[Loris-dev] Errors when using delete_imaging_upload.pl

[Ling Ma]

Hi Alfredo and Cecile,

Sorry for the erroneous information provided, I just checked, the program
execution order seems to be correct, the order should be first to delete
from image_upload, then tarchive table record. You need to check data to
see what happened, possibly the first deletion was not successful in
image_upload then the second deletion attempt broke out.

Ling Ma

On Mon, Apr 6, 2020 at 6:14 PM Ling Ma <lingyun.ma at mcin.ca> wrote:

> *tarchive*, not archive, the email automatically corrected my writing.
>
> On Mon, Apr 6, 2020 at 6:09 PM Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>> 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.
>>>>
>>>> _______________________________________________
>>>> 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/20200406/991f239c/attachment-0001.html>