[imaging_uploader] Loris-MRI - imaging pipeline fails

[regisoc]

Describe the bug

A bug on Loris-MRI side that blocks the imaging pipeline execution.
Execution fails, but nothing is visible on the UI side.

To Reproduce

You need back-end access to run scripts. By blocking the auto-launch config (ImagingUploaderAutoLaunch = No), pipeline can be triggered server-side after uploading a file.

Steps to reproduce the behavior (attach screenshots if applicable):
2. Go to menu > admin > configuration
3. Click on 'Study'
4. Change the ImagingUploaderAutoLaunch to No
5. Go back to the imaging_uploader (menu > imaging > imaging_uploader)
6. Go to upload tab and upload an valid archive
7. Connect to back-end.
8. Execute the following script by changing the upload_id (visible on the UI side for your file) and path_to_file (path to the uploaded file) arguments to run the imaging pipeline inside Loris-MRI that should end with the mentioned error:

(loris-mri-python env) user@machine:/opt/Loris-MRI/bin/mri$ perl uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 132 -verbose /data/incoming/$user_upload_folder/DCC090_587630_V1.tar.gz

 find \/tmp\/ImagingUpload\-9\-46\-wPzJP8 -name '__MACOSX' -exec rm -rf {} +  
Use of uninitialized value $living_phantom_regex in concatenation (.) or string at /opt/Loris-MRI/bin/mri/uploadNeuroDB/NeuroDB/ImagingUpload.pm line 298.

dicomTar.pl \/tmp\/ImagingUpload\-9\-46\-wPzJP8 \/data\/Loris\-MRI\/data\/tarchive -database -profile prod -verbose 
 Source: /tmp/ImagingUpload-9-46-wPzJP8
Target: /data/Loris-MRI/data/tarchive

Testing for database connectivity.
Database is available.

You will archive the dir		: ImagingUpload-9-46-wPzJP8

You are creating a tar with the following command:
        
tar -cf /data/Loris-MRI/data/tarchive/ImagingUpload-9-46-wPzJP8.tar ImagingUpload-9-46-wPzJP8


getting md5sums and gzipping!!

* Taken from dir                   :    /tmp/ImagingUpload-9-46-wPzJP8
* Archive target location          :    /data/Loris-MRI/data/tarchive/DCM_2016-08-17_ImagingUpload-9-46-wPzJP8.tar
* Name of creating host            :    ip
* Name of host OS                  :    Linux
* Created by user                  :    user
* Archived on                      :    2023-04-12 09:47:01
* dicomSummary version             :    1
* dicomTar version                 :    1
* md5sum for DICOM tarball         :    e6ca5d1b495a2ae3c88a33291ab3ec46  ImagingUpload-9-46-wPzJP8.tar
* md5sum for DICOM tarball gzipped :    456bfef47a592f9729a71b65bb4b0f4c  ImagingUpload-9-46-wPzJP8.tar.gz
* md5sum for complete archive      :    bd51f19d7766200ddd857f11cebe29e5  DCM_2016-08-17_ImagingUpload-9-46-wPzJP8.tar

Adding archive info into database

Removing temporary files from target location


Done adding archive info into database

\/opt\/Loris\-MRI\/bin\/mri/uploadNeuroDB/tarchiveLoader.pl -profile prod \/data\/Loris\-MRI\/data\/tarchive\/DCM_2016\-08\-17_ImagingUpload\-9\-46\-wPzJP8\.tar -uploadID 132 -verbose 
 md5sum /data/Loris-MRI/data/tarchive/DCM_2016-08-17_ImagingUpload-9-46-wPzJP8.tar
PSCID is: DCC090
 CandID id: 587630
 visit_label is: V1
DBD::mysql::db do failed: Field 'RegistrationProjectID' doesn't have a default value at /opt/Loris-MRI/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1026.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
	PREPARE s FROM 'INSERT INTO mri_scanner (Manufacturer,Software,Serial_number,CandID,Model) VALUES (?,?,?,?,?)';
	SET @x1='SIEMENS',@x2='syngo MR B17',@x3='35014',@x4='601025',@x5='TrioTim';
	EXECUTE s USING @x1,@x2,@x3,@x4,@x5;
Error obtained:Cannot add or update a child row: a foreign key constraint fails (`db`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)

 ERROR: The validation has failed. Either re-run the validation again and fix the problem. Or re-run tarchiveLoader.pl using -force to force the execution.

What did you expect to happen?

The script should not be blocked with a default_project in configuration.

[laemtl]

Fixed by aces/Loris-MRI#914