Issue uploading a Skyline Document to Panorama with a library file (.clib)

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Issue uploading a Skyline Document to Panorama with a library file (.clib) hogan  2020-06-18
 

Hello,

I have encountered an issue uploading a Skyline document to panorama that includes a .clib file. When I remove the .clib file using the peptide settings -> Library tab I am able to upload the file to panorama without issue. I would like to be able to include the .clib file in the document as the library dot product is data we would like to keep in the doc and it is not available if the library file is removed. Here is the error I receive from panorama when I attempt the upload. Thanks for your support!

18 Jun 2020 17:18:19,750 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
18 Jun 2020 17:18:19,762 INFO : Starting to import Skyline document from 20200615_H9407_1280777_1280778_2020-06-18_17-14-33.sky.zip
18 Jun 2020 17:18:19,772 INFO : Expanding Popeye Chromatogram Library 20min_rev7.clib
18 Jun 2020 17:18:19,876 INFO : Expanding 20200615_H9407_1280777_1280778.skyd
18 Jun 2020 17:18:21,030 INFO : Expanding 20200615_H9407_1280777_1280778.sky.view
18 Jun 2020 17:18:21,059 INFO : Expanding 20200615_H9407_1280777_1280778.sky
18 Jun 2020 17:18:21,367 WARN : The version of this Skyline document is 20.1. This is newer than the highest supported version 4.1
18 Jun 2020 17:18:21,390 INFO : 1% Done
18 Jun 2020 17:18:24,287 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
18 Jun 2020 17:18:24,314 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 "spectrumlibrary" violates foreign key constraint "fk_spectrumlibrary_librarysourceid"
Detail: Key (librarysourceid)=(0) is not present in table "librarysource".
18 Jun 2020 17:18:24,378 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import - 20200615_H9407_1280777_1280778_2020-06-18_17-14-33.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 "spectrumlibrary" violates foreign key constraint "fk_spectrumlibrary_librarysourceid"
Detail: Key (librarysourceid)=(0) is not present in table "librarysource".

 
 
Vagisha responded:  2020-06-18

Hi Kyle,

Are you trying to upload this document to PanoramaWeb (https://panoramaweb.org) or your own LabKey Server? We fixed this issue on PanoramaWeb sometime in April so it shouldn't be happening on that server. But if it is, please send me a link to your folder on PanoramaWeb. The fix should also be available in the latest release of LabKey Server 20.3. If you are running your own LabKey Server could you please upgrade?

Thanks,
Vagisha

 
hogan responded:  2020-06-22

Hello Vagisha,

I am attempting this in our own instance of the labkey server. I have reached out to the software team to request an upgrade of the server version to 20.3. I will update if that fixed the issue as soon as they are able to install the upgrade. Thank you for your prompt reply and clear instructions for fixing the issue.

Best,

Kyle