[Loris-dev] Errors when using delete_imaging_upload.pl

[Ling Ma]

*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.
>>>
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