23.12.1 (#296) · biocompute-objects/portal_userdb@769d35c

Commit

23.12.1 (#296)

* Add BCO API endpoints for UserDB
- one to submit and one to retreive
Changes to be committed:
	new file:   server/authentication/selectors.py
	modified:   server/authentication/services.py
	modified:   server/bcodb/admin.py
	modified:   server/bcodb/apis.py
	modified:   server/bcodb/models.py
	modified:   server/bcodb/services.py
	modified:   server/bcodb/urls.py
	modified:   server/portaluserdb/settings.py
	modified:   server/portaluserdb/urls.py
	modified:   server/requirements.txt

* Add functions to retreive Temp Draft
Changes to be committed:
	modified:   client/src/components/builder/index.js
	modified:   client/src/services/bco.service.js
	modified:   client/src/slices/bcoSlice.js

* Refine request and response for AddTempDraftBcoAPI
Changes to be committed:
	modified:   server/authentication/services.py
	modified:   server/bcodb/apis.py
	modified:   server/bcodb/urls.py

* Updates to ProvD form checking
Changes to be committed:
	modified:   client/src/components/builder/provenanceDomain.js

* Update BCO model and polish for apis

- add ORCID support for authentication in `/authentication/services.py`
- customized Django Admin for BCODB and BCO in `bcodb/admin.py`
- Updates to model in `bcodb/apis.py`
- Update to API function name in `bcodb/urls.py`

Changes to be committed:
	modified:   server/authentication/services.py
	modified:   server/bcodb/admin.py
	modified:   server/bcodb/apis.py
	new file:   server/bcodb/migrations/0007_bco.py
	modified:   server/bcodb/models.py
	modified:   server/bcodb/urls.py

* Add test for Temp BCO Add

Fix #246
Changes to be committed:
	modified:   server/bcodb/apis.py
	new file:   server/tests/fixtures/testing_example_bcos.json
	new file:   server/tests/test_views/test_draft_bco_add.py

* Test for Get Temp BCO
Fix #247
Changes to be committed:
	modified:   server/authentication/selectors.py
	modified:   server/bcodb/apis.py
	modified:   server/tests/fixtures/testing_data.json
	modified:   server/tests/test_views/test_draft_bco_add.py
	new file:   server/tests/test_views/test_draft_bco_get.py

* Add test for Temp BCO Delete

Fix #248
Changes to be committed:
	modified:   server/authentication/selectors.py
	modified:   server/authentication/services.py
	modified:   server/bcodb/apis.py
	modified:   server/bcodb/services.py
	modified:   server/bcodb/urls.py
	modified:   server/portaluserdb/settings.py
	new file:   server/tests/test_views/test_draft_bco_delete.py
	modified:   server/tests/test_views/test_draft_bco_get.py

* Added testing CI

Fix #207
Changes to be committed:
	new file:   .github/workflows/django.yml

* Fix path errors
Changes to be committed:
	modified:   .github/workflows/django.yml

* Path Again
Changes to be committed:
	modified:   .github/workflows/django.yml

* d

* again

* debugging

* debug

* deb

* added secrets
Changes to be committed:
	modified:   .github/workflows/django.yml

* s

* s

* s

* s

* s

* s

* Adjusted CustomJSONWebTokenAuthentication for CI

Changes to be committed:
	modified:   server/authentication/selectors.py
	modified:   server/authentication/services.py
	modified:   server/bcodb/apis.py
	modified:   server/portaluserdb/settings.py
	modified:   server/tests/test_views/test_draft_bco_delete.py
	modified:   server/tests/test_views/test_draft_bco_get.py

* Fix validation issues with removeEmptyValues function
Changes to be committed:
	modified:   client/src/components/builder/components.js
	modified:   client/src/components/builder/provenanceDomain.js
	modified:   client/src/layouts/shared/ToolsDropDown.js

* UPdate docs

* Update localDeployment.md

* CSS and organization fixes
Changes to be committed:
	modified:   client/package-lock.json
	modified:   client/package.json
	modified:   client/src/App.css
	modified:   client/src/App.js
	modified:   client/src/components/about/BCOnexus.js
	modified:   client/src/components/about/MeetOurTeam.js

* Css implementation
Changes to be committed:
	modified:   client/src/components/about/Overview.js
	modified:   client/src/components/about/SB.js
	modified:   client/src/components/about/Story.js

* Home page css
Changes to be committed:
	modified:   client/src/App.css
	modified:   client/src/components/home/BcoDb.js
	modified:   client/src/components/home/BioComputeResources.js
	modified:   client/src/components/home/Builder.js
	modified:   client/src/components/home/Documentation.js
	modified:   client/src/components/home/FdaBox.js
	modified:   client/src/components/home/Galaxy.js
	modified:   client/src/components/home/Hive.js
	modified:   client/src/components/home/Intro.js
	modified:   client/src/components/home/NewsBar.js
	modified:   client/src/components/home/Specification.js
	modified:   client/src/components/home/Tsc.js
	modified:   client/src/components/home/Workshop.js
	modified:   client/src/components/home/index.js

* css for resources page
Changes to be committed:
	modified:   client/src/components/account/Servers.js
	modified:   client/src/components/bcodbs/SearchResults.js
	modified:   client/src/components/resources/Builder.js
	modified:   client/src/components/resources/DNAnexus.js
	modified:   client/src/components/resources/Galaxy.js
	modified:   client/src/components/resources/Hive.js
	modified:   client/src/components/resources/Packages.js
	modified:   client/src/components/resources/index.js

* slice fix

* Builder css
Changes to be committed:
	modified:   client/src/components/builder/components.js
	modified:   client/src/components/builder/descriptionDomain.js
	modified:   client/src/components/builder/errorDomain.js
	modified:   client/src/components/builder/executionDomain.js
	modified:   client/src/components/builder/extensionDomain.js
	modified:   client/src/components/builder/index.js
	modified:   client/src/components/builder/ioDomain.js
	modified:   client/src/components/builder/parametricDomain.js
	modified:   client/src/components/builder/provenanceDomain.js
	modified:   client/src/components/builder/rawJson.js
	modified:   client/src/components/builder/reviewer.js
	modified:   client/src/components/builder/specialFeilds.js
	modified:   client/src/components/builder/treeView.js
	modified:   client/src/components/builder/usabilityDomain.js

* more resources updates
Changes to be committed:
	modified:   client/src/components/resources/CGC.js
	modified:   client/src/components/resources/Citations.js

* Index css
Changes to be committed:
	modified:   client/src/index.html
	modified:   client/src/layouts/MainNavBar.js
	modified:   client/src/layouts/ObjectNavBar.js

* testdata update

Changes to be committed:
	modified:   server/tests/fixtures/testing_data.json

* Add ORCID Auth api

Fix #276
Changes to be committed:
	modified:   server/authentication/apis.py
	new file:   server/tests/test_views/test_orcid_auth.py

* Fixes for Playbook integration
Changes to be committed:
	modified:   client/src/components/builder/index.js
	modified:   server/authentication/apis.py
	modified:   server/authentication/selectors.py

* Changing ORCID should require validation

When a user changes or adds an ORCID to their account it should require validation to save it.
This was a fix for #90 in 23.07. Somehow it was reverted and needed to be added again.
Changes to be committed:
	modified:   client/src/components/account/Profile.js
	modified:   client/src/services/auth.service.js
	modified:   client/src/slices/accountSlice.js
	modified:   server/authentication/apis.py
	modified:   server/authentication/services.py
	modified:   server/authentication/urls.py
	modified:   server/bcodb/services.py

* Add tests for new APIs and Swagger Docs

- /orcid/add/
- /orcid/remove/
Changes to be committed:
	modified:   server/authentication/apis.py
	new file:   server/tests/test_views/test_orcid_add.py
	modified:   server/tests/test_views/test_orcid_auth.py
	new file:   server/tests/test_views/test_orcid_remove.py
	modified:   server/users/selectors.py

* Updates for Swagger and Logout
Changes to be committed:
	modified:   server/authentication/apis.py
	modified:   server/authentication/urls.py
	modified:   server/prefix/apis.py

* Add logout endpoint for client
Changes to be committed:
	modified:   client/src/components/account/index.js
	modified:   client/src/services/auth.service.js
	modified:   client/src/slices/accountSlice.js

* Error Handling for auth failure #256
Changes to be committed:
	modified:   client/src/components/auth/Login.js
	modified:   client/src/slices/accountSlice.js

* Disable select box on BCO search page
Changes to be committed:
	modified:   client/src/components/bcodbs/SearchResults.js

* Remove Twitter NewsBar
Changes to be committed:
	modified:   client/src/components/home/FdaBox.js
	deleted:    client/src/components/home/NewsBar.js
	modified:   client/src/components/home/index.js
	modified:   server/.secrets.example

* Update for Playbook draft.ts

Update for "Temp Draft" submission
Changes to be committed:
	modified:   server/bcodb/apis.py

* Modified tests for merge
Changes to be committed:
	modified:   server/tests/test_views/test_draft_bco_add.py

---------

Co-authored-by: Tianyi Wang <[email protected]>

Loading branch information

HadleyKing and tiwa1154 authored Feb 14, 2024

1 parent 3950675 commit 769d35c

.github/workflows/django.yml

-Original file line number
+Diff line change
@@ -0,0 +1,47 @@
+    name: Django CI
+    on:
+      push:
+        branches: [main]
+      pull_request:
+    jobs:
+      build:
+        runs-on: ubuntu-latest
+        strategy:
+          max-parallel: 4
+          matrix:
+            python-version: [3.9]
+        steps:
+          - name: Checkout code
+            uses: actions/checkout@v3
+          - name: Set up Python ${{ matrix.python-version }}
+            uses: actions/setup-python@v3
+            with:
+              python-version: ${{ matrix.python-version }}
+          - name: Debugging Step
+            run: |
+                ls -R server # List all files and directories recursively
+                cat server/requirements.txt  # Print the contents of the requirements file
+          - name: Install Dependencies
+            run: |
+              python -m pip install --upgrade pip
+              pip install -r server/requirements.txt
+          - name: Run Tests
+            env:
+                SECRET_KEY: ${{ secrets.SECRET_KEY }}
+                DJANGO_GOOGLE_OAUTH2_CLIENT_ID: ${{ secrets.DJANGO_GOOGLE_OAUTH2_CLIENT_ID }}
+                DJANGO_GOOGLE_OAUTH2_CLIENT_SECRET: ${{ secrets.DJANGO_GOOGLE_OAUTH2_CLIENT_SECRET }}
+                DJANGO_ORCID_OAUTH2_CLIENT_URL: ${{ secrets.DJANGO_ORCID_OAUTH2_CLIENT_URL }}
+                DJANGO_ORCID_OAUTH2_CLIENT_ID: ${{ secrets.DJANGO_ORCID_OAUTH2_CLIENT_ID }}
+                DJANGO_ORCID_OAUTH2_CLIENT_SECRET: ${{ secrets.DJANGO_ORCID_OAUTH2_CLIENT_SECRET }}
+                DJANGO_ORCID_OAUTH2_URL: ${{ secrets.DJANGO_ORCID_OAUTH2_URL }}
+                SERVER_VERSION: ${{ secrets.SERVER_VERSION }}
+                SERVER_URL: ${{ secrets.SERVER_URL }}
+                DATABASE: ${{ secrets.DATABASE }}
+            run: |
+              cd server  # Change to the subdirectory
+              python3.9 manage.py test

client/README.md

-Original file line number
+Diff line change
@@ -0,0 +1,6 @@
+    # BCO Portal Client (AKA Portal)
+    This directory contains the Portal application. It utilizes Redux Toolkit (React JS) and a Fromik. Below are a few genral rules for how the code is structured and maintained.
+    - All deployment specific modifications should be made in the `.env` file. This is also where the keys for other applications are kept. This file should be created by copying the `.env.example` and filling in the fields.
+    - For the most part each page has it's own directory within the [components](client/src/components/) directory.

client/package-lock.json

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

client/package.json

-Original file line number
+Diff line change
@@ Expand Up / @@ -20,6 +20,7 @@ @@
         "axios": "^1.2.1",
         "bootstrap": "^5.2.3",
         "dayjs": "^1.11.7",
+        "focus-trap-react": "^10.2.3",
         "formik": "^2.2.9",
         "jslint": "^0.12.1",
         "object-hash": "^3.0.0",
@@ Expand All / @@ -33,6 +34,7 @@ @@
         "react-helmet": "^6.1.0",
         "react-json-view": "^1.21.3",
         "react-redux": "^8.0.4",
+        "react-multi-select-component": "^4.3.4",
         "react-router-dom": "^6.6.0",
         "react-scripts": "5.0.1",
         "react-twitter-embed": "^4.0.4",
@@ Expand Down @@

0 comments on commit `769d35c`

Please sign in to comment.

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Commit

There are no files selected for viewing

0 comments on commit `769d35c`

Commit

There are no files selected for viewing

0 comments on commit 769d35c

0 comments on commit `769d35c`