Migrate mri_scanner to the new database abstraction
#1232
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maximemulder
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mri_scanner to the new database abstraction
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Refactoring
Area: ORM
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@maximemulder branch has conflicts after merging #1224 |
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@cmadjar rebased ! |
maximemulder
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Feb 20, 2025
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| # TODO: Move this function to a more appropriate place. | ||
| def generate_new_cand_id(db: Database) -> int: | ||
| """ | ||
| Generate a new random CandID that is not already in the database. | ||
| """ | ||
|
|
||
| while True: | ||
| cand_id = random.randint(100000, 999999) | ||
| candidate = try_get_candidate_with_cand_id(db, cand_id) | ||
| if candidate is None: | ||
| return cand_id |
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Eventually I'd like to move this function to lib.candidate, but this is future work. I think with the changes in the incremental BIDS importer it might become easier.
cmadjar
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Feb 25, 2025
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* remove trailing whitespaces (#1149) Co-authored-by: Maxime Mulder <[email protected]> * SQLAlchemy proof-of-concept (#1152) * add sqlalchemy * fix lints * add comment --------- Co-authored-by: Maxime Mulder <[email protected]> * fix (#1168) Co-authored-by: Maxime Mulder <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * Add literal regex leading r (#1176) Co-authored-by: Maxime Mulder <[email protected]> * fix (#1178) Co-authored-by: Maxime Mulder <[email protected]> * 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 <[email protected]> * update docker install (#1171) Co-authored-by: Maxime Mulder <[email protected]> * 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 <[email protected]> --------- Co-authored-by: Cécile Madjar <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Maxime Mulder <[email protected]> Co-authored-by: Shen <[email protected]>
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Builds on top of #1224. This PR migrates
lib.database_lib.mri_scannerto the new database abstraction, and migrates the existing code that uses it to the new abstraction.This PR does not migrate the configuration file that still indirectly uses this code, but this can be done in a follow-up PR (or this PR if wanted).