diff --git a/.github/ISSUE_TEMPLATE/README.md b/.github/ISSUE_TEMPLATE/README.md new file mode 100644 index 000000000..0ae02773e --- /dev/null +++ b/.github/ISSUE_TEMPLATE/README.md @@ -0,0 +1,10 @@ +## 'ISSUE_TEMPLATE' Directory Contents + +### Files + +bug_report.yml + +feature_request.yaml + +voxl.yml + diff --git a/.github/workflows/README.md b/.github/workflows/README.md new file mode 100644 index 000000000..7a4b38642 --- /dev/null +++ b/.github/workflows/README.md @@ -0,0 +1,6 @@ +## 'workflows' Directory Contents + +### Files + +main.yml + diff --git a/README.md b/README.md index e9a30860d..bf779e8d8 100644 --- a/README.md +++ b/README.md @@ -6,13 +6,19 @@ PIXL Image eXtraction Laboratory `PIXL` is a system for extracting, linking and de-identifying DICOM imaging data, structured EHR data and free-text data from radiology reports at UCLH. -Please see the [rolling-skeleton]([https://github.com/SAFEHR-data/the-rolling-skeleton=](https://github.com/SAFEHR-data/the-rolling-skeleton/blob/main/docs/design/100-day-design.md)) for more details. -PIXL is intended run on one of the [GAE (General Application Environments)](https://github.com/SAFEHR-data/Book-of-FlowEHR/blob/main/glossary.md#gaes)s and comprises -several services orchestrated by [Docker Compose](https://docs.docker.com/compose/). +It comprises several services orchestrated by [Docker Compose](https://docs.docker.com/compose/). + +
UCLH SPECIFIC + +PIXL is intended run on one of the [GAE (General Application Environments)](https://github.com/SAFEHR-data/Book-of-FlowEHR/blob/main/glossary.md#gaes)s. To get access to the GAE, [see the documentation on Slab](https://uclh.slab.com/posts/gae-access-7hkddxap). -Please request access to Slab and add further details in a [new blank issue](https://github.com/SAFEHR-data/PIXL/issues/new). + +Please request access to Slab and add further details in a [new blank issue](https://github.com/SAFEHR-data/PIXL/issues/new). + +
+ ## Installation @@ -67,7 +73,7 @@ destination. Provides helper functions for de-identifying DICOM data -### PostgreSQL +### [PostgreSQL](.postgres/README.md) RDBMS which stores DICOM metadata, application data and anonymised patient record data. @@ -79,7 +85,7 @@ HTTP API to export files (parquet and DICOM) from UCLH to endpoints. HTTP API to process messages from the `imaging` queue and populate the raw orthanc instance with images from PACS/VNA. -## Setup `PIXL` in GAE +## Setup `PIXL`
Click here to expand steps and configurations @@ -202,7 +208,7 @@ These variables can be set in the `.env` file. For testing, they can be set in the `test/.secrets.env` file. For dev purposes find the `pixl-dev-secrets.env` note on LastPass for the necessary values. -If an Azure Keyvault hasn't been set up yet, follow [these instructions](./docs/setup/azure-keyvault.md). +At UCLH if an Azure Keyvault hasn't been set up yet, follow [these instructions](./docs/setup/azure-keyvault.md). A second Azure Keyvault is used to store hashing keys and salts for the `hasher` service. This kevyault is configured with the following environment variables: @@ -218,7 +224,7 @@ See the [hasher documentation](./hasher/README.md) for more information.
-## Run `PIXL` in GAE +## Run `PIXL`
Click here to view detailed steps @@ -278,6 +284,9 @@ test/resources/omop/public /*.parquet ### OMOP ES extract dir (input to PIXL) +>[!NOTE] +> OMOP ES is the tool used to extract Electronic Health Records that may be linked to images. + EXTRACT_DIR is the directory passed to `pixl populate` as the input `PARQUET_PATH` argument. ``` @@ -288,8 +297,8 @@ EXTRACT_DIR/public /*.parquet ### PIXL Export dir (PIXL intermediate) -The directory where PIXL will copy the public OMOP extract files (which now contain -the radiology reports) to. +The directory where PIXL will copy the public OMOP extract files and the radiology reports. + These files will subsequently be uploaded to the `parquet` destination specified in the [project config](#3-configure-a-new-project). @@ -310,10 +319,63 @@ FTPROOT/PROJECT_SLUG/EXTRACT_DATETIME/parquet/radiology/radiology.parquet ..............................................omop/public/*.parquet ``` -## :octocat: Cloning repository -* Generate your SSH keys as suggested [here](https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent) -* Clone the repository by typing (or copying) the following lines in a terminal -``` -git clone git@github.com:SAFEHR-data/PIXL.git -``` +## 'PIXL' Directory Contents + +
+ + +

Subdirectories with links to the relevant README

+ + + + +[bin](./bin/README.md) + +[cli](./cli/README.md) + +[docker](./docker/README.md) + +[docs](./docs/README.md) + +[hasher](./hasher/README.md) + +[orthanc](./orthanc/README.md) + +[pixl_core](./pixl_core/README.md) + +[pixl_dcmd](./pixl_dcmd/README.md) + +[pixl_export](./pixl_export/README.md) + +[pixl_imaging](./pixl_imaging/README.md) + +[postgres](./postgres/README.md) + +[projects](./projects/README.md) + +[pytest-pixl](./pytest-pixl/README.md) + +[schemas](./schemas/README.md) + +[scripts](./scripts/README.md) + +[test](./test/README.md) +
+
+ + +### Files + + + +| **Configuration** | **User docs** | **Housekeeping** | +| :--- | :--- | :--- | +| .env.sample | CODE_OF_CONDUCT.md | .renovaterc.json5 | +| .pre-commit-config.yaml | CONTRIBUTING.md | codecov.yml | +| docker-compose.yml | LICENSE | | +| mypy.ini | NOTICE | | +| pytest.ini | README.md | | +| ruff.toml | | | +| template_config.yaml | | | +
\ No newline at end of file diff --git a/bin/README.md b/bin/README.md new file mode 100644 index 000000000..eedf89797 --- /dev/null +++ b/bin/README.md @@ -0,0 +1,6 @@ +## 'PIXL/bin' Directory Contents + +### Subdirectories + +[linters](./linters/README.md) + diff --git a/bin/linters/README.md b/bin/linters/README.md new file mode 100644 index 000000000..a03874a75 --- /dev/null +++ b/bin/linters/README.md @@ -0,0 +1,6 @@ +## 'PIXL/bin/linters' Directory Contents + +### Files + +check_headers_exist.sh + diff --git a/cli/README.md b/cli/README.md index 374c358bd..bbbddeef6 100644 --- a/cli/README.md +++ b/cli/README.md @@ -142,3 +142,18 @@ The CLI tests require a running instance of the `rabbitmq` service, for which we pytest -vs tests #for all tests pytest -vs tests/test_docker_commands.py #e.g., for particular tests ``` + +## 'PIXL/cli' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/cli/src/README.md b/cli/src/README.md new file mode 100644 index 000000000..807a572b5 --- /dev/null +++ b/cli/src/README.md @@ -0,0 +1,6 @@ +## 'PIXL/cli/src' Directory Contents + +### Subdirectories + +[pixl_cli](./pixl_cli/README.md) + diff --git a/cli/src/pixl_cli/README.md b/cli/src/pixl_cli/README.md new file mode 100644 index 000000000..11f286869 --- /dev/null +++ b/cli/src/pixl_cli/README.md @@ -0,0 +1,18 @@ +## 'PIXL/cli/src/pixl_cli' Directory Contents + +### Files + +main.py + +_config.py + +_database.py + +_docker_commands.py + +_io.py + +_message_processing.py + +__init__.py + diff --git a/cli/tests/README.md b/cli/tests/README.md index 280d3bf6b..85977d651 100644 --- a/cli/tests/README.md +++ b/cli/tests/README.md @@ -5,3 +5,25 @@ Remove the db container and associated data docker container rm pixl-test-db -v -f ``` +## 'PIXL/cli/tests' Directory Contents + +### Files + +conftest.py + +README.md + +test_check_env.py + +test_database.py + +test_docker_commands.py + +test_io.py + +test_messages_from_files.py + +test_message_processing.py + +test_populate.py + diff --git a/docker/README.md b/docker/README.md new file mode 100644 index 000000000..d423d8cb6 --- /dev/null +++ b/docker/README.md @@ -0,0 +1,22 @@ +## 'PIXL/docker' Directory Contents + +### Subdirectories + +[export-api](./export-api/README.md) + +[hasher-api](./hasher-api/README.md) + +[imaging-api](./imaging-api/README.md) + +[orthanc-anon](./orthanc-anon/README.md) + +[orthanc-raw](./orthanc-raw/README.md) + +[postgres](./postgres/README.md) + +### Files + +.dockerignore + +common.env + diff --git a/docker/hasher-api/README.md b/docker/hasher-api/README.md new file mode 100644 index 000000000..f54e14972 --- /dev/null +++ b/docker/hasher-api/README.md @@ -0,0 +1,6 @@ +## 'PIXL/docker/hasher-api' Directory Contents + +### Files + +Dockerfile + diff --git a/docker/imaging-api/README.md b/docker/imaging-api/README.md new file mode 100644 index 000000000..400bee965 --- /dev/null +++ b/docker/imaging-api/README.md @@ -0,0 +1,6 @@ +## 'PIXL/docker/imaging-api' Directory Contents + +### Files + +Dockerfile + diff --git a/docker/orthanc-anon/README.md b/docker/orthanc-anon/README.md new file mode 100644 index 000000000..b1f2a60bc --- /dev/null +++ b/docker/orthanc-anon/README.md @@ -0,0 +1,6 @@ +## 'PIXL/docker/orthanc-anon' Directory Contents + +### Files + +Dockerfile + diff --git a/docker/orthanc/README.md b/docker/orthanc/README.md new file mode 100644 index 000000000..a137fb98a --- /dev/null +++ b/docker/orthanc/README.md @@ -0,0 +1,6 @@ +## 'PIXL/docker/orthanc-raw' Directory Contents + +### Files + +Dockerfile + diff --git a/docker/pixl-python/README.md b/docker/pixl-python/README.md new file mode 100644 index 000000000..f12d22846 --- /dev/null +++ b/docker/pixl-python/README.md @@ -0,0 +1,6 @@ +## 'PIXL/docker/export-api' Directory Contents + +### Files + +Dockerfile + diff --git a/docker/postgres/README.md b/docker/postgres/README.md new file mode 100644 index 000000000..f43084e01 --- /dev/null +++ b/docker/postgres/README.md @@ -0,0 +1,6 @@ +## 'PIXL/docker/postgres' Directory Contents + +### Files + +Dockerfile + diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 000000000..26ff7826b --- /dev/null +++ b/docs/README.md @@ -0,0 +1,14 @@ +## 'PIXL/docs' Directory Contents + +### Subdirectories + +[design](./design/README.md) + +[file_types](./file_types/README.md) + +[joss-publication](./joss-publication/README.md) + +[services](./services/README.md) + +[setup](./setup/README.md) + diff --git a/docs/design/README.md b/docs/design/README.md new file mode 100644 index 000000000..f2b57d6bd --- /dev/null +++ b/docs/design/README.md @@ -0,0 +1,10 @@ +## 'PIXL/docs/design' Directory Contents + +### Subdirectories + +[diagrams](./diagrams/README.md) + +### Files + +bigger_picture.md + diff --git a/docs/design/diagrams/README.md b/docs/design/diagrams/README.md new file mode 100644 index 000000000..7da298bcc --- /dev/null +++ b/docs/design/diagrams/README.md @@ -0,0 +1,8 @@ +## 'PIXL/docs/design/diagrams' Directory Contents + +### Files + +pixl-multi-project-config.drawio + +pixl-multi-project-config.png + diff --git a/docs/file_types/README.md b/docs/file_types/README.md new file mode 100644 index 000000000..a24a35216 --- /dev/null +++ b/docs/file_types/README.md @@ -0,0 +1,6 @@ +## 'PIXL/docs/file_types' Directory Contents + +### Files + +parquet_files.md + diff --git a/docs/joss-publication/README.md b/docs/joss-publication/README.md new file mode 100644 index 000000000..83800df8e --- /dev/null +++ b/docs/joss-publication/README.md @@ -0,0 +1,12 @@ +## 'PIXL/docs/joss-publication' Directory Contents + +### Subdirectories + +[figures](./figures/README.md) + +### Files + +paper.bib + +paper.md + diff --git a/docs/joss-publication/figures/README.md b/docs/joss-publication/figures/README.md new file mode 100644 index 000000000..c6147e300 --- /dev/null +++ b/docs/joss-publication/figures/README.md @@ -0,0 +1,2 @@ +## 'PIXL/docs/joss-publication/figures' Directory Contents + diff --git a/docs/joss-publication/paper.bib b/docs/joss-publication/paper.bib new file mode 100644 index 000000000..e69de29bb diff --git a/docs/joss-publication/paper.md b/docs/joss-publication/paper.md new file mode 100644 index 000000000..c6c0206c8 --- /dev/null +++ b/docs/joss-publication/paper.md @@ -0,0 +1 @@ +This is the file where the paper must be written \ No newline at end of file diff --git a/docs/services/README.md b/docs/services/README.md new file mode 100644 index 000000000..f0337901a --- /dev/null +++ b/docs/services/README.md @@ -0,0 +1,8 @@ +## 'PIXL/docs/services' Directory Contents + +### Files + +ftp-server.md + +pixl_database.md + diff --git a/docs/setup/README.md b/docs/setup/README.md new file mode 100644 index 000000000..fd9845552 --- /dev/null +++ b/docs/setup/README.md @@ -0,0 +1,10 @@ +## 'PIXL/docs/setup' Directory Contents + +### Files + +azure-keyvault.md + +developer.md + +uclh-infrastructure-setup.md + diff --git a/hasher/README.md b/hasher/README.md index 3119a298f..b9055be2c 100644 --- a/hasher/README.md +++ b/hasher/README.md @@ -67,3 +67,18 @@ HASHER_API_AZ_CLIENT_PASSWORD= HASHER_API_AZ_TENANT_ID= HASHER_API_AZ_KEY_VAULT_NAME= ``` + +## 'PIXL/hasher' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/hasher/src/README.md b/hasher/src/README.md new file mode 100644 index 000000000..99a56a701 --- /dev/null +++ b/hasher/src/README.md @@ -0,0 +1,6 @@ +## 'PIXL/hasher/src' Directory Contents + +### Subdirectories + +[hasher](./hasher/README.md) + diff --git a/hasher/src/hasher/README.md b/hasher/src/hasher/README.md new file mode 100644 index 000000000..40b064a8d --- /dev/null +++ b/hasher/src/hasher/README.md @@ -0,0 +1,12 @@ +## 'PIXL/hasher/src/hasher' Directory Contents + +### Files + +endpoints.py + +hashing.py + +main.py + +__init__.py + diff --git a/hasher/tests/README.md b/hasher/tests/README.md new file mode 100644 index 000000000..1a161940e --- /dev/null +++ b/hasher/tests/README.md @@ -0,0 +1,12 @@ +## 'PIXL/hasher/tests' Directory Contents + +### Files + +conftest.py + +test_endpoints.py + +test_hashing.py + +__init__.py + diff --git a/orthanc/README.md b/orthanc/README.md index 1683a2e5d..674d7d272 100644 --- a/orthanc/README.md +++ b/orthanc/README.md @@ -9,3 +9,18 @@ PIXL defines 2 types of ORTHANC instances: For both instances we define a plugin in `orthanc-*/plugin/pixl.py` that implements the custom functionality . + +## 'PIXL/orthanc' Directory Contents + +### Subdirectories + +[assets](./assets/README.md) + +[orthanc-anon](./orthanc-anon/README.md) + +[orthanc-raw](./orthanc-raw/README.md) + +### Files + +README.md + diff --git a/orthanc/assets/README.md b/orthanc/assets/README.md new file mode 100644 index 000000000..e6468fad6 --- /dev/null +++ b/orthanc/assets/README.md @@ -0,0 +1,10 @@ +## 'PIXL/orthanc/assets' Directory Contents + +### Files + +orthanc-anon-az-dicom.png + +orthanc-anon-web.png + +orthanc-raw-web.png + diff --git a/orthanc/orthanc-anon/README.md b/orthanc/orthanc-anon/README.md index 784084e9c..5b386ea5e 100644 --- a/orthanc/orthanc-anon/README.md +++ b/orthanc/orthanc-anon/README.md @@ -104,3 +104,18 @@ start. ## References - [Cheat sheet of the REST API](https://book.orthanc-server.com/users/rest-cheatsheet.html) + +## 'orthanc' Directory Contents + +### Subdirectories + +[assets](./assets/README.md) + +[orthanc-anon](./orthanc-anon/README.md) + +[orthanc-raw](./orthanc-raw/README.md) + +### Files + +README.md + diff --git a/orthanc/orthanc-anon/config/README.md b/orthanc/orthanc-anon/config/README.md new file mode 100644 index 000000000..ef5de4dce --- /dev/null +++ b/orthanc/orthanc-anon/config/README.md @@ -0,0 +1,8 @@ +## 'PIXL/orthanc/orthanc-anon/config' Directory Contents + +### Files + +dicom.json + +orthanc.json + diff --git a/orthanc/orthanc-anon/docs/README.md b/orthanc/orthanc-anon/docs/README.md new file mode 100644 index 000000000..8a6fa25bf --- /dev/null +++ b/orthanc/orthanc-anon/docs/README.md @@ -0,0 +1,10 @@ +## 'PIXL/orthanc/orthanc-anon/docs' Directory Contents + +### Subdirectories + +[assets](./assets/README.md) + +### Files + +DicomServiceViaAAD.md + diff --git a/orthanc/orthanc-anon/docs/assets/README.md b/orthanc/orthanc-anon/docs/assets/README.md new file mode 100644 index 000000000..484b4f3e3 --- /dev/null +++ b/orthanc/orthanc-anon/docs/assets/README.md @@ -0,0 +1,6 @@ +## 'PIXL/orthanc/orthanc-anon/docs/assets' Directory Contents + +### Files + +DicomServiceAuthority.png + diff --git a/orthanc/orthanc-anon/plugin/README.md b/orthanc/orthanc-anon/plugin/README.md new file mode 100644 index 000000000..6f5c0eba0 --- /dev/null +++ b/orthanc/orthanc-anon/plugin/README.md @@ -0,0 +1,8 @@ +## 'PIXL/orthanc/orthanc-anon/plugin' Directory Contents + +### Files + +download_dicom_spec.py + +pixl.py + diff --git a/orthanc/orthanc-raw/README.md b/orthanc/orthanc-raw/README.md index eec29a5a0..2e695cc3a 100644 --- a/orthanc/orthanc-raw/README.md +++ b/orthanc/orthanc-raw/README.md @@ -110,3 +110,16 @@ team. ## References - [Cheat sheet of the REST API](https://book.orthanc-server.com/users/rest-cheatsheet.html) + +## 'PIXL/orthanc/orthanc-raw' Directory Contents + +### Subdirectories + +[config](./config/README.md) + +[plugin](./plugin/README.md) + +### Files + +README.md + diff --git a/orthanc/orthanc-raw/config/README.md b/orthanc/orthanc-raw/config/README.md new file mode 100644 index 000000000..6d345e63e --- /dev/null +++ b/orthanc/orthanc-raw/config/README.md @@ -0,0 +1,10 @@ +## 'PIXL/orthanc/orthanc-raw/config' Directory Contents + +### Files + +dicom.json + +orthanc.json + +postgres.json + diff --git a/orthanc/orthanc-raw/plugin/README.md b/orthanc/orthanc-raw/plugin/README.md new file mode 100644 index 000000000..bfebf0781 --- /dev/null +++ b/orthanc/orthanc-raw/plugin/README.md @@ -0,0 +1,6 @@ +## 'PIXL/orthanc/orthanc-raw/plugin' Directory Contents + +### Files + +pixl.py + diff --git a/pixl_core/README.md b/pixl_core/README.md index 8116ba49e..5b9f784fb 100644 --- a/pixl_core/README.md +++ b/pixl_core/README.md @@ -234,3 +234,18 @@ Note, it can take several minutes for the server to start up. Once the server has started, you can log in by visiting `http://localhost:8080` with the username and password set in the `XNAT_USER_NAME` and `XNAT_PASSWORD` environment variables. + +## 'PIXL/pixl_core' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pixl_core/src/README.md b/pixl_core/src/README.md new file mode 100644 index 000000000..56763ccf2 --- /dev/null +++ b/pixl_core/src/README.md @@ -0,0 +1,6 @@ +## 'PIXL/pixl_core/src' Directory Contents + +### Subdirectories + +[core](./core/README.md) + diff --git a/pixl_core/src/core/README.md b/pixl_core/src/core/README.md new file mode 100644 index 000000000..c450b32c7 --- /dev/null +++ b/pixl_core/src/core/README.md @@ -0,0 +1,26 @@ +## 'PIXL/pixl_core/src/core' Directory Contents + +### Subdirectories + +[db](./db/README.md) + +[patient_queue](./patient_queue/README.md) + +[project_config](./project_config/README.md) + +[rest_api](./rest_api/README.md) + +[token_buffer](./token_buffer/README.md) + +[uploader](./uploader/README.md) + +### Files + +dicom_tags.py + +exceptions.py + +exports.py + +__init__.py + diff --git a/pixl_core/src/core/db/README.md b/pixl_core/src/core/db/README.md new file mode 100644 index 000000000..2b3e187dd --- /dev/null +++ b/pixl_core/src/core/db/README.md @@ -0,0 +1,10 @@ +## 'PIXL/pixl_core/src/core/db' Directory Contents + +### Files + +models.py + +queries.py + +__init__.py + diff --git a/pixl_core/src/core/patient_queue/README.md b/pixl_core/src/core/patient_queue/README.md new file mode 100644 index 000000000..f53cead1f --- /dev/null +++ b/pixl_core/src/core/patient_queue/README.md @@ -0,0 +1,14 @@ +## 'PIXL/pixl_core/src/core/patient_queue' Directory Contents + +### Files + +message.py + +producer.py + +subscriber.py + +_base.py + +__init__.py + diff --git a/pixl_core/src/core/project_config/README.md b/pixl_core/src/core/project_config/README.md new file mode 100644 index 000000000..4a8232810 --- /dev/null +++ b/pixl_core/src/core/project_config/README.md @@ -0,0 +1,12 @@ +## 'PIXL/pixl_core/src/core/project_config' Directory Contents + +### Files + +pixl_config_model.py + +secrets.py + +tag_operations.py + +__init__.py + diff --git a/pixl_core/src/core/rest_api/README.md b/pixl_core/src/core/rest_api/README.md new file mode 100644 index 000000000..2d481757b --- /dev/null +++ b/pixl_core/src/core/rest_api/README.md @@ -0,0 +1,8 @@ +## 'PIXL/pixl_core/src/core/rest_api' Directory Contents + +### Files + +router.py + +__init__.py + diff --git a/pixl_core/src/core/token_buffer/README.md b/pixl_core/src/core/token_buffer/README.md new file mode 100644 index 000000000..d25fd7b64 --- /dev/null +++ b/pixl_core/src/core/token_buffer/README.md @@ -0,0 +1,10 @@ +## 'PIXL/pixl_core/src/core/token_buffer' Directory Contents + +### Files + +models.py + +tokens.py + +__init__.py + diff --git a/pixl_core/src/core/uploader/README.md b/pixl_core/src/core/uploader/README.md new file mode 100644 index 000000000..1a0e6a444 --- /dev/null +++ b/pixl_core/src/core/uploader/README.md @@ -0,0 +1,16 @@ +## 'PIXL/pixl_core/src/core/uploader' Directory Contents + +### Files + +base.py + +_dicomweb.py + +_ftps.py + +_orthanc.py + +_xnat.py + +__init__.py + diff --git a/pixl_core/tests/README.md b/pixl_core/tests/README.md new file mode 100644 index 000000000..621d1b3c7 --- /dev/null +++ b/pixl_core/tests/README.md @@ -0,0 +1,22 @@ +## 'PIXL/pixl_core/tests' Directory Contents + +### Subdirectories + +[data](./data/README.md) + +[patient_queue](./patient_queue/README.md) + +[project_config](./project_config/README.md) + +[token_buffer](./token_buffer/README.md) + +[uploader](./uploader/README.md) + +### Files + +conftest.py + +docker-compose.yml + +test_exports.py + diff --git a/pixl_core/tests/data/README.md b/pixl_core/tests/data/README.md new file mode 100644 index 000000000..065c917e7 --- /dev/null +++ b/pixl_core/tests/data/README.md @@ -0,0 +1,10 @@ +## 'PIXL/pixl_core/tests/data' Directory Contents + +### Files + +dicom_series.zip + +public.zip + +xnat_project.xml + diff --git a/pixl_core/tests/patient_queue/README.md b/pixl_core/tests/patient_queue/README.md new file mode 100644 index 000000000..895a4d9fc --- /dev/null +++ b/pixl_core/tests/patient_queue/README.md @@ -0,0 +1,10 @@ +## 'PIXL/pixl_core/tests/patient_queue' Directory Contents + +### Files + +test_message.py + +test_producer.py + +test_subscriber.py + diff --git a/pixl_core/tests/project_config/README.md b/pixl_core/tests/project_config/README.md new file mode 100644 index 000000000..eb889f4e8 --- /dev/null +++ b/pixl_core/tests/project_config/README.md @@ -0,0 +1,8 @@ +## 'PIXL/pixl_core/tests/project_config' Directory Contents + +### Files + +test_project_config.py + +test_secrets.py + diff --git a/pixl_core/tests/token_buffer/README.md b/pixl_core/tests/token_buffer/README.md new file mode 100644 index 000000000..259ef6888 --- /dev/null +++ b/pixl_core/tests/token_buffer/README.md @@ -0,0 +1,6 @@ +## 'PIXL/pixl_core/tests/token_buffer' Directory Contents + +### Files + +test_tokens.py + diff --git a/pixl_core/tests/uploader/README.md b/pixl_core/tests/uploader/README.md new file mode 100644 index 000000000..e960568d5 --- /dev/null +++ b/pixl_core/tests/uploader/README.md @@ -0,0 +1,12 @@ +## 'PIXL/pixl_core/tests/uploader' Directory Contents + +### Files + +test_base.py + +test_dicomweb.py + +test_ftps.py + +test_xnat.py + diff --git a/pixl_dcmd/README.md b/pixl_dcmd/README.md index 2c8b57682..d1710c24b 100644 --- a/pixl_dcmd/README.md +++ b/pixl_dcmd/README.md @@ -62,3 +62,18 @@ and optionally a `manufacturer_overrides`. If a `manufacturer_overrides` is defined, it will be used to override the `base` tags, if the manufacturer of the DICOM file matches the manufacturer in the `manufacturer_overrides`. Any tags in the `manufacturer_overrides` that are not in the `base` will be added to the scheme as well. + +## 'PIXL/pixl_dcmd' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pixl_dcmd/src/README.md b/pixl_dcmd/src/README.md new file mode 100644 index 000000000..2ba0cd0e1 --- /dev/null +++ b/pixl_dcmd/src/README.md @@ -0,0 +1,6 @@ +## 'PIXL/pixl_dcmd/src' Directory Contents + +### Subdirectories + +[pixl_dcmd](./pixl_dcmd/README.md) + diff --git a/pixl_dcmd/src/pixl_dcmd/README.md b/pixl_dcmd/src/pixl_dcmd/README.md new file mode 100644 index 000000000..e94fbfd07 --- /dev/null +++ b/pixl_dcmd/src/pixl_dcmd/README.md @@ -0,0 +1,22 @@ +## 'PIXL/pixl_dcmd/src/pixl_dcmd' Directory Contents + +### Subdirectories + +[resources](./resources/README.md) + +### Files + +main.py + +tagrecording.py + +_database.py + +_dicom_helpers.py + +_tag_schemes.py + +_version.py + +__init__.py + diff --git a/pixl_dcmd/src/pixl_dcmd/resources/README.md b/pixl_dcmd/src/pixl_dcmd/resources/README.md new file mode 100644 index 000000000..b6d19ecc6 --- /dev/null +++ b/pixl_dcmd/src/pixl_dcmd/resources/README.md @@ -0,0 +1,6 @@ +## 'PIXL/pixl_dcmd/src/pixl_dcmd/resources' Directory Contents + +### Files + +recorded-headers.yml + diff --git a/pixl_dcmd/tests/README.md b/pixl_dcmd/tests/README.md new file mode 100644 index 000000000..9f05da066 --- /dev/null +++ b/pixl_dcmd/tests/README.md @@ -0,0 +1,16 @@ +## 'PIXL/pixl_dcmd/tests' Directory Contents + +### Files + +conftest.py + +test_database.py + +test_dicom_validator.py + +test_main.py + +test_tagrecording.py + +test_tag_schemes.py + diff --git a/pixl_export/README.md b/pixl_export/README.md index 9e34f283e..89481df38 100644 --- a/pixl_export/README.md +++ b/pixl_export/README.md @@ -43,3 +43,18 @@ Usage should be from the CLI driver, which calls the HTTP endpoints. ## Notes - The height/weight/GCS value is extracted only within a 24 h time window + +## 'PIXL/pixl_export' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pixl_export/src/README.md b/pixl_export/src/README.md new file mode 100644 index 000000000..06ab4efea --- /dev/null +++ b/pixl_export/src/README.md @@ -0,0 +1,6 @@ +## 'PIXL/pixl_export/src' Directory Contents + +### Subdirectories + +[pixl_export](./pixl_export/README.md) + diff --git a/pixl_export/src/pixl_export/README.md b/pixl_export/src/pixl_export/README.md new file mode 100644 index 000000000..c21da40db --- /dev/null +++ b/pixl_export/src/pixl_export/README.md @@ -0,0 +1,12 @@ +## 'PIXL/pixl_export/src/pixl_export' Directory Contents + +### Files + +main.py + +_databases.py + +_queries.py + +__init__.py + diff --git a/pixl_export/tests/README.md b/pixl_export/tests/README.md new file mode 100644 index 000000000..607a81078 --- /dev/null +++ b/pixl_export/tests/README.md @@ -0,0 +1,10 @@ +## 'PIXL/pixl_export/tests' Directory Contents + +### Files + +conftest.py + +docker-compose.yml + +test_app.py + diff --git a/pixl_imaging/README.md b/pixl_imaging/README.md index 9f3419db8..26463b37c 100644 --- a/pixl_imaging/README.md +++ b/pixl_imaging/README.md @@ -60,3 +60,22 @@ The `SKIP_ALEMBIC` environmental variable is used to control whether migrations - `SKIP_ALEMBIC` is set to true for tests that do not use the database (e.g. `SKIP_ALEMBIC=true`). Otherwise you probably want to run this. - If you wanted to test out new migrations from a test/dev deployment on the GAE with data in, then you can redeploy just the `imaging-api` container while keeping the `postgres` container up. + +## 'PIXL/pixl_imaging' Directory Contents + +### Subdirectories + +[alembic](./alembic/README.md) + +[scripts](./scripts/README.md) + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pixl_imaging/alembic/README.md b/pixl_imaging/alembic/README.md index fa1a34d83..d7054661f 100644 --- a/pixl_imaging/alembic/README.md +++ b/pixl_imaging/alembic/README.md @@ -29,3 +29,24 @@ There's a couple of manual steps: - Check the changes autogenerated and update to match your intention - Commit the changes and review in a pull request as normal + +## 'PIXL/pixl_imaging/alembic' Directory Contents + +### Subdirectories + +[versions](./versions/README.md) + +### Files + +alembic.ini + +autogenerate-migration.sh + +env.py + +migrations.env + +README.md + +script.py.mako + diff --git a/pixl_imaging/alembic/versions/README.md b/pixl_imaging/alembic/versions/README.md new file mode 100644 index 000000000..ea043622a --- /dev/null +++ b/pixl_imaging/alembic/versions/README.md @@ -0,0 +1,12 @@ +## 'PIXL/pixl_imaging/alembic/versions' Directory Contents + +### Files + +83dcb3812628_add_study_uid_column_to_image_table.py + +bcaef54e2bfe_create_extract_and_image_tables.py + +cb5ee12a6e20_replace_hashed_id_with_pseudo_study_uid.py + +d947cc715eb1_add_pseudo_patient_id_column_to_image_table.py + diff --git a/pixl_imaging/scripts/README.md b/pixl_imaging/scripts/README.md new file mode 100644 index 000000000..afd8a5659 --- /dev/null +++ b/pixl_imaging/scripts/README.md @@ -0,0 +1,6 @@ +## 'PIXL/pixl_imaging/scripts' Directory Contents + +### Files + +migrate_and_run.sh + diff --git a/pixl_imaging/src/README.md b/pixl_imaging/src/README.md new file mode 100644 index 000000000..a8f1b4ac5 --- /dev/null +++ b/pixl_imaging/src/README.md @@ -0,0 +1,6 @@ +## 'PIXL/pixl_imaging/src' Directory Contents + +### Subdirectories + +[pixl_imaging](./pixl_imaging/README.md) + diff --git a/pixl_imaging/src/pixl_imaging/README.md b/pixl_imaging/src/pixl_imaging/README.md new file mode 100644 index 000000000..8250982db --- /dev/null +++ b/pixl_imaging/src/pixl_imaging/README.md @@ -0,0 +1,12 @@ +## 'PIXL/pixl_imaging/src/pixl_imaging' Directory Contents + +### Files + +main.py + +_orthanc.py + +_processing.py + +__init__.py + diff --git a/pixl_imaging/tests/README.md b/pixl_imaging/tests/README.md new file mode 100644 index 000000000..8903dd81c --- /dev/null +++ b/pixl_imaging/tests/README.md @@ -0,0 +1,14 @@ +## 'PIXL/pixl_imaging/tests' Directory Contents + +### Subdirectories + +[orthanc_raw_config](./orthanc_raw_config/README.md) + +### Files + +conftest.py + +docker-compose.yml + +test_imaging_processing.py + diff --git a/pixl_imaging/tests/orthanc_raw_config/README.md b/pixl_imaging/tests/orthanc_raw_config/README.md new file mode 100644 index 000000000..3b95d29ca --- /dev/null +++ b/pixl_imaging/tests/orthanc_raw_config/README.md @@ -0,0 +1,8 @@ +## 'PIXL/pixl_imaging/tests/orthanc_raw_config' Directory Contents + +### Files + +dicom.json + +orthanc.json + diff --git a/postgres/README.md b/postgres/README.md index b161ebf78..e532b9469 100644 --- a/postgres/README.md +++ b/postgres/README.md @@ -5,3 +5,14 @@ container and the pixl_imaging api uses [alembic](https://alembic.sqlalchemy.org This allows a reproducible way to update (or rollback) alterations to the PIXL pipeline's database schema. See [/pixl_imaging/alembic](../pixl_imaging/alembic) for how these are defined and how to create new migrations. + +## 'PIXL/postgres' Directory Contents + +### Files + +pixl-db_init.sh + +postgres.conf + +README.md + diff --git a/projects/README.md b/projects/README.md new file mode 100644 index 000000000..dcfdcd654 --- /dev/null +++ b/projects/README.md @@ -0,0 +1,8 @@ +## 'PIXL/projects' Directory Contents + +### Subdirectories + +[configs](./configs/README.md) + +[exports](./exports/README.md) + diff --git a/projects/configs/README.md b/projects/configs/README.md new file mode 100644 index 000000000..351680b9b --- /dev/null +++ b/projects/configs/README.md @@ -0,0 +1,22 @@ +## 'PIXL/projects/configs' Directory Contents + +### Subdirectories + +[tag-operations](./tag-operations/README.md) + +### Files + +ms-pinpoint.yaml + +test-external-user.yaml + +test-extract-uclh-omop-cdm-dicomweb.yaml + +test-extract-uclh-omop-cdm-xnat.yaml + +test-extract-uclh-omop-cdm.yaml + +uclh-nasogastric-tube-project-ngt-only-full-dataset.yaml + +uclh-prostate-mri-external-dataset.yaml + diff --git a/projects/configs/tag-operations/README.md b/projects/configs/tag-operations/README.md new file mode 100644 index 000000000..83c53c681 --- /dev/null +++ b/projects/configs/tag-operations/README.md @@ -0,0 +1,24 @@ +## 'PIXL/projects/configs/tag-operations' Directory Contents + +### Subdirectories + +[manufacturer-overrides](./manufacturer-overrides/README.md) + +### Files + +base.yaml + +diffusion-weighted-mri.yaml + +mri.yaml + +ms-pinpoint.yaml + +test-external-user.yaml + +test-extract-uclh-omop-cdm.yaml + +uclh-nasogastric-tube-project-ngt-only-full-dataset.yaml + +xray.yaml + diff --git a/projects/configs/tag-operations/manufacturer-overrides/README.md b/projects/configs/tag-operations/manufacturer-overrides/README.md new file mode 100644 index 000000000..b77c531e3 --- /dev/null +++ b/projects/configs/tag-operations/manufacturer-overrides/README.md @@ -0,0 +1,8 @@ +## 'manufacturer-overrides' Directory Contents + +### Files + +mri-diffusion.yaml + +mri.yaml + diff --git a/pytest-pixl/README.md b/pytest-pixl/README.md index 4c4e9666e..30c8c4c21 100644 --- a/pytest-pixl/README.md +++ b/pytest-pixl/README.md @@ -102,3 +102,19 @@ default DICOM tag values used to generate fake DICOM data in `generate_dicom_dat The JSON file was created by running [`scripts/create_default_dicom_tags_json.py`](./scripts/create_default_dicom_tags_json.py), with the details implemented in [`pytest_pixl.dicom._create_default_json`](./src/pytest_pixl/dicom.py). +## 'PIXL/pytest-pixl' Directory Contents + +### Subdirectories + +[scripts](./scripts/README.md) + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pytest-pixl/scripts/README.md b/pytest-pixl/scripts/README.md new file mode 100644 index 000000000..65085443d --- /dev/null +++ b/pytest-pixl/scripts/README.md @@ -0,0 +1,6 @@ +## 'PIXL/pytest-pixl/scripts' Directory Contents + +### Files + +create_default_dicom_tags_json.py + diff --git a/pytest-pixl/src/README.md b/pytest-pixl/src/README.md new file mode 100644 index 000000000..138dffa26 --- /dev/null +++ b/pytest-pixl/src/README.md @@ -0,0 +1,8 @@ +## 'PIXL/pytest-pixl/src' Directory Contents + +### Subdirectories + +[pytest_pixl](./pytest_pixl/README.md) + +[resources](./resources/README.md) + diff --git a/pytest-pixl/src/pytest_pixl/README.md b/pytest-pixl/src/pytest_pixl/README.md new file mode 100644 index 000000000..98744d18c --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/README.md @@ -0,0 +1,18 @@ +## 'PIXL/pytest-pixl/src/pytest_pixl' Directory Contents + +### Subdirectories + +[data](./data/README.md) + +### Files + +dicom.py + +ftpserver.py + +helpers.py + +plugin.py + +__init__.py + diff --git a/pytest-pixl/src/pytest_pixl/data/README.md b/pytest-pixl/src/pytest_pixl/data/README.md new file mode 100644 index 000000000..cfa58b0bb --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/data/README.md @@ -0,0 +1,12 @@ +## 'PIXL/pytest-pixl/src/pytest_pixl/data' Directory Contents + +### Subdirectories + +[omop-resources](./omop-resources/README.md) + +### Files + +default_dicom_tags.json + +volume_dicom_variables.json + diff --git a/pytest-pixl/src/pytest_pixl/data/omop-resources/README.md b/pytest-pixl/src/pytest_pixl/data/omop-resources/README.md new file mode 100644 index 000000000..7a457c566 --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/data/omop-resources/README.md @@ -0,0 +1,18 @@ +## 'omop-resources' Directory Contents + +### Subdirectories + +[omop](./omop/README.md) + +### Files + +batch_input.csv + +duplicate_input.csv + +multiple_projects.csv + +participant_id.csv + +test.csv + diff --git a/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/README.md b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/README.md new file mode 100644 index 000000000..e5d45c492 --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/README.md @@ -0,0 +1,12 @@ +## 'omop' Directory Contents + +### Subdirectories + +[private](./private/README.md) + +[public](./public/README.md) + +### Files + +extract_summary.json + diff --git a/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/private/README.md b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/private/README.md new file mode 100644 index 000000000..2e47873ed --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/private/README.md @@ -0,0 +1,8 @@ +## 'private' Directory Contents + +### Files + +PERSON_LINKS.parquet + +PROCEDURE_OCCURRENCE_LINKS.parquet + diff --git a/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/public/README.md b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/public/README.md new file mode 100644 index 000000000..d35e10141 --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/public/README.md @@ -0,0 +1,6 @@ +## 'public' Directory Contents + +### Files + +PROCEDURE_OCCURRENCE.parquet + diff --git a/pytest-pixl/src/resources/README.md b/pytest-pixl/src/resources/README.md new file mode 100644 index 000000000..8c118dc40 --- /dev/null +++ b/pytest-pixl/src/resources/README.md @@ -0,0 +1,6 @@ +## 'PIXL/pytest-pixl/src/resources' Directory Contents + +### Subdirectories + +[ssl](./ssl/README.md) + diff --git a/pytest-pixl/src/resources/ssl/README.md b/pytest-pixl/src/resources/ssl/README.md new file mode 100644 index 000000000..20c619682 --- /dev/null +++ b/pytest-pixl/src/resources/ssl/README.md @@ -0,0 +1,8 @@ +## 'PIXL/pytest-pixl/src/resources/ssl' Directory Contents + +### Files + +localhost.crt + +localhost.key + diff --git a/pytest-pixl/tests/README.md b/pytest-pixl/tests/README.md new file mode 100644 index 000000000..d7c2900b2 --- /dev/null +++ b/pytest-pixl/tests/README.md @@ -0,0 +1,12 @@ +## 'PIXL/pytest-pixl/tests' Directory Contents + +### Subdirectories + +[samples_for_fixture_tests](./samples_for_fixture_tests/README.md) + +### Files + +conftest.py + +test_ftpserver_fixture.py + diff --git a/pytest-pixl/tests/samples_for_fixture_tests/README.md b/pytest-pixl/tests/samples_for_fixture_tests/README.md new file mode 100644 index 000000000..ee9d21902 --- /dev/null +++ b/pytest-pixl/tests/samples_for_fixture_tests/README.md @@ -0,0 +1,6 @@ +## 'PIXL/pytest-pixl/tests/samples_for_fixture_tests' Directory Contents + +### Subdirectories + +[test_ftpserver_fixture](./test_ftpserver_fixture/README.md) + diff --git a/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture/README.md b/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture/README.md new file mode 100644 index 000000000..06effc923 --- /dev/null +++ b/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture/README.md @@ -0,0 +1,6 @@ +## 'PIXL/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture' Directory Contents + +### Files + +test_ftpserver_login.py + diff --git a/schemas/README.md b/schemas/README.md new file mode 100644 index 000000000..432a9cc7b --- /dev/null +++ b/schemas/README.md @@ -0,0 +1,6 @@ +## 'PIXL/schemas' Directory Contents + +### Files + +github-issue-forms.json + diff --git a/scripts/README.md b/scripts/README.md new file mode 100644 index 000000000..26ff995a3 --- /dev/null +++ b/scripts/README.md @@ -0,0 +1,12 @@ +## 'PIXL/scripts' Directory Contents + +### Files + +cmove_all_studies.py + +delete_oldest_n_studies.py + +filter_cohort_for_those_present_in_raw.py + +list_newest_n_studies.py + diff --git a/test/README.md b/test/README.md index 2a3723cca..b1c25278f 100644 --- a/test/README.md +++ b/test/README.md @@ -10,7 +10,7 @@ consumers started. **Then** the DICOM study exists in the "anon" PIXL Orthanc instance. -After setting up your [.secrets.env](../README.md#project-secrets)), you can run the system test with: +After setting up your [.secrets.env](../README.md#project-secrets), you can run the system test with: ```bash ./run-system-test.sh @@ -69,3 +69,34 @@ but configured to upload to a [DICOMweb server](#dicomweb-config) ### DICOMWeb config `./dicomweb_config/` contains the Orthanc configuration files for the mock [DICOMweb server](../docs/services/dicomweb-server.md). + +## 'PIXL/test' Directory Contents + +### Subdirectories + +[dicomweb_config](./dicomweb_config/README.md) + +[resources](./resources/README.md) + +[vna_config](./vna_config/README.md) + +### Files + +.env + +.secrets.env.sample + +conftest.py + +docker-compose.yml + +README.md + +run-system-test.sh + +system_test.py + +test_parquet_exports.py + +utils.py + diff --git a/test/dicomweb_config/README.md b/test/dicomweb_config/README.md new file mode 100644 index 000000000..41729879a --- /dev/null +++ b/test/dicomweb_config/README.md @@ -0,0 +1,10 @@ +## 'PIXL/test/dicomweb_config' Directory Contents + +### Files + +.env + +dicom.json + +orthanc.json + diff --git a/test/resources/README.md b/test/resources/README.md new file mode 100644 index 000000000..132dcb141 --- /dev/null +++ b/test/resources/README.md @@ -0,0 +1,14 @@ +## 'PIXL/test/resources' Directory Contents + +### Subdirectories + +[omop](./omop/README.md) + +[omop-dicomweb](./omop-dicomweb/README.md) + +### Files + +Dicom1.dcm + +Dicom2.dcm + diff --git a/test/resources/omop-dicomweb/README.md b/test/resources/omop-dicomweb/README.md new file mode 100644 index 000000000..0847fb646 --- /dev/null +++ b/test/resources/omop-dicomweb/README.md @@ -0,0 +1,12 @@ +## 'omop-dicomweb' Directory Contents + +### Subdirectories + +[private](./private/README.md) + +[public](./public/README.md) + +### Files + +extract_summary.json + diff --git a/test/resources/omop-dicomweb/private/README.md b/test/resources/omop-dicomweb/private/README.md new file mode 100644 index 000000000..2e47873ed --- /dev/null +++ b/test/resources/omop-dicomweb/private/README.md @@ -0,0 +1,8 @@ +## 'private' Directory Contents + +### Files + +PERSON_LINKS.parquet + +PROCEDURE_OCCURRENCE_LINKS.parquet + diff --git a/test/resources/omop-dicomweb/public/README.md b/test/resources/omop-dicomweb/public/README.md new file mode 100644 index 000000000..d35e10141 --- /dev/null +++ b/test/resources/omop-dicomweb/public/README.md @@ -0,0 +1,6 @@ +## 'public' Directory Contents + +### Files + +PROCEDURE_OCCURRENCE.parquet + diff --git a/test/resources/omop/README.md b/test/resources/omop/README.md new file mode 100644 index 000000000..f8f0010b4 --- /dev/null +++ b/test/resources/omop/README.md @@ -0,0 +1,12 @@ +## 'PIXL/test/resources/omop' Directory Contents + +### Subdirectories + +[private](./private/README.md) + +[public](./public/README.md) + +### Files + +extract_summary.json + diff --git a/test/resources/omop/private/README.md b/test/resources/omop/private/README.md new file mode 100644 index 000000000..d0082ec64 --- /dev/null +++ b/test/resources/omop/private/README.md @@ -0,0 +1,8 @@ +## 'PIXL/test/resources/omop/private' Directory Contents + +### Files + +PERSON_LINKS.parquet + +PROCEDURE_OCCURRENCE_LINKS.parquet + diff --git a/test/resources/omop/public/README.md b/test/resources/omop/public/README.md new file mode 100644 index 000000000..be9075cd4 --- /dev/null +++ b/test/resources/omop/public/README.md @@ -0,0 +1,6 @@ +## 'PIXL/test/resources/omop/public' Directory Contents + +### Files + +PROCEDURE_OCCURRENCE.parquet + diff --git a/test/vna_config/README.md b/test/vna_config/README.md new file mode 100644 index 000000000..ee4cd9d44 --- /dev/null +++ b/test/vna_config/README.md @@ -0,0 +1,8 @@ +## 'PIXL/test/vna_config' Directory Contents + +### Files + +dicom.json + +orthanc.json +