CLI command to export radiology; fix system tests #227
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jeremyestein
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path explicitly because it's different depending on where it's running from, so there is no default that makes sense.
non-slugified version into the API.
any change in the source tree forced a rebuild.
test. Radiology parquet is still empty though.
* Slim down ehr tests Reduce use of docker containers and run tests in local pytest * Make sure output file is not owned by root * Awkward workaround for running containers as current user, so that any files created on mounts have the right ownership, and because running as root is bad... * Abandon attempt to run container as non-root; this doesn't work and needs a wider fix and further consideration anyway. Just try chowning the file. * chowning doesn't work either (breaks various tests). Just delete it from within the container that created it and we'll have to come back to this. * Disable check for now as we know it fails * Can't use container after it's been stopped * wrong dir * Correct container name * Don't assume "exports" dir is part of the path, just put the dir structure exactly where we're told. * Wait for healthy containers in better way * Rearrange export directory structure so it makes more sense, and there's only one symlink, which is only created by the CLI, not EHR. * Any FileNotFoundError will do * CLI test was asserting the wrong dir was a symlink. Defensively sort the results of `glob`; the order is not guaranteed. * Minor path error * Can't check for symlink in EHR-only test - radiology export no longer creates it * Update pixl_ehr/tests/test_processing.py * Don't blanket ignore security warning * doc error --------- Co-authored-by: Jeremy Stein <j.stein@ucl.ac.uk>
This reverts commit c5e9b5c.
jeremyestein
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jeremyestein
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jeremyestein
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stefpiatek
approved these changes
Jan 26, 2024
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TODO: