From 93dc6ba9e30ffa06d899d9223311d63fc5d8da22 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Wed, 27 Nov 2024 15:55:03 +0000 Subject: [PATCH] update main read me --- README.md | 94 +++++++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 78 insertions(+), 16 deletions(-) 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