09 Dec 2021 10:15:19,778 INFO : Copying experiment "Check of selected NTR peptide spectra by comparison with synthetic peptides" from folder /UGent - VIB09/Annelies_Bogaert to /Panorama Public/2021/UGent VIB09 - Annelies_Bogaert
09 Dec 2021 10:15:19,778 INFO : =======================================
09 Dec 2021 10:15:19,817 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask' at location 'webserver-high-priority'
09 Dec 2021 10:15:19,817 INFO : 
09 Dec 2021 10:15:19,817 INFO : Exporting experiment.
09 Dec 2021 10:16:57,287 INFO : 
09 Dec 2021 10:16:57,287 INFO : Experiment export completed successfully.
09 Dec 2021 10:16:57,287 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentExportTask'
09 Dec 2021 10:16:58,930 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask' at location 'webserver-high-priority'
09 Dec 2021 10:16:58,930 INFO : 
09 Dec 2021 10:16:58,930 INFO : Importing experiment.
09 Dec 2021 10:16:58,934 INFO : Loading folder properties (folder type, settings and active modules)
09 Dec 2021 10:16:59,010 INFO : Done importing folder properties (folder type, settings and active modules)
09 Dec 2021 10:16:59,013 INFO : Loading etl definitions
09 Dec 2021 10:16:59,015 INFO : Loading wikis
09 Dec 2021 10:16:59,017 INFO : 0 wikis imported
09 Dec 2021 10:16:59,017 INFO : Done importing wikis
09 Dec 2021 10:16:59,017 INFO : Starting to copy files
09 Dec 2021 10:18:33,946 INFO : Copied 15 files
09 Dec 2021 10:18:33,946 INFO : Ensuring exp.data rows exist for imported files
09 Dec 2021 10:18:34,046 INFO : Starting Sample Type and Data Class import
09 Dec 2021 10:18:34,046 INFO : No types XAR file to process.
09 Dec 2021 10:18:34,046 INFO : Finished importing Sample Types and Data Classes
09 Dec 2021 10:18:34,048 INFO : Loading xar
09 Dec 2021 10:18:34,272 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9410:TargetedMS.ImportSkyZip'
09 Dec 2021 10:18:34,274 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9410:TargetedMS.ImportSkyZip.Core'
09 Dec 2021 10:18:34,276 DEBUG: Finished loading Protocol with LSID 'urn:lsid:uw.edu:Protocol.Folder-9410:TargetedMS.ImportSkyZip.Output'
09 Dec 2021 10:18:34,276 DEBUG: Protocol import complete
09 Dec 2021 10:18:34,277 DEBUG: Finished loading Experiment with LSID 'urn:lsid:uw.edu:Experiment.Folder-9410:Check+of+selected+NTR+peptide+spectra+by+comparison+with+synthetic+peptides'
09 Dec 2021 10:18:34,277 DEBUG: Experiment/Run group import complete
09 Dec 2021 10:18:34,286 DEBUG: Protocol action set import complete
09 Dec 2021 10:18:34,297 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9410:TargetedMS.ImportSkyZip'
09 Dec 2021 10:18:34,303 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:skyd.Folder-9410:a2778df5-3a3a-103a-8339-fea6ddf5e014'
09 Dec 2021 10:18:34,307 DEBUG: Finished loading Data with LSID 'urn:lsid:uw.edu:UploadedFile.Folder-9410:a2778de6-3a3a-103a-8339-fea6ddf5e014'
09 Dec 2021 10:18:34,307 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9410:TargetedMS.ImportSkyZip.Core'
09 Dec 2021 10:18:34,310 DEBUG: Finished loading ProtocolApplication with LSID 'urn:lsid:uw.edu:Protocol.Folder-9410:TargetedMS.ImportSkyZip.Output'
09 Dec 2021 10:18:34,310 DEBUG: Finished loading ExperimentRun with LSID 'urn:lsid:uw.edu:Run.Folder-9410:a2778e14-3a3a-103a-8339-fea6ddf5e014'
09 Dec 2021 10:18:34,311 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UGent%20VIB09%20-%20Annelies_Bogaert_86fc2b3c-3b49-103a-8339-fea6ddf5e014/_temp__2021-12-09_10-15-19/export/xar/experiments_and_runs.xar.exploded/Run123443/Annelies_Ace-pep_panorama_2021-12-08_11-05-50/Annelies_Ace-pep_panorama.skyd into the system
09 Dec 2021 10:18:34,312 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UGent%20VIB09%20-%20Annelies_Bogaert_86fc2b3c-3b49-103a-8339-fea6ddf5e014/_temp__2021-12-09_10-15-19/export/xar/experiments_and_runs.xar.exploded/Run123443/Annelies_Ace-pep_panorama_2021-12-08_11-05-50/Annelies_Ace-pep_panorama.skyd into the system
09 Dec 2021 10:18:34,312 DEBUG: Trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UGent%20VIB09%20-%20Annelies_Bogaert_86fc2b3c-3b49-103a-8339-fea6ddf5e014/_temp__2021-12-09_10-15-19/export/xar/experiments_and_runs.xar.exploded/Run123443/Annelies_Ace-pep_panorama_2021-12-08_11-05-50.sky.zip into the system
09 Dec 2021 10:18:34,312 INFO : Starting import from Annelies_Ace-pep_panorama_2021-12-08_11-05-50.sky.zip
09 Dec 2021 10:18:34,315 INFO : Starting to import Skyline document from Annelies_Ace-pep_panorama_2021-12-08_11-05-50.sky.zip
09 Dec 2021 10:18:34,319 INFO : Expanding Annelies_Ace-pep_panorama.skyd
09 Dec 2021 10:18:34,442 INFO : Expanding Annelies_Ace-pep_panorama.sky.view
09 Dec 2021 10:18:34,442 INFO : Expanding Annelies_Ace-pep_panorama.sky
09 Dec 2021 10:18:34,447 WARN : The version of this Skyline document is 21.1. This is newer than the highest supported version 20.22
09 Dec 2021 10:18:34,452 INFO : 1% Done
09 Dec 2021 10:18:34,495 DEBUG: Starting to load chromatogram headers
09 Dec 2021 10:18:34,495 DEBUG: Done loading chromatogram headers
09 Dec 2021 10:18:34,555 INFO : 2% Done
09 Dec 2021 10:18:34,555 INFO : Inserting peptides1
09 Dec 2021 10:18:34,572 INFO : 15% Done
09 Dec 2021 10:18:34,648 INFO : 24% Done
09 Dec 2021 10:18:34,697 INFO : 29% Done
09 Dec 2021 10:18:34,727 INFO : 34% Done
09 Dec 2021 10:18:34,757 INFO : 40% Done
09 Dec 2021 10:18:34,789 INFO : 45% Done
09 Dec 2021 10:18:34,820 INFO : 51% Done
09 Dec 2021 10:18:34,853 INFO : 56% Done
09 Dec 2021 10:18:34,883 INFO : 61% Done
09 Dec 2021 10:18:34,914 INFO : 66% Done
09 Dec 2021 10:18:34,945 INFO : 72% Done
09 Dec 2021 10:18:34,976 INFO : 76% Done
09 Dec 2021 10:18:35,009 INFO : 82% Done
09 Dec 2021 10:18:35,044 INFO : 87% Done
09 Dec 2021 10:18:35,076 INFO : 93% Done
09 Dec 2021 10:18:35,106 INFO : 98% Done
09 Dec 2021 10:18:35,131 DEBUG: Total peptides inserted: 16
09 Dec 2021 10:18:35,132 INFO : Done parsing Skyline document.
09 Dec 2021 10:18:35,133 INFO : Creating and populating temp tables for Proportion values
09 Dec 2021 10:18:35,148 INFO : Setting PrecursorModifiedAreaProportion values on precursorchrominfo
09 Dec 2021 10:18:35,155 INFO : Setting ModifiedAreaProportion values on generalmoleculechrominfo
09 Dec 2021 10:18:35,160 INFO : Cleaning up temp tables
09 Dec 2021 10:18:35,389 INFO : Completed import of Skyline document from Annelies_Ace-pep_panorama_2021-12-08_11-05-50.sky.zip
09 Dec 2021 10:18:35,392 INFO : 100% Done
09 Dec 2021 10:18:35,396 DEBUG: Finished trying to load data file file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UGent%20VIB09%20-%20Annelies_Bogaert_86fc2b3c-3b49-103a-8339-fea6ddf5e014/_temp__2021-12-09_10-15-19/export/xar/experiments_and_runs.xar.exploded/Run123443/Annelies_Ace-pep_panorama_2021-12-08_11-05-50.sky.zip into the system
09 Dec 2021 10:18:35,402 INFO : Done importing xar
09 Dec 2021 10:18:35,404 INFO : Loading pages and webpart properties
09 Dec 2021 10:18:35,483 INFO : Done importing pages and webpart properties
09 Dec 2021 10:18:35,483 INFO : 
09 Dec 2021 10:18:35,483 INFO : Experiment import completed successfully.
09 Dec 2021 10:18:35,483 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.ExperimentImportTask'
09 Dec 2021 10:18:37,202 INFO : Starting to run task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask' at location 'webserver-high-priority'
09 Dec 2021 10:18:37,202 INFO : 
09 Dec 2021 10:18:37,202 INFO : Finishing up experiment copy.
09 Dec 2021 10:18:37,204 INFO : Creating a new TargetedMS experiment entry in panoramapublic.ExperimentAnnotations.
09 Dec 2021 10:18:37,205 INFO : Assigning a ProteomeXchange ID.
09 Dec 2021 10:18:37,479 INFO : Assigning a DOI.
09 Dec 2021 10:18:38,834 INFO : Assigned DOI: 10.6069/46ay-rw96
09 Dec 2021 10:18:38,837 INFO : Updating access URL to point to the new copy of the data.
09 Dec 2021 10:18:38,842 INFO : Setting the 'copied' timestamp and journalExperimentId on the JournalExperiment table.
09 Dec 2021 10:18:38,843 INFO : Removing copy permissions given to journal.
09 Dec 2021 10:18:38,855 INFO : Adding read permissions to all users that are folder admins in the source container.
09 Dec 2021 10:18:38,861 INFO : Setting the TargetedMS folder type to 'Experimental Data'
09 Dec 2021 10:18:38,867 INFO : Updating the 'Raw Data' tab configuration
09 Dec 2021 10:18:38,869 INFO : Updating dataFileUrls for run Annelies_Ace-pep_panorama_2021-12-08_11-05-50.sky.zip; targetedms run ID 126826
09 Dec 2021 10:18:38,869 INFO : Updating dataFileUrl...
09 Dec 2021 10:18:38,869 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UGent%20VIB09%20-%20Annelies_Bogaert_86fc2b3c-3b49-103a-8339-fea6ddf5e014/_temp__2021-12-09_10-15-19/export/xar/experiments_and_runs.xar.exploded/Run123443/Annelies_Ace-pep_panorama_2021-12-08_11-05-50/Annelies_Ace-pep_panorama.skyd
09 Dec 2021 10:18:38,869 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/UGent%20VIB09%20-%20Annelies_Bogaert/@files/Annelies_Ace-pep_panorama_2021-12-08_11-05-50/Annelies_Ace-pep_panorama.skyd
09 Dec 2021 10:18:38,870 INFO : Updating dataFileUrl...
09 Dec 2021 10:18:38,870 INFO : from: file:///data/apache-tomcat/instance/panoramaweb/temp/Pipeline_temp/UGent%20VIB09%20-%20Annelies_Bogaert_86fc2b3c-3b49-103a-8339-fea6ddf5e014/_temp__2021-12-09_10-15-19/export/xar/experiments_and_runs.xar.exploded/Run123443/Annelies_Ace-pep_panorama_2021-12-08_11-05-50.sky.zip
09 Dec 2021 10:18:38,870 INFO : to: file:///data/labkey/files/Panorama%20Public/2021/UGent%20VIB09%20-%20Annelies_Bogaert/@files/Annelies_Ace-pep_panorama_2021-12-08_11-05-50.sky.zip
09 Dec 2021 10:18:38,873 INFO : Creating a reviewer account.
09 Dec 2021 10:18:39,095 INFO : Created reviewer with email: User panorama+reviewer84@proteinms.net
09 Dec 2021 10:18:39,103 INFO : Hiding the Data Pipeline tab.
09 Dec 2021 10:18:39,166 INFO : Emailing submitter.
09 Dec 2021 10:18:39,269 INFO : Successfully completed task 'org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask'