Issue 720: Upload to Panorama fails when There are custom annotations for the Transitions

issues
Status:resolved
Assigned To:Brendan MacLean
Type:Defect
Area:Skyline
Priority:3
Milestone: 
Opened:2020-03-23 by hogan
Changed:2020-03-26 by Josh Eckels
Resolved:2020-03-26 by Josh Eckels
Resolution:Fixed
Closed:
2020-03-23 hogan
Title»Upload to Panorama fails when There are custom annotations for the Transitions
Assigned ToGuest»Brendan MacLean
Type»Defect
Area»Skyline
Priority»3
I have localized an error specifically to the custom annotation on a transition.

If there is any data filled in for the custom annotations of a transition the file will not upload to panorama correctly and I get the following error message:

23 Mar 2020 12:22:03,602 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
23 Mar 2020 12:22:03,612 INFO : Starting to import Skyline document from Panorama_Test_2020-03-23_12-20-46.sky.zip
23 Mar 2020 12:22:03,623 INFO : Expanding 20191028_Amyris_CenPK_DB.protdb
23 Mar 2020 12:22:04,997 INFO : Expanding Panorama_Test.skyd
23 Mar 2020 12:22:05,025 INFO : Expanding Panorama_Test.sky.view
23 Mar 2020 12:22:05,038 INFO : Expanding Panorama_Test.sky
23 Mar 2020 12:22:05,053 WARN : The version of this Skyline document is 20.1. This is newer than the highest supported version 4.1
23 Mar 2020 12:22:05,068 INFO : 80% Done
23 Mar 2020 12:22:05,122 INFO : Inserting Test
23 Mar 2020 12:22:05,238 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
23 Mar 2020 12:22:05,241 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: insert or update on table "transitionannotation" violates foreign key constraint "fk_transitionannotation_gtid"
  Detail: Key (transitionid)=(0) is not present in table "generaltransition".
23 Mar 2020 12:22:05,303 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import - Panorama_Test_2020-03-23_12-20-46.sky.zip
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: insert or update on table "transitionannotation" violates foreign key constraint "fk_transitionannotation_gtid"
  Detail: Key (transitionid)=(0) is not present in table "generaltransition".

If there is not information filled in at all for the custom annotations of a transition then the file uploads successfully.

Please see the attached document for screenshots.
 
 PanoramaUploadError.docx

2020-03-25 Josh Eckels
Notify»Josh Eckels
Hello,

Thanks for reporting and capturing your steps. I tried to reproduce the problem but couldn't recreate the error.

What version of Panorama and LabKey Server are you running? I notice that one of your annotations is using a list, which wasn't supported until newer versions of Panorama. We've just released version 20.3.0, which may resolve the problem (it's what I used for testing), though version 19.3 was when we first started supporting Skyline lists in Panorama.

https://www.labkey.org/Documentation/wiki-page.view?name=releasenotes193

If you can share a copy of your document that reproduces the error I'm happy to test it out as well. Maybe there's a subtle difference in the one I created.

Thanks,
Josh

2020-03-26 Josh Eckels
resolve as Fixed
Statusopen»resolved