncTable.tsx @@ -2,7 +2,7 @@ import React, {Component, ReactElement, BaseSyntheticEvent, ReactEventHandler} f import TableContainer from "@mui/material/TableContainer"; import Table from "@mui/material/Table"; import TableBody from "@mui/material/TableBody"; -import Connection, {APIConnection, APIObject} from "./APIConnection"; +import Connection, {APIConnection, APIObject, SingleAPIResponse} from "./APIConnection"; import TableRow from "@mui/material/TableRow"; import TableCell, {TableCellProps} from "@mui/material/TableCell"; import CircularProgress from "@mui/material/CircularProgress"; @@ -23,7 +23,9 @@ export type RowGeneratorContext = { columns: Column[]; update: ReactEventHandler; update_direct: (field_name: K, new_value: T[K]) => void; - refresh: () => void; + mark_loading: (state?: boolean) => void; + refresh: (row_data: any) => void; + refresh_from_api: () => void; refresh_all_rows: () => void; is_new_row: boolean; value_changed: boolean; @@ -44,7 +46,7 @@ type CompleteHeading = { export type AsyncTableProps = { columns: Column[]; row_generator: RowGenerator; - initial_url: string; + url: string; new_row_values?: Partial; styles?: any; } @@ -85,8 +87,6 @@ export const NEW_ROW_ID = -1 * This class abstracts away a lot of repetitive table-building code. */ export default class AsyncTable extends Component, AsyncTableState> { - current_url: string = ""; - state: AsyncTableState = { row_data: [], new_row: null, @@ -97,7 +97,6 @@ export default class AsyncTable extends Component) { super(props) - if (!this.current_url) this.current_url = props.initial_url if (props.new_row_values !== undefined) this.state.new_row = this.new_row_template } @@ -107,25 +106,40 @@ export default class AsyncTable extends Component) { - console.log("Updated AsyncTable", this, prevProps) + console.log("Updating AsyncTable...", this, prevProps) // Typical usage (don't forget to compare props): - if (this.props.initial_url !== prevProps.initial_url) { + if (this.props.url !== prevProps.url) { this.setState({row_data: []}) - this.get_data(this.props.initial_url) + this.get_data(this.props.url) } + console.log("Updated AsyncTable", this) } reset_new_row = () => this.setState({new_row: this.props.new_row_values? this.new_row_template : null}) - get_data: (url: string) => void = async (url) => { + mark_row_loading = (row_id: number, status: boolean = true) => { + const rows = this.state.loading_rows.filter(i => i !== row_id) + if (status) + rows.push(row_id) + this.setState({loading_rows: rows}) + } + + mark_row_changed = (row_id: number, status: boolean = true) => { + const rows = this.state.changed_rows.filter(i => i !== row_id) + if (status) + rows.push(row_id) + this.setState({changed_rows: rows}) + } + + get_data: (url?: string) => void = async (url) => { this.setState({loading: true}) - if (!url) return; - this.current_url = url; + if (!url) + url = this.props.url; await Connection.fetch(url) .then(APIConnection.get_result_array) .then((res) => { @@ -145,10 +159,20 @@ export default class AsyncTable extends Component { - const loading_rows = this.state.loading_rows.filter(i => i !== row.id) - loading_rows.push(row.id) - this.setState({loading_rows: loading_rows}) + refresh_row = async (row: SingleAPIResponse, is_result: boolean = true) => { + this.mark_row_loading(row.id) + + const _update = (row_data: SingleAPIResponse) => { + this.setState({ + row_data: this.state.row_data.map(r => r.id === row.id ? row_data : r) + }) + this.mark_row_changed(row.id, false) + this.mark_row_loading(row.id, false) + } + + if (is_result) + return _update(row) + await Connection.fetch(row.url) .then(APIConnection.get_result_array) .then((res) => { @@ -163,21 +187,18 @@ export default class AsyncTable extends Component r.id === row.id ? row_data : r), - changed_rows: this.state.changed_rows.filter(i => i !== row_data.id) - }) + _update(row_data) } }) .catch(e => console.error('AsyncTable.update_single_row error', e, row)) .finally( - () => this.setState({loading_rows: this.state.loading_rows.filter(i => i !== row.id)}) + () => this.mark_row_loading(row.id, false) ) } update_all = async () => { this.reset_new_row() - return this.get_data(this.current_url) + return this.get_data() } get header_row() { @@ -218,24 +239,27 @@ export default class AsyncTable extends Component { - let update_fun: RowGeneratorContext["update_direct"] = (name, value) => this.setState({ - // Amend row_data to include new value for [name] - row_data: this.state.row_data.map( - r => r.id === row.id ? {...row, [name]: value} : r - ), - changed_rows: [...this.state.changed_rows, row.id] - }) - if (is_new_row) - update_fun = (name, value) => this.setState({ - new_row: {...this.state.new_row, [name]: value, _changed: true}, - changed_rows: [...this.state.changed_rows, row.id] + let update_fun: RowGeneratorContext["update_direct"] = (name, value) => { + this.setState({ + // Amend row_data to include new value for [name] + row_data: this.state.row_data.map(r => r.id === row.id ? {...row, [name]: value} : r) }) + this.mark_row_changed(row.id) + } + if (is_new_row) { + update_fun = (name, value) => { + this.setState({new_row: {...this.state.new_row, [name]: value}}) + this.mark_row_changed(row.id) + } + } return { columns: this.props.columns, update: (event: BaseSyntheticEvent) => update_fun(event.target.name, event.target.value), update_direct: update_fun, - refresh: () => this.refresh_row(row), + mark_loading: (state: boolean = true) => this.mark_row_loading(row.id, state), + refresh: (r: any) => this.refresh_row(r, true), + refresh_from_api: () => this.refresh_row(row, false), refresh_all_rows: this.update_all, is_new_row, value_changed: this.state.changed_rows.includes(row.id) @@ -250,6 +274,8 @@ export default class AsyncTable extends Component { + if (!row) + return null const is_new_row = row_index === NEW_ROW_ID if (is_new_row) row_index = -1 diff --git a/frontend/src/Cells.tsx b/frontend/src/Cells.tsx index 6304e2f3..2fe31af1 100644 --- a/frontend/src/Cells.tsx +++ b/frontend/src/Cells.tsx @@ -9,7 +9,8 @@ import Container from '@mui/material/Container'; import SaveIcon from '@mui/icons-material/Save'; import DeleteIcon from '@mui/icons-material/Delete'; import Connection from "./APIConnection"; -import AsyncTable from "./AsyncTable"; +import AsyncTable, {RowGeneratorContext} from "./AsyncTable"; +import Typography from "@mui/material/Typography"; export type CellFields = { url: string; @@ -81,12 +82,14 @@ export default function Cells() { } } - const addNewCell = (data: CellFields) => { + const addNewCell = (data: CellFields, context: RowGeneratorContext) => { + context.mark_loading(true) const insert_data = get_write_data(data) return Connection.fetch('cells/', {body: JSON.stringify(insert_data), method: 'POST'}) }; - const updateCell = (data: CellFields) => { + const updateCell = (data: CellFields, context: RowGeneratorContext) => { + context.mark_loading(true) const insert_data = get_write_data(data) return Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) }; @@ -103,6 +106,7 @@ export default function Cells() { ), - - + cell.in_use? : + addNewCell(cell).then(context.refresh_all_rows) : - () => updateCell(cell).then(context.refresh)} + context.is_new_row? + () => addNewCell(cell, context).then(context.refresh_all_rows) : + () => updateCell(cell, context).then(context.refresh)} > {context.is_new_row? : } , - context.is_new_row? : + context.is_new_row || cell.in_use? : - deleteCell(cell).then(context.refresh)} - > + deleteCell(cell).then(context.refresh)}> @@ -157,8 +162,11 @@ export default function Cells() { name: '', manufacturer: '', form_factor: '', link_to_datasheet: '', anode_chemistry: '', cathode_chemistry: '', nominal_capacity: 0, nominal_cell_weight: 0 }} - initial_url="cells/?all=true" + url="cells/?all=true" /> + + Note: Cells assigned to existing datasets cannot be changed. + ); diff --git a/frontend/src/Datasets.tsx b/frontend/src/Datasets.tsx index b749ae8b..bec2ecd0 100644 --- a/frontend/src/Datasets.tsx +++ b/frontend/src/Datasets.tsx @@ -11,7 +11,7 @@ import DialogActions from '@mui/material/DialogActions'; import DialogContent from '@mui/material/DialogContent'; import DialogTitle from '@mui/material/DialogTitle'; import Connection, {APIConnection} from "./APIConnection" -import AsyncTable from "./AsyncTable" +import AsyncTable, {RowGeneratorContext} from "./AsyncTable" import Paper from "@mui/material/Paper"; import Select from "@mui/material/Select"; import SaveIcon from "@mui/icons-material/Save"; @@ -23,6 +23,9 @@ import {CellFields} from "./Cells"; import MenuItem from "@mui/material/MenuItem"; import CircularProgress from "@mui/material/CircularProgress"; import {EquipmentFields} from "./Equipment"; +import OutlinedInput from "@mui/material/OutlinedInput"; +import Box from "@mui/material/Box"; +import Chip from "@mui/material/Chip"; export type DatasetFields = { url: string; @@ -65,9 +68,11 @@ export default function Datasets() { const [selected, setSelected] = useState(null) const [cellListLoading, setCellListLoading] = useState(true) const [cellList, setCellList] = useState([]) + const [equipmentListLoading, setEquipmentListLoading] = useState(true) + const [equipmentList, setEquipmentList] = useState([]) useEffect(() => { - Connection.fetch('cells/?all=true') + Connection.fetch('cells/?all=true', {}, 0) .then(APIConnection.get_result_array) .then(r => { if (typeof r === 'number') @@ -78,14 +83,27 @@ export default function Datasets() { }) }, []) - const updateRow = (data: DatasetFields) => { - const insert_data = { + useEffect(() => { + Connection.fetch('equipment/?all=true', {}, 0) + .then(APIConnection.get_result_array) + .then(r => { + if (typeof r === 'number') + throw new Error(`equipment/?all=true -> ${r}`) + // @ts-ignore + setEquipmentList(r) + setEquipmentListLoading(false) + }) + }, []) + + const updateRow = (data: DatasetFields, context: RowGeneratorContext) => { + context.mark_loading(true) + const insert_data: any = { name: data.name, type: data.type, - purpose: data.purpose, - cell: data.cell || null, - equipment: data.equipment.map(e => e.id) + cell: data.cell?.url || null, + equipment: data.equipment.map(e => e.url) } + if (data.purpose) insert_data.purpose = data.purpose return Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) } @@ -96,6 +114,7 @@ export default function Datasets() { {label: 'Type', help: 'File type determined by Harvester'}, {label: 'Purpose', help: 'Short description of dataset purpose'}, {label: 'Cell', help: 'Cell that generated the dataset'}, + {label: 'Equipment', help: 'Equipment used to generate the dataset'}, {label: 'Details', help: 'Advanced dataset properties'}, {label: 'Save', help: 'Save changes'}, ] @@ -122,7 +141,7 @@ export default function Datasets() { setMatlabCodeOpen(false); }; - const get_items = (dataset: DatasetFields) => { + const get_cell_items = (dataset: DatasetFields) => { const menuItem = (cell: CellFields) => {cell.name} const items: ReactElement[] = [] if (dataset?.cell) { @@ -139,6 +158,26 @@ export default function Datasets() { return items } + const get_equipment_items = (dataset: DatasetFields) => { + const menuItem = (equipment: EquipmentFields) => + {equipment.name} + const items: ReactElement[] = [] + const current_equipment_ids: number[] = [] + if (dataset?.equipment) { + items.push(...dataset.equipment.map(e => menuItem(e))) + current_equipment_ids.push(...dataset.equipment.map(e => e.id)) + if (!equipmentListLoading) + items.push(None) + } + if (equipmentListLoading) + items.push() + if (equipmentList.length) + items.push(...equipmentList.filter(e => !current_equipment_ids.includes(e.id)).map(menuItem)) + if (!items.length) + items.push(No equipment defined) + return items + } + return ( @@ -171,7 +210,35 @@ export default function Datasets() { (e) => context.update_direct('cell', cellList?.find(c => c.id === e.target.value) || null) } > - {get_items(dataset)} + {get_cell_items(dataset)} + + , + + , @@ -182,13 +249,13 @@ export default function Datasets() { updateRow(dataset).then(context.refresh)} + onClick={() => updateRow(dataset, context).then(context.refresh)} > ]} - initial_url={`datasets/?all=true`} + url={`datasets/?all=true`} styles={classes} /> diff --git a/frontend/src/Equipment.tsx b/frontend/src/Equipment.tsx index 8c4132b6..d4afb0de 100644 --- a/frontend/src/Equipment.tsx +++ b/frontend/src/Equipment.tsx @@ -118,7 +118,7 @@ export default function Equipment() { ]} new_row_values={{name: '', type: ''}} - initial_url={`equipment/?all=true`} + url={`equipment/?all=true`} styles={classes} /> diff --git a/frontend/src/Files.tsx b/frontend/src/Files.tsx index 18ff734c..99bf1a3d 100644 --- a/frontend/src/Files.tsx +++ b/frontend/src/Files.tsx @@ -93,7 +93,7 @@ export default function Files(props: FilesProps) { forceReimport(file).then(context.refresh)}> ]} - initial_url={`files/?monitored_path__id=${props.path.id}&all=true`} + url={`files/?monitored_path__id=${props.path.id}&all=true`} styles={classes} /> diff --git a/frontend/src/HarvesterDetail.tsx b/frontend/src/HarvesterDetail.tsx index 80a518a1..9eb00db4 100644 --- a/frontend/src/HarvesterDetail.tsx +++ b/frontend/src/HarvesterDetail.tsx @@ -153,7 +153,7 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { , ]} - initial_url={`monitored_paths/?harvester__id=${harvester.id}&all=true`} + url={`monitored_paths/?harvester__id=${harvester.id}&all=true`} new_row_values={{path: "", stable_time: 60}} styles={classes} /> diff --git a/frontend/src/Harvesters.tsx b/frontend/src/Harvesters.tsx index 040cb880..03df0de2 100644 --- a/frontend/src/Harvesters.tsx +++ b/frontend/src/Harvesters.tsx @@ -142,7 +142,7 @@ export default function Harvesters() { , ]} - initial_url="harvesters/?all=true" + url="harvesters/?all=true" />} {selected !== null && } diff --git a/harvester/harvester/api.py b/harvester/harvester/api.py index 385bf652..29597986 100644 --- a/harvester/harvester/api.py +++ b/harvester/harvester/api.py @@ -2,6 +2,7 @@ import json import requests from .settings import get_setting, get_settings, get_settings_file, get_logger +import time logger = get_logger(__file__) @@ -12,6 +13,7 @@ def report_harvest_result( file: os.PathLike|str = None, error: BaseException = None ): + start = time.time() try: if error is not None: data = {'status': 'error', 'error': ";".join(error.args)} @@ -21,17 +23,19 @@ def report_harvest_result( if file is not None: data['file'] = file logger.debug(f"{get_setting('url')}report/; {json.dumps(data)}") - return requests.post( + out = requests.post( f"{get_setting('url')}report/", headers={ 'Authorization': f"Harvester {get_setting('api_key')}" }, json=data, - timeout=120 + timeout=600 ) except BaseException as e: logger.error(e) - return None + out = None + logger.info(f"API call finished in {time.time() - start}") + return out def update_config(): diff --git a/harvester/harvester/harvest.py b/harvester/harvester/harvest.py index 82a40124..7edb9fc9 100644 --- a/harvester/harvester/harvest.py +++ b/harvester/harvester/harvest.py @@ -4,6 +4,8 @@ import datetime import json import os +import time + import dateutil import sys from .parse.exceptions import UnsupportedFileTypeError @@ -98,6 +100,7 @@ def import_file(core_path: str, file_path: str) -> bool: } ) if report is None: + logger.error(f"API Error") return False if not report.ok: try: @@ -105,29 +108,48 @@ def import_file(core_path: str, file_path: str) -> bool: except BaseException: logger.error(f"API Error: {report.status_code}") return False + upload_info = report.json()['upload_info'] + last_uploaded_record = upload_info.get('last_record_number') + columns = upload_info.get('columns') # Figure out column data column_data = {} - mapping = input_file.get_file_column_to_standard_column_mapping() + if len(columns): + mapping = {c.get('name'): c.get('id') for c in columns} + value_map = {c.get('name'): c.get('keymap') for c in columns if len(c.get('keymap'))} + else: + mapping = input_file.get_file_column_to_standard_column_mapping() + value_map = {} next_key = 0 # limit size of requests. 1kb/column is an arbitrary buffer size. size = 0 - max_size = (max_upload_size / 1) - (1000 * len(extra_metadata)) + max_size = max_upload_size nth_part = 0 - start_row = 0 + start_row = last_uploaded_record if last_uploaded_record is not None else 0 # Find out if there's a Sample number column, otherwise we use the row number record_number_column = [k for k, v in mapping.items() if v == default_column_ids['Sample Number']] record_number_column = record_number_column[0] if len(record_number_column) else None - generator = input_file.load_data(input_file.file_path, input_file.column_info.keys()) + # TODO: is this actually determined correctly? Seems there are actually lots of data columns we miss?? + # Anyway, leaving this as instructed because everyone's happy with it as is. + columns_with_data = [c for c in input_file.column_info.keys() if input_file.column_info[c].get('has_data')] + generator = input_file.load_data(input_file.file_path, columns_with_data) + start = time.process_time() + new_row = {} for i, r in enumerate(generator): + if int(r.get(record_number_column, i)) <= start_row: + continue # Data are stored up in rows and shipped out when # adding the current row would exceed the server data # size limit. # If sent, sent data are wiped from column_data. # New row data are added to column_data below. - size = sys.getsizeof(json.dumps(column_data)) + size += sys.getsizeof(json.dumps(new_row)) if size > max_size: + if start_row == i: + logger.error(f"Row too large to upload {len(r.keys())} columns, size={sys.getsizeof(r)}") + return False logger.info(f"Upload part {nth_part} (rows {start_row}-{i - 1}; {size}bytes)") + logger.info(f"Read took {time.process_time() - start}") nth_part += 1 start_row = i report = report_harvest_result(path=core_path, file=file_path, content={ @@ -137,6 +159,7 @@ def import_file(core_path: str, file_path: str) -> bool: 'test_date': serialize_datetime(core_metadata['Date of Test']) }) if report is None: + logger.error(f"API Error") return False if not report.ok: try: @@ -146,6 +169,8 @@ def import_file(core_path: str, file_path: str) -> bool: return False for k in column_data.keys(): column_data[k]['values'] = {} + start = time.process_time() + size = 0 if i > 0: for k, v in new_row.items(): @@ -179,6 +204,153 @@ def import_file(core_path: str, file_path: str) -> bool: column_data[k]['value_map'] = {v: next_key} new_row[k] = next_key next_key += 1 + else: + column_data[k] = {} + if k in mapping: + column_data[k]['column_id'] = mapping[k] + else: + column_data[k]['column_name'] = k + if 'unit' in input_file.column_info[k]: + column_data[k]['unit_symbol'] = input_file.column_info[k].get('unit') + else: + column_data[k]['unit_id'] = default_units['Unitless'] + if k in value_map: + column_data[k]['value_map'] = value_map[k] + column_data[k]['values'] = {} + + # Send data + report = report_harvest_result(path=core_path, file=file_path, content={ + 'task': 'import', + 'status': 'in_progress', + 'data': [v for v in column_data.values()], + 'test_date': serialize_datetime(core_metadata['Date of Test']) + }) + if report is None: + logger.error(f"API Error") + return False + if not report.ok: + try: + logger.error(f"API responded with Error: {report.json()['error']}") + except BaseException: + logger.error(f"API Error: {report.status_code}") + return False + + logger.info("File successfully imported") + except Exception as e: + logger.error(e) + report_harvest_result(path=core_path, file=file_path, error=e) + return False + return True + + +def import_file_direct(core_path: str, file_path: str) -> bool: + """ + Attempts to import a given file + """ + default_column_ids = get_standard_columns() + default_units = get_standard_units() + max_upload_size = get_setting('max_upload_bytes') + full_file_path = os.sep.join([core_path, file_path]) + if not os.path.isfile(full_file_path): + logger.warn(f"{full_file_path} is not a file, skipping") + report_harvest_result(path=core_path, file=file_path, error=FileNotFoundError()) + return False + logger.info("Importing " + full_file_path + " [direct]") + + try: + # Attempt reading the file before updating the database to avoid + # creating rows for a file we can't read. + # TODO handle rows in the dataset and access tables with no + # corresponding data since the import might fail while reading the data + # anyway + input_file = None + load_start = time.process_time() + for input_file_cls in registered_input_files: + try: + logger.debug('Tried input reader {}'.format(input_file_cls)) + input_file = input_file_cls( + file_path=full_file_path, + standard_units=default_units, + standard_columns=default_column_ids + ) + except Exception as e: + logger.debug('...failed with: ', type(e), e) + else: + logger.debug('...succeeded...') + break + if input_file is None: + raise UnsupportedFileTypeError + + logger.info(f"Loaded file in {time.process_time() - load_start}") + # Send metadata + load_meta = time.process_time() + core_metadata, extra_metadata = input_file.load_metadata() + logger.info(f"Loaded metadata in {time.process_time() - load_meta}") + report = report_harvest_result( + path=core_path, + file=file_path, + content={ + 'task': 'import', + 'status': 'begin', + 'core_metadata': serialize_datetime(core_metadata), + 'extra_metadata': serialize_datetime(extra_metadata), + 'test_date': serialize_datetime(core_metadata['Date of Test']) + } + ) + if report is None: + logger.error(f"API Error") + return False + if not report.ok: + try: + logger.error(f"API responded with Error: {report.json()['error']}") + except BaseException: + logger.error(f"API Error: {report.status_code}") + return False + + # Figure out column data + load_data = time.process_time() + column_data = {} + mapping = input_file.get_file_column_to_standard_column_mapping() + next_key = 0 + # limit size of requests. 1kb/column is an arbitrary buffer size. + size = 0 + max_size = (max_upload_size / 1) - (1000 * len(extra_metadata)) + nth_part = 0 + start_row = 0 + # Find out if there's a Sample number column, otherwise we use the row number + record_number_column = [k for k, v in mapping.items() if v == default_column_ids['Sample Number']] + record_number_column = record_number_column[0] if len(record_number_column) else None + # TODO: is this actually determined correctly? Seems there are actually lots of data columns we miss?? + # Anyway, leaving this as instructed because everyone's happy with it as is. + columns_with_data = [c for c in input_file.column_info.keys() if input_file.column_info[c].get('has_data')] + generator = input_file.load_data(input_file.file_path, columns_with_data) + for i, r in enumerate(generator): + record_number = int(r.get(record_number_column, i)) + for k, v in r.items(): + if k == record_number_column: + continue + if k in column_data: + # Numeric data are stored directly + try: + column_data[k]['values'][record_number] = int(v) + except ValueError: + try: + column_data[k]['values'][record_number] = float(v) + # Timestamps are stored using float conversion + except ValueError: + try: + column_data[k]['values'][record_number] = dateutil.parser.parse(v).timestamp() + # Strings are mapped to integer values using a value map which is also sent to the database + except ValueError: + if 'value_map' in column_data[k] and v in column_data[k]['value_map']: + column_data[k]['values'][record_number] = column_data[k]['value_map'][v] + else: + if 'value_map' in column_data[k]: + column_data[k]['value_map'][v] = next_key + else: + column_data[k]['value_map'] = {v: next_key} + column_data[k]['values'][record_number] = next_key + next_key += 1 else: column_data[k] = {} if k in mapping: @@ -191,14 +363,18 @@ def import_file(core_path: str, file_path: str) -> bool: column_data[k]['unit_id'] = default_units['Unitless'] column_data[k]['values'] = {} + logger.info(f"Loaded and parsed data in {time.process_time() - load_data}") # Send data + send_data = time.process_time() report = report_harvest_result(path=core_path, file=file_path, content={ 'task': 'import', 'status': 'in_progress', 'data': [v for v in column_data.values()], 'test_date': serialize_datetime(core_metadata['Date of Test']) }) + logger.info(f"Sent data in {time.process_time() - send_data}") if report is None: + logger.error(f"API Error") return False if not report.ok: try: diff --git a/harvester/harvester/run.py b/harvester/harvester/run.py index 71be675e..07d423b4 100644 --- a/harvester/harvester/run.py +++ b/harvester/harvester/run.py @@ -2,7 +2,7 @@ import time from .settings import get_logger, get_setting from .api import report_harvest_result, update_config -from .harvest import import_file +from .harvest import import_file, import_file_direct logger = get_logger(__file__) diff --git a/harvester/harvester/settings.py b/harvester/harvester/settings.py index 6131a2f6..116d4be8 100644 --- a/harvester/harvester/settings.py +++ b/harvester/harvester/settings.py @@ -57,7 +57,9 @@ def get_logger(name): # stream_handler = logging.StreamHandler(sys.stdout) # stream_handler.setLevel(logging.INFO) # logger.addHandler(stream_handler) + formatter = logging.Formatter('%(asctime)s %(levelname)s %(message)s [%(name)s]', datefmt='%Y-%m-%d %H:%M:%S') file_handler = logging.handlers.RotatingFileHandler(get_logfile(), maxBytes=5_000_000, backupCount=5) file_handler.setLevel(logging.INFO) + file_handler.setFormatter(formatter) logger.addHandler(file_handler) return logger From 2609c72737784a154f62a842c081c2d8ede0bec6 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Tue, 7 Feb 2023 16:15:44 +0000 Subject: [PATCH 36/79] tidy import --- django/backend_django/galvanalyser/utils.py | 62 ++++++++++++++++++++ django/backend_django/galvanalyser/views.py | 63 +-------------------- 2 files changed, 63 insertions(+), 62 deletions(-) create mode 100644 django/backend_django/galvanalyser/utils.py diff --git a/django/backend_django/galvanalyser/utils.py b/django/backend_django/galvanalyser/utils.py new file mode 100644 index 00000000..283bba8a --- /dev/null +++ b/django/backend_django/galvanalyser/utils.py @@ -0,0 +1,62 @@ +import io + + +class IteratorFile(io.TextIOBase): + """ given an iterator which yields strings, + return a file like object for reading those strings """ + + def __init__(self, it): + self._it = it + self._f = io.StringIO() + self.buffered_chars = 0 + + def read(self, length=sys.maxsize): + + try: + while self.buffered_chars < length: + self.buffered_chars += self._f.write(next(self._it) + "\n") + + except StopIteration as e: + # soak up StopIteration. this block is not necessary because + # of finally, but just to be explicit + pass + + except: # Exception as e: + raise + # print("uncaught exception: {}".format(e)) + + finally: + self._f.seek(0) + data = self._f.read(length) + + # save the remainder for next read + remainder = self._f.read() + self._f.seek(0) + self._f.truncate(0) + self.buffered_chars = self._f.write(remainder) + return data + + def readline(self): + try: + # load up a line to make sure that there is one to read + self._f.write(next(self._it) + "\n") + except StopIteration as e: + # soak up StopIteration. this block is not necessary because + # of finally, but just to be explicit + pass + + except: # Exception as e: + raise + # print("uncaught exception: {}".format(e)) + + finally: + self._f.seek(0) + data = self._f.readline() + + # save the remainder for next read + remainder = self._f.read() + self._f.seek(0) + self._f.truncate(0) + # store size of data in buffer for the read method + self.buffered_chars = self._f.write(remainder) + return data diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 7a7cc725..bea38305 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -1,6 +1,3 @@ -import io -import sys - from django.db.models import Q from .serializers import HarvesterSerializer, \ HarvesterConfigSerializer, \ @@ -40,6 +37,7 @@ from rest_framework.response import Response from knox.views import LoginView as KnoxLoginView from rest_framework.authentication import BasicAuthentication +from .utils import IteratorFile import json import time import logging @@ -319,65 +317,6 @@ def report(self, request, pk: int = None): time_ts_prep = time.time() from django.db import connection - class IteratorFile(io.TextIOBase): - """ given an iterator which yields strings, - return a file like object for reading those strings """ - - def __init__(self, it): - self._it = it - self._f = io.StringIO() - self.buffered_chars = 0 - - def read(self, length=sys.maxsize): - - try: - while self.buffered_chars < length: - self.buffered_chars += self._f.write(next(self._it) + "\n") - - except StopIteration as e: - # soak up StopIteration. this block is not necessary because - # of finally, but just to be explicit - pass - - except: # Exception as e: - raise - # print("uncaught exception: {}".format(e)) - - finally: - self._f.seek(0) - data = self._f.read(length) - - # save the remainder for next read - remainder = self._f.read() - self._f.seek(0) - self._f.truncate(0) - self.buffered_chars = self._f.write(remainder) - return data - - def readline(self): - try: - # load up a line to make sure that there is one to read - self._f.write(next(self._it) + "\n") - except StopIteration as e: - # soak up StopIteration. this block is not necessary because - # of finally, but just to be explicit - pass - - except: # Exception as e: - raise - # print("uncaught exception: {}".format(e)) - - finally: - self._f.seek(0) - data = self._f.readline() - - # save the remainder for next read - remainder = self._f.read() - self._f.seek(0) - self._f.truncate(0) - # store size of data in buffer for the read method - self.buffered_chars = self._f.write(remainder) - return data rows = [] for s, v in column_data['values'].items(): rows.append(f"{int(s)}\t{column.id}\t{int(v)}") From 803dde62e1eefafb11c6ef97377769b17513eb78 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Tue, 7 Feb 2023 16:15:53 +0000 Subject: [PATCH 37/79] tests for harvester --- harvester/harvester/api.py | 5 +- harvester/harvester/harvest.py | 148 ------------------ harvester/harvester/run.py | 2 +- harvester/test/__init__.py | 0 harvester/test/test_harvester.py | 248 +++++++++++++++++++++++++++++++ 5 files changed, 251 insertions(+), 152 deletions(-) create mode 100644 harvester/test/__init__.py create mode 100644 harvester/test/test_harvester.py diff --git a/harvester/harvester/api.py b/harvester/harvester/api.py index 29597986..358ebd8b 100644 --- a/harvester/harvester/api.py +++ b/harvester/harvester/api.py @@ -28,8 +28,7 @@ def report_harvest_result( headers={ 'Authorization': f"Harvester {get_setting('api_key')}" }, - json=data, - timeout=600 + json=data ) except BaseException as e: logger.error(e) @@ -71,7 +70,7 @@ def update_config(): dirty = True if dirty: - with open(get_settings_file(), 'w') as f: + with open(get_settings_file(), 'w+') as f: json.dump(result.json(), f) else: logger.error(f"Unable to fetch {url}config/ -- received HTTP {result.status_code}") diff --git a/harvester/harvester/harvest.py b/harvester/harvester/harvest.py index 7edb9fc9..8074dc86 100644 --- a/harvester/harvester/harvest.py +++ b/harvester/harvester/harvest.py @@ -241,151 +241,3 @@ def import_file(core_path: str, file_path: str) -> bool: report_harvest_result(path=core_path, file=file_path, error=e) return False return True - - -def import_file_direct(core_path: str, file_path: str) -> bool: - """ - Attempts to import a given file - """ - default_column_ids = get_standard_columns() - default_units = get_standard_units() - max_upload_size = get_setting('max_upload_bytes') - full_file_path = os.sep.join([core_path, file_path]) - if not os.path.isfile(full_file_path): - logger.warn(f"{full_file_path} is not a file, skipping") - report_harvest_result(path=core_path, file=file_path, error=FileNotFoundError()) - return False - logger.info("Importing " + full_file_path + " [direct]") - - try: - # Attempt reading the file before updating the database to avoid - # creating rows for a file we can't read. - # TODO handle rows in the dataset and access tables with no - # corresponding data since the import might fail while reading the data - # anyway - input_file = None - load_start = time.process_time() - for input_file_cls in registered_input_files: - try: - logger.debug('Tried input reader {}'.format(input_file_cls)) - input_file = input_file_cls( - file_path=full_file_path, - standard_units=default_units, - standard_columns=default_column_ids - ) - except Exception as e: - logger.debug('...failed with: ', type(e), e) - else: - logger.debug('...succeeded...') - break - if input_file is None: - raise UnsupportedFileTypeError - - logger.info(f"Loaded file in {time.process_time() - load_start}") - # Send metadata - load_meta = time.process_time() - core_metadata, extra_metadata = input_file.load_metadata() - logger.info(f"Loaded metadata in {time.process_time() - load_meta}") - report = report_harvest_result( - path=core_path, - file=file_path, - content={ - 'task': 'import', - 'status': 'begin', - 'core_metadata': serialize_datetime(core_metadata), - 'extra_metadata': serialize_datetime(extra_metadata), - 'test_date': serialize_datetime(core_metadata['Date of Test']) - } - ) - if report is None: - logger.error(f"API Error") - return False - if not report.ok: - try: - logger.error(f"API responded with Error: {report.json()['error']}") - except BaseException: - logger.error(f"API Error: {report.status_code}") - return False - - # Figure out column data - load_data = time.process_time() - column_data = {} - mapping = input_file.get_file_column_to_standard_column_mapping() - next_key = 0 - # limit size of requests. 1kb/column is an arbitrary buffer size. - size = 0 - max_size = (max_upload_size / 1) - (1000 * len(extra_metadata)) - nth_part = 0 - start_row = 0 - # Find out if there's a Sample number column, otherwise we use the row number - record_number_column = [k for k, v in mapping.items() if v == default_column_ids['Sample Number']] - record_number_column = record_number_column[0] if len(record_number_column) else None - # TODO: is this actually determined correctly? Seems there are actually lots of data columns we miss?? - # Anyway, leaving this as instructed because everyone's happy with it as is. - columns_with_data = [c for c in input_file.column_info.keys() if input_file.column_info[c].get('has_data')] - generator = input_file.load_data(input_file.file_path, columns_with_data) - for i, r in enumerate(generator): - record_number = int(r.get(record_number_column, i)) - for k, v in r.items(): - if k == record_number_column: - continue - if k in column_data: - # Numeric data are stored directly - try: - column_data[k]['values'][record_number] = int(v) - except ValueError: - try: - column_data[k]['values'][record_number] = float(v) - # Timestamps are stored using float conversion - except ValueError: - try: - column_data[k]['values'][record_number] = dateutil.parser.parse(v).timestamp() - # Strings are mapped to integer values using a value map which is also sent to the database - except ValueError: - if 'value_map' in column_data[k] and v in column_data[k]['value_map']: - column_data[k]['values'][record_number] = column_data[k]['value_map'][v] - else: - if 'value_map' in column_data[k]: - column_data[k]['value_map'][v] = next_key - else: - column_data[k]['value_map'] = {v: next_key} - column_data[k]['values'][record_number] = next_key - next_key += 1 - else: - column_data[k] = {} - if k in mapping: - column_data[k]['column_id'] = mapping[k] - else: - column_data[k]['column_name'] = k - if 'unit' in input_file.column_info[k]: - column_data[k]['unit_symbol'] = input_file.column_info[k].get('unit') - else: - column_data[k]['unit_id'] = default_units['Unitless'] - column_data[k]['values'] = {} - - logger.info(f"Loaded and parsed data in {time.process_time() - load_data}") - # Send data - send_data = time.process_time() - report = report_harvest_result(path=core_path, file=file_path, content={ - 'task': 'import', - 'status': 'in_progress', - 'data': [v for v in column_data.values()], - 'test_date': serialize_datetime(core_metadata['Date of Test']) - }) - logger.info(f"Sent data in {time.process_time() - send_data}") - if report is None: - logger.error(f"API Error") - return False - if not report.ok: - try: - logger.error(f"API responded with Error: {report.json()['error']}") - except BaseException: - logger.error(f"API Error: {report.status_code}") - return False - - logger.info("File successfully imported") - except Exception as e: - logger.error(e) - report_harvest_result(path=core_path, file=file_path, error=e) - return False - return True diff --git a/harvester/harvester/run.py b/harvester/harvester/run.py index 07d423b4..71be675e 100644 --- a/harvester/harvester/run.py +++ b/harvester/harvester/run.py @@ -2,7 +2,7 @@ import time from .settings import get_logger, get_setting from .api import report_harvest_result, update_config -from .harvest import import_file, import_file_direct +from .harvest import import_file logger = get_logger(__file__) diff --git a/harvester/test/__init__.py b/harvester/test/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/harvester/test/test_harvester.py b/harvester/test/test_harvester.py new file mode 100644 index 00000000..f00760f0 --- /dev/null +++ b/harvester/test/test_harvester.py @@ -0,0 +1,248 @@ +import unittest +from unittest.mock import patch +import os +from pathlib import Path +import datetime + +from harvester.harvester.parse.input_file import InputFile +import harvester.harvester.run +import harvester.harvester.harvest + +class ConfigResponse: + status_code = 200 + + def json(self): + return { + "url": "http://app:5000/harvesters/1/", + "id": 1, + "api_key": "galv_hrv_x", + "name": "Test Harvester", + "sleep_time": 0, + "monitored_paths": [ + { + "path": "/usr/test_data", + "stable_time": 0 + } + ], + "standard_units": [ + { + "id": 1, + "name": "Unitless" + }, + { + "id": 2, + "name": "Time" + }, + { + "id": 3, + "name": "Volts" + }, + { + "id": 4, + "name": "Amps" + }, + { + "id": 5, + "name": "Energy" + }, + { + "id": 6, + "name": "Charge" + }, + { + "id": 7, + "name": "Temperature" + }, + { + "id": 8, + "name": "Power" + }, + { + "id": 9, + "name": "Ohm" + }, + { + "id": 10, + "name": "Degrees" + }, + { + "id": 11, + "name": "Frequency" + } + ], + "standard_columns": [ + { + "id": 1, + "name": "Unknown", + "unit": None + }, + { + "id": 2, + "name": "Sample Number", + "unit": "http://app:5000/units/1/" + }, + { + "id": 3, + "name": "Time", + "unit": "http://app:5000/units/2/" + }, + { + "id": 4, + "name": "Volts", + "unit": "http://app:5000/units/3/" + }, + { + "id": 5, + "name": "Amps", + "unit": "http://app:5000/units/4/" + }, + { + "id": 6, + "name": "Energy Capacity", + "unit": "http://app:5000/units/5/" + }, + { + "id": 7, + "name": "Charge Capacity", + "unit": "http://app:5000/units/6/" + }, + { + "id": 8, + "name": "Temperature", + "unit": "http://app:5000/units/7/" + }, + { + "id": 9, + "name": "Step Time", + "unit": "http://app:5000/units/8/" + }, + { + "id": 10, + "name": "Impedence Magnitude", + "unit": "http://app:5000/units/9/" + }, + { + "id": 11, + "name": "Impedence Phase", + "unit": "http://app:5000/units/10/" + }, + { + "id": 12, + "name": "Frequency", + "unit": "http://app:5000/units/11/" + } + ], + "max_upload_bytes": 2621440 + } + + +class JSONResponse: + def __init__(self, status_code = 200, json_data=None): + self.status_code = status_code + self.ok = 200 <= self.status_code < 400 + self.json_data = json_data if json_data else {} + + def json(self): + return self.json_data + + +def fail(e, *kwargs): + raise Exception(e) + + +class TestHarvester(unittest.TestCase): + @patch('requests.get') + @patch('harvester.harvester.api.logger') + @patch('harvester.harvester.run.logger') + @patch('harvester.harvester.api.get_settings_file') + @patch('harvester.harvester.settings.get_settings_file') + @patch('harvester.harvester.settings.get_logfile') + def test_config_update( + self, + mock_settings_log, + mock_settings_file, + mock_api_settings_file, + mock_run_logger, + mock_api_logger, + mock_get + ): + mock_settings_log.return_value = '/tmp/harvester.log' + mock_settings_file.return_value = '/tmp/harvester.json' + mock_api_settings_file.return_value = '/tmp/harvester.json' + mock_api_logger.error = fail + mock_run_logger.error = fail + mock_get.return_value = ConfigResponse() + harvester.harvester.run.update_config() + if not os.path.isfile(mock_settings_file()): + raise AssertionError(f"Expected JSON file '{mock_settings_file()}' not found") + + @patch('harvester.harvester.run.report_harvest_result') + @patch('harvester.harvester.run.import_file') + @patch('harvester.harvester.run.logger') + def test_harvest_path(self, mock_logger, mock_import, mock_report): + mock_logger.error = fail + mock_report.return_value = JSONResponse(200, {'state': 'STABLE'}) + mock_import.return_value = True + harvester.harvester.run.harvest_path(Path('/usr/test_data')) + files = [] + for c in mock_import.call_args_list: + if c.args[1] not in files: + files.append(c.args[1]) + if len(files) != 5: + raise AssertionError(f"Did not find 5 files in path /usr/test_data") + for f in files: + for task in ['file_size', 'import']: + ok = False + for c in mock_report.call_args_list: + if c.kwargs['content']['task'] == task: + if not task == 'import' or c.kwargs['content']['status'] == 'complete': + ok = True + break + if not ok: + raise AssertionError(f"{f} did not make call with 'task'={task}") + + @patch('harvester.harvester.harvest.report_harvest_result') + @patch('harvester.harvester.harvest.logger') + @patch('harvester.harvester.settings.get_settings') + def import_file(self, filename, mock_settings, mock_logger, mock_report): + mock_settings.return_value = ConfigResponse().json() + mock_logger.error = fail + mock_report.return_value = JSONResponse( + 200, {'upload_info': {'last_record_number': 0, 'columns': []}} + ) + if not harvester.harvester.harvest.import_file('/usr/test_data', filename): + raise AssertionError(f"Import failed for /usr/test_data/{filename}") + self.validate_report_calls(mock_report.call_args_list) + + def validate_report_calls(self, calls): + begun = False + for c in calls: + if not 'content' in c.kwargs: + raise AssertionError(f"Report made with no content") + if not begun: + if c.kwargs['content']['status'] != 'begin': + raise AssertionError(f"Expected result reports to start with status='begin'") + if 'core_metadata' not in c.kwargs['content']: + raise AssertionError(f"Expected result report to contain core_metadata") + begun = True + continue + if c.kwargs['content']['status'] != 'in_progress': + raise AssertionError(f"Expected result report status to be 'in_progress'") + if not c.kwargs['content']['data']: + raise AssertionError(f"Expected result report to contain 'data'") + row = c.kwargs['content']['data'][0] + if not 'values' in row: + raise AssertionError(f"'data' contains no 'values' field") + + def test_import_mpr(self): + self.import_file('adam_3_C05.mpr') + + def test_import_idf(self): + self.import_file('Ivium_Cell+1.idf') + + # def test_import_txt(self): + # self.import_file('TPG1+-+Cell+15+-+002.txt') + + +if __name__ == '__main__': + unittest.main() From e3a6e1010c15869952c6cd73901585533dfde2f9 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Wed, 8 Feb 2023 15:44:52 +0000 Subject: [PATCH 38/79] clearer harvester error --- harvester/start.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/harvester/start.py b/harvester/start.py index 56d2a745..a354fd08 100644 --- a/harvester/start.py +++ b/harvester/start.py @@ -15,7 +15,10 @@ def query(url: str, data: object = None) -> object: click.echo(f"POST {url}; {json.dumps(data)}") result = requests.post(url, data=data) if result.status_code != 200: - raise ConnectionError(f"Unable to connect to {url}") + try: + raise ConnectionError(result.json()['error']) + except (json.JSONDecodeError, AttributeError, KeyError): + raise ConnectionError(f"Unable to connect to {url}") return result.json() From 71c2021ded9ea3d8f5d91ba89323adfcfceac34a Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Wed, 8 Feb 2023 15:46:08 +0000 Subject: [PATCH 39/79] cellfamily, docs --- backend/galvanalyser/routes.py | 4 +- .../galvanalyser/migrations/0001_initial.py | 194 ++++++++++++++++++ .../0002_alter_observedfile_state.py | 18 ++ .../0003_alter_observedfile_state.py | 18 ++ django/backend_django/galvanalyser/models.py | 21 +- .../galvanalyser/serializers.py | 43 +++- django/backend_django/galvanalyser/utils.py | 1 + django/backend_django/galvanalyser/views.py | 98 ++++++--- docker-compose.override.yml | 2 + frontend/src/AsyncTable.tsx | 7 +- frontend/src/CellList.tsx | 134 ++++++++++++ frontend/src/Cells.tsx | 82 ++++---- frontend/src/DatasetDetail.js | 4 +- frontend/src/Datasets.tsx | 13 +- 14 files changed, 541 insertions(+), 98 deletions(-) create mode 100644 django/backend_django/galvanalyser/migrations/0001_initial.py create mode 100644 django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py create mode 100644 django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py create mode 100644 frontend/src/CellList.tsx diff --git a/backend/galvanalyser/routes.py b/backend/galvanalyser/routes.py index 4d7e0074..d2fbf1f6 100644 --- a/backend/galvanalyser/routes.py +++ b/backend/galvanalyser/routes.py @@ -345,8 +345,8 @@ def equipment(id_=None): return jsonify({'success': True}), 200 -@ app.route('/CellData', methods=['GET', 'POST']) -@ app.route('/CellData/', methods=['GET', 'PUT', 'DELETE']) +@ app.route('/CellFamily', methods=['GET', 'POST']) +@ app.route('/CellFamily/', methods=['GET', 'PUT', 'DELETE']) @ cross_origin() @ jwt_required() def cell(id_=None): diff --git a/django/backend_django/galvanalyser/migrations/0001_initial.py b/django/backend_django/galvanalyser/migrations/0001_initial.py new file mode 100644 index 00000000..0edb05db --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0001_initial.py @@ -0,0 +1,194 @@ +# Generated by Django 4.1.4 on 2023-02-08 11:13 + +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + initial = True + + dependencies = [ + ('auth', '0012_alter_user_first_name_max_length'), + ] + + operations = [ + migrations.CreateModel( + name='TimeseriesData', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample', models.PositiveBigIntegerField()), + ('column_id', models.PositiveIntegerField()), + ('value', models.FloatField()), + ], + options={ + 'db_table': 'timeseries_data', + 'managed': False, + }, + ), + migrations.CreateModel( + name='Cell', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('display_name', models.TextField(null=True, unique=True)), + ], + ), + migrations.CreateModel( + name='CellFamily', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField(unique=True)), + ('form_factor', models.TextField()), + ('link_to_datasheet', models.TextField()), + ('anode_chemistry', models.TextField()), + ('cathode_chemistry', models.TextField()), + ('nominal_capacity', models.FloatField()), + ('nominal_cell_weight', models.FloatField()), + ('manufacturer', models.TextField()), + ], + ), + migrations.CreateModel( + name='Dataset', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField(null=True)), + ('date', models.DateTimeField()), + ('type', models.TextField(null=True)), + ('purpose', models.TextField()), + ('json_data', models.JSONField(null=True)), + ('cell', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='datasets', to='galvanalyser.cell')), + ], + ), + migrations.CreateModel( + name='DataUnit', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField()), + ('symbol', models.TextField()), + ('description', models.TextField()), + ('is_default', models.BooleanField(default=False)), + ], + ), + migrations.CreateModel( + name='Harvester', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField(unique=True)), + ('api_key', models.TextField(null=True)), + ('last_check_in', models.DateTimeField(null=True)), + ('sleep_time', models.IntegerField(default=10)), + ('admin_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='editable_harvesters', to='auth.group')), + ('user_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='readable_harvesters', to='auth.group')), + ], + ), + migrations.CreateModel( + name='MonitoredPath', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('path', models.TextField()), + ('stable_time', models.PositiveSmallIntegerField(default=60)), + ('admin_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='editable_paths', to='auth.group')), + ('harvester', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='monitored_paths', to='galvanalyser.harvester')), + ('user_group', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='readable_paths', to='auth.group')), + ], + options={ + 'unique_together': {('harvester', 'path')}, + }, + ), + migrations.CreateModel( + name='TimeseriesRangeLabel', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('label', models.TextField()), + ('range_start', models.PositiveBigIntegerField()), + ('range_end', models.PositiveBigIntegerField()), + ('info', models.TextField()), + ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='range_labels', to='galvanalyser.dataset')), + ], + ), + migrations.CreateModel( + name='ObservedFile', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('relative_path', models.TextField()), + ('last_observed_size', models.PositiveBigIntegerField(default=0)), + ('last_observed_time', models.DateTimeField(null=True)), + ('state', models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE')), + ('monitored_path', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='files', to='galvanalyser.monitoredpath')), + ], + options={ + 'unique_together': {('monitored_path', 'relative_path')}, + }, + ), + migrations.CreateModel( + name='HarvestError', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('error', models.TextField()), + ('timestamp', models.DateTimeField(auto_now=True, null=True)), + ('file', models.ForeignKey(on_delete=django.db.models.deletion.DO_NOTHING, related_name='errors', to='galvanalyser.observedfile')), + ('harvester', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='paths', to='galvanalyser.harvester')), + ('path', models.ForeignKey(on_delete=django.db.models.deletion.DO_NOTHING, to='galvanalyser.monitoredpath')), + ], + ), + migrations.CreateModel( + name='Equipment', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField(unique=True)), + ('type', models.TextField()), + ('datasets', models.ManyToManyField(related_name='equipment', to='galvanalyser.dataset')), + ], + ), + migrations.AddField( + model_name='dataset', + name='file', + field=models.ForeignKey(on_delete=django.db.models.deletion.DO_NOTHING, related_name='datasets', to='galvanalyser.observedfile'), + ), + migrations.CreateModel( + name='DataColumnType', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField()), + ('description', models.TextField()), + ('is_default', models.BooleanField(default=False)), + ('unit', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='galvanalyser.dataunit')), + ], + options={ + 'unique_together': {('unit', 'name')}, + }, + ), + migrations.CreateModel( + name='DataColumn', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.TextField()), + ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='columns', to='galvanalyser.dataset')), + ('type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='galvanalyser.datacolumntype')), + ], + options={ + 'unique_together': {('dataset', 'name')}, + }, + ), + migrations.AddField( + model_name='cell', + name='family', + field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='cells', to='galvanalyser.cellfamily'), + ), + migrations.AlterUniqueTogether( + name='dataset', + unique_together={('file', 'date')}, + ), + migrations.CreateModel( + name='DataColumnStringKeys', + fields=[ + ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('key', models.PositiveBigIntegerField()), + ('string', models.TextField()), + ('column', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='string_keys', to='galvanalyser.datacolumn')), + ], + options={ + 'unique_together': {('column', 'key', 'string')}, + }, + ), + ] diff --git a/django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py new file mode 100644 index 00000000..81e4ba6e --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0002_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-02-08 11:23 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0001_initial'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py b/django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py new file mode 100644 index 00000000..513ecc04 --- /dev/null +++ b/django/backend_django/galvanalyser/migrations/0003_alter_observedfile_state.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1.4 on 2023-02-08 11:38 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('galvanalyser', '0002_alter_observedfile_state'), + ] + + operations = [ + migrations.AlterField( + model_name='observedfile', + name='state', + field=models.TextField(choices=[('RETRY IMPORT', 'Retry Import'), ('IMPORT FAILED', 'Import Failed'), ('UNSTABLE', 'Unstable'), ('GROWING', 'Growing'), ('STABLE', 'Stable'), ('IMPORTING', 'Importing'), ('IMPORTED', 'Imported')], default='UNSTABLE'), + ), + ] diff --git a/django/backend_django/galvanalyser/models.py b/django/backend_django/galvanalyser/models.py index 3c18b21c..34e48e68 100644 --- a/django/backend_django/galvanalyser/models.py +++ b/django/backend_django/galvanalyser/models.py @@ -44,19 +44,9 @@ def save(self, *args, **kwargs): self.api_key = f"galv_hrv_{''.join(random.choices(text, k=60))}" super(Harvester, self).save(*args, **kwargs) - # Perform harvesting - def run(self): - paths = MonitoredPath.objects.filter(harvester=self) - for path in paths: - files = ObservedFile.objects.filter(monitored_path=path) - for file in files: - if file.state == FileState.STABLE: - file.import_content() - self.last_successful_run = timezone.now() - class MonitoredPath(models.Model): - harvester = models.ForeignKey(to=Harvester, related_name='monitored_paths', on_delete=models.DO_NOTHING) + harvester = models.ForeignKey(to=Harvester, related_name='monitored_paths', on_delete=models.SET_NULL, null=True) path = models.TextField() stable_time = models.PositiveSmallIntegerField(default=60) # seconds files must remain stable to be processed admin_group = models.ForeignKey( @@ -95,7 +85,7 @@ class HarvestError(models.Model): timestamp = models.DateTimeField(auto_now=True, null=True) -class CellData(models.Model): +class CellFamily(models.Model): name = models.TextField(null=False, unique=True) form_factor = models.TextField() link_to_datasheet = models.TextField() @@ -106,8 +96,13 @@ class CellData(models.Model): manufacturer = models.TextField() +class Cell(models.Model): + display_name = models.TextField(null=True, unique=True) + family = models.ForeignKey(to=CellFamily, related_name='cells', on_delete=models.SET_NULL, null=True) + + class Dataset(models.Model): - cell = models.ForeignKey(to=CellData, on_delete=models.SET_NULL, null=True) + cell = models.ForeignKey(to=Cell, related_name='datasets', on_delete=models.SET_NULL, null=True) file = models.ForeignKey(to=ObservedFile, on_delete=models.DO_NOTHING, related_name='datasets') name = models.TextField(null=True) date = models.DateTimeField(null=False) diff --git a/django/backend_django/galvanalyser/serializers.py b/django/backend_django/galvanalyser/serializers.py index 3c355943..355e6ff6 100644 --- a/django/backend_django/galvanalyser/serializers.py +++ b/django/backend_django/galvanalyser/serializers.py @@ -2,7 +2,8 @@ HarvestError, \ MonitoredPath, \ ObservedFile, \ - CellData, \ + Cell, \ + CellFamily, \ Dataset, \ Equipment, \ DataUnit, \ @@ -10,7 +11,7 @@ DataColumn, \ TimeseriesData, \ TimeseriesRangeLabel, \ - FileState, DataColumnStringKeys + DataColumnStringKeys from django.db import connection from django.contrib.auth.models import User, Group from django.conf.global_settings import DATA_UPLOAD_MAX_MEMORY_SIZE @@ -177,22 +178,44 @@ class Meta: fields = ['url', 'id', 'harvester', 'path', 'file', 'error', 'timestamp'] -class CellDataSerializer(serializers.HyperlinkedModelSerializer): - in_use = serializers.SerializerMethodField() - - def get_in_use(self, instance): - return Dataset.objects.filter(cell=instance).exists() +class CellFamilySerializer(serializers.HyperlinkedModelSerializer): class Meta: - model = CellData + model = CellFamily fields = [ 'url', 'id', 'name', 'form_factor', 'link_to_datasheet', 'anode_chemistry', 'cathode_chemistry', 'nominal_capacity', 'nominal_cell_weight', 'manufacturer', - 'in_use' + 'cells' ] - read_only_fields = ['id', 'url', 'in_use'] + read_only_fields = ['id', 'url', 'cells'] + + +class CellSerializer(serializers.HyperlinkedModelSerializer): + + class Meta: + model = Cell + fields = ['url', 'id', 'display_name', 'family', 'datasets'] + read_only_fields = ['id', 'url', 'datasets'] + extra_kwargs = {'display_name': {'allow_blank': True, 'allow_null': True}} + + def validate_display_name(self, value): + if isinstance(value, str): + return value + return "" + + def validate_family(self, value): + if not isinstance(value, CellFamily): + raise serializers.ValidationError("family property must be a CellFamily instance") + return value + + def create(self, validated_data): + display_name = validated_data.pop('display_name') + family = validated_data.pop('family') + if display_name is '': + display_name = f"{family.name}_{family.cells.count()}" + return Cell.objects.create(family=family, display_name=display_name) class EquipmentSerializer(serializers.HyperlinkedModelSerializer): diff --git a/django/backend_django/galvanalyser/utils.py b/django/backend_django/galvanalyser/utils.py index 283bba8a..1fc39a44 100644 --- a/django/backend_django/galvanalyser/utils.py +++ b/django/backend_django/galvanalyser/utils.py @@ -1,4 +1,5 @@ import io +import sys class IteratorFile(io.TextIOBase): diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index bea38305..82a4deeb 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -3,7 +3,8 @@ HarvesterConfigSerializer, \ MonitoredPathSerializer, \ ObservedFileSerializer, \ - CellDataSerializer, \ + CellSerializer, \ + CellFamilySerializer, \ DatasetSerializer, \ EquipmentSerializer, \ DataUnitSerializer, \ @@ -18,7 +19,8 @@ HarvestError, \ MonitoredPath, \ ObservedFile, \ - CellData, \ + Cell, \ + CellFamily, \ Dataset, \ Equipment, \ DataUnit, \ @@ -77,6 +79,8 @@ class HarvesterViewSet(viewsets.ModelViewSet): When Harvesters communicate with the API they do so using special Harvester API Keys. These provide access to the report and configuration endpoints. + + Harvesters are created by a separate software package available within Galvanalyser. """ serializer_class = HarvesterSerializer filterset_fields = ['name'] @@ -93,7 +97,7 @@ def create(self, request, *args, **kwargs): """ Create a Harvester and the user Groups required to control it. """ - + # TODO: move to serializer? # Validate input if not request.data['name']: return error_response('No name specified for Harvester.') @@ -115,7 +119,7 @@ def create(self, request, *args, **kwargs): user.groups.add(harvester.admin_group) user.save() - return Response(self.get_serializer(harvester).data) + return Response(HarvesterConfigSerializer(harvester, context={'request': request}).data) def update(self, request, *args, **kwargs): try: @@ -143,11 +147,7 @@ def update(self, request, *args, **kwargs): harvester.save() return Response(self.get_serializer(harvester).data) - # @action(detail=True, methods=['GET']) - # def env(self, request, pk: int = None): - # harvester = Harvester.objects.get(id=pk) - # result = get_env.apply_async(queue=harvester.name) - # return Response(result.get()) + # TODO: handle harvester envvars? @action(detail=True, methods=['GET']) def config(self, request, pk: int = None): @@ -155,17 +155,22 @@ def config(self, request, pk: int = None): Return a full configuration file including MonitoredPaths under paths. Used by the API for updating the Harvester. """ - # TODO: Restrict access to Harvester or harvester user harvester = get_object_or_404(Harvester, id=pk) - return Response(HarvesterConfigSerializer(harvester, context={'request': request}).data) + try: + key = request.META.get('HTTP_AUTHORIZATION', '') + key = key[len('Harvester '):] + assert key == harvester.api_key + return Response(HarvesterConfigSerializer(harvester, context={'request': request}).data) + except AssertionError: + return error_response("Invalid AUTHORIZATION header. Required 'Harvester [api_key]'.") @action(detail=True, methods=['POST']) def report(self, request, pk: int = None): """ - Process a harvester's report on its activity. + Process a Harvester's report on its activity. This will spawn various other database updates depending on payload content. - Only harvesters are authorised to issue reports. + Only Harvesters are authorised to issue reports. """ # TODO access class Harvester harvester = Harvester.objects.get(id=pk) @@ -354,7 +359,12 @@ def report(self, request, pk: int = None): class MonitoredPathViewSet(viewsets.ModelViewSet): """ - TODO: document + A MonitoredPath refers to a directory accessible by a Harvester in which + data files will reside. Those files will be scanned periodically by the Harvester, + becoming ObservedFiles once they are reported to Galvanalyser by the Harvester. + + MonitoredPaths can be created or updated by a Harvester's admins and users, as + well as any users who have been given explicit permissions to edit the MonitoredPath. """ serializer_class = MonitoredPathSerializer filterset_fields = ['path', 'harvester__id', 'harvester__name'] @@ -434,7 +444,13 @@ def update(self, request, *args, **kwargs): class ObservedFileViewSet(viewsets.ModelViewSet): """ - TODO: document + ObservedFiles are files that exist (or have existed) in a MonitoredPath and have + been reported to Galvanalyser by the Harvester. + + An ObservedFile instance will have file metadata (size, modification time), and a + status representing its import state. It may be linked to HarvestErrors + encountered while importing the file, and/or to Datasets representing the content + of imported files. """ serializer_class = ObservedFileSerializer filterset_fields = ['monitored_path__id', 'relative_path', 'state'] @@ -462,10 +478,13 @@ def reimport(self, request, pk: int = None): class DatasetViewSet(viewsets.ModelViewSet): """ - TODO: document + A Dataset contains structured data from an ObservedFile. + + Datasets are decomposed within Galvanalyser into columns and datapoints, + providing an ability flexibly handle any kind of tabular data. """ serializer_class = DatasetSerializer - filterset_fields = ['name', 'type', 'cell__name'] + filterset_fields = ['name', 'type', 'cell__family__name'] search_fields = ['@name', 'type'] queryset = Dataset.objects.none().order_by('-date', '-id') @@ -480,7 +499,8 @@ def get_queryset(self): class HarvestErrorViewSet(viewsets.ModelViewSet): """ - TODO: document + HarvestErrors are problems encountered by Harvesters during the crawling of + MonitoredPaths or the importing or inspection of ObservedFiles. """ serializer_class = HarvestErrorSerializer filterset_fields = ['file', 'path', 'harvester'] @@ -496,17 +516,33 @@ def get_queryset(self): ).order_by('-timestamp') -class CellDataViewSet(viewsets.ModelViewSet): +class CellFamilyViewSet(viewsets.ModelViewSet): + """ + CellFamilies describe types of Cell. + """ + serializer_class = CellFamilySerializer + filterset_fields = [ + 'name', 'form_factor', 'anode_chemistry', 'cathode_chemistry', 'nominal_capacity', + 'nominal_cell_weight', 'manufacturer' + ] + search_fields = ['@name', '@manufacturer', 'form_factor'] + queryset = CellFamily.objects.all().order_by('-id') + + +class CellViewSet(viewsets.ModelViewSet): """ - TODO: document + Cells are specific cells which have generated data stored in Datasets/ObservedFiles. """ - serializer_class = CellDataSerializer - queryset = CellData.objects.all().order_by('-id') + serializer_class = CellSerializer + filterset_fields = ['display_name', 'family__id'] + search_fields = ['@display_name'] + queryset = Cell.objects.all().order_by('-id') class EquipmentViewSet(viewsets.ModelViewSet): """ - TODO: document + Equipment can be attached to Datasets and used to view Datasets which + have used similar equipment. """ serializer_class = EquipmentSerializer queryset = Equipment.objects.all() @@ -514,7 +550,7 @@ class EquipmentViewSet(viewsets.ModelViewSet): class DataUnitViewSet(viewsets.ModelViewSet): """ - TODO: document + DataUnits are units used to characterise data in a DataColumn. """ serializer_class = DataUnitSerializer filterset_fields = ['name', 'symbol', 'is_default'] @@ -524,7 +560,8 @@ class DataUnitViewSet(viewsets.ModelViewSet): class DataColumnTypeViewSet(viewsets.ModelViewSet): """ - TODO: document + DataColumnTypes support reuse of DataColumns over multiple DataSets + by abstracting their information. """ serializer_class = DataColumnTypeSerializer filterset_fields = ['name', 'unit__symbol', 'unit__name', 'is_default'] @@ -534,7 +571,7 @@ class DataColumnTypeViewSet(viewsets.ModelViewSet): class DataColumnViewSet(viewsets.ModelViewSet): """ - TODO: document + DataColumns describe which columns are in a Dataset's data. """ serializer_class = DataColumnSerializer queryset = DataColumn.objects.all() @@ -542,7 +579,8 @@ class DataColumnViewSet(viewsets.ModelViewSet): class TimeseriesDataViewSet(viewsets.ModelViewSet): """ - TODO: document + TimeseriesData link observation identifiers (rows) with DataColumns, + and therefore hold the actual values in the cells of a dataset. """ serializer_class = TimeseriesDataSerializer queryset = TimeseriesData.objects.all() @@ -550,7 +588,7 @@ class TimeseriesDataViewSet(viewsets.ModelViewSet): class TimeseriesRangeLabelViewSet(viewsets.ModelViewSet): """ - TODO: document + TimeseriesRangeLabels mark contiguous observations using start and endpoints. """ serializer_class = TimeseriesRangeLabelSerializer queryset = TimeseriesRangeLabel.objects.all() @@ -558,7 +596,7 @@ class TimeseriesRangeLabelViewSet(viewsets.ModelViewSet): class UserViewSet(viewsets.ModelViewSet): """ - TODO: document + Users are Django User instances custom-serialized for convenience. """ serializer_class = UserSerializer queryset = User.objects.all() @@ -566,7 +604,7 @@ class UserViewSet(viewsets.ModelViewSet): class GroupViewSet(viewsets.ModelViewSet): """ - TODO: document + Groups are Django Group instances custom-serialized for convenience. """ serializer_class = GroupSerializer queryset = Group.objects.none().order_by('-id') diff --git a/docker-compose.override.yml b/docker-compose.override.yml index d3705b2c..24e7929a 100644 --- a/docker-compose.override.yml +++ b/docker-compose.override.yml @@ -27,6 +27,7 @@ services: # command: tail -F anything depends_on: - app + restart: unless-stopped volumes: - ./harvester:/usr/harvester - ./.harvester:/harvester_files @@ -42,6 +43,7 @@ services: ports: - "3000:3000" command: yarn start + restart: unless-stopped # old_worker: # build: diff --git a/frontend/src/AsyncTable.tsx b/frontend/src/AsyncTable.tsx index 310237a6..ed6097bf 100644 --- a/frontend/src/AsyncTable.tsx +++ b/frontend/src/AsyncTable.tsx @@ -47,6 +47,7 @@ export type AsyncTableProps = { columns: Column[]; row_generator: RowGenerator; url: string; + fetch_depth?: number; new_row_values?: Partial; styles?: any; } @@ -94,11 +95,13 @@ export default class AsyncTable extends Component) { super(props) if (props.new_row_values !== undefined) this.state.new_row = this.new_row_template + this.fetch_depth = props.fetch_depth === undefined? 1 : props.fetch_depth } get new_row_template() { @@ -140,7 +143,7 @@ export default class AsyncTable extends Component { if (typeof(res) === 'number') @@ -173,7 +176,7 @@ export default class AsyncTable extends Component { // If we deleted the row, delete it in state diff --git a/frontend/src/CellList.tsx b/frontend/src/CellList.tsx new file mode 100644 index 00000000..3b0034ad --- /dev/null +++ b/frontend/src/CellList.tsx @@ -0,0 +1,134 @@ +import React, {Fragment, useState} from 'react'; +import TextField from '@mui/material/TextField'; +import { makeStyles } from '@mui/styles' +import Paper from '@mui/material/Paper'; +import Tooltip from '@mui/material/Tooltip'; +import AddIcon from '@mui/icons-material/Add'; +import IconButton from '@mui/material/IconButton'; +import Container from '@mui/material/Container'; +import SaveIcon from '@mui/icons-material/Save'; +import DeleteIcon from '@mui/icons-material/Delete'; +import Connection from "./APIConnection"; +import AsyncTable, {RowGeneratorContext} from "./AsyncTable"; +import Typography from "@mui/material/Typography"; +import {CellFamilyFields} from "./Cells"; + +export type CellFields = { + id: number; + url: string; + display_name: string; + family: string; + datasets: string[]; +} +type CellDetailProps = { + family: CellFamilyFields, + [key: string]: any +} + +const useStyles = makeStyles((theme) => ({ + container: { + paddingTop: theme.spacing(4), + paddingBottom: theme.spacing(4), + }, + table: { + minWidth: 650, + }, + resize: { + fontSize: '10pt', + }, + input: { + marginLeft: theme.spacing(0), + flex: 1, + }, + iconButton: { + padding: 10, + }, + paper: {} +})); + +const columns = [ + {label: 'Display Name', help: 'Human-friendly name for the cell'}, + {label: 'Linked Datasets', help: 'Number of datasets linked to this cell'}, + {label: 'Save', help: 'Click to save edits to a row. Edits are disabled for cells that are in use'}, + {label: 'Delete', help: 'Delete a cell that is not in use'}, +] + +export default function CellList(props: CellDetailProps) { + const classes = useStyles(); + + const addNewCell = (data: CellFields, context: RowGeneratorContext) => { + context.mark_loading(true) + const insert_data = {display_name: data.display_name, family: props.family.url} + return Connection.fetch('cells/', {body: JSON.stringify(insert_data), method: 'POST'}) + }; + + const updateCell = (data: CellFields, context: RowGeneratorContext) => { + context.mark_loading(true) + const insert_data = {display_name: data.display_name, family: props.family.url} + return Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) + }; + + const deleteCell = (data: CellFields) => Connection.fetch(data.url, {method: 'DELETE'}) + + return ( + + + + columns={columns} + row_generator={(cell, context) => [ + + 0} + placeholder={`${props.family.name}_#`} + InputProps={{ + classes: { + input: classes.resize, + }, + }} + onChange={context.update} + /> + , + context.is_new_row? : + {cell.datasets.length} + , + cell.datasets.length > 0? : + 0? "Cannot update a cell that is used by datasets." : + context.is_new_row? "Add cell" : "Save changes to cell" + }> + + 0} + onClick={ + context.is_new_row? + () => addNewCell(cell, context).then(context.refresh_all_rows) : + () => updateCell(cell, context).then(context.refresh)} + > + {context.is_new_row? : } + + + + , + context.is_new_row || cell.datasets.length > 0? : + + + deleteCell(cell).then(context.refresh)}> + + + + + + ]} + new_row_values={{display_name: '', datasets: []}} + url={`cells/?all=true&family__id=${props.family.id}`} + fetch_depth={0} + /> + + Note: Cells assigned to existing datasets cannot be changed. + + + + ); +} diff --git a/frontend/src/Cells.tsx b/frontend/src/Cells.tsx index 2fe31af1..afed1976 100644 --- a/frontend/src/Cells.tsx +++ b/frontend/src/Cells.tsx @@ -1,4 +1,4 @@ -import React, { Fragment } from 'react'; +import React, {Fragment, useState} from 'react'; import TextField from '@mui/material/TextField'; import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; @@ -11,8 +11,10 @@ import DeleteIcon from '@mui/icons-material/Delete'; import Connection from "./APIConnection"; import AsyncTable, {RowGeneratorContext} from "./AsyncTable"; import Typography from "@mui/material/Typography"; +import SearchIcon from "@mui/icons-material/Search"; +import CellList, {CellFields} from "./CellList"; -export type CellFields = { +export type CellFamilyFields = { url: string; id: number; name: string; @@ -23,7 +25,7 @@ export type CellFields = { nominal_capacity: number; nominal_cell_weight: number; manufacturer: string; - in_use: boolean; + cells: CellFields[]; } const useStyles = makeStyles((theme) => ({ @@ -48,17 +50,17 @@ const useStyles = makeStyles((theme) => ({ })); const columns = [ - // {label: 'ID', help: 'Id in database'}, {label: 'Name', help: ''}, - {label: 'Manufacturer', help: 'Manufacturer of the cell'}, - {label: 'Form Factor', help: 'Form factor of the cell'}, - {label: 'Datasheet', help: 'Link to the cell\'s datasheet'}, - {label: 'Anode Chemistry', help: 'Chemistry of the cell\'s anode'}, - {label: 'Cathode Chemistry', help: 'Chemistry of the cell\'s cathode'}, - {label: 'Nominal Capacity', help: 'Nominal cell capacity'}, - {label: 'Nominal Weight', help: 'Nominal cell weight'}, - {label: 'Save', help: 'Click to save edits to a row. Edits are disabled for cells that are in use'}, - {label: 'Delete', help: 'Delete a cell that is not in use'}, + {label: 'Manufacturer', help: 'Manufacturer of the cell family'}, + {label: 'Form Factor', help: 'Form factor of the cell family'}, + {label: 'Datasheet', help: 'Link to the cell family\'s datasheet'}, + {label: 'Anode Chemistry', help: 'Chemistry of the cell family\'s anode'}, + {label: 'Cathode Chemistry', help: 'Chemistry of the cell family\'s cathode'}, + {label: 'Nominal Capacity', help: 'Nominal cell family capacity'}, + {label: 'Nominal Weight', help: 'Nominal cell family weight'}, + {label: 'Details', help: 'View cells in this family'}, + {label: 'Save', help: 'Click to save edits to a row. Edits are disabled for cell families that are in use'}, + {label: 'Delete', help: 'Delete a cell family that is not in use'}, ] const string_fields = [ @@ -68,8 +70,9 @@ const number_fields = ['nominal_capacity', 'nominal_cell_weight'] as const export default function Cells() { const classes = useStyles(); + const [selected, setSelected] = useState(null) - const get_write_data: (data: CellFields) => Partial = (data) => { + const get_write_data: (data: CellFamilyFields) => Partial = (data) => { return { name: data.name, form_factor: data.form_factor, @@ -82,31 +85,31 @@ export default function Cells() { } } - const addNewCell = (data: CellFields, context: RowGeneratorContext) => { + const addNewCell = (data: CellFamilyFields, context: RowGeneratorContext) => { context.mark_loading(true) const insert_data = get_write_data(data) - return Connection.fetch('cells/', {body: JSON.stringify(insert_data), method: 'POST'}) + return Connection.fetch('cell_families/', {body: JSON.stringify(insert_data), method: 'POST'}) }; - const updateCell = (data: CellFields, context: RowGeneratorContext) => { + const updateCell = (data: CellFamilyFields, context: RowGeneratorContext) => { context.mark_loading(true) const insert_data = get_write_data(data) return Connection.fetch(data.url, {body: JSON.stringify(insert_data), method: 'PATCH'}) }; - const deleteCell = (data: CellFields) => Connection.fetch(data.url, {method: 'DELETE'}) + const deleteCell = (data: CellFamilyFields) => Connection.fetch(data.url, {method: 'DELETE'}) return ( - + columns={columns} - row_generator={(cell, context) => [ + row_generator={(family, context) => [ ...string_fields.map(n => 0} InputProps={{ classes: { input: classes.resize, @@ -120,8 +123,8 @@ export default function Cells() { name={n} style={{width: 60}} type={"number"} - value={cell[n]} - disabled={cell.in_use} + value={family[n]} + disabled={family.cells.length > 0} InputProps={{ classes: { input: classes.resize, @@ -130,28 +133,33 @@ export default function Cells() { onChange={context.update} /> ), - cell.in_use? : + context.is_new_row? : + selected?.id === family.id? setSelected(null) : setSelected(family)}> + + + , + family.cells.length > 0? : 0? "Cannot update a cell family that is used by cells." : + context.is_new_row? "Add cell family" : "Save changes to cell family" }> 0} onClick={ context.is_new_row? - () => addNewCell(cell, context).then(context.refresh_all_rows) : - () => updateCell(cell, context).then(context.refresh)} + () => addNewCell(family, context).then(context.refresh_all_rows) : + () => updateCell(family, context).then(context.refresh)} > {context.is_new_row? : } , - context.is_new_row || cell.in_use? : - + context.is_new_row || family.cells.length > 0? : + - deleteCell(cell).then(context.refresh)}> + deleteCell(family).then(context.refresh)}> @@ -160,14 +168,16 @@ export default function Cells() { ]} new_row_values={{ name: '', manufacturer: '', form_factor: '', link_to_datasheet: '', anode_chemistry: '', cathode_chemistry: '', - nominal_capacity: 0, nominal_cell_weight: 0 + nominal_capacity: 0, nominal_cell_weight: 0, cells: [] }} - url="cells/?all=true" + url="cell_families/?all=true" + fetch_depth={0} /> - Note: Cells assigned to existing datasets cannot be changed. + Note: Cell families with cells cannot be changed. + {selected !== null && } ); } diff --git a/frontend/src/DatasetDetail.js b/frontend/src/DatasetDetail.js index ca92c1b6..80f6fb3f 100644 --- a/frontend/src/DatasetDetail.js +++ b/frontend/src/DatasetDetail.js @@ -132,7 +132,7 @@ export default function DatasetDetail() { const { id } = useParams(); const classes = useStyles(); - const [cellData, setCellData] = useState([]) + const [cellData, setCellFamily] = useState([]) const [equipmentData, setEquipmentData] = useState(null) const [dataset, setDataset] = useState(null) const [userData, setUserData] = useState([]) @@ -146,7 +146,7 @@ export default function DatasetDetail() { }); cells().then((response) => { if (response.ok) { - return response.json().then(setCellData); + return response.json().then(setCellFamily); } }); datasets(id).then((response) => { diff --git a/frontend/src/Datasets.tsx b/frontend/src/Datasets.tsx index bec2ecd0..a0e19757 100644 --- a/frontend/src/Datasets.tsx +++ b/frontend/src/Datasets.tsx @@ -19,7 +19,7 @@ import TextField from "@mui/material/TextField"; import IconButton from "@mui/material/IconButton"; import {UserSet} from "./UserRoleSet"; import SettingsIcon from "@mui/icons-material/Settings"; -import {CellFields} from "./Cells"; +import {CellFields} from "./CellList"; import MenuItem from "@mui/material/MenuItem"; import CircularProgress from "@mui/material/CircularProgress"; import {EquipmentFields} from "./Equipment"; @@ -142,7 +142,7 @@ export default function Datasets() { }; const get_cell_items = (dataset: DatasetFields) => { - const menuItem = (cell: CellFields) => {cell.name} + const menuItem = (cell: CellFields) => {cell.display_name} const items: ReactElement[] = [] if (dataset?.cell) { items.push(menuItem(dataset.cell)) @@ -185,7 +185,14 @@ export default function Datasets() { columns={columns} row_generator={(dataset, context) => [ {dataset.id}, - {dataset.date}, + + { + Intl.DateTimeFormat( + 'en-GB', + {dateStyle: 'long', timeStyle: 'long'}) + .format(Date.parse(dataset.date)) + } + , // these fields have the same shape, so condense the code. // as const stops TypeScript from complaining about strings assigned to keyof DatasetFields ...(['name', 'type', 'purpose'] as const).map( From 97ea47aed650cd73091fdabd23439c8df7090d97 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Thu, 9 Feb 2023 18:25:12 +0000 Subject: [PATCH 40/79] reduce display width; unite action buttons --- frontend/src/APIConnection.ts | 7 +- frontend/src/ActionButtons.tsx | 87 ++++++++++++ frontend/src/CellList.tsx | 75 +++-------- frontend/src/Cells.tsx | 222 +++++++++++++++++-------------- frontend/src/Datasets.tsx | 164 ++++++++++++----------- frontend/src/Equipment.tsx | 74 +++-------- frontend/src/Files.tsx | 23 +--- frontend/src/HarvesterDetail.tsx | 72 +++------- frontend/src/Harvesters.tsx | 64 ++------- frontend/src/UseStyles.ts | 57 ++++++++ 10 files changed, 427 insertions(+), 418 deletions(-) create mode 100644 frontend/src/ActionButtons.tsx create mode 100644 frontend/src/UseStyles.ts diff --git a/frontend/src/APIConnection.ts b/frontend/src/APIConnection.ts index e56ea90d..fc663c95 100644 --- a/frontend/src/APIConnection.ts +++ b/frontend/src/APIConnection.ts @@ -6,11 +6,6 @@ export type User = { last_name: string, is_staff: boolean, is_superuser: boolean, - // groups: { - // url: string, - // name: string, - // permissions: [] - // }[], token: string, } @@ -78,7 +73,7 @@ export class APIConnection { return cookie !== undefined && this.user !== null; } - async fetch(url: string, options?: any, depth: number = 1): Promise { + async fetch(url: string, options?: any, depth: number = 0): Promise { await this.get_is_logged_in(); console.info(`Fetch ${url} for ${this.user?.username}`) console.info('fetch options', options) diff --git a/frontend/src/ActionButtons.tsx b/frontend/src/ActionButtons.tsx new file mode 100644 index 00000000..01f0ff74 --- /dev/null +++ b/frontend/src/ActionButtons.tsx @@ -0,0 +1,87 @@ +import React, {Component} from "react"; +import Stack, {StackProps} from "@mui/material/Stack"; +import IconButton, {IconButtonProps} from "@mui/material/IconButton"; +import Icon from "@mui/material/Icon"; +import SearchIcon from "@mui/icons-material/Search"; +import SaveIcon from "@mui/icons-material/Save"; +import DeleteIcon from "@mui/icons-material/Delete"; +import {SvgIconProps} from "@mui/material/SvgIcon" +import useStyles from "./UseStyles"; + +export type ActionButtonsProps = { + classes: ReturnType; + onInspect?: () => void; + onSave?: () => void; + onDelete?: () => void; + inspectButtonProps?: IconButtonProps; + saveButtonProps?: IconButtonProps; + deleteButtonProps?: IconButtonProps; + inspectIconProps?: SvgIconProps & {component?: any}; + saveIconProps?: SvgIconProps & {component?: any}; + deleteIconProps?: SvgIconProps & {component?: any}; + wrapperElementProps?: StackProps; +} + +/** + * Group together commonly displayed action buttons. + * + * Buttons included are: + * - Inspect + * - Save + * - Delete + * + * Buttons are included where the on[ButtonName] property is specified. + * Their properties can be customised with [buttonName]ButtonProps, + * and the properties of the child SvgIcon by [buttonName]IconProps. + * + * The wrapper element is a element and + * can be customised with the wrapperElementProps prop. + */ +export default class ActionButtons extends Component { + render() { + return ( + + { + this.props.onInspect !== undefined && + + + + } + { + this.props.onSave !== undefined && + + + + } + { + this.props.onDelete !== undefined && + + + + } + + ) + } +} \ No newline at end of file diff --git a/frontend/src/CellList.tsx b/frontend/src/CellList.tsx index 3b0034ad..673c207c 100644 --- a/frontend/src/CellList.tsx +++ b/frontend/src/CellList.tsx @@ -1,17 +1,15 @@ -import React, {Fragment, useState} from 'react'; +import React, {Fragment} from 'react'; import TextField from '@mui/material/TextField'; -import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; -import Tooltip from '@mui/material/Tooltip'; import AddIcon from '@mui/icons-material/Add'; -import IconButton from '@mui/material/IconButton'; import Container from '@mui/material/Container'; import SaveIcon from '@mui/icons-material/Save'; -import DeleteIcon from '@mui/icons-material/Delete'; import Connection from "./APIConnection"; import AsyncTable, {RowGeneratorContext} from "./AsyncTable"; import Typography from "@mui/material/Typography"; import {CellFamilyFields} from "./Cells"; +import useStyles from "./UseStyles"; +import ActionButtons from "./ActionButtons"; export type CellFields = { id: number; @@ -25,32 +23,10 @@ type CellDetailProps = { [key: string]: any } -const useStyles = makeStyles((theme) => ({ - container: { - paddingTop: theme.spacing(4), - paddingBottom: theme.spacing(4), - }, - table: { - minWidth: 650, - }, - resize: { - fontSize: '10pt', - }, - input: { - marginLeft: theme.spacing(0), - flex: 1, - }, - iconButton: { - padding: 10, - }, - paper: {} -})); - const columns = [ {label: 'Display Name', help: 'Human-friendly name for the cell'}, {label: 'Linked Datasets', help: 'Number of datasets linked to this cell'}, - {label: 'Save', help: 'Click to save edits to a row. Edits are disabled for cells that are in use'}, - {label: 'Delete', help: 'Delete a cell that is not in use'}, + {label: 'Actions', help: 'Save / Delete a cell. Edits are disabled for cells that are in use'} ] export default function CellList(props: CellDetailProps) { @@ -93,32 +69,23 @@ export default function CellList(props: CellDetailProps) { context.is_new_row? : {cell.datasets.length} , - cell.datasets.length > 0? : - 0? "Cannot update a cell that is used by datasets." : - context.is_new_row? "Add cell" : "Save changes to cell" - }> - - 0} - onClick={ - context.is_new_row? - () => addNewCell(cell, context).then(context.refresh_all_rows) : - () => updateCell(cell, context).then(context.refresh)} - > - {context.is_new_row? : } - - - - , - context.is_new_row || cell.datasets.length > 0? : - - - deleteCell(cell).then(context.refresh)}> - - - - + + addNewCell(cell, context).then(context.refresh_all_rows) : + () => updateCell(cell, context).then(context.refresh) + } + saveButtonProps={{disabled: !context.value_changed || cell.datasets.length > 0}} + saveIconProps={{component: context.is_new_row? AddIcon : SaveIcon}} + onDelete={ + () => + window.confirm(`Delete cell ${cell.display_name}?`) && + deleteCell(cell).then(context.refresh) + } + deleteButtonProps={{disabled: context.is_new_row || cell.datasets.length > 0}} + /> ]} new_row_values={{display_name: '', datasets: []}} diff --git a/frontend/src/Cells.tsx b/frontend/src/Cells.tsx index afed1976..a9eaa842 100644 --- a/frontend/src/Cells.tsx +++ b/frontend/src/Cells.tsx @@ -1,18 +1,17 @@ import React, {Fragment, useState} from 'react'; import TextField from '@mui/material/TextField'; -import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; import Tooltip from '@mui/material/Tooltip'; import AddIcon from '@mui/icons-material/Add'; -import IconButton from '@mui/material/IconButton'; import Container from '@mui/material/Container'; import SaveIcon from '@mui/icons-material/Save'; -import DeleteIcon from '@mui/icons-material/Delete'; import Connection from "./APIConnection"; import AsyncTable, {RowGeneratorContext} from "./AsyncTable"; import Typography from "@mui/material/Typography"; -import SearchIcon from "@mui/icons-material/Search"; import CellList, {CellFields} from "./CellList"; +import Stack from "@mui/material/Stack"; +import useStyles from "./UseStyles"; +import ActionButtons from "./ActionButtons"; export type CellFamilyFields = { url: string; @@ -28,46 +27,14 @@ export type CellFamilyFields = { cells: CellFields[]; } -const useStyles = makeStyles((theme) => ({ - container: { - paddingTop: theme.spacing(4), - paddingBottom: theme.spacing(4), - }, - table: { - minWidth: 650, - }, - resize: { - fontSize: '10pt', - }, - input: { - marginLeft: theme.spacing(0), - flex: 1, - }, - iconButton: { - padding: 10, - }, - paper: {} -})); - const columns = [ - {label: 'Name', help: ''}, - {label: 'Manufacturer', help: 'Manufacturer of the cell family'}, - {label: 'Form Factor', help: 'Form factor of the cell family'}, - {label: 'Datasheet', help: 'Link to the cell family\'s datasheet'}, - {label: 'Anode Chemistry', help: 'Chemistry of the cell family\'s anode'}, - {label: 'Cathode Chemistry', help: 'Chemistry of the cell family\'s cathode'}, - {label: 'Nominal Capacity', help: 'Nominal cell family capacity'}, - {label: 'Nominal Weight', help: 'Nominal cell family weight'}, - {label: 'Details', help: 'View cells in this family'}, - {label: 'Save', help: 'Click to save edits to a row. Edits are disabled for cell families that are in use'}, - {label: 'Delete', help: 'Delete a cell family that is not in use'}, + {label: 'Source', help: ''}, + {label: 'Type', help: ''}, + {label: 'Chemistry', help: ''}, + {label: 'Statistics', help: 'Nominal values for cell'}, + {label: 'Actions', help: 'View Cells / Save / Delete cell families'}, ] -const string_fields = [ - 'name', 'manufacturer', 'form_factor', 'link_to_datasheet', 'anode_chemistry', 'cathode_chemistry' -] as const -const number_fields = ['nominal_capacity', 'nominal_cell_weight'] as const - export default function Cells() { const classes = useStyles(); const [selected, setSelected] = useState(null) @@ -105,65 +72,124 @@ export default function Cells() { columns={columns} row_generator={(family, context) => [ - ...string_fields.map(n => - 0} - InputProps={{ - classes: { - input: classes.resize, - }, - }} - onChange={context.update} - /> - ), - ...number_fields.map(n => - 0} - InputProps={{ - classes: { - input: classes.resize, - }, - }} - onChange={context.update} - /> - ), - context.is_new_row? : - selected?.id === family.id? setSelected(null) : setSelected(family)}> - - + + + + + + + + + , - family.cells.length > 0? : - 0? "Cannot update a cell family that is used by cells." : - context.is_new_row? "Add cell family" : "Save changes to cell family" - }> - - 0} - onClick={ - context.is_new_row? - () => addNewCell(family, context).then(context.refresh_all_rows) : - () => updateCell(family, context).then(context.refresh)} - > - {context.is_new_row? : } - - - + + + + + + + + + , - context.is_new_row || family.cells.length > 0? : - - - deleteCell(family).then(context.refresh)}> - - - - + + + + + + + + + + , + + + + + + + + + + , + + selected?.id === family.id? setSelected(null) : setSelected(family)} + inspectButtonProps={{disabled: context.is_new_row}} + inspectIconProps={selected?.id === family.id ? {color: 'info'} : {}} + onSave={ + context.is_new_row? + () => addNewCell(family, context).then(context.refresh_all_rows) : + () => updateCell(family, context).then(context.refresh) + } + saveButtonProps={{disabled: !context.value_changed || family.cells.length > 0}} + saveIconProps={{component: context.is_new_row? AddIcon : SaveIcon}} + onDelete={ + () => + window.confirm(`Delete cell family ${family.name}?`) && + deleteCell(family).then(context.refresh) + } + deleteButtonProps={{disabled: context.is_new_row || family.cells.length > 0}} + /> ]} new_row_values={{ diff --git a/frontend/src/Datasets.tsx b/frontend/src/Datasets.tsx index a0e19757..1aa3eac1 100644 --- a/frontend/src/Datasets.tsx +++ b/frontend/src/Datasets.tsx @@ -1,7 +1,5 @@ - import React, {useEffect, useState, Fragment, ReactElement} from "react"; import Container from '@mui/material/Container'; -import { makeStyles } from '@mui/styles' import Button from '@mui/material/Button'; import { useNavigate } from "react-router-dom"; import GetDatasetPython from "./GetDatasetPython" @@ -13,12 +11,10 @@ import DialogTitle from '@mui/material/DialogTitle'; import Connection, {APIConnection} from "./APIConnection" import AsyncTable, {RowGeneratorContext} from "./AsyncTable" import Paper from "@mui/material/Paper"; +import FormControl from "@mui/material/FormControl"; import Select from "@mui/material/Select"; -import SaveIcon from "@mui/icons-material/Save"; import TextField from "@mui/material/TextField"; -import IconButton from "@mui/material/IconButton"; import {UserSet} from "./UserRoleSet"; -import SettingsIcon from "@mui/icons-material/Settings"; import {CellFields} from "./CellList"; import MenuItem from "@mui/material/MenuItem"; import CircularProgress from "@mui/material/CircularProgress"; @@ -26,6 +22,11 @@ import {EquipmentFields} from "./Equipment"; import OutlinedInput from "@mui/material/OutlinedInput"; import Box from "@mui/material/Box"; import Chip from "@mui/material/Chip"; +import Tooltip from "@mui/material/Tooltip"; +import Grid from "@mui/material/Grid"; +import InputLabel from "@mui/material/InputLabel"; +import useStyles from "./UseStyles"; +import ActionButtons from "./ActionButtons"; export type DatasetFields = { url: string; @@ -39,30 +40,6 @@ export type DatasetFields = { user_sets: UserSet[]; } -const useStyles = makeStyles((theme) => ({ - button: { - margin: theme.spacing(1), - }, - container: { - paddingTop: theme.spacing(4), - paddingBottom: theme.spacing(4), - }, - table: { - minWidth: 650, - }, - resize: { - fontSize: '11pt', - }, - input: { - marginLeft: theme.spacing(1), - flex: 1, - }, - iconButton: { - padding: 10, - }, - paper: {} -})); - export default function Datasets() { const classes = useStyles(); const [selected, setSelected] = useState(null) @@ -108,15 +85,10 @@ export default function Datasets() { } const columns = [ - {label: 'ID', help: 'Unique ID in database'}, {label: 'Date', help: 'Date of Test'}, - {label: 'Name', help: ''}, - {label: 'Type', help: 'File type determined by Harvester'}, - {label: 'Purpose', help: 'Short description of dataset purpose'}, - {label: 'Cell', help: 'Cell that generated the dataset'}, + {label: 'Properties', help: ''}, {label: 'Equipment', help: 'Equipment used to generate the dataset'}, - {label: 'Details', help: 'Advanced dataset properties'}, - {label: 'Save', help: 'Save changes'}, + {label: 'Actions', help: 'Inspect / Save dataset'} ] const navigate = useNavigate(); @@ -146,11 +118,11 @@ export default function Datasets() { const items: ReactElement[] = [] if (dataset?.cell) { items.push(menuItem(dataset.cell)) - if (!cellListLoading) - items.push(None) } if (cellListLoading) - items.push() + items.push() + else + items.push(None) if (cellList.length) items.push(...cellList.filter(c => c.id !== dataset.cell?.id).map(menuItem)) if (!items.length) @@ -166,11 +138,11 @@ export default function Datasets() { if (dataset?.equipment) { items.push(...dataset.equipment.map(e => menuItem(e))) current_equipment_ids.push(...dataset.equipment.map(e => e.id)) - if (!equipmentListLoading) - items.push(None) } if (equipmentListLoading) - items.push() + items.push() + else + items.push(None) if (equipmentList.length) items.push(...equipmentList.filter(e => !current_equipment_ids.includes(e.id)).map(menuItem)) if (!items.length) @@ -184,41 +156,74 @@ export default function Datasets() { columns={columns} row_generator={(dataset, context) => [ - {dataset.id}, { Intl.DateTimeFormat( 'en-GB', - {dateStyle: 'long', timeStyle: 'long'}) + {dateStyle: 'short'}) .format(Date.parse(dataset.date)) } , - // these fields have the same shape, so condense the code. - // as const stops TypeScript from complaining about strings assigned to keyof DatasetFields - ...(['name', 'type', 'purpose'] as const).map( - (n) => - - - ), - + + + + + + + + + + + + + + + + + + + + + + Cell + + + + + , , - - selected?.id === dataset.id? setSelected(null) : setSelected(dataset)}> - - - , - - updateRow(dataset, context).then(context.refresh)} - > - - + + selected?.id === dataset.id? setSelected(null) : setSelected(dataset)} + inspectIconProps={selected?.id === dataset.id ? {color: 'info'} : {}} + onSave={() => updateRow(dataset, context).then(context.refresh)} + saveButtonProps={{disabled: !context.value_changed}} + /> ]} url={`datasets/?all=true`} diff --git a/frontend/src/Equipment.tsx b/frontend/src/Equipment.tsx index d4afb0de..26e538de 100644 --- a/frontend/src/Equipment.tsx +++ b/frontend/src/Equipment.tsx @@ -1,15 +1,13 @@ import React, { Fragment } from 'react'; import TextField from '@mui/material/TextField'; -import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; -import Tooltip from '@mui/material/Tooltip'; import AddIcon from '@mui/icons-material/Add'; -import IconButton from '@mui/material/IconButton'; import Container from '@mui/material/Container'; import SaveIcon from '@mui/icons-material/Save'; -import DeleteIcon from '@mui/icons-material/Delete'; import AsyncTable from './AsyncTable'; import Connection from "./APIConnection"; +import ActionButtons from "./ActionButtons"; +import useStyles from "./UseStyles"; export type EquipmentFields = { url: string; @@ -19,32 +17,10 @@ export type EquipmentFields = { in_use: boolean; } -const useStyles = makeStyles((theme) => ({ - container: { - paddingTop: theme.spacing(4), - paddingBottom: theme.spacing(4), - }, - table: { - minWidth: 650, - }, - resize: { - fontSize: '10pt', - }, - input: { - marginLeft: theme.spacing(1), - flex: 1, - }, - iconButton: { - padding: 10, - }, - paper: {} -})); - const columns = [ {label: 'Name', help: 'Equipment Name'}, {label: 'Type', help: 'Equipment Type'}, - {label: 'Save', help: 'Click to save edits to a row. Edits are disabled for equipment that is in use'}, - {label: 'Delete', help: 'Delete equipment that is not in use'}, + {label: 'Save', help: 'Save / Delete equipment. Edits are disabled for equipment that is in use'}, ] const string_fields = ['name', 'type'] as const @@ -88,33 +64,23 @@ export default function Equipment() { /> } ), - - - - addNewEquipment(equipment).then(context.refresh_all_rows) : - () => updateEquipment(equipment).then(context.refresh) - } - > - {context.is_new_row? : } - - - - , - context.is_new_row? : - - - deleteEquipment(equipment).then(context.refresh)} - > - - - - + + addNewEquipment(equipment).then(context.refresh_all_rows) : + () => updateEquipment(equipment).then(context.refresh) + } + saveButtonProps={{disabled: !context.value_changed || equipment.in_use}} + saveIconProps={{component: context.is_new_row? AddIcon : SaveIcon}} + onDelete={ + () => + window.confirm(`Delete equipment ${equipment.name}?`) && + deleteEquipment(equipment).then(context.refresh) + } + deleteButtonProps={{disabled: context.is_new_row || equipment.in_use}} + /> ]} new_row_values={{name: '', type: ''}} diff --git a/frontend/src/Files.tsx b/frontend/src/Files.tsx index 99bf1a3d..3f4efcc7 100644 --- a/frontend/src/Files.tsx +++ b/frontend/src/Files.tsx @@ -9,24 +9,7 @@ import Connection from "./APIConnection"; import {MonitoredPathFields} from "./HarvesterDetail"; import IconButton from "@mui/material/IconButton"; import RefreshIcon from "@mui/icons-material/Refresh"; - - -const useStyles = makeStyles((theme) => ({ - head: { - backgroundColor: theme.palette.primary.light, - }, - headCell: { - color: theme.palette.common.black, - }, - container: { - paddingTop: theme.spacing(4), - paddingBottom: theme.spacing(4), - }, - table: { - minWidth: 650, - }, - paper: {} -})); +import useStyles from "./UseStyles"; export type FileFields = { url: string; @@ -90,7 +73,9 @@ export default function Files(props: FilesProps) { {file_state(file)}, {file.datasets.length}, - forceReimport(file).then(context.refresh)}> + forceReimport(file).then(context.refresh)}> + + ]} url={`files/?monitored_path__id=${props.path.id}&all=true`} diff --git a/frontend/src/HarvesterDetail.tsx b/frontend/src/HarvesterDetail.tsx index 9eb00db4..48622e67 100644 --- a/frontend/src/HarvesterDetail.tsx +++ b/frontend/src/HarvesterDetail.tsx @@ -1,7 +1,6 @@ import React, {useState, Fragment} from 'react'; import TextField from '@mui/material/TextField'; import Typography from '@mui/material/Typography'; -import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; import AddIcon from '@mui/icons-material/Add'; import IconButton from '@mui/material/IconButton'; @@ -13,35 +12,8 @@ import {HarvesterFields} from "./Harvesters"; import UserRoleSet, {UserSet} from "./UserRoleSet"; import AsyncTable from "./AsyncTable"; import SearchIcon from "@mui/icons-material/Search"; - -const useStyles = makeStyles((theme) => ({ - paper: { - marginTop: theme.spacing(4), - }, - table: { - minWidth: 650, - }, - resize: { - fontSize: '11pt', - }, - input: { - marginLeft: theme.spacing(1), - flex: 1, - }, - inputAdornment: { - color: theme.palette.text.disabled, - }, - iconButton: { - padding: 10, - }, - chips: { - display: 'flex', - flexWrap: 'wrap', - }, - chip: { - margin: 2, - }, -})); +import useStyles from "./UseStyles"; +import ActionButtons from "./ActionButtons"; export type MonitoredPathFields = { url: string; @@ -78,14 +50,12 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { {label: 'Path', help: 'Directory to watch'}, {label: 'Stable Time (s)', help: 'Seconds files must remain unchanged to be considered stable and imported'}, {label: 'Users', help: 'Users with access to this path\'s datasets'}, - {label: 'Files', help: 'View files in this directory'}, - {label: 'Save', help: 'Save changes'}, - {label: 'Delete', help: 'Delete monitored path (imported datasets will remain)'}, + {label: 'Actions', help: 'Inspect / Save / Delete monitored path (imported datasets will remain)'}, ] return ( - + {harvester.name} - monitored paths @@ -127,31 +97,23 @@ export default function HarvesterDetail(props: HarvesterDetailProps) { set_last_updated={context.refresh} /> , - context.is_new_row? : - selected?.id === row.id? setSelected(null) : setSelected(row)}> - - - , - - + selected?.id === row.id? setSelected(null) : setSelected(row)} + inspectButtonProps={{disabled: context.is_new_row}} + inspectIconProps={selected?.id === row.id ? {color: 'info'} : {}} + onSave={ context.is_new_row? () => addNewPath(row).then(context.refresh_all_rows) : () => updatePath(row).then(context.refresh) } - > - {context.is_new_row? : } - - , - context.is_new_row? : - deletePath(row).then(context.refresh)} - > - - - , + saveButtonProps={{disabled: !context.value_changed}} + saveIconProps={{component: context.is_new_row? AddIcon : SaveIcon}} + onDelete={() => window.confirm(`Delete ${row.path}?`) && deletePath(row).then(context.refresh)} + deleteButtonProps={{disabled: context.is_new_row}} + /> + ]} url={`monitored_paths/?harvester__id=${harvester.id}&all=true`} new_row_values={{path: "", stable_time: 60}} diff --git a/frontend/src/Harvesters.tsx b/frontend/src/Harvesters.tsx index 03df0de2..71fd4a37 100644 --- a/frontend/src/Harvesters.tsx +++ b/frontend/src/Harvesters.tsx @@ -1,18 +1,14 @@ import React, { useState, Fragment } from 'react'; import TextField from '@mui/material/TextField'; -import { makeStyles } from '@mui/styles' import Paper from '@mui/material/Paper'; import Typography from '@mui/material/Typography'; -import IconButton from '@mui/material/IconButton'; import Container from '@mui/material/Container'; -import SaveIcon from '@mui/icons-material/Save'; -import SearchIcon from '@mui/icons-material/Search'; -import DeleteIcon from '@mui/icons-material/Delete'; - import HarvesterDetail from './HarvesterDetail'; import Connection from "./APIConnection"; import {UserSet} from "./UserRoleSet"; import AsyncTable, {Column} from "./AsyncTable"; +import useStyles from "./UseStyles"; +import ActionButtons from "./ActionButtons"; export type HarvesterWriteableFields = { name: string; @@ -26,27 +22,6 @@ export type HarvesterFields = HarvesterWriteableFields & { user_sets: UserSet[]; } -const useStyles = makeStyles((theme) => ({ - container: { - paddingTop: theme.spacing(4), - paddingBottom: theme.spacing(4), - }, - table: { - minWidth: 650, - }, - resize: { - fontSize: '11pt', - }, - input: { - marginLeft: theme.spacing(1), - flex: 1, - }, - iconButton: { - padding: 10, - }, - paper: {} -})); - export default function Harvesters() { const classes = useStyles(); @@ -73,9 +48,7 @@ export default function Harvesters() { {label: 'Name', help: 'Harvester name'}, {label: 'Last Check In', help: 'Datetime of last harvester run that successfully contacted the database'}, {label: 'Sleep Time (s)', help: 'Time harvester waits after completing a cycle before beginning the next'}, - {label: 'Details', help: 'View harvester path information'}, - {label: 'Save', help: 'Click to save edits to a row'}, - {label: 'Delete', help: 'Delete a harvester'}, + {label: 'Actions', help: 'Inspect / Add / Save / Delete harvester path information'} ] return ( @@ -119,27 +92,16 @@ export default function Harvesters() { > , - - selected?.id === row.id? setSelected(null) : setSelected(row)}> - - - , - - updateHarvester(row).then(context.refresh)} - > - - - , - - deleteHarvester(row).then(context.refresh)} - > - - + + selected?.id === row.id? setSelected(null) : setSelected(row)} + inspectIconProps={selected?.id === row.id ? {color: 'info'} : {}} + onSave={() => updateHarvester(row).then(context.refresh)} + saveButtonProps={{disabled: !userIsAdmin(row) || !context.value_changed}} + onDelete={() => window.confirm(`Delete ${row.name}?`) && deleteHarvester(row).then(context.refresh)} + deleteButtonProps={{disabled: !userIsAdmin(row)}} + /> , ]} url="harvesters/?all=true" diff --git a/frontend/src/UseStyles.ts b/frontend/src/UseStyles.ts new file mode 100644 index 00000000..e5e0f4ae --- /dev/null +++ b/frontend/src/UseStyles.ts @@ -0,0 +1,57 @@ +import {makeStyles} from "@mui/styles"; + +export default makeStyles((theme) => ({ + button: { + margin: theme.spacing(1), + }, + chips: { + display: 'flex', + flexWrap: 'wrap', + }, + chip: { + margin: 2, + }, + container: { + paddingTop: theme.spacing(4), + paddingBottom: theme.spacing(4), + }, + deleteIcon: { + "&:hover": {color: theme.palette.error.light}, + "&:focus": {color: theme.palette.error.light} + }, + head: { + backgroundColor: theme.palette.primary.light, + }, + headCell: { + color: theme.palette.common.black, + }, + iconButton: { + padding: 10, + }, + infoIcon: { + "&:hover": {color: theme.palette.info.light}, + "&:focus": {color: theme.palette.info.light} + }, + input: { + marginLeft: theme.spacing(0), + flex: 1, + }, + inputAdornment: { + color: theme.palette.text.disabled, + }, + paper: {}, + refreshIcon: { + "&:hover": {color: theme.palette.warning.light}, + "&:focus": {color: theme.palette.warning.light} + }, + resize: { + fontSize: '10pt', + }, + saveIcon: { + "&:hover": {color: theme.palette.success.light}, + "&:focus": {color: theme.palette.success.light} + }, + table: { + minWidth: 650, + }, +})); From 0b87d40532f25aab44f30bed1ea9a98f4befbb30 Mon Sep 17 00:00:00 2001 From: Matt Jaquiery Date: Fri, 10 Feb 2023 13:34:54 +0000 Subject: [PATCH 41/79] frontend tweaks and performance NOTE: Dataset Cell select not working --- django/backend_django/galvanalyser/views.py | 5 +- frontend/src/APIConnection.ts | 31 +++++----- frontend/src/ActionButtons.tsx | 4 +- frontend/src/App.jsx | 4 +- frontend/src/AsyncTable.tsx | 55 ++++++++++++------ frontend/src/CellList.tsx | 1 + frontend/src/Cells.tsx | 1 + frontend/src/{Core.js => Core.tsx} | 43 +++++--------- frontend/src/Datasets.tsx | 64 ++++++++++++++------- frontend/src/Equipment.tsx | 1 + frontend/src/Files.tsx | 2 +- frontend/src/HarvesterDetail.tsx | 5 +- frontend/src/Harvesters.tsx | 1 + frontend/src/{Login.js => Login.tsx} | 43 +++++++------- frontend/src/UseStyles.ts | 2 + 15 files changed, 145 insertions(+), 117 deletions(-) rename frontend/src/{Core.js => Core.tsx} (88%) rename frontend/src/{Login.js => Login.tsx} (73%) diff --git a/django/backend_django/galvanalyser/views.py b/django/backend_django/galvanalyser/views.py index 82a4deeb..c23b8e12 100644 --- a/django/backend_django/galvanalyser/views.py +++ b/django/backend_django/galvanalyser/views.py @@ -88,9 +88,10 @@ class HarvesterViewSet(viewsets.ModelViewSet): queryset = Harvester.objects.none().order_by('-last_check_in', '-id') def get_queryset(self): + user_groups = self.request.user.groups.all() return Harvester.objects.filter( - Q(user_group__in=self.request.user.groups.all()) | - Q(admin_group__in=self.request.user.groups.all()) + Q(user_group__in=user_groups) | + Q(admin_group__in=user_groups) ).order_by('-last_check_in', '-id') def create(self, request, *args, **kwargs): diff --git a/frontend/src/APIConnection.ts b/frontend/src/APIConnection.ts index fc663c95..cd1bc9f7 100644 --- a/frontend/src/APIConnection.ts +++ b/frontend/src/APIConnection.ts @@ -48,8 +48,12 @@ export class APIConnection { token: r.token } console.info(`Logged in as ${this.user?.username}`) + return true + }) + .catch(e => { + console.error("Login failure", e) + return false }) - .catch(e => console.error("Login failure", e)) } logout() { @@ -64,6 +68,10 @@ export class APIConnection { return null } + get is_logged_in() { + return this.user !== null + } + async get_is_logged_in(skip: boolean = true): Promise { await this.login('admin', 'admin') const cookie = this.get_cookie('csrf_access_token'); @@ -74,9 +82,10 @@ export class APIConnection { } async fetch(url: string, options?: any, depth: number = 0): Promise { - await this.get_is_logged_in(); - console.info(`Fetch ${url} for ${this.user?.username}`) - console.info('fetch options', options) + if (!this.is_logged_in) + return -1 + console.info(`Fetch ${url} for ${this.user?.username}`, options) + // console.info('fetch options', options) const token = this.user?.token; let newOptions = {...options}; newOptions.credentials = 'same-origin'; @@ -115,18 +124,12 @@ export class APIConnection { } return await this.fetch_children(json, options, depth - 1) }) - .then(r => { - console.log(url, options, depth, r); return r - }) + // .then(r => { + // console.log(url, options, depth, r); return r + // }) .catch(e => { console.error(e); - return { - count: 0, - previous: null, - next: null, - results: [], - error: true - }; + return -1; }); } diff --git a/frontend/src/ActionButtons.tsx b/frontend/src/ActionButtons.tsx index 01f0ff74..aea0d14c 100644 --- a/frontend/src/ActionButtons.tsx +++ b/frontend/src/ActionButtons.tsx @@ -57,7 +57,7 @@ export default class ActionButtons extends Component { { this.props.onSave !== undefined && { { this.props.onDelete !== undefined && diff --git a/frontend/src/App.jsx b/frontend/src/App.jsx index 9f441526..ca65e9d3 100644 --- a/frontend/src/App.jsx +++ b/frontend/src/App.jsx @@ -1,11 +1,11 @@ /* -* Theme wrapper for the app. Body in Core.js +* Theme wrapper for the app. Body in Core.tsx */ import React from "react"; import { createTheme, StyledEngineProvider } from '@mui/material/styles'; import { ThemeProvider } from "@mui/styles"; -import Core from "./Core.js" +import Core from "./Core.tsx" const theme = createTheme(); diff --git a/frontend/src/AsyncTable.tsx b/frontend/src/AsyncTable.tsx index ed6097bf..385ad44e 100644 --- a/frontend/src/AsyncTable.tsx +++ b/frontend/src/AsyncTable.tsx @@ -9,6 +9,7 @@ import CircularProgress from "@mui/material/CircularProgress"; import Tooltip, {TooltipProps} from "@mui/material/Tooltip"; import Typography, {TypographyProps} from "@mui/material/Typography"; import TableHead from "@mui/material/TableHead"; +import useStyles from "./UseStyles"; export type Column = { label: string; @@ -44,6 +45,7 @@ type CompleteHeading = { } export type AsyncTableProps = { + classes: ReturnType; columns: Column[]; row_generator: RowGenerator; url: string; @@ -116,10 +118,10 @@ export default class AsyncTable extends Component) { console.log("Updating AsyncTable...", this, prevProps) // Typical usage (don't forget to compare props): - if (this.props.url !== prevProps.url) { - this.setState({row_data: []}) + if (this.props.url !== prevProps.url) this.get_data(this.props.url) - } + if (this.props.new_row_values !== prevProps.new_row_values) + this.reset_new_row() console.log("Updated AsyncTable", this) } @@ -139,11 +141,11 @@ export default class AsyncTable extends Component void = async (url) => { - this.setState({loading: true}) + get_data: (url?: string) => void = (url) => { + this.setState({loading: true, row_data: []}) if (!url) url = this.props.url; - await Connection.fetch(url, {}, this.fetch_depth) + Connection.fetch(url, {}, this.fetch_depth) .then(APIConnection.get_result_array) .then((res) => { if (typeof(res) === 'number') @@ -162,7 +164,7 @@ export default class AsyncTable extends Component { + refresh_row = (row: SingleAPIResponse, is_result: boolean = true) => { this.mark_row_loading(row.id) const _update = (row_data: SingleAPIResponse) => { @@ -176,7 +178,7 @@ export default class AsyncTable extends Component { // If we deleted the row, delete it in state @@ -271,23 +273,38 @@ export default class AsyncTable extends Component { const cells = contents.map((cell: any, i: number) => - {cell} + n !== undefined).join(' ')} + key={`cell-${i}`} + >{cell} ) - return {cells} + return {cells} } row_data_to_tablerow = (row: T, row_index: number) => { - if (!row) - return null - const is_new_row = row_index === NEW_ROW_ID - if (is_new_row) - row_index = -1 + try { + if (!row) + return null + const is_new_row = row_index === NEW_ROW_ID + if (is_new_row) + row_index = -1 - if (this.state.loading_rows.includes(row.id)) - return this.loading_row(row.id) + if (this.state.loading_rows.includes(row.id)) + return this.loading_row(row.id) - const row_contents = this.props.row_generator(row, this.row_conversion_context(row, is_new_row)) - return this.wrap_cells_in_row(row_contents, row_index) + const row_contents = this.props.row_generator(row, this.row_conversion_context(row, is_new_row)) + return this.wrap_cells_in_row(row_contents, row_index) + } catch(e) { + console.info('Error constructing table row:', e) + return null + } } render() { diff --git a/frontend/src/CellList.tsx b/frontend/src/CellList.tsx index 673c207c..92ed49fb 100644 --- a/frontend/src/CellList.tsx +++ b/frontend/src/CellList.tsx @@ -50,6 +50,7 @@ export default function CellList(props: CellDetailProps) { + classes={classes} columns={columns} row_generator={(cell, context) => [ diff --git a/frontend/src/Cells.tsx b/frontend/src/Cells.tsx index a9eaa842..909feb03 100644 --- a/frontend/src/Cells.tsx +++ b/frontend/src/Cells.tsx @@ -70,6 +70,7 @@ export default function Cells() { + classes={classes} columns={columns} row_generator={(family, context) => [ diff --git a/frontend/src/Core.js b/frontend/src/Core.tsx similarity index 88% rename from frontend/src/Core.js rename to frontend/src/Core.tsx index 2fae4af6..4f0c6952 100644 --- a/frontend/src/Core.js +++ b/frontend/src/Core.tsx @@ -24,7 +24,6 @@ import DialogContentText from '@mui/material/DialogContentText'; import DialogTitle from '@mui/material/DialogTitle'; import BatteryUnknownIcon from '@mui/icons-material/BatteryUnknown'; import BackupIcon from '@mui/icons-material/Backup'; -import {loggedIn, handleLogin, logout, getToken, getUser, isAdmin} from "./Api" import { makeStyles} from "@mui/styles"; import CssBaseline from '@mui/material/CssBaseline'; @@ -44,9 +43,10 @@ import ListItem from '@mui/material/ListItem'; import ListItemIcon from '@mui/material/ListItemIcon'; import ListItemText from '@mui/material/ListItemText'; import { ReactComponent as GalvanalyserLogo } from './Galvanalyser-logo.svg'; +import Connection from "./APIConnection"; -const PrivateRoute = (component) => { - const logged = loggedIn(); +const PrivateRoute = (component: JSX.Element) => { + const logged = Connection.is_logged_in; return logged? component : ; } @@ -136,33 +136,20 @@ const useStyles = makeStyles((theme) => ({ }, })); - - export default function Core() { const { pathname } = useLocation(); const classes = useStyles(); - const user = getUser() - - const userIsAdmin = isAdmin() - - let userDisplayName = '' - if (user) { - userDisplayName = userIsAdmin ? - user.username + " (Admin)" : - user.username - } + const userDisplayName = Connection.is_logged_in? Connection.user?.username : '' const datasetsPath = "/" - const isDatasetPath = matchPath({path: datasetsPath, exact:true}, pathname) !== null + const isDatasetPath = matchPath({path: datasetsPath, end: true}, pathname) !== null const harvestersPath = "/harvesters" - const isHarvestersPath = matchPath({path: harvestersPath, exact:true}, pathname) !== null + const isHarvestersPath = matchPath({path: harvestersPath, end: true}, pathname) !== null const cellsPath = "/cells" - const isCellsPath = matchPath({path: cellsPath, exact:true}, pathname) !== null + const isCellsPath = matchPath({path: cellsPath, end: true}, pathname) !== null const equipmentPath = "/equipment" - const isEquipmentPath = matchPath({path: equipmentPath, exact:true}, pathname) !== null - console.log('paths:', isDatasetPath, isHarvestersPath) - + const isEquipmentPath = matchPath({path: equipmentPath, end: true}, pathname) !== null const [open, setOpen] = React.useState(false); const handleDrawerOpen = () => { @@ -173,13 +160,11 @@ export default function Core() { }; const [tokenOpen, setTokenOpen] = React.useState(false); - const [token, setToken] = React.useState(); + const [token, setToken] = React.useState(); const handleTokenOpen = () => { - getToken().then(response => response.json()).then(data => { - setToken(data.access_token) - setTokenOpen(true); - }); + setToken(Connection.user?.token) + setTokenOpen(true); }; const handleTokenClose = () => { @@ -189,7 +174,7 @@ export default function Core() { const tokenGenerator = ( {tokenGenerator} @@ -305,7 +290,7 @@ export default function Core() { /* A looks through its children s and renders the first one that matches the current URL. */ return ( - }/> + }/> diff --git a/frontend/src/Datasets.tsx b/frontend/src/Datasets.tsx index 1aa3eac1..08c34731 100644 --- a/frontend/src/Datasets.tsx +++ b/frontend/src/Datasets.tsx @@ -52,11 +52,13 @@ export default function Datasets() { Connection.fetch('cells/?all=true', {}, 0) .then(APIConnection.get_result_array) .then(r => { - if (typeof r === 'number') - throw new Error(`cells/?all=true -> ${r}`) + setCellListLoading(false) + if (typeof r === 'number') { + console.error(`cells/?all=true -> ${r}`) + setCellList([]) + } // @ts-ignore setCellList(r) - setCellListLoading(false) }) }, []) @@ -64,11 +66,13 @@ export default function Datasets() { Connection.fetch('equipment/?all=true', {}, 0) .then(APIConnection.get_result_array) .then(r => { - if (typeof r === 'number') - throw new Error(`equipment/?all=true -> ${r}`) + setEquipmentListLoading(false) + if (typeof r === 'number') { + console.error(`equipment/?all=true -> ${r}`) + setEquipmentList([]) + } // @ts-ignore setEquipmentList(r) - setEquipmentListLoading(false) }) }, []) @@ -150,10 +154,24 @@ export default function Datasets() { return items } + const purposeOptions = [ + 'Ageing', + 'Real world/drive cycling', + 'Characterisation/check-up', + 'Thermal performance', + 'Pulse', + 'Charge', + 'Discharge', + 'EIS', + 'GITT', + 'Pseudo-OCV', + ] + return ( + classes={classes} columns={columns} row_generator={(dataset, context) => [ @@ -180,33 +198,37 @@ export default function Datasets() { - - - + + Purpose + + - + - + Cell