22 Nov 2021 14:33:48,513 INFO : Copying experiment "Uncovering Xenobiotics in the Dark Metabolome using Ion Mobility Spectrometry, Mass Defect Analysis and Machine Learning" from folder /NCSU - Baker Lab/PFAS Library to /Panorama Public/2021/NCSU Baker Lab - PFAS Library
22 Nov 2021 14:33:48,513 INFO : =======================================
22 Nov 2021 14:33:48,567 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
22 Nov 2021 14:33:48,567 INFO :
22 Nov 2021 14:33:48,567 INFO : Exporting experiment.
22 Nov 2021 14:33:48,858 INFO :
22 Nov 2021 14:33:48,858 INFO : Experiment export completed successfully.
22 Nov 2021 14:33:48,858 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
22 Nov 2021 14:33:48,890 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
22 Nov 2021 14:33:48,890 INFO :
22 Nov 2021 14:33:48,890 INFO : Importing experiment.
22 Nov 2021 14:33:48,895 INFO : Loading folder properties (folder type, settings and active modules)
22 Nov 2021 14:33:48,982 INFO : Done importing folder properties (folder type, settings and active modules)
22 Nov 2021 14:33:48,985 INFO : Loading etl definitions
22 Nov 2021 14:33:48,987 INFO : Loading wikis
22 Nov 2021 14:33:48,990 INFO : 0 wikis imported
22 Nov 2021 14:33:48,990 INFO : Done importing wikis
22 Nov 2021 14:33:48,990 INFO : Starting to copy files
22 Nov 2021 14:33:49,000 INFO : Copied 13 files
22 Nov 2021 14:33:49,000 INFO : Ensuring exp.data rows exist for imported files
22 Nov 2021 14:33:49,094 INFO : Starting Sample Type and Data Class import
22 Nov 2021 14:33:49,094 INFO : No types XAR file to process.
22 Nov 2021 14:33:49,094 INFO : Finished importing Sample Types and Data Classes
22 Nov 2021 14:33:49,096 INFO : Loading xar
22 Nov 2021 14:33:49,110 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9350:TargetedMS.ImportSkyZip'
22 Nov 2021 14:33:49,112 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9350:TargetedMS.ImportSkyZip.Core'
22 Nov 2021 14:33:49,114 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9350:TargetedMS.ImportSkyZip.Output'
22 Nov 2021 14:33:49,114 DEBUG: Protocol import complete
22 Nov 2021 14:33:49,116 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-9350:Uncovering+Xenobiotics+in+the+Dark+Metabolome+using+Ion+Mobility+Spectrometry%2C+Mass+Defect+Analysis+and+Machine+Learning'
22 Nov 2021 14:33:49,116 DEBUG: Experiment/Run group import complete
22 Nov 2021 14:33:49,126 DEBUG: Protocol action set import complete
22 Nov 2021 14:33:49,136 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9350:TargetedMS.ImportSkyZip'
22 Nov 2021 14:33:49,146 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-9350:8cafe768-2df5-103a-bfdd-fea6ddf55ce4'
22 Nov 2021 14:33:49,146 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9350:TargetedMS.ImportSkyZip.Core'
22 Nov 2021 14:33:49,148 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9350:TargetedMS.ImportSkyZip.Output'
22 Nov 2021 14:33:49,149 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-9350:8cafe7ca-2df5-103a-bfdd-fea6ddf55ce4'
22 Nov 2021 14:33:49,150 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/NCSU%20Baker%20Lab%20-%20PFAS%20Library_80f7d9e7-2e10-103a-bfdd-fea6ddf55ce4/_temp__2021-11-22_14-33-47/export/xar/experiments_and_runs.xar.exploded/Run122313/PFAS%20Library_2021-11-22_14-16-54.sky.zip into the system
22 Nov 2021 14:33:49,152 INFO : Starting import from PFAS Library_2021-11-22_14-16-54.sky.zip
22 Nov 2021 14:33:49,155 INFO : Starting to import Skyline document from PFAS Library_2021-11-22_14-16-54.sky.zip
22 Nov 2021 14:33:49,156 INFO : Expanding PFAS Library.sky.view
22 Nov 2021 14:33:49,157 INFO : Expanding PFAS Library.sky
22 Nov 2021 14:33:49,157 INFO : Expanding PFAS Library.skyl
22 Nov 2021 14:33:49,159 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.22
22 Nov 2021 14:33:49,164 INFO : 4% Done
22 Nov 2021 14:33:49,164 WARN : Unable to find file /data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/NCSU Baker Lab - PFAS Library_80f7d9e7-2e10-103a-bfdd-fea6ddf55ce4/_temp__2021-11-22_14-33-47/export/xar/experiments_and_runs.xar.exploded/Run122313/PFAS Library_2021-11-22_14-16-54/PFAS Library.skyd, unable to import chromatograms
22 Nov 2021 14:33:49,194 INFO : Inserting PFAS (-) SIL
22 Nov 2021 14:33:49,202 INFO : 10% Done
22 Nov 2021 14:33:49,214 INFO : 14% Done
22 Nov 2021 14:33:49,223 INFO : 19% Done
22 Nov 2021 14:33:49,226 DEBUG: Total molecules inserted: 14
22 Nov 2021 14:33:49,227 INFO : Inserting PFAS (-) PFCA
22 Nov 2021 14:33:49,232 INFO : 24% Done
22 Nov 2021 14:33:49,242 INFO : 28% Done
22 Nov 2021 14:33:49,254 INFO : 32% Done
22 Nov 2021 14:33:49,262 INFO : 37% Done
22 Nov 2021 14:33:49,272 INFO : 42% Done
22 Nov 2021 14:33:49,276 DEBUG: Total molecules inserted: 17
22 Nov 2021 14:33:49,277 INFO : Inserting PFAS (-) PFSA
22 Nov 2021 14:33:49,283 INFO : 47% Done
22 Nov 2021 14:33:49,292 INFO : 51% Done
22 Nov 2021 14:33:49,297 DEBUG: Total molecules inserted: 11
22 Nov 2021 14:33:49,298 INFO : Inserting PFAS (-) FT
22 Nov 2021 14:33:49,300 INFO : 56% Done
22 Nov 2021 14:33:49,307 DEBUG: Total molecules inserted: 5
22 Nov 2021 14:33:49,307 INFO : Inserting PFAS (-) PFECA
22 Nov 2021 14:33:49,309 INFO : 61% Done
22 Nov 2021 14:33:49,317 INFO : 66% Done
22 Nov 2021 14:33:49,325 DEBUG: Total molecules inserted: 10
22 Nov 2021 14:33:49,325 INFO : Inserting PFAS (-) PFESA
22 Nov 2021 14:33:49,327 INFO : 70% Done
22 Nov 2021 14:33:49,335 INFO : 74% Done
22 Nov 2021 14:33:49,342 DEBUG: Total molecules inserted: 9
22 Nov 2021 14:33:49,344 INFO : 79% Done
22 Nov 2021 14:33:49,344 INFO : Inserting PFAS (-) PFASA
22 Nov 2021 14:33:49,350 INFO : 84% Done
22 Nov 2021 14:33:49,356 INFO : 89% Done
22 Nov 2021 14:33:49,360 DEBUG: Total molecules inserted: 11
22 Nov 2021 14:33:49,360 INFO : Inserting PFAS (-) PFP
22 Nov 2021 14:33:49,363 INFO : 93% Done
22 Nov 2021 14:33:49,371 INFO : 98% Done
22 Nov 2021 14:33:49,377 DEBUG: Total molecules inserted: 12
22 Nov 2021 14:33:49,377 INFO : Done parsing Skyline document.
22 Nov 2021 14:33:49,404 INFO : Creating and populating temp tables for Proportion values
22 Nov 2021 14:33:49,410 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
22 Nov 2021 14:33:49,410 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
22 Nov 2021 14:33:49,411 INFO : Cleaning up temp tables
22 Nov 2021 14:33:49,412 INFO : Completed import of Skyline document from PFAS Library_2021-11-22_14-16-54.sky.zip
22 Nov 2021 14:33:49,414 INFO : 100% Done
22 Nov 2021 14:33:49,417 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/NCSU%20Baker%20Lab%20-%20PFAS%20Library_80f7d9e7-2e10-103a-bfdd-fea6ddf55ce4/_temp__2021-11-22_14-33-47/export/xar/experiments_and_runs.xar.exploded/Run122313/PFAS%20Library_2021-11-22_14-16-54.sky.zip into the system
22 Nov 2021 14:33:49,423 INFO : Done importing xar
22 Nov 2021 14:33:49,424 INFO : Loading pages and webpart properties
22 Nov 2021 14:33:49,533 INFO : Done importing pages and webpart properties
22 Nov 2021 14:33:49,533 INFO :
22 Nov 2021 14:33:49,533 INFO : Experiment import completed successfully.
22 Nov 2021 14:33:49,533 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
22 Nov 2021 14:33:49,559 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
22 Nov 2021 14:33:49,559 INFO :
22 Nov 2021 14:33:49,559 INFO : Finishing up experiment copy.
22 Nov 2021 14:33:49,560 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
22 Nov 2021 14:33:49,561 INFO : Assigning a DOI.
22 Nov 2021 14:33:51,628 INFO : Assigned DOI: 10.6069/kehx-qa53
22 Nov 2021 14:33:51,632 INFO : Updating access URL to point to the new copy of the data.
22 Nov 2021 14:33:51,637 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
22 Nov 2021 14:33:51,638 INFO : Removing copy permissions given to journal.
22 Nov 2021 14:33:51,648 INFO : Adding read permissions to all users that are folder admins in the source container.
22 Nov 2021 14:33:51,656 INFO : Setting the TargetedMS folder type to 'Experimental Data'
22 Nov 2021 14:33:51,658 INFO : Updating the 'Raw Data' tab configuration
22 Nov 2021 14:33:51,660 INFO : Updating dataFileUrls for run PFAS Library_2021-11-22_14-16-54.sky.zip; targetedms run ID 125490
22 Nov 2021 14:33:51,668 INFO : Targetedms run 125490 in container org.labkey.api.data.Container@251056904 /Panorama Public/2021/NCSU Baker Lab - PFAS Library/ 80f7d9e7-2e10-103a-bfdd-fea6ddf55ce4 does not have a skydDataId.
22 Nov 2021 14:33:51,668 INFO : Updating dataFileUrl...
22 Nov 2021 14:33:51,668 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/NCSU%20Baker%20Lab%20-%20PFAS%20Library_80f7d9e7-2e10-103a-bfdd-fea6ddf55ce4/_temp__2021-11-22_14-33-47/export/xar/experiments_and_runs.xar.exploded/Run122313/PFAS%20Library_2021-11-22_14-16-54.sky.zip
22 Nov 2021 14:33:51,668 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/NCSU%20Baker%20Lab%20-%20PFAS%20Library/@files/PFAS%20Library_2021-11-22_14-16-54.sky.zip
22 Nov 2021 14:33:51,673 INFO : Creating a reviewer account.
22 Nov 2021 14:33:51,905 INFO : Created reviewer with email: User panorama+reviewer79@proteinms.net
22 Nov 2021 14:33:51,913 INFO : Hiding the Data Pipeline tab.
22 Nov 2021 14:33:51,964 INFO : Emailing submitter.
22 Nov 2021 14:33:52,078 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'