[Loris-dev] Errors when using delete_imaging_upload.pl

[Cecile Madjar]

Hi Alfredo,

See answers below in blue.

Error type 1:
> ===
> Error! File /ABC/data/pic/979907/IPMSA_979907_m00_NA_001_182_check.jpg
> exists in the database but was not found on the file system.
> Aborting.
> ===
>
> Error type 2:
> ===
> Error! File
> /ABC/data/assembly/677803/m12/mri/native/IPMSA_677803_m12_NA_002.nii exists
> in the database but was not found on the file system.
> Aborting.
> ===
>

The first two errors are the same. The delete script always checks first if
the file is on the filesystem. My guess is that when you ran the pipeline,
the path to the NIfTI file was inserted into the database even when the
NIfTI file was not created due to some mnc2nii conversion errors (known bug
that was fixed in release 22.0). You can use the option -ignore to ignore
the check between database and file system.


>
> Error type 3:
> ===
> /ABC/data/pic/819059/IPMSA_819059_m12_NA_006_3098_check.jpg
> /ABC/data/pic/819059/IPMSA_819059_m12_NA_007_3099_check.jpg
> /ABC/data/pic/819059/IPMSA_819059_m12_NA_008_3100_check.jpg
> /ABCdata/pic/819059/IPMSA_819059_m12_NA_009_3101_check.jpg
> /ABC/data/pic/819059/IPMSA_819059_m12_t1_001_3091_check.jpg
> /ABC/data/pic/819059/IPMSA_819059_m12_t1_002_3092_check.jpg
> /ABC/data/tarchive/2009/DCM_2009-12-10_ImagingUpload-7-57-r0hk9h.tar
>
> DBD::mysql::db do failed: Cannot delete or update a parent row: a foreign
> key constraint fails (`IPMSA_LORIS`.`mri_upload`, CONSTRAINT
> `FK_mriupload_TarchiveID` FOREIGN KEY (`TarchiveID`) REFERENCES `tarchive`
> (`TarchiveID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/tools//
> delete_imaging_upload.pl line 1612.
> Issuing rollback() due to DESTROY without explicit disconnect() of
> DBD::mysql::db handle database=IPMSA_LORIS;host=132.216.133.50;port=3306;
> at /data_/ipmsa/loris_data/IPMSA/bin/mri/tools//delete_imaging_upload.pl
> line 1612.
> ===
>

Not sure what is going on here. Could you point me to the file so I can
check where the issue comes from? Or the release version you are using. Are
there any processed output data for that upload ID?


>
> Error type 4:
> ===
> Cannot delete upload 1543: the MRI pipeline is currently processing it.
> ===
>

If you are sure you are not running the pipeline, you will need to update
the mri_upload table to reflect this. For some obscure reason, the
insertion status fields of the mri_upload table were not updated for that
UploadID. Maybe the pipeline got interrupted?
UPDATE mri_upload SET Inserting=0, InsertionComplete=1 WHERE UploadID=1543;
Then, rerun the delete script on that UploadID.

Hope this helps. Best,

Cécile


> Looking forward to hearing from you.
>
> Regards,
> Alfredo.
>
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