Panorama error with Skyline daily document

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Panorama error with Skyline daily document Chris Ashwood  2020-05-14
 

Hi all,

I hope you are well. I have been encountering a reproducible error lately, working on a Skyline document that uses the new log iRT feature. There are other niche features used including a spectral library of 500 molecules. The document itself is sensitive and sizeable (95 MB) but I can share it privately. Please find the Panorama warnings/errors below:

14 May 2020 20:23:29,961 WARN : The version of this Skyline document is 20.11. This is newer than the highest supported version 4.
14 May 2020 20:24:06,450 INFO : 98% Done

14 May 2020 20:24:06,677 INFO : Done parsing Skyline document.

14 May 2020 20:24:10,809 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'

14 May 2020 20:24:10,812 ERROR: SqlExecutor.execute(); uncategorized SQLException for SQL []; SQL state [25P02]; error code [0]; ERROR: current transaction is aborted, commands ignored until end of transaction block; nested exception is org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block

Caused by: org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block

Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "uix_auditlogentry_document"

Detail: Key (documentguid, entryhash)=(577e6540-bd2e-4a40-85dd-c009a80ba168, VeCVOeCev0LQhxtTovC3nshjfOY=) already exists.

14 May 2020 20:24:10,853 ERROR: SqlExecutor.execute(); uncategorized SQLException for SQL []; SQL state [25P02]; error code [0]; ERROR: current transaction is aborted, commands ignored until end of transaction block; nested exception is org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block

org.springframework.jdbc.UncategorizedSQLException: SqlExecutor.execute(); uncategorized SQLException for SQL []; SQL state [25P02]; error code [0]; ERROR: current transaction is aborted, commands ignored until end of transaction block; nested exception is org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block

Caused by: org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block

Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "uix_auditlogentry_document"

Detail: Key (documentguid, entryhash)=(577e6540-bd2e-4a40-85dd-c009a80ba168, VeCVOeCev0LQhxtTovC3nshjfOY=) already exists.

Cheers,
Chris

 
 
Nick Shulman responded:  2020-05-14
The error is: duplicate key value violates unique constraint "uix_auditlogentry_document"

We have seen that error before. It can happen if your audit log contains two identical entries, which can happen if an external tool (or, conceivably, a really fast human) made multiple identical changes to the Skyline document in less than a second.

If it does not seem plausible that multiple edits were made to your document in less than a second, then you can email us your .sky.zip file (or let us know where it is on Panorama) and we can take a look.

You can work around this bug by deleting your .skyl (Skyline log) file, but that will remove all of the audit log information from your document.

Here's the Panorama support request where someone reported this same issue, but it does not have any useful information on it because it was all resolved in email.
https://panoramaweb.org/home/support/announcements-thread.view?rowId=4170

-- Nick
 
Chris Ashwood responded:  2020-05-14
Thanks Nick!

Does this mean that any external tool that runs multiple commands needs to have a 1 second wait between identical changes?

I had deleted the .skyl file which fixed most issues but now I get a new error, please find the error and link to the files below:
https://panoramaweb.org/U%20of%20Nebraska%20Medical%20Center%20-%20Gundry%20Lab/N-Glycan%20Catalog%20%28N-GlyCat%29/pipeline-status-details.view?rowId=87023

14 May 2020 21:34:06,598 WARN : The version of this Skyline document is 20.11. This is newer than the highest supported version 4.1
14 May 2020 21:34:34,995 INFO : Done parsing Skyline document.

14 May 2020 21:34:35,576 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'

14 May 2020 21:34:35,579 ERROR: Index 0 out of bounds for length 0

14 May 2020 21:34:35,726 ERROR: Index 0 out of bounds for length 0

java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0

Cheers,
Chris
 
Vagisha responded:  2020-05-15
Hi Chris,

The IndexOutOfBoundsException error happens if the document has an audit log with zero entries in it. If you expand the log by clicking the "Show Full Log File" link you will be able to see that the source of the error is in the code that is saving the audit log. Here is the related bug report:
https://www.labkey.org/home/Developer/issues/issues-details.view?issueId=39455

Until this bug is fixed, one way to get this document to upload to Panorama is to disable audit logging. To do this open the audit log (View > Other Grids > Audit Log). You should see a checkbox for "Enable audit logging" in the top right corner of the window. If you are not seeing the checkbox make the window bigger or click the little triangle icon in the top right corner to see the checkbox. Uncheck this box. You will see a warning dialog with a message like "This will clear the audit log and delete it permanently.....". Click "Yes" and save the document.

You should enable audit logging again after the document is uploaded to Panorama.

Thanks,
Vagisha