[Loris-dev] [IPMSA] MRI batch uploader cannot handle visits labels with "_"

[Morales Pinzon, Alfredo]

Dear LORIS-dev team,

In the IPMSA project for the first time we are using visit labels for the MRI visits including the character "_" in the visit label, for instance ADDTC_1. This however cannot be handle by the MRI batch uploader because it uses the first part the name as visit label, in the previous example it uses "ADDTC" which is not a valid visit label. I can help modifying the code where the split using "_" is used (if this is used) but need indications on where to do it.

Here is the log from the file log_batch_imageuploader_YYY12345_123456_ADDTC_1.txt (I modified the PSCID to be YYY12345, the CandidateId to be 123456, and the path to the project to the location of loris to /XXX/):


---------------------------------------------------------------------------------------
Running now the following command: /XXX/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 8299 /XXX/YYY12345_123456_ADDTC_1.tar.gz -verbose

/XXX/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-17-7-AkVEyo /XXX/data/tarchive -clobber -database -profile prod -verbose
 Source: /tmp/ImagingUpload-17-7-AkVEyo
Target: /XXX/data/tarchive

Testing for database connectivity.
Database is available.

You will archive the dir                : ImagingUpload-17-7-AkVEyo

You are creating a tar with the following command:
tar -cf /XXX/data/tarchive/ImagingUpload-17-7-AkVEyo.tar ImagingUpload-17-7-AkVEyo


getting md5sums and gzipping!!

* Taken from dir                   :    /tmp/ImagingUpload-17-7-AkVEyo
* Archive target location          :    /XXX/data/tarchive/DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar
* Name of creating host            :    132.206.178.78
* Name of host OS                  :    Linux
* Created by user                  :    lorisadmin
* Archived on                      :    2019-02-04 17:07:43
* dicomSummary version             :    1
* dicomTar version                 :    1
* md5sum for DICOM tarball         :    6ca6a6e5c3a77bb8a15dc1eeae3147a7  ImagingUpload-17-7-AkVEyo.tar
* md5sum for DICOM tarball gzipped :    eda7f62c570818aa0d96a73ded441345  ImagingUpload-17-7-AkVEyo.tar.gz
* md5sum for complete archive      :    79d919f5676aadeea91762a4a07c165e  DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar

Adding archive info into database

Removing temporary files from target location


Done adding archive info into database

/XXX/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod /XXX/data/tarchive/DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar -verbose
 md5sum /XXX/data/tarchive/DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar
PSCID is: YYY12345
 CandID id: 123456
 visit_label is: ADDTC
candidate id 123456

=> No Visit labelVisit label does not exist
Set newVisitNo = 5 and centerID = 316
PSCID is: YYY12345
 CandID id: 123456
 visit_label is: ADDTC

Number of MINC files that will be considered for inserting into the database: 5
---------------------------------------------------------------------------------------

Let me know if the issue is clear and if you need more information. We have more than 20 visit label with "_" in the name.

Best,
Alfredo.

P.S. We previously modified the name of the visit label to replace the character "-" with "_" because the API cannot handle "-" in the url.


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