Support configuration for multiple projects #309
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Looks great! I've not used pydantic before, pretty cool! I would consider having the tag operations be an array to allow for multilevel configuration sharing, as we could have e.g.
or have groups of tags, or something else. Just an idea though, not sure if it actually reflects the project needs, this should be enough for the time being |
…lidator is also a classmethod Setting the validators as `classmethod` will fail for some validations
…n base data object
`config.py` needs it
## Project configs ## Common - add env variable for project configs location - mount project configs location - make tag operations a list in config (limited to length 1 for now) - make config functions return `PixlConfig | Any` to get type hints - replace deprecated pydantic features - add utility function to load project config by slug only ### CLI - install cli as editable to find env files correctly - add function to check env for all env.sample keys ### orthanc-anon project config - orthanc anon now cofigurable (tag ops, modalities, destionation) - add query for project slug by non-hashed values - move anonymisation logic to dcmd package ### EHR project config - mark only processing tests with run_containers fixture - use project config to determine destination --------- Co-authored-by: Milan Malfait <[email protected]>
* Add documentation for Parquet files and export process * Formatting * Move `TODO` to issue #306 * Remove PR references * Formatting * Move specific details to `pixl_core` docs and add links * Update directory structure on the FTPS server * Formatting * Rename docs/data -> docs/file_types * Link to `file_types` documentation * Add directory structures to docstrings * Update upload.py Co-authored-by: Stef Piatek <[email protected]> * Fix docs link Co-authored-by: Jeremy Stein <[email protected]> * Clarify that the radiology reports go through Cogstack Co-authored-by: Jeremy Stein <[email protected]> * Add note about test files Co-authored-by: Jeremy Stein <[email protected]> --------- Co-authored-by: Stef Piatek <[email protected]> Co-authored-by: Jeremy Stein <[email protected]>
* docs: better editable install instructions * docs: editable install of pytest-pixl
9 tasks
`field_validator` is only available in `pydantic>-2.0`
peshence
reviewed
Feb 29, 2024
stefpiatek
approved these changes
Mar 1, 2024
Avoids circular imports
This reverts commit 6ce589e.
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Current status
config-template/example-config.ymlpydanticmodel of project configurationpydanticmodelcore.uploadso it now has anUploaderinterface for uploading DICOM and Parquet files to the right destination depending on the project's configTo do
.secrets.envwith the relevant envvars on GitHub CIFixes #232