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Bug #4585

Parser fails to launch from within Morpho!

Added by Sandeep Namilikonda over 9 years ago. Updated over 9 years ago.

Status:
Resolved
Priority:
Immediate
Category:
dataserver
Target version:
Start date:
11/25/2009
Due date:
% Done:

0%

Estimated time:
Bugzilla-Id:
4585

Description

Using the latest Morpho build, when creating a new package or re-visiting an
existing assessment, the parser component cannot be launched with the console
displaying the following messages and errors.

(NOTE: The following only shows messages output corresponding to the object
that resulted in the error. The messages below were generated when trying to
re-open a parsed assessment by clicking "Assessment Items" option under
"Documentation" menu on the Morpho interface.)

Creating new DataPackage Object
id: namilikonda.41.4
location: local
opening local file
local file opened
Current ClassLoader is: sun.misc.Launcher$AppClassLoader
Parser created is: org.apache.xerces.jaxp.DocumentBuilderImpl
Current ClassLoader is: sun.misc.Launcher$AppClassLoader
Parser created is: org.apache.xerces.jaxp.DocumentBuilderImpl
the second line string is: edml:edml packageId="namilikonda.41.4" system="first" xmlns:edml="edml://ecoinformatics.org/edml" xmlns:lom="http://ltsc.ieee.org/xsd/LOM" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="edml://ecoinformatics.org/edml edml.xsd"
Creating new DataPackage Object
id: namilikonda.41.4
location: local
opening local file
local file opened
Current ClassLoader is: sun.misc.Launcher$AppClassLoader
Parser created is: org.apache.xerces.jaxp.DocumentBuilderImpl
Current ClassLoader is: sun.misc.Launcher$AppClassLoader
Parser created is: org.apache.xerces.jaxp.DocumentBuilderImpl
The external package is namilikonda.41.4
The reference id in external package is 1236231088109
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at java.util.Calendar.setTime(Unknown Source)
at java.text.SimpleDateFormat.format(Unknown Source)
at java.text.SimpleDateFormat.format(Unknown Source)
at java.text.DateFormat.format(Unknown Source)
at edu.ucsb.nceas.morpho.first.plugins.wizard.pages.AssessmentPage.getPageData(AssessmentPage.java:652)
at edu.ucsb.nceas.morpho.first.plugins.wizard.pages.AssessmentPage.rememberPreviousValues(AssessmentPage.java:934)
at edu.ucsb.nceas.morpho.first.plugins.wizard.pages.AssessmentPage.onLoadAction(AssessmentPage.java:515)
at edu.ucsb.nceas.morpho.first.plugins.wizard.EdMLWizardContainerFrame.setCurrentPage(EdMLWizardContainerFrame.java:182)
at edu.ucsb.nceas.morpho.first.plugins.wizard.EdMLWizardContainerFrame.nextAction(EdMLWizardContainerFrame.java:506)
at edu.ucsb.nceas.morpho.first.plugins.wizard.EdMLWizardContainerFrame$7.actionPerformed(EdMLWizardContainerFrame.java:409)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Wizard complete - Will now create an AbstractDataPackage..
AbstractDataPackage complete
/xpathKeyMap/contextNode[@name='package']/accessionNumber maps to [#text: /*[local-name()='edml']/@packageId]
node path is /*[local-name()='edml']/@packageId
setting value to temporary.1.1
Exception in thread "AWT-EventQueue-0" java.lang.AbstractMethodError: edu.ucsb.nceas.morpho.first.edml.EdmlPackagePlugin.openNewDataPackage(Ledu/ucsb/nceas/morpho/datapackage/AbstractDataPackage;Ledu/ucsb/nceas/morpho/framework/ButterflyFlapCoordinator;)Ledu/ucsb/nceas/morpho/framework/MorphoFrame;
at edu.ucsb.nceas.morpho.first.edml.commands.CreateNewDataPackageCommand$1.wizardComplete(CreateNewDataPackageCommand.java:102)
at edu.ucsb.nceas.morpho.first.plugins.wizard.EdMLWizardContainerFrame.finishAction(EdMLWizardContainerFrame.java:526)
at edu.ucsb.nceas.morpho.first.plugins.wizard.EdMLWizardContainerFrame$8.actionPerformed(EdMLWizardContainerFrame.java:415)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Parser created is: org.apache.xerces.parsers.SAXParser
Created root query group.
(2) Executing local query...
(3.0) Creating DOM parser...
Current ClassLoader is: sun.misc.Launcher$AppClassLoader
Parser created is: org.apache.xerces.jaxp.DocumentBuilderImpl
(3.1) DOM parser created...
selectedId is: namilikonda.918.2
the package name is: namilikonda.918
the number of previous version is: 1
selectedId is: namilikonda.918.2
the package name is: namilikonda.918
the number of previous version is: 1
DataPackage: Got service request to open: namilikonda.918.2 from local.
the second line string is: edml:edml packageId="namilikonda.918.2" system="first" xmlns:edml="edml://ecoinformatics.org/edml" xmlns:lom="http://ltsc.ieee.org/xsd/LOM" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="edml://ecoinformatics.org/edml edml.xsd"
Creating new DataPackage Object
id: namilikonda.918.2
location: local
opening local file
local file opened
Current ClassLoader is: sun.misc.Launcher$AppClassLoader
Parser created is: org.apache.xerces.jaxp.DocumentBuilderImpl
Current ClassLoader is: sun.misc.Launcher$AppClassLoader
Parser created is: org.apache.xerces.jaxp.DocumentBuilderImpl
Adding window: Data Package: namilikonda.918.2
ViewContainer startUp time: 281
entityList is null!
genericName: /xpathKeyMap/contextNode[@name='package']/title
path: /*[local-name()='edml']/assessment/title
Document root node has 6 attributes
genericName: /xpathKeyMap/contextNode[@name='package']/accessionNumber
path: /*[local-name()='edml']/@packageId
Document root node has 6 attributes
EntityItems vector is null
XMLTransformer: ClassLoader would have been: sun.misc.Launcher$AppClassLoader
XMLTransformer: ...but from Morpho, setting ClassLoader to: sun.misc.Launcher$AppClassLoader
genericName: /xpathKeyMap/contextNode[@name='package']/accessionNumber
path: /*[local-name()='edml']/@packageId
Document root node has 6 attributes
DVCP startUp time: 2156
genericName: /xpathKeyMap/contextNode[@name='package']/accessionNumber
path: /*[local-name()='edml']/@packageId
Document root node has 6 attributes
Exception in thread "AWT-EventQueue-0" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
at java.lang.String.substring(Unknown Source)
at edu.ucsb.nceas.morpho.datapackage.AccessionNumber.getParts(AccessionNumber.java:283)
at edu.ucsb.nceas.morpho.first.edml.commands.RunAssessmentParseCommand.execute(RunAssessmentParseCommand.java:76)
at edu.ucsb.nceas.morpho.util.GUIAction.actionPerformed(GUIAction.java:410)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

History

#1 Updated by Sandeep Namilikonda over 9 years ago

An attempt to create a new data package result in the following error message
and the parser not being launched!

Action fired: New Data Package

  • Error in AbstractDataPackage insertSubtree():
    XMLUtilities.getNodeListWithXPath() returned NULL for xpath: /xpathKeyMap/insertionList[@name='projectTitle']/prevNode and /xpathKeyMap/insertionList[@name='projectTitle']/nextNode
    genericName: /xpathKeyMap/contextNode[@name='package']/accessionNumber
    path: /*[local-name()='edml']/@packageId
    Document root node has 6 attributes
    Parser created is: org.apache.xerces.parsers.SAXParser

#2 Updated by ben leinfelder over 9 years ago

there was a NPE when trying to clear a non-existent temporary save directory that was part of the parsing process. i added a check to avoid this null pointer. I do not believe this had anything to do with the morpho.jar

#3 Updated by Redmine Admin over 6 years ago

Original Bugzilla ID was 4585

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