…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)

…es#825)

* 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

…sertion.pl (aces#829)

…to make it executable (aces#830)

… been rerun (aces#831)

aces#833)

…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)

…edFor (aces#862)

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>