Migrate ImagingUpload and MriUploadDB to the new database abstraction
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maximemulder
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ImagingUpload and MriUploadDB to sqlalchemyImagingUpload and MriUploadDB to the new database abstraction
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@maximemulder very nice!! A few minor suggestions/questions. I did not test it yet.
use dicom archive id instead of tarchiveid because it is prettier ruff check
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* remove trailing whitespaces (#1149) Co-authored-by: Maxime Mulder <maxime.mulder@mcgill.ca> * SQLAlchemy proof-of-concept (#1152) * add sqlalchemy * fix lints * add comment --------- Co-authored-by: Maxime Mulder <maxime.mulder@mcgill.ca> * fix (#1168) Co-authored-by: Maxime Mulder <maxime.mulder@mcgill.ca> * integration test (#1138) * test * main Loris here * ignore Loris python * clone Loris * rm loris * override test * override test * override RB data * fix folder * test php files * test * try * test * try install loris mri * os * test * rm modules * Update flake8_python_linter.yml * Small linting improvements (#1167) * better linting * remove tab in comment --------- Co-authored-by: Maxime Mulder <maxime.mulder@mcgill.ca> * Improve Python subject determination and validation error handling (#1146) * improve subjects determination and validation * use tuple for database query arguments * query on single line --------- Co-authored-by: Maxime Mulder <maxime.mulder@mcgill.ca> * Add literal regex leading r (#1176) Co-authored-by: Maxime Mulder <maxime.mulder@mcgill.ca> * fix (#1178) Co-authored-by: Maxime Mulder <maxime.mulder@mcgill.ca> * LORIS-MRI tooling configuration (#1170) * add pyproject.toml * keep flake8 (for now) * double type checking * Use Pyright as main type checker * remove comment * test * test * change configuration * add python environment variables * try factorization * test * test * test * test * remove temporary things * test ruff error * ruff output github * further test errors * test pyright output github * test * test * test * change comment * remove test errors * test --------- Co-authored-by: Maxime Mulder <maxime.mulder@mcgill.ca> * update docker install (#1171) Co-authored-by: Maxime Mulder <maxime.mulder@mcgill.ca> * add RB override tables for the MRI side (#1173) * Remove php 8.1 and 8.2 from the LORIS tests to keep only test on PHP 8.3 (#1175) * remove php 8.1 and 8.2 testing * update to 8.3 in Dockerfile.test.php8 * ADD minc tools install in gitactions (#1179) * todo install loris mri * test * run pytest in gitaction (#1172) * test * ttt * test * test * test * test * test * test * test * test * test * test * test * test * test * test * test * test * test * Delete test_example.py * rename * done * Delete test/Dockerfile.test.py * test (#1187) * unit tests poc (#1188) * add more pytest global rules (#1194) * Stricter linter configuration (#1193) * stricter ruff config * do not ignore N818 * lint for sorted imports * add python scripts directory (#1196) * Bunch of SQLAlchemy definitions (#1192) * bunch of sqlalchemy definitions * add project orm definition * fix candidate to site query function * optimize docker image (#1195) * fix pytest config (#1197) * fix python scripts (#1199) * remove mysql-connector (#1200) * Improve subject configuration structure (#1150) * refacor subject config * remove suspicious phantom code * change naming * fix rebase lints * cleaner database url * Cecile CandID path join bug fix Co-authored-by: Cécile Madjar <cecile.madjar@mcin.ca> --------- Co-authored-by: Cécile Madjar <cecile.madjar@mcin.ca> * Integration test to check that the ORM definitions match the LORIS SQL database (#1198) * orm sync integration test * add docker health check * use integration config file * test error * Revert "test error" This reverts commit d1a70e6. * Clean up Docker database scripts (#1202) * clean docker database * remove docker warning * remove unused attribute (#1201) * try fix perl ci * Add file, file_parameter and scanner SQLAlchemy models (#1207) * add tables * rename file model * rename parameter_file * fix lints (#1210) * Unify LORIS-MRI logging (#1191) * new env * change print order in database log * create notification type if needed * fix typing pyright update * Integration test for `run_dicom_archive_loader.py` (#1203) add integration test put keys in github repo debugging add database check add comments and debugging remove s3 keys change converter in test check file tree fix doc fix docs 2 rename variable go back to using s3 keys fix path try fix * rename database sub-namepaces (#1214) * fix warnings (#1215) * Factorize get subject session (#1190) * factorize subject session * re-add site log * Migrate "get all sites from the database" to the SQLAlchemy abstraction (#1216) * Fix new PEP585 Ruff lint (#1218) * Clean-up database scan type (#1139) Complementary PR of LORIS #9304 * Migrate DICOM archive files to new database abstraction (#1217) * wip * use self.dicom_archive.id instead of self.tarchive_id * fix todo * Fix SQLAlchemy file model (#1221) * Improve Python requirements order (#1222) * add python documentation (#1223) * Update SQLAlchemy bindings to match LORIS#9556 (#1229) * trigger_tests * try update * fix old queries for integration tests * Migrate `ImagingUpload` and `MriUploadDB` to the new database abstraction (#1224) * migrate mri upload to sqlalchemy * fix concurrency bug * fix clean up * display mri upload ids use dicom archive id instead of tarchiveid because it is prettier ruff check * migrate scanner to new abstraction (#1232) * Fix install script (#1234) * fix install script and move files related to install into the install directory * fix install script and move files related to install into the install directory * fix install script and move files related to install into the install directory * fix paths in imaging_install_test.sh * fix paths in imaging_install_test.sh * fix SQL error in install script * fix tests * fix tests * fix github action * add cpanfile * copy cpanfile in MRI dockerfile * add new dependency in order to be able to source the Digest::BLAKE2 in the cpanfile * fix Digest::BLAKE2 installation though cpanfile * move config templates to a templates directory and requirements files into a requirements directory * remove copy * fix test * fix test * fix test * fix test * Maxime's feedback * specify python version (#1237) * fix large file hash memory (#1236) * add lib.util module (#1238) * New DICOM study import script (#1117) * rewrite dicom archive * update * remove --year and --target options * get session from config file * remove unused upload argument * fix little oopsie for --session * handle large files hash * fix unhandled modalities * use new lib.util module * Add support to be able to read headers from enhanced DICOMs (#7) * print * print * print * print * add support for enhanced DICOMs * add support for enhanced DICOMs * rework associate files with series * sort dicom series and files before inserting in the database * handle null scanner --------- Co-authored-by: Cécile Madjar <cecile.madjar@mcin.ca> * refactoring of CandID on the non-ORM python side * tests * fix insertion in mri_protocol_violation_scans * alphabetical order is hard sometimes * FIx `get_candidate_id` documentation --------- Co-authored-by: Maxime Mulder <maxime-mulder@outlook.com> Co-authored-by: Maxime Mulder <maxime.mulder@mcgill.ca> Co-authored-by: Shen <kongtiaowangshen@gmail.com>
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Migrate
ImagingUploadandMriUploadDBto the new database abstraction.The current input checking is very complex and this should simplify it a little. The previous code seems to sometimes accept or forget to check if the DICOM archive or MRI upload is null in a few specific places, but I do not see how it can work as a whole in these conditions. I therefore assume the DICOM archive and MRI upload must not be null.
The integration test will check if this works broadly, but since this touches the argument validation, I will need to test the pipeline manually with:
Tested and there does not seem to be any regression:
run_dicom_archive_loader.pyexpects either (exclusive)--upload_idor--tarchive_path, and requires the DICOM archive to be associated with exactly one MRI upload.