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Batch upload and insertion of scans for projects not using the front-end imaging uploader #133
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@MounaSafiHarab This looks like a major change for existing projects, and information that should be easily available to New projects as well. |
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. |
@MounaSafiHarab, please add -profile prod option to the example on how to run this tool. |
thanks for the catch! |
"matches the file name $base in $path\n"; | ||
exit(2); | ||
} | ||
if (($phantom eq '') || ($phantom ne 'N') || ($phantom eq 'Y')) { |
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@MounaSafiHarab If you modify your logic for this line to:
if (($phantom eq '') || (($phantom ne 'N') && ($phantom ne 'Y')))
the phantoms will get inserted.
…ntries, and leaving imaging_upload_file.pl untouched
** IsCandidateInfoValid
** dicomTar.pl
** tarchiveLoader which triggers minc_insertion.pl (mri_protocol checks), pic/jiv/nii files generation.
$ ./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