[Loris-dev] Errors when using delete_imaging_upload.pl

[Nicolas Brossard]

Hi all,

Regarding the foreign key constraint fail error, my guess is that you have
two records in mri_uploads that are tied to the same archive and you are
trying to delete one of them. What I am saying is that you have two
uploads, say U1 and U2, which have the same tarchive ID, say A1. If you try
to delete U1, the script will try to delete everything associated to it,
including archive A1, which will fail because of the foreign key constraint
still tying U2 to A1. This is unfortunately a bug of the delete script.

You should be able to delete *all* the uploads that have the same tarchive
ID though, but you'd have to do it in the same script invocation. So back
to our example, you could delete U1 and U2 but you'd have to delete them at
the same time by supplying both upload IDs in a comma-separated list via
the -uploadID switch (see the perldoc for the delete script).

I hope this makes sense. Let me know if I you need more information.


Regards,
Nicolas



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.
>>
>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20200407/3451764e/attachment.html>