Clean-up database scan type #1139
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I am having some troubles testing this PR because my dev database config got changed recently, but this should work. According to the files changed, only the DICOM to MINC ingestion pipeline needs to be tested. |
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@maximemulder there is a conflict in this PR. Could you rebase and let @nicolasbrossard and I when it is ready to test/review? Thank you :) |
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cmadjar
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Nov 12, 2024
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Tested following scripts:
- delete script 🟢
- minc_insertion.pl 🔴 see suggested code changes in functions
scan_type_text_to_idandscan_type_id_to_textofMRI.pm - imaging_non_minc_insertion.pl 🟢
- minc_to_bids_converter.pl 🔴 see suggested code change in function
getFileListoftools/minc_to_bids_converter.pl - get_dicom_files.pl 🟢
- run_defacing_script.pl 🔴 see suggested code change in function
check_if_deface_files_already_in_dbfunction oftools/run_defacing_script.pl - register_processed_data.pl 🟢
- run_dicom_archive_loader.py 🟢
🟢 = test successful 🥳
🔴 = bugs found, see attached comments for the bug resolution.
Co-authored-by: Cécile Madjar <cecile.madjar@mcin.ca>
Co-authored-by: Cécile Madjar <cecile.madjar@mcin.ca>
Co-authored-by: Cécile Madjar <cecile.madjar@mcin.ca>
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@cmadjar Thank you a lot for the testing and suggestions ! This dates a while back now but the testing I did was certainly not exhaustive enough... |
Co-authored-by: Cécile Madjar <cecile.madjar@mcin.ca>
cmadjar
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Dec 3, 2024
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This is ready to go once aces/Loris#9304 is merged on the LORIS. However, I believe that some of the tests might fail after the merge on the LORIS code base since the table structure will change. @maximemulder @laemtl I will let you fix those while I am away. Thanks! |
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Merging because @cmadjar said to merge this if the other was merged |
cmadjar
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Mar 21, 2025
* 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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Complementary PR of LORIS #9304