Details
-
Type: Bug
-
Status: Closed (View Workflow)
-
Priority: Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 10.0.0 Major Release
-
Labels:None
-
Story Points:1
-
Epic Link:
-
Sprint:Fall 1 - Sep 5, Fall 2 2023 Sep 17
Description
Situation: When starting IGB 9.1.10 the below error is occurring, causing the DAS data to fail to load.
Task: Investigate the DAS error.
Attachments
Issue Links
- relates to
-
IGBF-3103 Enable IGB to follow http to https redirect for Quickload meta-data files
- Closed
Activity
Error:
10:21:14.674 ERROR o.l.igb.das.utils.DasServerUtils - Could not initialize JAXBContext for org.lorainelab.igb.das.model.dsn.DasDsn javax.xml.bind.UnmarshalException: null at javax.xml.bind.helpers.AbstractUnmarshallerImpl.createUnmarshalException(AbstractUnmarshallerImpl.java:335) ~[na:1.8.0_332] at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.createUnmarshalException(UnmarshallerImpl.java:563) ~[na:1.8.0_332] at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:249) ~[na:1.8.0_332] at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal(UnmarshallerImpl.java:214) ~[na:1.8.0_332] at javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(AbstractUnmarshallerImpl.java:140) ~[na:1.8.0_332] at javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(AbstractUnmarshallerImpl.java:123) ~[na:1.8.0_332] at org.lorainelab.igb.das.utils.DasServerUtils.retrieveDsnResponse(DasServerUtils.java:68) ~[das-9.1.10.jar:na] at org.lorainelab.igb.das.DasDataProvider.initialize(DasDataProvider.java:103) [das-9.1.10.jar:na] at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:333) [igb-9.1.10.jar:na] at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$87(DataProviderManager.java:324) [igb-9.1.10.jar:na] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) ~[na:1.8.0_332] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_332] at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_332] at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_332] at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_332] at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_332] at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) ~[na:1.8.0_332] at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_332] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) ~[na:1.8.0_332] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) ~[na:1.8.0_332] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) ~[na:1.8.0_332] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) ~[na:1.8.0_332] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) ~[na:1.8.0_332] at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ~[na:1.8.0_332] Caused by: org.xml.sax.SAXParseException: White spaces are required between publicId and systemId. at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:204) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:178) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:399) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:326) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1466) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.impl.XMLScanner.scanExternalID(XMLScanner.java:1066) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.scanDoctypeDecl(XMLDocumentScannerImpl.java:641) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:923) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:601) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:504) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:841) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:770) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) ~[na:1.8.0_332] at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:642) ~[na:1.8.0_332] at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:243) ~[na:1.8.0_332] ... 21 common frames omitted
Nowlan Freese
added a comment - Error:
10:21:14.674 ERROR o.l.igb.das.utils.DasServerUtils - Could not initialize JAXBContext for org.lorainelab.igb.das.model.dsn.DasDsn
javax.xml.bind.UnmarshalException: null
at javax.xml.bind.helpers.AbstractUnmarshallerImpl.createUnmarshalException(AbstractUnmarshallerImpl.java:335) ~[na:1.8.0_332]
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.createUnmarshalException(UnmarshallerImpl.java:563) ~[na:1.8.0_332]
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:249) ~[na:1.8.0_332]
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal(UnmarshallerImpl.java:214) ~[na:1.8.0_332]
at javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(AbstractUnmarshallerImpl.java:140) ~[na:1.8.0_332]
at javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(AbstractUnmarshallerImpl.java:123) ~[na:1.8.0_332]
at org.lorainelab.igb.das.utils.DasServerUtils.retrieveDsnResponse(DasServerUtils.java:68) ~[das-9.1.10.jar:na]
at org.lorainelab.igb.das.DasDataProvider.initialize(DasDataProvider.java:103) [das-9.1.10.jar:na]
at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:333) [igb-9.1.10.jar:na]
at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$87(DataProviderManager.java:324) [igb-9.1.10.jar:na]
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) ~[na:1.8.0_332]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_332]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_332]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_332]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_332]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_332]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) ~[na:1.8.0_332]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_332]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) ~[na:1.8.0_332]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) ~[na:1.8.0_332]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) ~[na:1.8.0_332]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) ~[na:1.8.0_332]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) ~[na:1.8.0_332]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) ~[na:1.8.0_332]
Caused by: org.xml.sax.SAXParseException: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:204) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:178) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:399) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:326) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1466) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.impl.XMLScanner.scanExternalID(XMLScanner.java:1066) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.scanDoctypeDecl(XMLDocumentScannerImpl.java:641) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:923) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:601) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:504) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:841) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:770) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) ~[na:1.8.0_332]
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:642) ~[na:1.8.0_332]
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:243) ~[na:1.8.0_332]
... 21 common frames omitted
Tested the installer in https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/. No errors found.
Moving to close.