[Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
Olano.María
molano at ext.cnio.es
Thu Nov 17 10:24:22 EST 2022
Good afternoon!
We managed to solve the issue with the scanner_id by linking the CandID to the scanner
mysql> SELECT * FROM `mri_scanner`;
+----+--------------+---------+---------------+----------+--------+
| ID | Manufacturer | Model | Serial_number | Software | CandID |
+----+--------------+---------+---------------+----------+--------+
| 0 | NULL | NULL | NULL | NULL | NULL |
| 1 | SIEMENS | TrioTim | 35008 | Python | 359572 |
| 10 | NULL | NULL | NULL | NULL | NULL |
+----+--------------+---------+---------------+----------+--------+
And later got the upload_id error:
(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose
log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-11-48-F5qW5R.log.
ERROR: Invalid UploadID 1.
Managed to side step this error by using the front end Imaging Uploader which filled out the mri_upload table with the UploadID 1
mysql> SELECT * FROM `mri_upload`;
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
| UploadID | UploadedBy | UploadDate | UploadLocation | DecompressedLocation | InsertionComplete | Inserting | PatientName | number_of_mincInserted | number_of_mincCreated | TarchiveID | SessionID | IsCandidateInfoValidated | IsTarchiveValidated | IsPhantom |
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
| 1 | lorisadmin | 2022-11-17 14:40:58 | /data/incoming/lorisadmin/DCC0000_359572_V3.zip | | 0 | NULL | DCC0000_359572_V3 | NULL | NULL | NULL | 1 | NULL | 0 | N |
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
However! It didn't manage to upload correctly so we tried to use the back end again with imaging_non_minc_insertion.pl (as this isn't a DICOM file) and we are presented with our last error:
(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /data/incoming/lorisadmin/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose
log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-16-0-_g35H2.log.
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3.zip
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3.zip
=> No Visit label
ERROR: Candidate IDs mismatch for /data/incoming/lorisadmin/DCC0000_359572_V3.zip.
This Visit label has been populated in the MySQL visit table, so we don't know what mismatch it is referring to.
Any help would be much appreciated.
María
De: Olano.María
Enviado el: miércoles, 16 de noviembre de 2022 14:11
Para: 'loris-dev at bic.mni.mcgill.ca' <loris-dev at bic.mni.mcgill.ca>
Asunto: imaging_non_minc_insertion.pl issue with scanner_id
Good afternoon,
Hope this email finds you well. We are having problems using the imaging_non_minc_insertion.pl as when we execute the command this what pops up in the terminal.
(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 0 -coordin_space native -reckless -verbose
This script inserts a file in the files and parameter_file tables.
Usage: perl imaging_non_minc_insertion.pl [options]
-help for options
ERROR: missing -scanner_id argument
As you can see, scanner_id is included in the options accompanying the command, but when changing the ID from 0 to 10 it does recognize scanner_id, shown as followed:
(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 10 -coordin_space native -reckless -verbose
log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-12-49-8uubDY.log.
ERROR: Invalid ScannerID 10.
Both IDs are in the MYSQL table "mri_scanner" so we don't know what the problem could be.
mysql> SELECT * FROM `mri_scanner`;
+----+--------------+-------+---------------+----------+--------+
| ID | Manufacturer | Model | Serial_number | Software | CandID |
+----+--------------+-------+---------------+----------+--------+
| 0 | NULL | NULL | NULL | NULL | NULL |
| 10 | NULL | NULL | NULL | NULL | NULL |
+----+--------------+-------+---------------+----------+--------+
Any help would be much appreciated.
Best regards,
María
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