[Loris-dev] Errors when using delete_imaging_upload.pl

[Ling Ma]

Hi Alfredo and Cecile

The third question comes most likely from the fact the
delete_imaging_upload.pl tries to delete from image_upload table, which
references some record in the archive table. You need to check the related
record in your DB to see what that record was referring to, then delete the
record from archive if you are sure what you are doing. Possibly this is a
bug of the delete_imaging_upload.pl, also possibly this bug has been fixed
in the more recent version. Cecile knows more about that.

Best regards,
Ling Ma

On Mon, Apr 6, 2020 at 6:02 PM Cecile Madjar <cecile.madjar at mcin.ca> wrote:

> 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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