Merge 24.1.7 into main #879
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…n the `converter` Config setting (aces#815) * modifies the dcm2niix command to use the Config converter value instead of hardcoding dcm2niix * add a check to make sure the converter is a dcm2niix binary
* Reload the mri_upload dictionary before checking if a tarchive has been validated (aces#783) * reload mri_upload object * remove debugging exit and print statements * fix minor bugs when dealing with scans.tsv files (aces#774) * fix regex search for excluded series description patterns (aces#786) * fix_return_statement_of_create_imaging_upload_dict_from_upload_id_function (aces#787) * [dcm2bids] Insert into MRICandidateErrors if there is a Candidate PatientName mismatch (aces#790) * insert into MRICandidateErrors when candidate mismatch or pname not matching between DICOMs and NIfTI * remove exit * fix table name to MRICandidateErrors instead of MriCandidateErrors as apparently, it makes a difference on MariaDB/Linux VMs while it just worked on local install on Mac... (aces#793) * Set DICOM dates to undef if the date does not follow proper DICOM standard (aces#794) * set date to undef if it does not follow proper DICOM formats * fix all dates set to NULL * Installation and pet fixes (aces#818) Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mcgill.ca> * Update VERSION file for next bug fix release Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mail.mcgill.ca> Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mcgill.ca>
…t proper logging is done (aces#824)
* add capability to download file from s3 * fix flake8 error
… upload (aces#827) * add capability to download file from s3 * fix flake8 error * add ability to remove s3://bucketname/ from the object name before upload
…to make it executable (aces#830)
…stem before adding them to the list of files to push to S3 (aces#834)
* Reload the mri_upload dictionary before checking if a tarchive has been validated (aces#783) * reload mri_upload object * remove debugging exit and print statements * fix minor bugs when dealing with scans.tsv files (aces#774) * fix regex search for excluded series description patterns (aces#786) * fix_return_statement_of_create_imaging_upload_dict_from_upload_id_function (aces#787) * [dcm2bids] Insert into MRICandidateErrors if there is a Candidate PatientName mismatch (aces#790) * insert into MRICandidateErrors when candidate mismatch or pname not matching between DICOMs and NIfTI * remove exit * fix table name to MRICandidateErrors instead of MriCandidateErrors as apparently, it makes a difference on MariaDB/Linux VMs while it just worked on local install on Mac... (aces#793) * Set DICOM dates to undef if the date does not follow proper DICOM standard (aces#794) * set date to undef if it does not follow proper DICOM formats * fix all dates set to NULL * Installation and pet fixes (aces#818) Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mcgill.ca> * Update VERSION file for next bug fix release * Project, event validation and protobuf update (aces#823) * Project, event validation and protobuf update * Site and project search when creating candidate * missing import * correct pscid search * Events validation * flake rules update * review, and NULL value filtered out for site and project * flake * flake Co-authored-by: regisoc <regis.ongaro-carcy@mcin.ca> * fix conflict * fix version * fix version Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mail.mcgill.ca> Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mcgill.ca> Co-authored-by: regisoc <regis.ongaro-carcy@mcin.ca>
…es are already pushed to S3 and not on filesystem anymore (aces#846) * fix bug * fix listing of filenames * comment new function
* Chunk creation subprocess failure check Raise error when the chunk creation subprocess fails. Fix aces#843 * Update python/lib/physiological.py Print actual error message Co-authored-by: Cécile Madjar <cecile.madjar@mcin.ca> Co-authored-by: Cécile Madjar <cecile.madjar@mcin.ca>
* add some missing exit codes * add some missing exit codes
…tion was an S3 URL (aces#860)
Tested on sandbox with Config `data_dir` = `/data/loris/data`
…eline_lib/dicom_archive_loader_pipeline.py, line 346, in _add_intended_for_to_fieldmap_json_files (aces#867) Tested on HBCD sandbox on the dataset that caused the issue.
…ns of the pipeline are run (aces#868) * update mri_upload to inserting=0 when push to s3 pipeline is finished * fix Inserting flag being properly set when pipeline is running
… IntendedFor written in them (aces#874) * add download from S3 for fmap that needs to have IntendedFor written in them * add print
* Reload the mri_upload dictionary before checking if a tarchive has been validated (aces#783) * reload mri_upload object * remove debugging exit and print statements * fix minor bugs when dealing with scans.tsv files (aces#774) * fix regex search for excluded series description patterns (aces#786) * fix_return_statement_of_create_imaging_upload_dict_from_upload_id_function (aces#787) * [dcm2bids] Insert into MRICandidateErrors if there is a Candidate PatientName mismatch (aces#790) * insert into MRICandidateErrors when candidate mismatch or pname not matching between DICOMs and NIfTI * remove exit * fix table name to MRICandidateErrors instead of MriCandidateErrors as apparently, it makes a difference on MariaDB/Linux VMs while it just worked on local install on Mac... (aces#793) * Set DICOM dates to undef if the date does not follow proper DICOM standard (aces#794) * set date to undef if it does not follow proper DICOM formats * fix all dates set to NULL * Installation and pet fixes (aces#818) Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mcgill.ca> * Update VERSION file for next bug fix release * Project, event validation and protobuf update (aces#823) * Project, event validation and protobuf update * Site and project search when creating candidate * missing import * correct pscid search * Events validation * flake rules update * review, and NULL value filtered out for site and project * flake * flake Co-authored-by: regisoc <regis.ongaro-carcy@mcin.ca> * DICOM Archive broken archive link fix (aces#872) * update version to 24.0.4 (aces#877) Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mail.mcgill.ca> Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mcgill.ca> Co-authored-by: regisoc <regis.ongaro-carcy@mcin.ca>
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