Batch upload and insertion of scans for projects not using the front-end imaging uploader

[MounaSafiHarab]

• This file is intended to mimic the bahviour of the front-end imaging uploader, but without having to upload scans, one file at a time
• It allows projects with candidates having a registered timepoint in the Loris database to upload multiple scans (see "Usage" section below) to populate the mri_upload table in the database and launch the insertion scripts, more specifically, launching imaging_upload_file.pl which in turns performs the execution of the following main steps:
  ** IsCandidateInfoValid
  ** dicomTar.pl
  ** tarchiveLoader which triggers minc_insertion.pl (mri_protocol checks), pic/jiv/nii files generation.
• This file is similar in functionality to batch_uploads_tarchive which performs the tarchiveLoader step on multiple files at once, but extends the functionality of batch_uploads_tarchive to include the 3 steps highlighted in the previous point
• Usage: Run it as follows form where the Loris-MRI code base is:

$ ./batch_uploads_imageuploader -profile prod < imageuploader_list >log_batch_imageuploader.txt 2>&1

where imageuploader_list is a text file that has one scan details per line (example for 2 entries shown below); and each line (for each scan) consists of space delimited 1) the full path to the DICOM zipped scan, 2) Y or N depending on whether the scan is for a phantom or not, and 3) patient name following the PSCID_CandID_VisitLabel Loris convention for real candidates and left BLANK for phantoms

An example of uploading 2 entries/scans to be uploaded:
/data/incoming/PSC0001_123456_V1.tar.gz N PSC0001_123456_V1
/data/incoming/Lego_Phantom_MNI_20140101.zip Y

[christinerogers]

@MounaSafiHarab This looks like a major change for existing projects, and information that should be easily available to New projects as well.
Let's create/add tag "add to documentation" as it should definitely go in the wiki as well.

[MounaSafiHarab]

@christinerogers

This is a new feature that should not impact at all existing projects. imaging_upload_file.pl should run for existing projects without any change (the extra options added to the script are not required for existing projects, and are needed for those using batch_uploads_imageuploader which is a new script).

Bye yes, it should be documented and tested more thoroughly.

[gluneau]

@MounaSafiHarab, please add -profile prod option to the example on how to run this tool.

[MounaSafiHarab]

@gluneau,

thanks for the catch!

[gluneau]

@MounaSafiHarab If you modify your logic for this line to:

if (($phantom eq '') || (($phantom ne 'N') && ($phantom ne 'Y')))

the phantoms will get inserted.