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  1. IGB
  2. IGBF-2475

Fix the org.xml.sax.SAXParseException occurrence in IGB

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:

          Description

          When we run the IGB following exception is getting thrown: (the exception is occurring in the survey plugin of IGB)

          [Fatal Error] :1:50: White spaces are required between publicId and systemId.
          com.affymetrix.igb.survey.Activator - Exception in Activator.registerService() -> White spaces are required between publicId and systemId.
          org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.
          at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
          at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
          at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
          at com.affymetrix.igb.survey.SurveyParser.parse(SurveyParser.java:40)
          at com.affymetrix.igb.survey.Activator.getServices(Activator.java:59)
          at com.affymetrix.igb.survey.Activator.getServices(Activator.java:40)
          at org.lorainelab.igb.services.XServiceRegistrar.getServices(XServiceRegistrar.java:26)
          at org.lorainelab.igb.services.SimpleServiceRegistrar.registerService(SimpleServiceRegistrar.java:19)
          at org.lorainelab.igb.services.XServiceRegistrar.access$001(XServiceRegistrar.java:13)
          at org.lorainelab.igb.services.XServiceRegistrar$1.addingService(XServiceRegistrar.java:47)
          at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:941)
          at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:870)
          at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:256)
          at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:229)
          at org.osgi.util.tracker.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:901)
          at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:987)
          at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:838)
          at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:545)
          at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4560)
          at org.apache.felix.framework.Felix.registerService(Felix.java:3542)
          at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:348)
          at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:355)
          at com.affymetrix.igb.Activator$1.initializeWindowService(Activator.java:143)
          at com.affymetrix.igb.Activator$1.addingService(Activator.java:134)
          at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:941)
          at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:870)
          at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:256)
          at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:229)
          at org.osgi.util.tracker.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:901)
          at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:987)
          at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:838)
          at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:545)
          at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4560)
          at org.apache.felix.framework.Felix.registerService(Felix.java:3542)
          at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:348)
          at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003)
          at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992)
          at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134)
          at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044)
          at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841)
          at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931)
          at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895)
          at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480)
          at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401)
          at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210)
          at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148)
          at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432)
          at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:987)
          at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:838)
          at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:545)
          at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4560)
          at org.apache.felix.framework.Felix.registerService(Felix.java:3542)
          at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:348)
          at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003)
          at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992)
          at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134)
          at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044)
          at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841)
          at org.apache.felix.scr.impl.manager.AbstractComponentManager.enable(AbstractComponentManager.java:419)
          at org.apache.felix.scr.impl.config.ConfigurableComponentHolder.enableComponents(ConfigurableComponentHolder.java:376)
          at org.apache.felix.scr.impl.BundleComponentActivator.initialize(BundleComponentActivator.java:172)
          at org.apache.felix.scr.impl.BundleComponentActivator.<init>(BundleComponentActivator.java:120)
          at org.apache.felix.scr.impl.Activator.loadComponents(Activator.java:258)
          at org.apache.felix.scr.impl.Activator.access$000(Activator.java:45)
          at org.apache.felix.scr.impl.Activator$ScrExtension.start(Activator.java:185)
          at org.apache.felix.utils.extender.AbstractExtender.createExtension(AbstractExtender.java:259)
          at org.apache.felix.utils.extender.AbstractExtender.modifiedBundle(AbstractExtender.java:232)
          at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:479)
          at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:414)
          at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:232)
          at org.osgi.util.tracker.BundleTracker$Tracked.bundleChanged(BundleTracker.java:443)
          at org.apache.felix.framework.util.EventDispatcher.invokeBundleListenerCallback(EventDispatcher.java:913)
          at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:834)
          at org.apache.felix.framework.util.EventDispatcher.fireBundleEvent(EventDispatcher.java:516)
          at org.apache.felix.framework.Felix.fireBundleEvent(Felix.java:4544)
          at org.apache.felix.framework.Felix.startBundle(Felix.java:2166)
          at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:977)
          at org.apache.felix.fileinstall.internal.DirectoryWatcher.startBundle(DirectoryWatcher.java:1245)
          at org.apache.felix.fileinstall.internal.DirectoryWatcher.startBundles(DirectoryWatcher.java:1217)
          at org.apache.felix.fileinstall.internal.DirectoryWatcher.doProcess(DirectoryWatcher.java:509)
          at org.apache.felix.fileinstall.internal.DirectoryWatcher.process(DirectoryWatcher.java:358)
          at org.apache.felix.fileinstall.internal.DirectoryWatcher.run(DirectoryWatcher.java:310)

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              prutha Prutha Kulkarni (Inactive) created issue -
              prutha Prutha Kulkarni (Inactive) made changes -
              Field Original Value New Value
              Epic Link IGBF-1765 [ 17855 ]
              prutha Prutha Kulkarni (Inactive) made changes -
              Rank Ranked higher
              pbadzuh Philip Badzuh (Inactive) made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              pbadzuh Philip Badzuh (Inactive) made changes -
              Assignee Philip Badzuh [ pbadzuh ]
              pbadzuh Philip Badzuh (Inactive) made changes -
              Story Points 1 2
              pbadzuh Philip Badzuh (Inactive) made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              pbadzuh Philip Badzuh (Inactive) made changes -
              Assignee Philip Badzuh [ pbadzuh ]
              ann.loraine Ann Loraine made changes -
              Comment [ Maybe also look at this file? (It creates a "non-validating" parser.)

              * core/quickload/src/main/java/org/lorainelab/igb/quickload/util/AnnotsParser.java ]
              ann.loraine Ann Loraine made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
              ann.loraine Ann Loraine made changes -
              Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Rank Ranked lower
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              prutha Prutha Kulkarni (Inactive) made changes -
              Assignee Prutha Kulkarni [ prutha ]
              prutha Prutha Kulkarni (Inactive) made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              prutha Prutha Kulkarni (Inactive) made changes -
              Story Points 2 3.5
              prutha Prutha Kulkarni (Inactive) made changes -
              Summary Investigate on the org.xml.sax.SAXParseException occurrence on running IGB Fix the org.xml.sax.SAXParseException occurrence in IGB
              prutha Prutha Kulkarni (Inactive) made changes -
              Assignee Prutha Kulkarni [ prutha ]
              prutha Prutha Kulkarni (Inactive) made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              ann.loraine Ann Loraine made changes -
              Sprint Summer 4: 14 Jul - 28 Jul [ 99 ] Summer 4: 14 Jul - 28 Jul, Summer 5: 29 Jul - 12 Aug [ 99, 100 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              ann.loraine Ann Loraine made changes -
              Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
              rweidenh Logan Weidenhammer (Inactive) made changes -
              Assignee Rachel Weidenhammer [ rweidenh ]
              rweidenh Logan Weidenhammer (Inactive) made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              rweidenh Logan Weidenhammer (Inactive) made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              rweidenh Logan Weidenhammer (Inactive) made changes -
              Assignee Rachel Weidenhammer [ rweidenh ] Prutha Kulkarni [ prutha ]
              prutha Prutha Kulkarni (Inactive) made changes -
              Assignee Prutha Kulkarni [ prutha ]
              prutha Prutha Kulkarni (Inactive) made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              ann.loraine Ann Loraine made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              ann.loraine Ann Loraine made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              shamika Shamika Gajanan Kulkarni (Inactive) made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              shamika Shamika Gajanan Kulkarni (Inactive) made changes -
              Assignee Shamika Gajanan Kulkarni [ shamika ]
              shamika Shamika Gajanan Kulkarni (Inactive) made changes -
              Resolution Done [ 10000 ]
              Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
              shamika Shamika Gajanan Kulkarni (Inactive) made changes -
              Assignee Shamika Gajanan Kulkarni [ shamika ] Prutha Kulkarni [ prutha ]

                People

                • Assignee:
                  prutha Prutha Kulkarni (Inactive)
                  Reporter:
                  prutha Prutha Kulkarni (Inactive)
                • Votes:
                  0 Vote for this issue
                  Watchers:
                  5 Start watching this issue

                  Dates

                  • Created:
                    Updated:
                    Resolved: