[IGBF-3441] Fix DAS error - JIRA UNCC

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:
Improve IGB for users
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.

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Issue Links

relates to

IGBF-3103 Enable IGB to follow http to https redirect for Quickload meta-data files

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Nowlan Freese added a comment - 13/Sep/23 1:45 PM

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

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Nowlan Freese added a comment - 13/Sep/23 1:45 PM 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

4 older comments

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Karthik Raveendran added a comment - 17/Sep/23 1:40 AM

No errors in logs. Requesting Pull Request.

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Karthik Raveendran added a comment - 17/Sep/23 1:40 AM No errors in logs. Requesting Pull Request.

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Nowlan Freese added a comment - 18/Sep/23 10:01 AM - edited

[~aloraine] - Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/948

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Nowlan Freese added a comment - 18/Sep/23 10:01 AM - edited [~aloraine] - Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/948

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Ann Loraine added a comment - 18/Sep/23 1:27 PM

PR is merged into main-JDK8.

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Ann Loraine added a comment - 18/Sep/23 1:27 PM PR is merged into main-JDK8.

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Karthik Raveendran added a comment - 20/Sep/23 10:37 AM

After including this changes in main-JDK8-r6, I tested it with no errors.

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Karthik Raveendran added a comment - 20/Sep/23 10:37 AM After including this changes in main-JDK8-r6, I tested it with no errors.

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Karthik Raveendran added a comment - 21/Sep/23 10:37 AM

Tested the installer in https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/. No errors found.

Moving to close.

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Karthik Raveendran added a comment - 21/Sep/23 10:37 AM Tested the installer in https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/ . No errors found. Moving to close.

People

Assignee:

Nowlan Freese

Reporter:

Nowlan Freese

Votes:

0 Vote for this issue

Watchers:

3 Start watching this issue

Dates

Created:

13/Sep/23 1:44 PM

Updated:

07/Feb/24 1:52 PM

Resolved:

21/Sep/23 10:37 AM