[dcm2bids pipeline] Delete temporary directory created by the pipeline once it is done running #806
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cmadjar
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that referenced
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Oct 6, 2022
* Turn off column statistics option when running mysqldump (#771) * turn off column statistics option when running mysqldump * add new option to the script to provide additional mysqldump options * run mass perldoc * fix perldoc * fix perldoc * check if date exists otherwise set it to null when inserting into the files table (#777) * [dcm2bids] Get scanner candidate's RegistrationProjectID based on the scanned candidate's visit ProjectID (#779) * add registrationProjectID to the function creating the candidate scanner * missed function call in base_pipeline * flake8 * Pull 24.0-release to 24.1-release (#788) * Reload the mri_upload dictionary before checking if a tarchive has been validated (#783) * reload mri_upload object * remove debugging exit and print statements * fix minor bugs when dealing with scans.tsv files (#774) * fix regex search for excluded series description patterns (#786) * fix_return_statement_of_create_imaging_upload_dict_from_upload_id_function (#787) * merge 24.0 release to 24.1-release (#791) * Reload the mri_upload dictionary before checking if a tarchive has been validated (#783) * reload mri_upload object * remove debugging exit and print statements * fix minor bugs when dealing with scans.tsv files (#774) * fix regex search for excluded series description patterns (#786) * fix_return_statement_of_create_imaging_upload_dict_from_upload_id_function (#787) * [dcm2bids] Insert into MRICandidateErrors if there is a Candidate PatientName mismatch (#790) * insert into MRICandidateErrors when candidate mismatch or pname not matching between DICOMs and NIfTI * remove exit * Add PhaseEncodingDirection and EchoNumber to files and mri_violations_log insert statements (#785) * modify insertion into the mri_violations_log * modify is_file_unique function perl side * modify minc_insertion.pl script to add PhaseEncodingDirectin and EchoNumber to the file data object - perl side * check uniqueness of file based on seriesUID, EchoTime, EchoNumber and PhaseEncodingDirection in python scripts * populate PhaseEncDir, EchoTime, EchoNumber in insertion to files table for bids_import * set PhaseEncDir and EchoNb to none if not present in JSON file * update file non unique message * insert PhaseEncDir and EchoNb in mri_violations_log and files tables in python pipeline * fix missing parentheses * fix extra brackets in nifti_insertion.py * file matching type with regex instead of text as pybids returns either json or .json etc depending on it version * fix bug * fix phaseencodingdirection and echonumber set to null when inserting into files table for perl pipeline * Add phase encoding direction and echo number to mri protocol and mri protocol violated scans (#782) * add PhaseEncodingDirection and ScanOptions to mri_protocol and mri_protocol_violated_scans queries in the python code * update perl code to add the new fields in mri_protocol and mri_protocol_violated_scans * fix ScanOptions not being inserted correctly * use EchoNumber instead of ScanOptions as more generic * update doc * fix seriesUID not being inserted in mri_protocol_violated_scans * some print to figure out why scan is not inserted? * some print to figure out why scan is not inserted? * fix tiny bug * other prints * other prints * fix comparison of int and str for echo number comparison between protocol and json file content * Merge 24.0-release into 24.1-release (#796) * Reload the mri_upload dictionary before checking if a tarchive has been validated (#783) * reload mri_upload object * remove debugging exit and print statements * fix minor bugs when dealing with scans.tsv files (#774) * fix regex search for excluded series description patterns (#786) * fix_return_statement_of_create_imaging_upload_dict_from_upload_id_function (#787) * [dcm2bids] Insert into MRICandidateErrors if there is a Candidate PatientName mismatch (#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... (#793) * Set DICOM dates to undef if the date does not follow proper DICOM standard (#794) * set date to undef if it does not follow proper DICOM formats * fix all dates set to NULL * set file number to undef if it is '' (#800) * [dcm2bids] Add missing get_scanner_candid function in imaging.py (#801) * add missing function called from database_config.py get_subject_ids function * add python function documentation * Add TaskName field to JSON side car file for modalities with task-* names (#802) * add taskName to JSON side car file for modalities with task-* names * add relevant comments * Add required IntendedFor BIDS field in fieldmap JSON files (#803) * add IntendedFor to fieldmaps automatically add visit_label in intended for paths * add method documentation * fix line too long * fix line too long * Update VERSION to 24.1.0 * Update release version in the README.md file * Fix batch_uploads_tarchive to redirect to dcm2bids pipeline when dcm2niix is set as a converter in the Configs (#804) * modify batch_uploads_tarchive so that it can run dcm2bids or dcm2mnc pipeline depending on the converter mentioned in the Config module * fix typo identified by Christine (#807) * [dcm2bids pipeline] Delete temporary directory created by the pipeline once it is done running (#806) * remove tmp dirs before exiting pipeline * add comments
zaliqarosli
pushed a commit
to zaliqarosli/Loris-MRI
that referenced
this pull request
Mar 9, 2023
* Turn off column statistics option when running mysqldump (aces#771) * turn off column statistics option when running mysqldump * add new option to the script to provide additional mysqldump options * run mass perldoc * fix perldoc * fix perldoc * check if date exists otherwise set it to null when inserting into the files table (aces#777) * [dcm2bids] Get scanner candidate's RegistrationProjectID based on the scanned candidate's visit ProjectID (aces#779) * add registrationProjectID to the function creating the candidate scanner * missed function call in base_pipeline * flake8 * Pull 24.0-release to 24.1-release (aces#788) * 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) * merge 24.0 release to 24.1-release (aces#791) * 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 * Add PhaseEncodingDirection and EchoNumber to files and mri_violations_log insert statements (aces#785) * modify insertion into the mri_violations_log * modify is_file_unique function perl side * modify minc_insertion.pl script to add PhaseEncodingDirectin and EchoNumber to the file data object - perl side * check uniqueness of file based on seriesUID, EchoTime, EchoNumber and PhaseEncodingDirection in python scripts * populate PhaseEncDir, EchoTime, EchoNumber in insertion to files table for bids_import * set PhaseEncDir and EchoNb to none if not present in JSON file * update file non unique message * insert PhaseEncDir and EchoNb in mri_violations_log and files tables in python pipeline * fix missing parentheses * fix extra brackets in nifti_insertion.py * file matching type with regex instead of text as pybids returns either json or .json etc depending on it version * fix bug * fix phaseencodingdirection and echonumber set to null when inserting into files table for perl pipeline * Add phase encoding direction and echo number to mri protocol and mri protocol violated scans (aces#782) * add PhaseEncodingDirection and ScanOptions to mri_protocol and mri_protocol_violated_scans queries in the python code * update perl code to add the new fields in mri_protocol and mri_protocol_violated_scans * fix ScanOptions not being inserted correctly * use EchoNumber instead of ScanOptions as more generic * update doc * fix seriesUID not being inserted in mri_protocol_violated_scans * some print to figure out why scan is not inserted? * some print to figure out why scan is not inserted? * fix tiny bug * other prints * other prints * fix comparison of int and str for echo number comparison between protocol and json file content * Merge 24.0-release into 24.1-release (aces#796) * 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 * set file number to undef if it is '' (aces#800) * [dcm2bids] Add missing get_scanner_candid function in imaging.py (aces#801) * add missing function called from database_config.py get_subject_ids function * add python function documentation * Add TaskName field to JSON side car file for modalities with task-* names (aces#802) * add taskName to JSON side car file for modalities with task-* names * add relevant comments * Add required IntendedFor BIDS field in fieldmap JSON files (aces#803) * add IntendedFor to fieldmaps automatically add visit_label in intended for paths * add method documentation * fix line too long * fix line too long * Update VERSION to 24.1.0 * Update release version in the README.md file * Fix batch_uploads_tarchive to redirect to dcm2bids pipeline when dcm2niix is set as a converter in the Configs (aces#804) * modify batch_uploads_tarchive so that it can run dcm2bids or dcm2mnc pipeline depending on the converter mentioned in the Config module * fix typo identified by Christine (aces#807) * [dcm2bids pipeline] Delete temporary directory created by the pipeline once it is done running (aces#806) * remove tmp dirs before exiting pipeline * add comments
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Description
The temporary directories created by the dcm2bids pipeline were not being deleted. This fixes this issue by deleting temporary directories once the pipeline has finished running.