Protein name too long for upload to Panorama

support
Protein name too long for upload to Panorama rj8  2022-07-14
 

I'm in the habit of using the Associate Proteins... feature of skyline, which correctly combines protein names that are grouped together. A problem seems to arise when I then upload the Skyline file to Panorama. Panorama seems to have an upper limit of 500 characters for a protein name, but when many proteins are grouped together I can get very large names (from large numbers of proteins in the same group). I can manually delete some of the characters to bring the size below 500, but maybe Panorama should set an upper limit of several thousand characters. Here's an example of the error message from within Panorama:

14 Jul 2022 11:46:18,743 ERROR: PreferredName: Value is too long for column 'PreferredName', a maximum length of 500 is allowed. The supplied value, 'A2AE18_MOUSE/tr|Q6PEE4|Q.../tr|L7N1Z0|L7N1Z0_MOUSE', was 1231 characters long.
org.labkey.api.pipeline.PipelineJobException: PreferredName: Value is too long for column 'PreferredName', a maximum length of 500 is allowed. The supplied value, 'A2AE18_MOUSE/tr|Q6PEE4|Q.../tr|L7N1Z0|L7N1Z0_MOUSE', was 1231 characters long.
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:275)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:841)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1077)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:577)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$CallerRunsPolicy.rejectedExecution(ThreadPoolExecutor.java:1486)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:391)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:865)
at org.mule.impl.work.ScheduleWorkExecutor.doExecute(ScheduleWorkExecutor.java:39)
at org.mule.impl.work.MuleWorkManager.executeWork(MuleWorkManager.java:277)
at org.mule.impl.work.MuleWorkManager.scheduleWork(MuleWorkManager.java:244)
at org.mule.impl.model.seda.SedaComponent.run(SedaComponent.java:483)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: org.labkey.api.query.RuntimeValidationException: PreferredName: Value is too long for column 'PreferredName', a maximum length of 500 is allowed. The supplied value, 'A2AE18_MOUSE/tr|Q6PEE4|Q.../tr|L7N1Z0|L7N1Z0_MOUSE', was 1231 characters long.
at org.labkey.api.data.Table.insert(Table.java:751)
at org.labkey.targetedms.SkylineDocImporter.insertPeptideGroup(SkylineDocImporter.java:1319)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:405)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:248)
... 23 more
Caused by: PreferredName: Value is too long for column 'PreferredName', a maximum length of 500 is allowed. The supplied value, 'A2AE18_MOUSE/tr|Q6PEE4|Q.../tr|L7N1Z0|L7N1Z0_MOUSE', was 1231 characters long.
at org.labkey.api.query.RuntimeValidationException.<init>(RuntimeValidationException.java:36)
... 27 more