2016-07-27 11:57:17,476 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.features.repos.cfg 2016-07-27 11:57:17,482 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.org.apache.karaf.security.jmx.cfg 2016-07-27 11:57:17,489 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.config.cfg 2016-07-27 11:57:17,493 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.java.lang.Memory.cfg 2016-07-27 11:57:17,497 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.bundle.cfg 2016-07-27 11:57:17,506 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.ops4j.pax.url.mvn.cfg 2016-07-27 11:57:17,511 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.kar.cfg 2016-07-27 11:57:17,515 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.management.cfg 2016-07-27 11:57:17,522 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.cfg 2016-07-27 11:57:17,527 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.jaas.cfg 2016-07-27 11:57:17,532 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.scope_bundle.cfg 2016-07-27 11:57:17,535 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.system.cfg 2016-07-27 11:57:17,540 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.jaas.cfg 2016-07-27 11:57:17,547 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.feature.cfg 2016-07-27 11:57:17,557 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.features.cfg 2016-07-27 11:57:19,213 [FelixStartLevel] WARN org.apache.karaf.features.internal.FeatureValidationUtil - Old style feature file without namespace found (URI: mvn:org.cytoscape.distribution/features/3.4.0/xml/features). This format is deprecated and support for it will soon be removed 2016-07-27 11:57:19,296 [FelixStartLevel] INFO org.apache.karaf.features.internal.FeaturesServiceImpl - Installing feature standard 3.0.3 2016-07-27 11:57:19,428 [FelixStartLevel] INFO org.apache.karaf.features.internal.FeaturesServiceImpl - Installing feature cytoscape-gui 3.4.0 2016-07-27 11:57:20,620 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.features.command is waiting for namespace handlers [http://karaf.apache.org/xmlns/shell/v1.1.0] 2016-07-27 11:57:20,743 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.feature into service ACL configs [org.apache.karaf.service.acl.command.feature.uninstall, org.apache.karaf.service.acl.command.feature.install] 2016-07-27 11:57:20,756 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.jaas into service ACL configs [org.apache.karaf.service.acl.command.jaas.update] 2016-07-27 11:57:20,762 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.config into service ACL configs [org.apache.karaf.service.acl.command.config.property-append, org.apache.karaf.service.acl.command.config.property-delete, org.apache.karaf.service.acl.command.config.property-set, org.apache.karaf.service.acl.command.config.edit, org.apache.karaf.service.acl.command.config.update, org.apache.karaf.service.acl.command.config.cancel, org.apache.karaf.service.acl.command.config.delete] 2016-07-27 11:57:20,786 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.shell into service ACL configs [org.apache.karaf.service.acl.command.shell.java, org.apache.karaf.service.acl.command.shell.new, org.apache.karaf.service.acl.command.shell.edit, org.apache.karaf.service.acl.command.shell.exec] 2016-07-27 11:57:20,802 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.system into service ACL configs [org.apache.karaf.service.acl.command.system.property, org.apache.karaf.service.acl.command.system.shutdown, org.apache.karaf.service.acl.command.system.start-level] 2016-07-27 11:57:20,812 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.scope_bundle into service ACL configs [org.apache.karaf.service.acl.command.scope_bundle.shell, org.apache.karaf.service.acl.command.scope_bundle.packages, org.apache.karaf.service.acl.command.scope_bundle.admin, org.apache.karaf.service.acl.command.scope_bundle.ssh, org.apache.karaf.service.acl.command.scope_bundle.osgi, org.apache.karaf.service.acl.command.scope_bundle.config, org.apache.karaf.service.acl.command.scope_bundle.jaas, org.apache.karaf.service.acl.command.scope_bundle.features, org.apache.karaf.service.acl.command.scope_bundle.log] 2016-07-27 11:57:20,834 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.kar into service ACL configs [org.apache.karaf.service.acl.command.kar.uninstall, org.apache.karaf.service.acl.command.kar.install] 2016-07-27 11:57:20,842 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.bundle into service ACL configs [org.apache.karaf.service.acl.command.bundle.watch, org.apache.karaf.service.acl.command.bundle.update, org.apache.karaf.service.acl.command.bundle.install, org.apache.karaf.service.acl.command.bundle.uninstall, org.apache.karaf.service.acl.command.bundle.refresh, org.apache.karaf.service.acl.command.bundle.restart, org.apache.karaf.service.acl.command.bundle.stop, org.apache.karaf.service.acl.command.bundle.start] 2016-07-27 11:57:20,955 [Blueprint Extender: 1] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.features.command is waiting for dependencies [(objectClass=org.apache.karaf.features.FeaturesService)] 2016-07-27 11:57:20,967 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.jaas.modules is waiting for namespace handlers [http://karaf.apache.org/xmlns/jaas/v1.0.0] 2016-07-27 11:57:21,094 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.instance.command is waiting for dependencies [(objectClass=org.apache.karaf.features.FeaturesService)] 2016-07-27 11:57:23,439 [FelixStartLevel] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default 2016-07-27 11:57:23,458 [FelixStartLevel] INFO org.cytoscape.application.internal.CyApplicationConfigurationImpl - Setting file directory = /Users/johannavillen/CytoscapeConfiguration 2016-07-27 11:57:23,500 [FelixStartLevel] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'groupSettings.props' in jar. 2016-07-27 11:57:24,029 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Custom Graphics Image property file loaded from: /Users/johannavillen/CytoscapeConfiguration/images3 2016-07-27 11:57:24,029 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Image loading process finished in 0.003 sec. 2016-07-27 11:57:24,029 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Currently, -1 images are available. 2016-07-27 11:57:24,194 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Image saving process finished in 0.168 sec. 2016-07-27 11:57:24,663 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,664 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,665 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,666 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,666 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,667 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,667 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,668 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,668 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,669 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,669 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,670 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,672 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,673 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:24,674 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:25,915 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.grid.props' in jar. 2016-07-27 11:57:27,214 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@1b6b2b62,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Copy Style...] with gravity: 2.0 2016-07-27 11:57:27,215 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu separator with gravity: 5.9999 2016-07-27 11:57:27,215 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@1b6b2b62,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create Legend...] with gravity: 6.0 2016-07-27 11:57:27,216 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@1b6b2b62,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create New Style...] with gravity: 1.0 2016-07-27 11:57:27,217 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@1b6b2b62,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Rename Style...] with gravity: 3.0 2016-07-27 11:57:27,218 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu separator with gravity: 4.9999 2016-07-27 11:57:27,219 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@1b6b2b62,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Make Current Styles Default] with gravity: 5.0 2016-07-27 11:57:27,219 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@1b6b2b62,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Remove Style] with gravity: 4.0 2016-07-27 11:57:27,468 [FelixStartLevel] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ private tables created: ID = 2 2016-07-27 11:57:27,468 [FelixStartLevel] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ private tables created: Base Graph ID = 18 2016-07-27 11:57:27,889 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.hierarchical.props' in jar. 2016-07-27 11:57:27,893 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.circular.props' in jar. 2016-07-27 11:57:27,898 [pool-7-thread-3] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.attribute-circle.props' in jar. 2016-07-27 11:57:27,902 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.stacked-node-layout.props' in jar. 2016-07-27 11:57:27,906 [pool-7-thread-3] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.attributes-layout.props' in jar. 2016-07-27 11:57:27,909 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.degree-circle.props' in jar. 2016-07-27 11:57:27,926 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.isom.props' in jar. 2016-07-27 11:57:27,927 [pool-7-thread-3] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.kamada-kawai.props' in jar. 2016-07-27 11:57:27,932 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.fruchterman-rheingold.props' in jar. 2016-07-27 11:57:28,150 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.force-directed.props' in jar. 2016-07-27 11:57:28,797 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:28,992 [pool-8-thread-1] INFO org.cytoscape.app.internal.net.server.CyHttpdImpl - Server socket started on 127.0.0.1:2607 2016-07-27 11:57:29,155 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: DEGREE 2016-07-27 11:57:29,155 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: INDEGREE 2016-07-27 11:57:29,156 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: OUTDEGREE 2016-07-27 11:57:29,156 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: SOURCEID 2016-07-27 11:57:29,156 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: TARGETID 2016-07-27 11:57:30,332 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = BioPAX 2016-07-27 11:57:30,332 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: BioPAX 2016-07-27 11:57:30,332 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 2 2016-07-27 11:57:30,409 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = BioPAX_SIF 2016-07-27 11:57:30,409 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: BioPAX_SIF 2016-07-27 11:57:30,409 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 3 2016-07-27 11:57:30,656 [pool-9-thread-1] INFO org.cytoscape.webservice.internal.ui.WebServiceImportDialog - New network import client registered: Universal Interaction Database Client 2016-07-27 11:57:30,670 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:30,670 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:30,726 [pool-9-thread-1] INFO org.cytoscape.webservice.internal.ui.WebServiceImportDialog - New network import client registered: BioMart Client 2016-07-27 11:57:30,870 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:30,871 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 11:57:30,872 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 11:57:30,873 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 11:57:30,873 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 11:57:31,599 [pool-9-thread-1] INFO org.cytoscape.rest.internal.CyActivator - Initializing cyREST API server... 2016-07-27 11:57:31,603 [pool-9-thread-1] INFO org.cytoscape.rest.internal.CyActivator - cyREST dependency import took: 1 msec. 2016-07-27 11:57:31,648 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Arabidopsis_thaliana_Columbia-3.4.129.mitab 2016-07-27 11:57:31,649 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - BioGRID release version is: 3.4.129 2016-07-27 11:57:31,650 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Caenorhabditis_elegans-3.4.129.mitab 2016-07-27 11:57:31,651 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Danio_rerio-3.4.129.mitab 2016-07-27 11:57:31,651 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Drosophila_melanogaster-3.4.129.mitab 2016-07-27 11:57:31,651 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Escherichia_coli_K12_MG1655-3.4.129.mitab 2016-07-27 11:57:31,652 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Homo_sapiens-3.4.129.mitab 2016-07-27 11:57:31,652 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Mus_musculus-3.4.129.mitab 2016-07-27 11:57:31,652 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Saccharomyces_cerevisiae_S288c-3.4.129.mitab 2016-07-27 11:57:32,191 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.io.internal.read.GenericReaderManager - Filter returns Accepted. Need to check priority: org.cytoscape.io.internal.read.vizmap.VizmapXMLReaderFactory@1e70fa5e 2016-07-27 11:57:32,191 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.io.internal.read.GenericReaderManager - Successfully found compatible ReaderFactory org.cytoscape.io.internal.read.vizmap.VizmapXMLReaderFactory@1e70fa5e 2016-07-27 11:57:32,351 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Curved 2016-07-27 11:57:32,367 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Gradient1 2016-07-27 11:57:32,605 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Big Labels 2016-07-27 11:57:32,609 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default 2016-07-27 11:57:32,614 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default black 2016-07-27 11:57:32,619 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Directed 2016-07-27 11:57:32,638 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Marquee 2016-07-27 11:57:32,648 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Minimal 2016-07-27 11:57:32,674 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Nested Network Style 2016-07-27 11:57:32,685 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Ripple 2016-07-27 11:57:32,701 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample1 2016-07-27 11:57:32,710 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample2 2016-07-27 11:57:32,722 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample3 2016-07-27 11:57:32,728 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Solid 2016-07-27 11:57:32,730 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Universe 2016-07-27 11:57:32,732 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample2 2016-07-27 11:57:32,732 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 4 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Big Labels 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 5 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Curved 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 6 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Minimal 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 7 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Solid 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 8 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Directed 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 9 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Gradient1 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 10 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample1 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 11 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: default black 2016-07-27 11:57:32,733 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 12 2016-07-27 11:57:32,734 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample3 2016-07-27 11:57:32,734 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 13 2016-07-27 11:57:32,734 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Ripple 2016-07-27 11:57:32,734 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 14 2016-07-27 11:57:32,734 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Universe 2016-07-27 11:57:32,734 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 15 2016-07-27 11:57:32,734 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Marquee 2016-07-27 11:57:32,734 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 16 2016-07-27 11:57:32,734 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Nested Network Style 2016-07-27 11:57:32,734 [Task-Thread-1-Factory-0x234347e4] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 17 2016-07-27 11:57:33,907 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.force-directed-cl.props' in jar. 2016-07-27 11:57:34,579 [pool-10-thread-1] WARN org.glassfish.jersey.internal.Errors - The following warnings have been detected: WARNING: Parameter taskManager of type org.cytoscape.work.SynchronousTaskManager from private org.cytoscape.work.SynchronousTaskManager org.cytoscape.rest.internal.commands.resources.CommandResource.taskManager is not resolvable to a concrete type. WARNING: The (sub)resource method getTables in org.cytoscape.rest.internal.resource.TableResource contains empty path annotation. WARNING: The (sub)resource method createNetworkView in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method getAllNetworkViews in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method deleteAllNetworkViews in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method getNetworks in org.cytoscape.rest.internal.resource.NetworkFullResource contains empty path annotation. WARNING: The (sub)resource method deleteSession in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method getSessionFromFile in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method createSessionFile in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method getAllGroups in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. WARNING: The (sub)resource method createGroup in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. WARNING: The (sub)resource method deleteAllGroups in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.GroupResource.expandGroup(java.lang.Long,java.lang.Long), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.GroupResource.collapseGroup(java.lang.Long,java.lang.Long), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". WARNING: The (sub)resource method getStatus in org.cytoscape.rest.internal.resource.MiscResource contains empty path annotation. HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.MiscResource.runGarbageCollection(), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". WARNING: The (sub)resource method getVersions in org.cytoscape.rest.internal.resource.RootResource contains empty path annotation. WARNING: Return type, java.util.List>, of method, public java.util.List> org.cytoscape.rest.internal.resource.NetworkNameResource.getNetworks(java.lang.String,java.lang.String), is not resolvable to a concrete type. WARNING: The (sub)resource method getNetworks in org.cytoscape.rest.internal.resource.NetworkNameResource contains empty path annotation. WARNING: The (sub)resource method getDesktop in org.cytoscape.rest.internal.resource.UIResource contains empty path annotation. WARNING: The (sub)resource method enumerateNamespaces in org.cytoscape.rest.internal.commands.resources.CommandResource contains empty path annotation. WARNING: The (sub)resource method enumerateNamespacesHtml in org.cytoscape.rest.internal.commands.resources.CommandResource contains empty path annotation. WARNING: The (sub)resource method getStyleNames in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method createStyle in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method deleteAllStyles in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method createNetwork in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. WARNING: The (sub)resource method getNetworksAsSUID in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. WARNING: The (sub)resource method deleteAllNetworks in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. 2016-07-27 11:57:34,951 [pool-10-thread-1] INFO org.cytoscape.rest.internal.task.GrizzlyServerManager - ========== Cytoscape RESTful API service started. Listening at port: 1234 ============== 2016-07-27 12:02:54,974 [Task-Thread-4-Factory-0x234347e4] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ public tables created: ID = 36 2016-07-27 12:02:54,978 [Task-Thread-4-Factory-0x234347e4] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ public tables created: Base Graph ID = 52 2016-07-27 12:04:14,416 [Task-Thread-4-Factory-0x234347e4] INFO org.cytoscape.io.internal.read.GenericReaderManager - Filter returns Accepted. Need to check priority: org.cytoscape.tableimport.internal.task.ImportNetworkTableReaderFactory@1312c555 2016-07-27 12:04:14,434 [Task-Thread-4-Factory-0x234347e4] INFO org.cytoscape.io.internal.read.GenericReaderManager - Successfully found compatible ReaderFactory org.cytoscape.tableimport.internal.task.ImportNetworkTableReaderFactory@1312c555 2016-07-27 12:10:16,343 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.features.repos.cfg 2016-07-27 12:10:16,348 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.org.apache.karaf.security.jmx.cfg 2016-07-27 12:10:16,355 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.config.cfg 2016-07-27 12:10:16,359 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.java.lang.Memory.cfg 2016-07-27 12:10:16,368 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.bundle.cfg 2016-07-27 12:10:16,378 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.ops4j.pax.url.mvn.cfg 2016-07-27 12:10:16,382 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.kar.cfg 2016-07-27 12:10:16,391 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.management.cfg 2016-07-27 12:10:16,394 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.cfg 2016-07-27 12:10:16,402 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.jaas.cfg 2016-07-27 12:10:16,406 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.scope_bundle.cfg 2016-07-27 12:10:16,409 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.system.cfg 2016-07-27 12:10:16,416 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.jaas.cfg 2016-07-27 12:10:16,420 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.feature.cfg 2016-07-27 12:10:16,425 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.features.cfg 2016-07-27 12:10:17,978 [FelixStartLevel] WARN org.apache.karaf.features.internal.FeatureValidationUtil - Old style feature file without namespace found (URI: mvn:org.cytoscape.distribution/features/3.4.0/xml/features). This format is deprecated and support for it will soon be removed 2016-07-27 12:10:18,074 [FelixStartLevel] INFO org.apache.karaf.features.internal.FeaturesServiceImpl - Installing feature standard 3.0.3 2016-07-27 12:10:18,168 [FelixStartLevel] INFO org.apache.karaf.features.internal.FeaturesServiceImpl - Installing feature cytoscape-gui 3.4.0 2016-07-27 12:10:19,091 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.features.command is waiting for namespace handlers [http://karaf.apache.org/xmlns/shell/v1.1.0] 2016-07-27 12:10:19,158 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.feature into service ACL configs [org.apache.karaf.service.acl.command.feature.uninstall, org.apache.karaf.service.acl.command.feature.install] 2016-07-27 12:10:19,170 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.jaas into service ACL configs [org.apache.karaf.service.acl.command.jaas.update] 2016-07-27 12:10:19,179 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.config into service ACL configs [org.apache.karaf.service.acl.command.config.property-append, org.apache.karaf.service.acl.command.config.property-delete, org.apache.karaf.service.acl.command.config.property-set, org.apache.karaf.service.acl.command.config.edit, org.apache.karaf.service.acl.command.config.update, org.apache.karaf.service.acl.command.config.cancel, org.apache.karaf.service.acl.command.config.delete] 2016-07-27 12:10:19,206 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.shell into service ACL configs [org.apache.karaf.service.acl.command.shell.java, org.apache.karaf.service.acl.command.shell.new, org.apache.karaf.service.acl.command.shell.edit, org.apache.karaf.service.acl.command.shell.exec] 2016-07-27 12:10:19,221 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.system into service ACL configs [org.apache.karaf.service.acl.command.system.property, org.apache.karaf.service.acl.command.system.shutdown, org.apache.karaf.service.acl.command.system.start-level] 2016-07-27 12:10:19,232 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.scope_bundle into service ACL configs [org.apache.karaf.service.acl.command.scope_bundle.shell, org.apache.karaf.service.acl.command.scope_bundle.packages, org.apache.karaf.service.acl.command.scope_bundle.admin, org.apache.karaf.service.acl.command.scope_bundle.ssh, org.apache.karaf.service.acl.command.scope_bundle.osgi, org.apache.karaf.service.acl.command.scope_bundle.config, org.apache.karaf.service.acl.command.scope_bundle.jaas, org.apache.karaf.service.acl.command.scope_bundle.features, org.apache.karaf.service.acl.command.scope_bundle.log] 2016-07-27 12:10:19,265 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.kar into service ACL configs [org.apache.karaf.service.acl.command.kar.uninstall, org.apache.karaf.service.acl.command.kar.install] 2016-07-27 12:10:19,270 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.bundle into service ACL configs [org.apache.karaf.service.acl.command.bundle.watch, org.apache.karaf.service.acl.command.bundle.update, org.apache.karaf.service.acl.command.bundle.install, org.apache.karaf.service.acl.command.bundle.uninstall, org.apache.karaf.service.acl.command.bundle.refresh, org.apache.karaf.service.acl.command.bundle.restart, org.apache.karaf.service.acl.command.bundle.stop, org.apache.karaf.service.acl.command.bundle.start] 2016-07-27 12:10:19,349 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.jaas.modules is waiting for namespace handlers [http://karaf.apache.org/xmlns/jaas/v1.0.0] 2016-07-27 12:10:19,350 [Blueprint Extender: 1] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.features.command is waiting for dependencies [(objectClass=org.apache.karaf.features.FeaturesService)] 2016-07-27 12:10:19,498 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.instance.command is waiting for dependencies [(objectClass=org.apache.karaf.features.FeaturesService)] 2016-07-27 12:10:21,433 [FelixStartLevel] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default 2016-07-27 12:10:21,450 [FelixStartLevel] INFO org.cytoscape.application.internal.CyApplicationConfigurationImpl - Setting file directory = /Users/johannavillen/CytoscapeConfiguration 2016-07-27 12:10:21,510 [FelixStartLevel] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'groupSettings.props' in jar. 2016-07-27 12:10:21,784 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Custom Graphics Image property file loaded from: /Users/johannavillen/CytoscapeConfiguration/images3 2016-07-27 12:10:21,785 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Image loading process finished in 0.001 sec. 2016-07-27 12:10:21,785 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Currently, -1 images are available. 2016-07-27 12:10:21,918 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Image saving process finished in 0.135 sec. 2016-07-27 12:10:22,284 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,285 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,285 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,286 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,287 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,287 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,288 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,289 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,289 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,290 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,291 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,292 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,293 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,293 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:22,294 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:23,382 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.grid.props' in jar. 2016-07-27 12:10:24,518 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu separator with gravity: 4.9999 2016-07-27 12:10:24,518 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@3f1b3e77,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Make Current Styles Default] with gravity: 5.0 2016-07-27 12:10:24,520 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@3f1b3e77,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Remove Style] with gravity: 4.0 2016-07-27 12:10:24,521 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@3f1b3e77,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create New Style...] with gravity: 1.0 2016-07-27 12:10:24,523 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu separator with gravity: 5.9999 2016-07-27 12:10:24,523 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@3f1b3e77,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create Legend...] with gravity: 6.0 2016-07-27 12:10:24,524 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@3f1b3e77,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Copy Style...] with gravity: 2.0 2016-07-27 12:10:24,526 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@3f1b3e77,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Rename Style...] with gravity: 3.0 2016-07-27 12:10:24,700 [FelixStartLevel] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ private tables created: ID = 2 2016-07-27 12:10:24,700 [FelixStartLevel] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ private tables created: Base Graph ID = 18 2016-07-27 12:10:25,057 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.hierarchical.props' in jar. 2016-07-27 12:10:25,061 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.circular.props' in jar. 2016-07-27 12:10:25,065 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.stacked-node-layout.props' in jar. 2016-07-27 12:10:25,068 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.attribute-circle.props' in jar. 2016-07-27 12:10:25,073 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.degree-circle.props' in jar. 2016-07-27 12:10:25,077 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.attributes-layout.props' in jar. 2016-07-27 12:10:25,091 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.kamada-kawai.props' in jar. 2016-07-27 12:10:25,095 [pool-7-thread-3] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.isom.props' in jar. 2016-07-27 12:10:25,099 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.fruchterman-rheingold.props' in jar. 2016-07-27 12:10:25,321 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.force-directed.props' in jar. 2016-07-27 12:10:26,023 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:26,223 [pool-8-thread-1] INFO org.cytoscape.app.internal.net.server.CyHttpdImpl - Server socket started on 127.0.0.1:2607 2016-07-27 12:10:26,382 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: DEGREE 2016-07-27 12:10:26,382 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: INDEGREE 2016-07-27 12:10:26,383 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: OUTDEGREE 2016-07-27 12:10:26,384 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: SOURCEID 2016-07-27 12:10:26,384 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: TARGETID 2016-07-27 12:10:27,584 [pool-9-thread-1] INFO org.cytoscape.webservice.internal.ui.WebServiceImportDialog - New network import client registered: BioMart Client 2016-07-27 12:10:27,689 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:27,689 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:27,714 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Arabidopsis_thaliana_Columbia-3.4.129.mitab 2016-07-27 12:10:27,714 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - BioGRID release version is: 3.4.129 2016-07-27 12:10:27,715 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Caenorhabditis_elegans-3.4.129.mitab 2016-07-27 12:10:27,715 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Danio_rerio-3.4.129.mitab 2016-07-27 12:10:27,715 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Drosophila_melanogaster-3.4.129.mitab 2016-07-27 12:10:27,716 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Escherichia_coli_K12_MG1655-3.4.129.mitab 2016-07-27 12:10:27,716 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Homo_sapiens-3.4.129.mitab 2016-07-27 12:10:27,716 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Mus_musculus-3.4.129.mitab 2016-07-27 12:10:27,716 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Saccharomyces_cerevisiae_S288c-3.4.129.mitab 2016-07-27 12:10:27,909 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:27,911 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 12:10:27,912 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 12:10:27,913 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 12:10:27,914 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 12:10:28,199 [pool-9-thread-1] INFO org.cytoscape.webservice.internal.ui.WebServiceImportDialog - New network import client registered: Universal Interaction Database Client 2016-07-27 12:10:29,006 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = BioPAX 2016-07-27 12:10:29,006 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: BioPAX 2016-07-27 12:10:29,006 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 2 2016-07-27 12:10:29,161 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = BioPAX_SIF 2016-07-27 12:10:29,161 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: BioPAX_SIF 2016-07-27 12:10:29,161 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 3 2016-07-27 12:10:29,375 [pool-9-thread-1] INFO org.cytoscape.rest.internal.CyActivator - Initializing cyREST API server... 2016-07-27 12:10:29,376 [pool-9-thread-1] INFO org.cytoscape.rest.internal.CyActivator - cyREST dependency import took: 1 msec. 2016-07-27 12:10:29,423 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.io.internal.read.GenericReaderManager - Filter returns Accepted. Need to check priority: org.cytoscape.io.internal.read.vizmap.VizmapXMLReaderFactory@5a3ceb03 2016-07-27 12:10:29,423 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.io.internal.read.GenericReaderManager - Successfully found compatible ReaderFactory org.cytoscape.io.internal.read.vizmap.VizmapXMLReaderFactory@5a3ceb03 2016-07-27 12:10:29,524 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Curved 2016-07-27 12:10:29,534 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Gradient1 2016-07-27 12:10:29,870 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Big Labels 2016-07-27 12:10:29,880 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default 2016-07-27 12:10:29,885 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default black 2016-07-27 12:10:29,889 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Directed 2016-07-27 12:10:29,946 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Marquee 2016-07-27 12:10:29,963 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Minimal 2016-07-27 12:10:29,967 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Nested Network Style 2016-07-27 12:10:29,985 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Ripple 2016-07-27 12:10:29,989 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample1 2016-07-27 12:10:29,992 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample2 2016-07-27 12:10:29,994 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample3 2016-07-27 12:10:29,996 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Solid 2016-07-27 12:10:30,001 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Universe 2016-07-27 12:10:30,004 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Directed 2016-07-27 12:10:30,004 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 4 2016-07-27 12:10:30,007 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Minimal 2016-07-27 12:10:30,007 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 5 2016-07-27 12:10:30,007 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample3 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 6 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Big Labels 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 7 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: default black 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 8 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Curved 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 9 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Universe 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 10 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample2 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 11 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Gradient1 2016-07-27 12:10:30,008 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 12 2016-07-27 12:10:30,009 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Nested Network Style 2016-07-27 12:10:30,009 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 13 2016-07-27 12:10:30,009 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample1 2016-07-27 12:10:30,009 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 14 2016-07-27 12:10:30,009 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Ripple 2016-07-27 12:10:30,009 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 15 2016-07-27 12:10:30,009 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Marquee 2016-07-27 12:10:30,009 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 16 2016-07-27 12:10:30,009 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Solid 2016-07-27 12:10:30,009 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 17 2016-07-27 12:10:31,020 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.force-directed-cl.props' in jar. 2016-07-27 12:10:32,262 [pool-12-thread-1] WARN org.glassfish.jersey.internal.Errors - The following warnings have been detected: WARNING: Parameter taskManager of type org.cytoscape.work.SynchronousTaskManager from private org.cytoscape.work.SynchronousTaskManager org.cytoscape.rest.internal.commands.resources.CommandResource.taskManager is not resolvable to a concrete type. WARNING: The (sub)resource method getTables in org.cytoscape.rest.internal.resource.TableResource contains empty path annotation. WARNING: The (sub)resource method createNetworkView in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method getAllNetworkViews in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method deleteAllNetworkViews in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method getNetworks in org.cytoscape.rest.internal.resource.NetworkFullResource contains empty path annotation. WARNING: The (sub)resource method deleteSession in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method getSessionFromFile in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method createSessionFile in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method createGroup in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. WARNING: The (sub)resource method getAllGroups in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. WARNING: The (sub)resource method deleteAllGroups in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.GroupResource.expandGroup(java.lang.Long,java.lang.Long), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.GroupResource.collapseGroup(java.lang.Long,java.lang.Long), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". WARNING: The (sub)resource method getStatus in org.cytoscape.rest.internal.resource.MiscResource contains empty path annotation. HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.MiscResource.runGarbageCollection(), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". WARNING: Return type, java.util.List>, of method, public java.util.List> org.cytoscape.rest.internal.resource.NetworkNameResource.getNetworks(java.lang.String,java.lang.String), is not resolvable to a concrete type. WARNING: The (sub)resource method getNetworks in org.cytoscape.rest.internal.resource.NetworkNameResource contains empty path annotation. WARNING: The (sub)resource method getVersions in org.cytoscape.rest.internal.resource.RootResource contains empty path annotation. WARNING: The (sub)resource method getDesktop in org.cytoscape.rest.internal.resource.UIResource contains empty path annotation. WARNING: The (sub)resource method enumerateNamespaces in org.cytoscape.rest.internal.commands.resources.CommandResource contains empty path annotation. WARNING: The (sub)resource method enumerateNamespacesHtml in org.cytoscape.rest.internal.commands.resources.CommandResource contains empty path annotation. WARNING: The (sub)resource method createNetwork in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. WARNING: The (sub)resource method getNetworksAsSUID in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. WARNING: The (sub)resource method deleteAllNetworks in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. WARNING: The (sub)resource method getStyleNames in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method deleteAllStyles in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method createStyle in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. 2016-07-27 12:10:32,631 [pool-12-thread-1] INFO org.cytoscape.rest.internal.task.GrizzlyServerManager - ========== Cytoscape RESTful API service started. Listening at port: 1234 ============== 2016-07-27 12:11:04,609 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.io.internal.read.GenericReaderManager - Filter returns Accepted. Need to check priority: org.cytoscape.tableimport.internal.task.ImportNetworkTableReaderFactory@7c14a67d 2016-07-27 12:11:04,626 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.io.internal.read.GenericReaderManager - Successfully found compatible ReaderFactory org.cytoscape.tableimport.internal.task.ImportNetworkTableReaderFactory@7c14a67d 2016-07-27 12:11:21,380 [AWT-EventQueue-0] INFO org.cytoscape.ding.customgraphicsmgr.internal.CustomGraphicsManagerImpl - Start Saving images to: /Users/johannavillen/CytoscapeConfiguration/images3 2016-07-27 12:11:21,385 [AWT-EventQueue-0] INFO org.cytoscape.ding.customgraphicsmgr.internal.CustomGraphicsManagerImpl - ========== Image saving process finished ============= 2016-07-27 12:11:21,399 [Task-Thread-1-Factory-0x55a89755] INFO org.cytoscape.ding.customgraphicsmgr.internal.PersistImageTask - Image saving process finished in 0.008 sec. 2016-07-27 12:11:21,455 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.service.command 2016-07-27 12:11:21,468 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.service.core 2016-07-27 12:11:21,469 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.log.command 2016-07-27 12:11:21,482 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.log.core 2016-07-27 12:11:21,485 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.diagnostic.command 2016-07-27 12:11:21,488 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.diagnostic.core 2016-07-27 12:11:21,491 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.command 2016-07-27 12:11:21,508 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.instance.command 2016-07-27 12:11:21,542 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.instance.core 2016-07-27 12:11:21,544 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.commands 2016-07-27 12:11:21,606 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.system.command 2016-07-27 12:11:21,616 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.system.core 2016-07-27 12:11:21,617 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.help 2016-07-27 12:11:21,619 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.bundle.command 2016-07-27 12:11:21,648 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.modules 2016-07-27 12:11:21,651 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.features.command 2016-07-27 12:11:21,672 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.features.core 2016-07-27 12:11:21,678 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.features 2016-07-27 12:11:21,680 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.cytoscape.scripting-impl 2016-07-27 12:11:21,683 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.bundle.core 2016-07-27 12:11:21,687 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.config 2016-07-27 12:11:21,691 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.console 2016-07-27 12:11:21,697 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.blueprint 2016-07-27 12:11:21,700 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.spring 2016-07-27 12:11:21,702 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.aries.blueprint.core 2016-07-27 12:11:21,705 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.aries.blueprint.cm 2016-07-27 12:11:21,720 [FelixStartLevel] INFO org.cytoscape.rest.internal.CyActivator - Shutting down REST server... 2016-07-27 13:22:01,911 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.features.repos.cfg 2016-07-27 13:22:01,921 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.org.apache.karaf.security.jmx.cfg 2016-07-27 13:22:01,928 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.config.cfg 2016-07-27 13:22:01,935 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.java.lang.Memory.cfg 2016-07-27 13:22:01,942 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.bundle.cfg 2016-07-27 13:22:01,952 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.ops4j.pax.url.mvn.cfg 2016-07-27 13:22:01,959 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.kar.cfg 2016-07-27 13:22:01,966 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.management.cfg 2016-07-27 13:22:01,971 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.cfg 2016-07-27 13:22:01,978 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.jaas.cfg 2016-07-27 13:22:01,982 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.scope_bundle.cfg 2016-07-27 13:22:01,989 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.system.cfg 2016-07-27 13:22:01,996 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.jaas.cfg 2016-07-27 13:22:02,004 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.feature.cfg 2016-07-27 13:22:02,008 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.features.cfg 2016-07-27 13:22:03,699 [FelixStartLevel] WARN org.apache.karaf.features.internal.FeatureValidationUtil - Old style feature file without namespace found (URI: mvn:org.cytoscape.distribution/features/3.4.0/xml/features). This format is deprecated and support for it will soon be removed 2016-07-27 13:22:03,783 [FelixStartLevel] INFO org.apache.karaf.features.internal.FeaturesServiceImpl - Installing feature standard 3.0.3 2016-07-27 13:22:03,880 [FelixStartLevel] INFO org.apache.karaf.features.internal.FeaturesServiceImpl - Installing feature cytoscape-gui 3.4.0 2016-07-27 13:22:05,003 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.features.command is waiting for namespace handlers [http://karaf.apache.org/xmlns/shell/v1.1.0] 2016-07-27 13:22:05,083 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.feature into service ACL configs [org.apache.karaf.service.acl.command.feature.uninstall, org.apache.karaf.service.acl.command.feature.install] 2016-07-27 13:22:05,090 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.jaas into service ACL configs [org.apache.karaf.service.acl.command.jaas.update] 2016-07-27 13:22:05,094 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.config into service ACL configs [org.apache.karaf.service.acl.command.config.property-append, org.apache.karaf.service.acl.command.config.property-delete, org.apache.karaf.service.acl.command.config.property-set, org.apache.karaf.service.acl.command.config.edit, org.apache.karaf.service.acl.command.config.update, org.apache.karaf.service.acl.command.config.cancel, org.apache.karaf.service.acl.command.config.delete] 2016-07-27 13:22:05,120 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.shell into service ACL configs [org.apache.karaf.service.acl.command.shell.java, org.apache.karaf.service.acl.command.shell.new, org.apache.karaf.service.acl.command.shell.edit, org.apache.karaf.service.acl.command.shell.exec] 2016-07-27 13:22:05,136 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.system into service ACL configs [org.apache.karaf.service.acl.command.system.property, org.apache.karaf.service.acl.command.system.shutdown, org.apache.karaf.service.acl.command.system.start-level] 2016-07-27 13:22:05,146 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.scope_bundle into service ACL configs [org.apache.karaf.service.acl.command.scope_bundle.shell, org.apache.karaf.service.acl.command.scope_bundle.packages, org.apache.karaf.service.acl.command.scope_bundle.admin, org.apache.karaf.service.acl.command.scope_bundle.ssh, org.apache.karaf.service.acl.command.scope_bundle.osgi, org.apache.karaf.service.acl.command.scope_bundle.config, org.apache.karaf.service.acl.command.scope_bundle.jaas, org.apache.karaf.service.acl.command.scope_bundle.features, org.apache.karaf.service.acl.command.scope_bundle.log] 2016-07-27 13:22:05,178 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.kar into service ACL configs [org.apache.karaf.service.acl.command.kar.uninstall, org.apache.karaf.service.acl.command.kar.install] 2016-07-27 13:22:05,185 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.bundle into service ACL configs [org.apache.karaf.service.acl.command.bundle.watch, org.apache.karaf.service.acl.command.bundle.update, org.apache.karaf.service.acl.command.bundle.install, org.apache.karaf.service.acl.command.bundle.uninstall, org.apache.karaf.service.acl.command.bundle.refresh, org.apache.karaf.service.acl.command.bundle.restart, org.apache.karaf.service.acl.command.bundle.stop, org.apache.karaf.service.acl.command.bundle.start] 2016-07-27 13:22:05,286 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.jaas.modules is waiting for namespace handlers [http://karaf.apache.org/xmlns/jaas/v1.0.0] 2016-07-27 13:22:05,315 [Blueprint Extender: 1] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.features.command is waiting for dependencies [(objectClass=org.apache.karaf.features.FeaturesService)] 2016-07-27 13:22:05,414 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.instance.command is waiting for dependencies [(objectClass=org.apache.karaf.features.FeaturesService)] 2016-07-27 13:22:08,253 [FelixStartLevel] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default 2016-07-27 13:22:08,274 [FelixStartLevel] INFO org.cytoscape.application.internal.CyApplicationConfigurationImpl - Setting file directory = /Users/johannavillen/CytoscapeConfiguration 2016-07-27 13:22:08,358 [FelixStartLevel] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'groupSettings.props' in jar. 2016-07-27 13:22:08,978 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Custom Graphics Image property file loaded from: /Users/johannavillen/CytoscapeConfiguration/images3 2016-07-27 13:22:08,980 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Image loading process finished in 0.005 sec. 2016-07-27 13:22:08,980 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Currently, -1 images are available. 2016-07-27 13:22:09,146 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Image saving process finished in 0.171 sec. 2016-07-27 13:22:09,571 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,572 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,573 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,574 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,575 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,576 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,576 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,578 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,579 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,580 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,581 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,582 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,583 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,584 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:09,584 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:11,154 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.grid.props' in jar. 2016-07-27 13:22:12,451 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu separator with gravity: 5.9999 2016-07-27 13:22:12,451 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@27a02cd8,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create Legend...] with gravity: 6.0 2016-07-27 13:22:12,453 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@27a02cd8,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Remove Style] with gravity: 4.0 2016-07-27 13:22:12,454 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@27a02cd8,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Rename Style...] with gravity: 3.0 2016-07-27 13:22:12,454 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@27a02cd8,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create New Style...] with gravity: 1.0 2016-07-27 13:22:12,456 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu separator with gravity: 4.9999 2016-07-27 13:22:12,456 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@27a02cd8,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Make Current Styles Default] with gravity: 5.0 2016-07-27 13:22:12,458 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@27a02cd8,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Copy Style...] with gravity: 2.0 2016-07-27 13:22:12,661 [FelixStartLevel] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ private tables created: ID = 2 2016-07-27 13:22:12,662 [FelixStartLevel] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ private tables created: Base Graph ID = 18 2016-07-27 13:22:12,983 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.hierarchical.props' in jar. 2016-07-27 13:22:12,987 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.circular.props' in jar. 2016-07-27 13:22:12,991 [pool-7-thread-3] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.attribute-circle.props' in jar. 2016-07-27 13:22:12,995 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.stacked-node-layout.props' in jar. 2016-07-27 13:22:12,999 [pool-7-thread-3] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.attributes-layout.props' in jar. 2016-07-27 13:22:13,003 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.degree-circle.props' in jar. 2016-07-27 13:22:13,008 [pool-7-thread-3] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.kamada-kawai.props' in jar. 2016-07-27 13:22:13,012 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.isom.props' in jar. 2016-07-27 13:22:13,015 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.fruchterman-rheingold.props' in jar. 2016-07-27 13:22:13,195 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.force-directed.props' in jar. 2016-07-27 13:22:13,794 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:13,965 [pool-8-thread-1] INFO org.cytoscape.app.internal.net.server.CyHttpdImpl - Server socket started on 127.0.0.1:2607 2016-07-27 13:22:14,132 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: DEGREE 2016-07-27 13:22:14,133 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: INDEGREE 2016-07-27 13:22:14,134 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: OUTDEGREE 2016-07-27 13:22:14,135 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: SOURCEID 2016-07-27 13:22:14,135 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: TARGETID 2016-07-27 13:22:15,223 [pool-9-thread-1] INFO org.cytoscape.rest.internal.CyActivator - Initializing cyREST API server... 2016-07-27 13:22:15,225 [pool-9-thread-1] INFO org.cytoscape.rest.internal.CyActivator - cyREST dependency import took: 1 msec. 2016-07-27 13:22:15,250 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:15,251 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:15,356 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Arabidopsis_thaliana_Columbia-3.4.129.mitab 2016-07-27 13:22:15,356 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - BioGRID release version is: 3.4.129 2016-07-27 13:22:15,357 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Caenorhabditis_elegans-3.4.129.mitab 2016-07-27 13:22:15,357 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Danio_rerio-3.4.129.mitab 2016-07-27 13:22:15,357 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Drosophila_melanogaster-3.4.129.mitab 2016-07-27 13:22:15,357 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Escherichia_coli_K12_MG1655-3.4.129.mitab 2016-07-27 13:22:15,357 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Homo_sapiens-3.4.129.mitab 2016-07-27 13:22:15,358 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Mus_musculus-3.4.129.mitab 2016-07-27 13:22:15,358 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Saccharomyces_cerevisiae_S288c-3.4.129.mitab 2016-07-27 13:22:15,588 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = BioPAX 2016-07-27 13:22:15,588 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: BioPAX 2016-07-27 13:22:15,588 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 2 2016-07-27 13:22:15,823 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = BioPAX_SIF 2016-07-27 13:22:15,824 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: BioPAX_SIF 2016-07-27 13:22:15,824 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 3 2016-07-27 13:22:16,421 [pool-9-thread-1] INFO org.cytoscape.webservice.internal.ui.WebServiceImportDialog - New network import client registered: Universal Interaction Database Client 2016-07-27 13:22:16,562 [pool-9-thread-1] INFO org.cytoscape.webservice.internal.ui.WebServiceImportDialog - New network import client registered: BioMart Client 2016-07-27 13:22:17,449 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:17,451 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:22:17,453 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 13:22:17,455 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 13:22:17,456 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 13:22:17,628 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.io.internal.read.GenericReaderManager - Filter returns Accepted. Need to check priority: org.cytoscape.io.internal.read.vizmap.VizmapXMLReaderFactory@8a36d72 2016-07-27 13:22:17,628 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.io.internal.read.GenericReaderManager - Successfully found compatible ReaderFactory org.cytoscape.io.internal.read.vizmap.VizmapXMLReaderFactory@8a36d72 2016-07-27 13:22:17,701 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Curved 2016-07-27 13:22:17,710 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Gradient1 2016-07-27 13:22:17,756 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.force-directed-cl.props' in jar. 2016-07-27 13:22:17,926 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Big Labels 2016-07-27 13:22:17,934 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default 2016-07-27 13:22:17,939 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default black 2016-07-27 13:22:17,944 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Directed 2016-07-27 13:22:17,949 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Marquee 2016-07-27 13:22:17,953 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Minimal 2016-07-27 13:22:17,958 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Nested Network Style 2016-07-27 13:22:17,971 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Ripple 2016-07-27 13:22:17,974 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample1 2016-07-27 13:22:17,977 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample2 2016-07-27 13:22:17,980 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample3 2016-07-27 13:22:17,992 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Solid 2016-07-27 13:22:18,005 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Universe 2016-07-27 13:22:18,007 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Big Labels 2016-07-27 13:22:18,007 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 4 2016-07-27 13:22:18,011 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Universe 2016-07-27 13:22:18,011 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 5 2016-07-27 13:22:18,012 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Minimal 2016-07-27 13:22:18,012 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 6 2016-07-27 13:22:18,012 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Gradient1 2016-07-27 13:22:18,012 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 7 2016-07-27 13:22:18,012 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Marquee 2016-07-27 13:22:18,012 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 8 2016-07-27 13:22:18,012 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Directed 2016-07-27 13:22:18,012 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 9 2016-07-27 13:22:18,012 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample1 2016-07-27 13:22:18,012 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 10 2016-07-27 13:22:18,013 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample2 2016-07-27 13:22:18,013 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 11 2016-07-27 13:22:18,013 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Ripple 2016-07-27 13:22:18,013 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 12 2016-07-27 13:22:18,013 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Nested Network Style 2016-07-27 13:22:18,013 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 13 2016-07-27 13:22:18,013 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Solid 2016-07-27 13:22:18,013 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 14 2016-07-27 13:22:18,013 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Curved 2016-07-27 13:22:18,013 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 15 2016-07-27 13:22:18,013 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample3 2016-07-27 13:22:18,014 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 16 2016-07-27 13:22:18,014 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: default black 2016-07-27 13:22:18,014 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 17 2016-07-27 13:22:22,786 [pool-10-thread-1] WARN org.glassfish.jersey.internal.Errors - The following warnings have been detected: WARNING: Parameter taskManager of type org.cytoscape.work.SynchronousTaskManager from private org.cytoscape.work.SynchronousTaskManager org.cytoscape.rest.internal.commands.resources.CommandResource.taskManager is not resolvable to a concrete type. WARNING: The (sub)resource method getTables in org.cytoscape.rest.internal.resource.TableResource contains empty path annotation. WARNING: The (sub)resource method createNetworkView in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method getAllNetworkViews in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method deleteAllNetworkViews in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method getNetworks in org.cytoscape.rest.internal.resource.NetworkFullResource contains empty path annotation. WARNING: The (sub)resource method deleteSession in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method getSessionFromFile in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method createSessionFile in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method getAllGroups in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. WARNING: The (sub)resource method createGroup in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. WARNING: The (sub)resource method deleteAllGroups in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.GroupResource.expandGroup(java.lang.Long,java.lang.Long), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.GroupResource.collapseGroup(java.lang.Long,java.lang.Long), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". WARNING: The (sub)resource method getStatus in org.cytoscape.rest.internal.resource.MiscResource contains empty path annotation. HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.MiscResource.runGarbageCollection(), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". WARNING: Return type, java.util.List>, of method, public java.util.List> org.cytoscape.rest.internal.resource.NetworkNameResource.getNetworks(java.lang.String,java.lang.String), is not resolvable to a concrete type. WARNING: The (sub)resource method getNetworks in org.cytoscape.rest.internal.resource.NetworkNameResource contains empty path annotation. WARNING: The (sub)resource method getVersions in org.cytoscape.rest.internal.resource.RootResource contains empty path annotation. WARNING: The (sub)resource method getDesktop in org.cytoscape.rest.internal.resource.UIResource contains empty path annotation. WARNING: The (sub)resource method enumerateNamespaces in org.cytoscape.rest.internal.commands.resources.CommandResource contains empty path annotation. WARNING: The (sub)resource method enumerateNamespacesHtml in org.cytoscape.rest.internal.commands.resources.CommandResource contains empty path annotation. WARNING: The (sub)resource method getStyleNames in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method deleteAllStyles in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method createStyle in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method createNetwork in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. WARNING: The (sub)resource method getNetworksAsSUID in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. WARNING: The (sub)resource method deleteAllNetworks in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. 2016-07-27 13:22:23,606 [pool-10-thread-1] INFO org.cytoscape.rest.internal.task.GrizzlyServerManager - ========== Cytoscape RESTful API service started. Listening at port: 1234 ============== 2016-07-27 13:22:25,263 [pool-16-thread-1] INFO org.cytoscape.webservice.psicquic.RegistryManager - Found 27 active PSICQUIC services. 2016-07-27 13:22:51,329 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.webservice.psicquic.PSICQUICRestClient - PSICQUIC DB search finished in 2.493 sec. 2016-07-27 13:23:42,929 [pool-18-thread-1] WARN org.cytoscape.webservice.psicquic.PSICQUICRestClient - MITAB 2.7 is not supported by: Spike 2016-07-27 13:23:48,008 [pool-18-thread-1] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ public tables created: ID = 36 2016-07-27 13:23:48,008 [pool-18-thread-1] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ public tables created: Base Graph ID = 52 2016-07-27 13:24:13,100 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.webservice.psicquic.PSICQUICRestClient - PSICUQIC Import Finished in 30.503 sec. 2016-07-27 13:24:27,767 [AWT-EventQueue-0] INFO org.cytoscape.ding.customgraphicsmgr.internal.CustomGraphicsManagerImpl - Start Saving images to: /Users/johannavillen/CytoscapeConfiguration/images3 2016-07-27 13:24:27,792 [AWT-EventQueue-0] INFO org.cytoscape.ding.customgraphicsmgr.internal.CustomGraphicsManagerImpl - ========== Image saving process finished ============= 2016-07-27 13:24:27,802 [Task-Thread-1-Factory-0x3c244898] INFO org.cytoscape.ding.customgraphicsmgr.internal.PersistImageTask - Image saving process finished in 0.006 sec. 2016-07-27 13:24:27,903 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.service.command 2016-07-27 13:24:27,920 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.service.core 2016-07-27 13:24:27,922 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.log.command 2016-07-27 13:24:27,947 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.log.core 2016-07-27 13:24:27,955 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.diagnostic.command 2016-07-27 13:24:27,975 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.diagnostic.core 2016-07-27 13:24:27,988 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.command 2016-07-27 13:24:28,046 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.instance.command 2016-07-27 13:24:28,077 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.instance.core 2016-07-27 13:24:28,079 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.commands 2016-07-27 13:24:28,138 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.system.command 2016-07-27 13:24:28,147 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.system.core 2016-07-27 13:24:28,149 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.help 2016-07-27 13:24:28,152 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.bundle.command 2016-07-27 13:24:28,191 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.modules 2016-07-27 13:24:28,195 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.features.command 2016-07-27 13:24:28,208 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.features.core 2016-07-27 13:24:28,219 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.features 2016-07-27 13:24:28,221 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.cytoscape.scripting-impl 2016-07-27 13:24:28,223 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.bundle.core 2016-07-27 13:24:28,226 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.config 2016-07-27 13:24:28,234 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.console 2016-07-27 13:24:28,244 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.blueprint 2016-07-27 13:24:28,246 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.spring 2016-07-27 13:24:28,248 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.aries.blueprint.core 2016-07-27 13:24:28,251 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.aries.blueprint.cm 2016-07-27 13:24:28,390 [FelixStartLevel] INFO org.cytoscape.rest.internal.CyActivator - Shutting down REST server... 2016-07-27 13:24:43,132 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.features.repos.cfg 2016-07-27 13:24:43,137 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.org.apache.karaf.security.jmx.cfg 2016-07-27 13:24:43,143 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.config.cfg 2016-07-27 13:24:43,150 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.java.lang.Memory.cfg 2016-07-27 13:24:43,153 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.bundle.cfg 2016-07-27 13:24:43,161 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.ops4j.pax.url.mvn.cfg 2016-07-27 13:24:43,166 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.kar.cfg 2016-07-27 13:24:43,175 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.management.cfg 2016-07-27 13:24:43,179 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.cfg 2016-07-27 13:24:43,186 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.jaas.cfg 2016-07-27 13:24:43,191 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.scope_bundle.cfg 2016-07-27 13:24:43,195 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.system.cfg 2016-07-27 13:24:43,202 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.jaas.cfg 2016-07-27 13:24:43,209 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.feature.cfg 2016-07-27 13:24:43,216 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.features.cfg 2016-07-27 13:24:43,970 [FelixStartLevel] WARN org.apache.karaf.features.internal.FeatureValidationUtil - Old style feature file without namespace found (URI: mvn:org.cytoscape.distribution/features/3.4.0/xml/features). This format is deprecated and support for it will soon be removed 2016-07-27 13:24:44,045 [FelixStartLevel] INFO org.apache.karaf.features.internal.FeaturesServiceImpl - Installing feature standard 3.0.3 2016-07-27 13:24:44,145 [FelixStartLevel] INFO org.apache.karaf.features.internal.FeaturesServiceImpl - Installing feature cytoscape-gui 3.4.0 2016-07-27 13:24:45,188 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.features.command is waiting for namespace handlers [http://karaf.apache.org/xmlns/shell/v1.1.0] 2016-07-27 13:24:45,225 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.feature into service ACL configs [org.apache.karaf.service.acl.command.feature.uninstall, org.apache.karaf.service.acl.command.feature.install] 2016-07-27 13:24:45,233 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.jaas into service ACL configs [org.apache.karaf.service.acl.command.jaas.update] 2016-07-27 13:24:45,238 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.config into service ACL configs [org.apache.karaf.service.acl.command.config.property-append, org.apache.karaf.service.acl.command.config.property-delete, org.apache.karaf.service.acl.command.config.property-set, org.apache.karaf.service.acl.command.config.edit, org.apache.karaf.service.acl.command.config.update, org.apache.karaf.service.acl.command.config.cancel, org.apache.karaf.service.acl.command.config.delete] 2016-07-27 13:24:45,264 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.shell into service ACL configs [org.apache.karaf.service.acl.command.shell.java, org.apache.karaf.service.acl.command.shell.new, org.apache.karaf.service.acl.command.shell.edit, org.apache.karaf.service.acl.command.shell.exec] 2016-07-27 13:24:45,285 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.system into service ACL configs [org.apache.karaf.service.acl.command.system.property, org.apache.karaf.service.acl.command.system.shutdown, org.apache.karaf.service.acl.command.system.start-level] 2016-07-27 13:24:45,297 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.scope_bundle into service ACL configs [org.apache.karaf.service.acl.command.scope_bundle.shell, org.apache.karaf.service.acl.command.scope_bundle.packages, org.apache.karaf.service.acl.command.scope_bundle.admin, org.apache.karaf.service.acl.command.scope_bundle.ssh, org.apache.karaf.service.acl.command.scope_bundle.osgi, org.apache.karaf.service.acl.command.scope_bundle.config, org.apache.karaf.service.acl.command.scope_bundle.jaas, org.apache.karaf.service.acl.command.scope_bundle.features, org.apache.karaf.service.acl.command.scope_bundle.log] 2016-07-27 13:24:45,327 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.kar into service ACL configs [org.apache.karaf.service.acl.command.kar.uninstall, org.apache.karaf.service.acl.command.kar.install] 2016-07-27 13:24:45,335 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.bundle into service ACL configs [org.apache.karaf.service.acl.command.bundle.watch, org.apache.karaf.service.acl.command.bundle.update, org.apache.karaf.service.acl.command.bundle.install, org.apache.karaf.service.acl.command.bundle.uninstall, org.apache.karaf.service.acl.command.bundle.refresh, org.apache.karaf.service.acl.command.bundle.restart, org.apache.karaf.service.acl.command.bundle.stop, org.apache.karaf.service.acl.command.bundle.start] 2016-07-27 13:24:45,413 [Blueprint Extender: 1] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.features.command is waiting for dependencies [(objectClass=org.apache.karaf.features.FeaturesService)] 2016-07-27 13:24:45,430 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.jaas.modules is waiting for namespace handlers [http://karaf.apache.org/xmlns/jaas/v1.0.0] 2016-07-27 13:24:45,567 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.instance.command is waiting for dependencies [(objectClass=org.apache.karaf.features.FeaturesService)] 2016-07-27 13:24:47,349 [FelixStartLevel] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default 2016-07-27 13:24:47,364 [FelixStartLevel] INFO org.cytoscape.application.internal.CyApplicationConfigurationImpl - Setting file directory = /Users/johannavillen/CytoscapeConfiguration 2016-07-27 13:24:47,408 [FelixStartLevel] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'groupSettings.props' in jar. 2016-07-27 13:24:47,595 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Custom Graphics Image property file loaded from: /Users/johannavillen/CytoscapeConfiguration/images3 2016-07-27 13:24:47,595 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Image loading process finished in 0.001 sec. 2016-07-27 13:24:47,595 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Currently, -1 images are available. 2016-07-27 13:24:47,757 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Image saving process finished in 0.163 sec. 2016-07-27 13:24:47,913 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,914 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,914 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,915 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,915 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,916 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,916 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,917 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,918 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,919 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,919 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,920 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,920 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,921 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:47,923 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:48,679 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.grid.props' in jar. 2016-07-27 13:24:49,310 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@740eb15c,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Remove Style] with gravity: 4.0 2016-07-27 13:24:49,311 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu separator with gravity: 5.9999 2016-07-27 13:24:49,312 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@740eb15c,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create Legend...] with gravity: 6.0 2016-07-27 13:24:49,314 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@740eb15c,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create New Style...] with gravity: 1.0 2016-07-27 13:24:49,315 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@740eb15c,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Rename Style...] with gravity: 3.0 2016-07-27 13:24:49,318 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu separator with gravity: 4.9999 2016-07-27 13:24:49,318 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@740eb15c,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Make Current Styles Default] with gravity: 5.0 2016-07-27 13:24:49,319 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@740eb15c,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Copy Style...] with gravity: 2.0 2016-07-27 13:24:49,395 [FelixStartLevel] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ private tables created: ID = 2 2016-07-27 13:24:49,396 [FelixStartLevel] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ private tables created: Base Graph ID = 18 2016-07-27 13:24:49,620 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.hierarchical.props' in jar. 2016-07-27 13:24:49,622 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.circular.props' in jar. 2016-07-27 13:24:49,625 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.stacked-node-layout.props' in jar. 2016-07-27 13:24:49,629 [pool-7-thread-3] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.degree-circle.props' in jar. 2016-07-27 13:24:49,633 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.attribute-circle.props' in jar. 2016-07-27 13:24:49,636 [pool-7-thread-3] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.isom.props' in jar. 2016-07-27 13:24:49,640 [pool-7-thread-5] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.kamada-kawai.props' in jar. 2016-07-27 13:24:49,645 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.fruchterman-rheingold.props' in jar. 2016-07-27 13:24:49,648 [pool-7-thread-4] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.attributes-layout.props' in jar. 2016-07-27 13:24:49,798 [pool-7-thread-4] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.force-directed.props' in jar. 2016-07-27 13:24:50,254 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:50,382 [pool-8-thread-1] INFO org.cytoscape.app.internal.net.server.CyHttpdImpl - Server socket started on 127.0.0.1:2607 2016-07-27 13:24:50,502 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: DEGREE 2016-07-27 13:24:50,502 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: INDEGREE 2016-07-27 13:24:50,503 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: OUTDEGREE 2016-07-27 13:24:50,503 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: SOURCEID 2016-07-27 13:24:50,503 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: TARGETID 2016-07-27 13:24:51,637 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:51,640 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:51,642 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 13:24:51,643 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 13:24:51,644 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 13:24:51,898 [pool-9-thread-1] INFO org.cytoscape.webservice.internal.ui.WebServiceImportDialog - New network import client registered: Universal Interaction Database Client 2016-07-27 13:24:52,288 [pool-9-thread-1] INFO org.cytoscape.rest.internal.CyActivator - Initializing cyREST API server... 2016-07-27 13:24:52,289 [pool-9-thread-1] INFO org.cytoscape.rest.internal.CyActivator - cyREST dependency import took: 1 msec. 2016-07-27 13:24:52,311 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:52,311 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:24:53,078 [pool-9-thread-1] INFO org.cytoscape.webservice.internal.ui.WebServiceImportDialog - New network import client registered: BioMart Client 2016-07-27 13:24:53,096 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Arabidopsis_thaliana_Columbia-3.4.129.mitab 2016-07-27 13:24:53,097 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - BioGRID release version is: 3.4.129 2016-07-27 13:24:53,097 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Caenorhabditis_elegans-3.4.129.mitab 2016-07-27 13:24:53,097 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Danio_rerio-3.4.129.mitab 2016-07-27 13:24:53,097 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Drosophila_melanogaster-3.4.129.mitab 2016-07-27 13:24:53,097 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Escherichia_coli_K12_MG1655-3.4.129.mitab 2016-07-27 13:24:53,097 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Homo_sapiens-3.4.129.mitab 2016-07-27 13:24:53,097 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Mus_musculus-3.4.129.mitab 2016-07-27 13:24:53,097 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Saccharomyces_cerevisiae_S288c-3.4.129.mitab 2016-07-27 13:24:53,487 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = BioPAX 2016-07-27 13:24:53,487 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: BioPAX 2016-07-27 13:24:53,487 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 2 2016-07-27 13:24:53,743 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = BioPAX_SIF 2016-07-27 13:24:53,743 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: BioPAX_SIF 2016-07-27 13:24:53,744 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 3 2016-07-27 13:24:54,125 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.io.internal.read.GenericReaderManager - Filter returns Accepted. Need to check priority: org.cytoscape.io.internal.read.vizmap.VizmapXMLReaderFactory@db6374f 2016-07-27 13:24:54,126 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.io.internal.read.GenericReaderManager - Successfully found compatible ReaderFactory org.cytoscape.io.internal.read.vizmap.VizmapXMLReaderFactory@db6374f 2016-07-27 13:24:54,211 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Curved 2016-07-27 13:24:54,226 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Gradient1 2016-07-27 13:24:54,424 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Big Labels 2016-07-27 13:24:54,427 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default 2016-07-27 13:24:54,429 [pool-7-thread-4] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.force-directed-cl.props' in jar. 2016-07-27 13:24:54,431 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default black 2016-07-27 13:24:54,434 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Directed 2016-07-27 13:24:54,437 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Marquee 2016-07-27 13:24:54,440 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Minimal 2016-07-27 13:24:54,443 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Nested Network Style 2016-07-27 13:24:54,447 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Ripple 2016-07-27 13:24:54,450 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample1 2016-07-27 13:24:54,453 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample2 2016-07-27 13:24:54,456 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample3 2016-07-27 13:24:54,458 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Solid 2016-07-27 13:24:54,462 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Universe 2016-07-27 13:24:54,463 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Nested Network Style 2016-07-27 13:24:54,463 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 4 2016-07-27 13:24:54,466 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample3 2016-07-27 13:24:54,466 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 5 2016-07-27 13:24:54,466 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Marquee 2016-07-27 13:24:54,467 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 6 2016-07-27 13:24:54,467 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Curved 2016-07-27 13:24:54,467 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 7 2016-07-27 13:24:54,467 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Big Labels 2016-07-27 13:24:54,467 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 8 2016-07-27 13:24:54,467 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: default black 2016-07-27 13:24:54,467 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 9 2016-07-27 13:24:54,467 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Directed 2016-07-27 13:24:54,467 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 10 2016-07-27 13:24:54,467 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample1 2016-07-27 13:24:54,467 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 11 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Gradient1 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 12 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Solid 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 13 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Ripple 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 14 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Minimal 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 15 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Universe 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 16 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample2 2016-07-27 13:24:54,468 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 17 2016-07-27 13:24:55,756 [pool-11-thread-1] WARN org.glassfish.jersey.internal.Errors - The following warnings have been detected: WARNING: Parameter taskManager of type org.cytoscape.work.SynchronousTaskManager from private org.cytoscape.work.SynchronousTaskManager org.cytoscape.rest.internal.commands.resources.CommandResource.taskManager is not resolvable to a concrete type. WARNING: The (sub)resource method getTables in org.cytoscape.rest.internal.resource.TableResource contains empty path annotation. WARNING: The (sub)resource method getNetworks in org.cytoscape.rest.internal.resource.NetworkFullResource contains empty path annotation. WARNING: The (sub)resource method createNetworkView in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method getAllNetworkViews in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method deleteAllNetworkViews in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method deleteSession in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method getSessionFromFile in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method createSessionFile in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method createGroup in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. WARNING: The (sub)resource method getAllGroups in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. WARNING: The (sub)resource method deleteAllGroups in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.GroupResource.expandGroup(java.lang.Long,java.lang.Long), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.GroupResource.collapseGroup(java.lang.Long,java.lang.Long), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". WARNING: The (sub)resource method getStatus in org.cytoscape.rest.internal.resource.MiscResource contains empty path annotation. HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.MiscResource.runGarbageCollection(), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". WARNING: Return type, java.util.List>, of method, public java.util.List> org.cytoscape.rest.internal.resource.NetworkNameResource.getNetworks(java.lang.String,java.lang.String), is not resolvable to a concrete type. WARNING: The (sub)resource method getNetworks in org.cytoscape.rest.internal.resource.NetworkNameResource contains empty path annotation. WARNING: The (sub)resource method getVersions in org.cytoscape.rest.internal.resource.RootResource contains empty path annotation. WARNING: The (sub)resource method getDesktop in org.cytoscape.rest.internal.resource.UIResource contains empty path annotation. WARNING: The (sub)resource method enumerateNamespaces in org.cytoscape.rest.internal.commands.resources.CommandResource contains empty path annotation. WARNING: The (sub)resource method enumerateNamespacesHtml in org.cytoscape.rest.internal.commands.resources.CommandResource contains empty path annotation. WARNING: The (sub)resource method getStyleNames in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method deleteAllStyles in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method createStyle in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method createNetwork in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. WARNING: The (sub)resource method getNetworksAsSUID in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. WARNING: The (sub)resource method deleteAllNetworks in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. 2016-07-27 13:24:56,065 [pool-11-thread-1] INFO org.cytoscape.rest.internal.task.GrizzlyServerManager - ========== Cytoscape RESTful API service started. Listening at port: 1234 ============== 2016-07-27 13:24:58,536 [pool-16-thread-1] INFO org.cytoscape.webservice.psicquic.RegistryManager - Found 27 active PSICQUIC services. 2016-07-27 13:25:16,644 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.webservice.psicquic.PSICQUICRestClient - PSICQUIC DB search finished in 2.077 sec. 2016-07-27 13:25:21,317 [pool-18-thread-1] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ public tables created: ID = 36 2016-07-27 13:25:21,317 [pool-18-thread-1] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ public tables created: Base Graph ID = 52 2016-07-27 13:25:21,460 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.webservice.psicquic.PSICQUICRestClient - PSICUQIC Import Finished in 0.575 sec. 2016-07-27 13:25:21,638 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = PSIMI 25 Style 2016-07-27 13:25:21,639 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: PSIMI 25 Style 2016-07-27 13:25:21,639 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 18 2016-07-27 13:25:21,819 [Task-Thread-1-Factory-0x2a7ef8a] INFO org.cytoscape.task.internal.creation.CreateNetworkViewTask - Network view creation finished in 131 msec. 2016-07-27 13:29:19,078 [AWT-EventQueue-0] INFO org.cytoscape.event.internal.CyEventHelperImpl - silencing event source: BioGrid (2016/07/27 1:25:20 em, CEST) default node 2016-07-27 13:29:19,083 [AWT-EventQueue-0] INFO org.cytoscape.event.internal.CyEventHelperImpl - unsilencing event source: BioGrid (2016/07/27 1:25:20 em, CEST) default node 2016-07-27 13:34:25,179 [AWT-EventQueue-0] INFO org.cytoscape.ding.customgraphicsmgr.internal.CustomGraphicsManagerImpl - Start Saving images to: /Users/johannavillen/CytoscapeConfiguration/images3 2016-07-27 13:34:25,215 [AWT-EventQueue-0] INFO org.cytoscape.ding.customgraphicsmgr.internal.CustomGraphicsManagerImpl - ========== Image saving process finished ============= 2016-07-27 13:34:25,287 [Task-Thread-4-Factory-0x2a7ef8a] INFO org.cytoscape.ding.customgraphicsmgr.internal.PersistImageTask - Image saving process finished in 0.047 sec. 2016-07-27 13:34:25,455 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.service.command 2016-07-27 13:34:25,513 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.service.core 2016-07-27 13:34:25,527 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.log.command 2016-07-27 13:34:25,545 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.log.core 2016-07-27 13:34:25,565 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.diagnostic.command 2016-07-27 13:34:25,568 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.diagnostic.core 2016-07-27 13:34:25,576 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.command 2016-07-27 13:34:25,648 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.instance.command 2016-07-27 13:34:25,707 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.instance.core 2016-07-27 13:34:25,709 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.commands 2016-07-27 13:34:25,824 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.system.command 2016-07-27 13:34:25,839 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.system.core 2016-07-27 13:34:25,845 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.help 2016-07-27 13:34:25,847 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.bundle.command 2016-07-27 13:34:25,904 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.modules 2016-07-27 13:34:25,917 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.features.command 2016-07-27 13:34:25,946 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.features.core 2016-07-27 13:34:25,961 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.features 2016-07-27 13:34:25,964 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.cytoscape.scripting-impl 2016-07-27 13:34:25,975 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.bundle.core 2016-07-27 13:34:25,991 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.config 2016-07-27 13:34:26,009 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.console 2016-07-27 13:34:26,034 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.blueprint 2016-07-27 13:34:26,039 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.spring 2016-07-27 13:34:26,040 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.aries.blueprint.core 2016-07-27 13:34:26,048 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.aries.blueprint.cm 2016-07-27 13:34:26,186 [FelixStartLevel] INFO org.cytoscape.rest.internal.CyActivator - Shutting down REST server... 2016-07-27 13:34:42,334 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.features.repos.cfg 2016-07-27 13:34:42,339 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.org.apache.karaf.security.jmx.cfg 2016-07-27 13:34:42,344 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.config.cfg 2016-07-27 13:34:42,351 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.java.lang.Memory.cfg 2016-07-27 13:34:42,359 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.bundle.cfg 2016-07-27 13:34:42,362 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.ops4j.pax.url.mvn.cfg 2016-07-27 13:34:42,367 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.kar.cfg 2016-07-27 13:34:42,376 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.management.cfg 2016-07-27 13:34:42,382 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from jmx.acl.cfg 2016-07-27 13:34:42,392 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.jaas.cfg 2016-07-27 13:34:42,396 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.scope_bundle.cfg 2016-07-27 13:34:42,400 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.system.cfg 2016-07-27 13:34:42,407 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.jaas.cfg 2016-07-27 13:34:42,411 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.command.acl.feature.cfg 2016-07-27 13:34:42,418 [FelixStartLevel] INFO org.apache.felix.fileinstall - Creating configuration from org.apache.karaf.features.cfg 2016-07-27 13:34:43,960 [FelixStartLevel] WARN org.apache.karaf.features.internal.FeatureValidationUtil - Old style feature file without namespace found (URI: mvn:org.cytoscape.distribution/features/3.4.0/xml/features). This format is deprecated and support for it will soon be removed 2016-07-27 13:34:44,037 [FelixStartLevel] INFO org.apache.karaf.features.internal.FeaturesServiceImpl - Installing feature standard 3.0.3 2016-07-27 13:34:44,135 [FelixStartLevel] INFO org.apache.karaf.features.internal.FeaturesServiceImpl - Installing feature cytoscape-gui 3.4.0 2016-07-27 13:34:45,333 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.features.command is waiting for namespace handlers [http://karaf.apache.org/xmlns/shell/v1.1.0] 2016-07-27 13:34:45,399 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.feature into service ACL configs [org.apache.karaf.service.acl.command.feature.uninstall, org.apache.karaf.service.acl.command.feature.install] 2016-07-27 13:34:45,406 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.jaas into service ACL configs [org.apache.karaf.service.acl.command.jaas.update] 2016-07-27 13:34:45,411 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.config into service ACL configs [org.apache.karaf.service.acl.command.config.property-append, org.apache.karaf.service.acl.command.config.property-delete, org.apache.karaf.service.acl.command.config.property-set, org.apache.karaf.service.acl.command.config.edit, org.apache.karaf.service.acl.command.config.update, org.apache.karaf.service.acl.command.config.cancel, org.apache.karaf.service.acl.command.config.delete] 2016-07-27 13:34:45,436 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.shell into service ACL configs [org.apache.karaf.service.acl.command.shell.java, org.apache.karaf.service.acl.command.shell.new, org.apache.karaf.service.acl.command.shell.edit, org.apache.karaf.service.acl.command.shell.exec] 2016-07-27 13:34:45,450 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.system into service ACL configs [org.apache.karaf.service.acl.command.system.property, org.apache.karaf.service.acl.command.system.shutdown, org.apache.karaf.service.acl.command.system.start-level] 2016-07-27 13:34:45,461 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.scope_bundle into service ACL configs [org.apache.karaf.service.acl.command.scope_bundle.shell, org.apache.karaf.service.acl.command.scope_bundle.packages, org.apache.karaf.service.acl.command.scope_bundle.admin, org.apache.karaf.service.acl.command.scope_bundle.ssh, org.apache.karaf.service.acl.command.scope_bundle.osgi, org.apache.karaf.service.acl.command.scope_bundle.config, org.apache.karaf.service.acl.command.scope_bundle.jaas, org.apache.karaf.service.acl.command.scope_bundle.features, org.apache.karaf.service.acl.command.scope_bundle.log] 2016-07-27 13:34:45,487 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.kar into service ACL configs [org.apache.karaf.service.acl.command.kar.uninstall, org.apache.karaf.service.acl.command.kar.install] 2016-07-27 13:34:45,495 [FelixStartLevel] INFO org.apache.karaf.shell.security.impl.SecuredCommandConfigTransformer - Generating command ACL config org.apache.karaf.command.acl.bundle into service ACL configs [org.apache.karaf.service.acl.command.bundle.watch, org.apache.karaf.service.acl.command.bundle.update, org.apache.karaf.service.acl.command.bundle.install, org.apache.karaf.service.acl.command.bundle.uninstall, org.apache.karaf.service.acl.command.bundle.refresh, org.apache.karaf.service.acl.command.bundle.restart, org.apache.karaf.service.acl.command.bundle.stop, org.apache.karaf.service.acl.command.bundle.start] 2016-07-27 13:34:45,567 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.jaas.modules is waiting for namespace handlers [http://karaf.apache.org/xmlns/jaas/v1.0.0] 2016-07-27 13:34:45,606 [Blueprint Extender: 1] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.features.command is waiting for dependencies [(objectClass=org.apache.karaf.features.FeaturesService)] 2016-07-27 13:34:45,719 [FelixStartLevel] INFO org.apache.aries.blueprint.container.BlueprintContainerImpl - Bundle org.apache.karaf.instance.command is waiting for dependencies [(objectClass=org.apache.karaf.features.FeaturesService)] 2016-07-27 13:34:47,968 [FelixStartLevel] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default 2016-07-27 13:34:47,983 [FelixStartLevel] INFO org.cytoscape.application.internal.CyApplicationConfigurationImpl - Setting file directory = /Users/johannavillen/CytoscapeConfiguration 2016-07-27 13:34:48,023 [FelixStartLevel] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'groupSettings.props' in jar. 2016-07-27 13:34:48,242 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Custom Graphics Image property file loaded from: /Users/johannavillen/CytoscapeConfiguration/images3 2016-07-27 13:34:48,243 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Image loading process finished in 0.003 sec. 2016-07-27 13:34:48,243 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Currently, -1 images are available. 2016-07-27 13:34:48,433 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.ding.customgraphicsmgr.internal.RestoreImageTask - Image saving process finished in 0.194 sec. 2016-07-27 13:34:48,753 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,754 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,755 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,756 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,757 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,758 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,759 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,760 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,760 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,761 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,762 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,763 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,766 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,766 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:48,767 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:49,876 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.grid.props' in jar. 2016-07-27 13:34:51,141 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu separator with gravity: 4.9999 2016-07-27 13:34:51,142 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@742ac1f6,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Make Current Styles Default] with gravity: 5.0 2016-07-27 13:34:51,144 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@742ac1f6,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Copy Style...] with gravity: 2.0 2016-07-27 13:34:51,146 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@742ac1f6,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create New Style...] with gravity: 1.0 2016-07-27 13:34:51,148 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu separator with gravity: 5.9999 2016-07-27 13:34:51,149 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@742ac1f6,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create Legend...] with gravity: 6.0 2016-07-27 13:34:51,149 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@742ac1f6,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Rename Style...] with gravity: 3.0 2016-07-27 13:34:51,150 [AWT-EventQueue-0] INFO org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=com.apple.laf.AquaMenuBorder@742ac1f6,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=true,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Remove Style] with gravity: 4.0 2016-07-27 13:34:51,384 [FelixStartLevel] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ private tables created: ID = 2 2016-07-27 13:34:51,384 [FelixStartLevel] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ private tables created: Base Graph ID = 18 2016-07-27 13:34:51,704 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.hierarchical.props' in jar. 2016-07-27 13:34:51,708 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.circular.props' in jar. 2016-07-27 13:34:51,712 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.stacked-node-layout.props' in jar. 2016-07-27 13:34:51,715 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.attribute-circle.props' in jar. 2016-07-27 13:34:51,719 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.degree-circle.props' in jar. 2016-07-27 13:34:51,723 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.attributes-layout.props' in jar. 2016-07-27 13:34:51,735 [pool-7-thread-3] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.isom.props' in jar. 2016-07-27 13:34:51,738 [pool-7-thread-1] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.fruchterman-rheingold.props' in jar. 2016-07-27 13:34:51,742 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.kamada-kawai.props' in jar. 2016-07-27 13:34:51,992 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.force-directed.props' in jar. 2016-07-27 13:34:52,673 [FelixStartLevel] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:52,888 [pool-8-thread-1] INFO org.cytoscape.app.internal.net.server.CyHttpdImpl - Server socket started on 127.0.0.1:2607 2016-07-27 13:34:53,209 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: DEGREE 2016-07-27 13:34:53,210 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: INDEGREE 2016-07-27 13:34:53,211 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: OUTDEGREE 2016-07-27 13:34:53,211 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: SOURCEID 2016-07-27 13:34:53,211 [FelixStartLevel] INFO org.cytoscape.equations.internal.EquationParserImpl - New Function Registered: TARGETID 2016-07-27 13:34:54,588 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = BioPAX 2016-07-27 13:34:54,588 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: BioPAX 2016-07-27 13:34:54,588 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 2 2016-07-27 13:34:54,710 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = BioPAX_SIF 2016-07-27 13:34:54,710 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: BioPAX_SIF 2016-07-27 13:34:54,710 [pool-9-thread-1] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 3 2016-07-27 13:34:54,993 [pool-9-thread-1] INFO org.cytoscape.webservice.internal.ui.WebServiceImportDialog - New network import client registered: Universal Interaction Database Client 2016-07-27 13:34:55,010 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:55,011 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:55,083 [pool-9-thread-1] INFO org.cytoscape.webservice.internal.ui.WebServiceImportDialog - New network import client registered: BioMart Client 2016-07-27 13:34:55,291 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:55,292 [pool-9-thread-1] INFO org.cytoscape.io.internal.write.AbstractWriterManager - adding IO taskFactory 2016-07-27 13:34:55,293 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 13:34:55,295 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 13:34:55,296 [pool-9-thread-1] WARN org.cytoscape.io.internal.write.AbstractWriterManager - Specified factory is null or has wrong DataCategory (SESSION) 2016-07-27 13:34:56,071 [pool-9-thread-1] INFO org.cytoscape.rest.internal.CyActivator - Initializing cyREST API server... 2016-07-27 13:34:56,072 [pool-9-thread-1] INFO org.cytoscape.rest.internal.CyActivator - cyREST dependency import took: 1 msec. 2016-07-27 13:34:56,103 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Arabidopsis_thaliana_Columbia-3.4.129.mitab 2016-07-27 13:34:56,104 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - BioGRID release version is: 3.4.129 2016-07-27 13:34:56,106 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Caenorhabditis_elegans-3.4.129.mitab 2016-07-27 13:34:56,106 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Danio_rerio-3.4.129.mitab 2016-07-27 13:34:56,106 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Drosophila_melanogaster-3.4.129.mitab 2016-07-27 13:34:56,106 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Escherichia_coli_K12_MG1655-3.4.129.mitab 2016-07-27 13:34:56,106 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Homo_sapiens-3.4.129.mitab 2016-07-27 13:34:56,106 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Mus_musculus-3.4.129.mitab 2016-07-27 13:34:56,107 [pool-9-thread-1] INFO org.cytoscape.datasource.biogrid.internal.BiogridDataLoader - * Processing local organism network file: BIOGRID-ORGANISM-Saccharomyces_cerevisiae_S288c-3.4.129.mitab 2016-07-27 13:34:56,981 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.io.internal.read.GenericReaderManager - Filter returns Accepted. Need to check priority: org.cytoscape.io.internal.read.vizmap.VizmapXMLReaderFactory@435fa3a1 2016-07-27 13:34:56,985 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.io.internal.read.GenericReaderManager - Successfully found compatible ReaderFactory org.cytoscape.io.internal.read.vizmap.VizmapXMLReaderFactory@435fa3a1 2016-07-27 13:34:57,169 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Curved 2016-07-27 13:34:57,178 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Gradient1 2016-07-27 13:34:57,539 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Big Labels 2016-07-27 13:34:57,577 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default 2016-07-27 13:34:57,645 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = default black 2016-07-27 13:34:57,652 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Directed 2016-07-27 13:34:57,658 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Marquee 2016-07-27 13:34:57,665 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Minimal 2016-07-27 13:34:57,670 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Nested Network Style 2016-07-27 13:34:57,678 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Ripple 2016-07-27 13:34:57,683 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample1 2016-07-27 13:34:57,688 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample2 2016-07-27 13:34:57,698 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Sample3 2016-07-27 13:34:57,710 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Solid 2016-07-27 13:34:57,713 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualStyleImpl - New Visual Style Created: Style Name = Universe 2016-07-27 13:34:57,715 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Marquee 2016-07-27 13:34:57,715 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 4 2016-07-27 13:34:57,716 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample1 2016-07-27 13:34:57,716 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 5 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Directed 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 6 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Universe 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 7 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Gradient1 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 8 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Minimal 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 9 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Curved 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 10 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample2 2016-07-27 13:34:57,717 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 11 2016-07-27 13:34:57,718 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Solid 2016-07-27 13:34:57,718 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 12 2016-07-27 13:34:57,718 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Ripple 2016-07-27 13:34:57,718 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 13 2016-07-27 13:34:57,718 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Nested Network Style 2016-07-27 13:34:57,718 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 14 2016-07-27 13:34:57,719 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: default black 2016-07-27 13:34:57,719 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 15 2016-07-27 13:34:57,719 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Sample3 2016-07-27 13:34:57,719 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 16 2016-07-27 13:34:57,719 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - New visual Style registered to VMM: Big Labels 2016-07-27 13:34:57,719 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl - Total Number of VS in VMM = 17 2016-07-27 13:34:58,919 [pool-7-thread-2] WARN org.cytoscape.property.AbstractConfigDirPropsReader - couldn't find resource 'layout.force-directed-cl.props' in jar. 2016-07-27 13:34:59,748 [pool-10-thread-1] WARN org.glassfish.jersey.internal.Errors - The following warnings have been detected: WARNING: Parameter taskManager of type org.cytoscape.work.SynchronousTaskManager from private org.cytoscape.work.SynchronousTaskManager org.cytoscape.rest.internal.commands.resources.CommandResource.taskManager is not resolvable to a concrete type. WARNING: The (sub)resource method getTables in org.cytoscape.rest.internal.resource.TableResource contains empty path annotation. WARNING: The (sub)resource method deleteAllNetworkViews in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method createNetworkView in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method getAllNetworkViews in org.cytoscape.rest.internal.resource.NetworkViewResource contains empty path annotation. WARNING: The (sub)resource method getNetworks in org.cytoscape.rest.internal.resource.NetworkFullResource contains empty path annotation. WARNING: The (sub)resource method deleteSession in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method getSessionFromFile in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method createSessionFile in org.cytoscape.rest.internal.resource.SessionResource contains empty path annotation. WARNING: The (sub)resource method createGroup in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. WARNING: The (sub)resource method getAllGroups in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. WARNING: The (sub)resource method deleteAllGroups in org.cytoscape.rest.internal.resource.GroupResource contains empty path annotation. HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.GroupResource.expandGroup(java.lang.Long,java.lang.Long), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.GroupResource.collapseGroup(java.lang.Long,java.lang.Long), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". WARNING: The (sub)resource method getStatus in org.cytoscape.rest.internal.resource.MiscResource contains empty path annotation. HINT: A HTTP GET method, public void org.cytoscape.rest.internal.resource.MiscResource.runGarbageCollection(), returns a void type. It can be intentional and perfectly fine, but it is a little uncommon that GET method returns always "204 No Content". WARNING: The (sub)resource method getVersions in org.cytoscape.rest.internal.resource.RootResource contains empty path annotation. WARNING: Return type, java.util.List>, of method, public java.util.List> org.cytoscape.rest.internal.resource.NetworkNameResource.getNetworks(java.lang.String,java.lang.String), is not resolvable to a concrete type. WARNING: The (sub)resource method getNetworks in org.cytoscape.rest.internal.resource.NetworkNameResource contains empty path annotation. WARNING: The (sub)resource method getDesktop in org.cytoscape.rest.internal.resource.UIResource contains empty path annotation. WARNING: The (sub)resource method enumerateNamespaces in org.cytoscape.rest.internal.commands.resources.CommandResource contains empty path annotation. WARNING: The (sub)resource method enumerateNamespacesHtml in org.cytoscape.rest.internal.commands.resources.CommandResource contains empty path annotation. WARNING: The (sub)resource method getStyleNames in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method deleteAllStyles in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method createStyle in org.cytoscape.rest.internal.resource.StyleResource contains empty path annotation. WARNING: The (sub)resource method deleteAllNetworks in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. WARNING: The (sub)resource method createNetwork in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. WARNING: The (sub)resource method getNetworksAsSUID in org.cytoscape.rest.internal.resource.NetworkResource contains empty path annotation. 2016-07-27 13:35:00,109 [pool-10-thread-1] INFO org.cytoscape.rest.internal.task.GrizzlyServerManager - ========== Cytoscape RESTful API service started. Listening at port: 1234 ============== 2016-07-27 13:35:07,496 [pool-16-thread-1] INFO org.cytoscape.webservice.psicquic.RegistryManager - Found 26 active PSICQUIC services. 2016-07-27 13:35:50,529 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.io.internal.read.GenericReaderManager - Filter returns Accepted. Need to check priority: org.cytoscape.tableimport.internal.task.ImportNetworkTableReaderFactory@4e5fc172 2016-07-27 13:35:50,545 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.io.internal.read.GenericReaderManager - Successfully found compatible ReaderFactory org.cytoscape.tableimport.internal.task.ImportNetworkTableReaderFactory@4e5fc172 2016-07-27 13:36:59,550 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ public tables created: ID = 36 2016-07-27 13:36:59,553 [Task-Thread-1-Factory-0x331a648c] INFO org.cytoscape.model.internal.CyNetworkFactoryImpl - CyNetwork w/ public tables created: Base Graph ID = 52 2016-07-27 13:39:40,624 [AWT-EventQueue-0] INFO org.cytoscape.ding.customgraphicsmgr.internal.CustomGraphicsManagerImpl - Start Saving images to: /Users/johannavillen/CytoscapeConfiguration/images3 2016-07-27 13:39:40,637 [AWT-EventQueue-0] INFO org.cytoscape.ding.customgraphicsmgr.internal.CustomGraphicsManagerImpl - ========== Image saving process finished ============= 2016-07-27 13:39:40,645 [Task-Thread-3-Factory-0x331a648c] INFO org.cytoscape.ding.customgraphicsmgr.internal.PersistImageTask - Image saving process finished in 0.004 sec. 2016-07-27 13:39:40,789 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.service.command 2016-07-27 13:39:40,800 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.service.core 2016-07-27 13:39:40,801 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.log.command 2016-07-27 13:39:40,823 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.log.core 2016-07-27 13:39:40,829 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.diagnostic.command 2016-07-27 13:39:40,832 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.diagnostic.core 2016-07-27 13:39:40,838 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.command 2016-07-27 13:39:40,876 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.instance.command 2016-07-27 13:39:41,343 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.instance.core 2016-07-27 13:39:41,346 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.commands 2016-07-27 13:39:41,407 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.system.command 2016-07-27 13:39:41,420 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.system.core 2016-07-27 13:39:41,422 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.help 2016-07-27 13:39:41,424 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.bundle.command 2016-07-27 13:39:41,465 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.modules 2016-07-27 13:39:41,468 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.features.command 2016-07-27 13:39:41,492 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.features.core 2016-07-27 13:39:41,498 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.features 2016-07-27 13:39:41,500 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.cytoscape.scripting-impl 2016-07-27 13:39:41,504 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.bundle.core 2016-07-27 13:39:41,508 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.jaas.config 2016-07-27 13:39:41,513 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.shell.console 2016-07-27 13:39:41,520 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.blueprint 2016-07-27 13:39:41,522 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.karaf.deployer.spring 2016-07-27 13:39:41,524 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.aries.blueprint.core 2016-07-27 13:39:41,527 [FelixShutdown] INFO org.apache.aries.blueprint.container.BlueprintExtender - Destroying BlueprintContainer for bundle org.apache.aries.blueprint.cm 2016-07-27 13:39:41,560 [FelixStartLevel] INFO org.cytoscape.rest.internal.CyActivator - Shutting down REST server...