[IGBF-2475] Fix the org.xml.sax.SAXParseException occurrence in IGB - JIRA UNCC

Details

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

Story Points:
3.5
Epic Link:
Improve IGB for users
Sprint:
Summer 4: 14 Jul - 28 Jul, Summer 5: 3 Aug - 14 Aug

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)

Attachments

Activity

Ascending order - Click to sort in descending order

Hide

Permalink

Philip Badzuh (Inactive) added a comment - 23/Jul/20 3:19 PM

Some notes on my deep dive into this issue:

The fatal error is being thrown in line 1071 of com.sun.org.apache.xerces.internal.impl.XMLScanner:

XMLScanner.java

if (!fEntityScanner.skipSpaces() && !optionalSystemId) {
    reportFatalError("SpaceRequiredBetweenPublicAndSystem", null);
}

I think the error has to do with the parser failing to validate the nonexistent doctype declaration.

I tried to configure the DTD in surveys.xml, as shown below, but the error persisted:

surveys.xml

<!DOCTYPE surveys [
    <!ELEMENT surveys (survey)>
    <!ELEMENT survey (name,description,link,startdate,enddate)>
    <!ELEMENT name (#PCDATA)>
    <!ELEMENT description (#PCDATA)>
    <!ELEMENT link (#PCDATA)>
    <!ELEMENT startdate (#PCDATA)>
    <!ELEMENT enddate (#PCDATA)>
]>

In trying to configure the DocumentBuilderFactory in SurveyParser to be less stringent with regards to xml formatting validation at [~aloraine]'s suggestion, I tried several options from the list here, in addition to those used in AnnotsParser, but I couldn't get any configuration to work.

I tried to make the implementation of SurveyParser mimic that of UpdateParser, however, the issue still persisted.

I have reverted to what seems to be the previously used deserialization method, which was commented out above the one that is currently causing this error. Although the Fatal Error is still printed, now no exception is thrown.
https://bitbucket.org/pbadzuh/igb_pbdev/branch/IGBF-2475#diff

This isn't exactly a solution, but I'm not entirely sure what the exact problem is and have a feeling that the fatal error message may be misleading. From my further research online, it appears to be a generic error. Please let me know what you think.

Show

Philip Badzuh (Inactive) added a comment - 23/Jul/20 3:19 PM Some notes on my deep dive into this issue: The fatal error is being thrown in line 1071 of com.sun.org.apache.xerces.internal.impl.XMLScanner: XMLScanner.java if (!fEntityScanner.skipSpaces() && !optionalSystemId) { reportFatalError( "SpaceRequiredBetweenPublicAndSystem" , null ); } I think the error has to do with the parser failing to validate the nonexistent doctype declaration. I tried to configure the DTD in surveys.xml, as shown below, but the error persisted: surveys.xml <!DOCTYPE surveys [ <!ELEMENT surveys (survey)> <!ELEMENT survey (name,description,link,startdate,enddate)> <!ELEMENT name (#PCDATA)> <!ELEMENT description (#PCDATA)> <!ELEMENT link (#PCDATA)> <!ELEMENT startdate (#PCDATA)> <!ELEMENT enddate (#PCDATA)> ]> In trying to configure the DocumentBuilderFactory in SurveyParser to be less stringent with regards to xml formatting validation at [~aloraine] 's suggestion, I tried several options from the list here , in addition to those used in AnnotsParser, but I couldn't get any configuration to work. I tried to make the implementation of SurveyParser mimic that of UpdateParser, however, the issue still persisted. I have reverted to what seems to be the previously used deserialization method, which was commented out above the one that is currently causing this error. Although the Fatal Error is still printed, now no exception is thrown. https://bitbucket.org/pbadzuh/igb_pbdev/branch/IGBF-2475#diff This isn't exactly a solution, but I'm not entirely sure what the exact problem is and have a feeling that the fatal error message may be misleading. From my further research online, it appears to be a generic error. Please let me know what you think.

4 older comments

Hide

Permalink

Logan Weidenhammer (Inactive) added a comment - 12/Aug/20 3:15 PM

Tested as instructed.
To run IGB through the console I used Git Bash and ran "$ java -Xmx1g -jar igb_exe.jar" at the location IGB was installed on my machine.

The output did contain the fatal error:
[ Fatal Error ] :1:50: White spaces are required between publicId and systemId.

And it did not contain the exception
org.xml.sax.SAXParseException

Prutha Kulkarni, is this a satisfactory result as far as the functional review goes?

Show

Logan Weidenhammer (Inactive) added a comment - 12/Aug/20 3:15 PM Tested as instructed. To run IGB through the console I used Git Bash and ran "$ java -Xmx1g -jar igb_exe.jar" at the location IGB was installed on my machine. The output did contain the fatal error: [ Fatal Error ] :1:50: White spaces are required between publicId and systemId. And it did not contain the exception org.xml.sax.SAXParseException Prutha Kulkarni , is this a satisfactory result as far as the functional review goes?

Hide

Permalink

Prutha Kulkarni (Inactive) added a comment - 12/Aug/20 3:48 PM

Logan Weidenhammer, the fatal error is because of other module i.e. "update" module to be specific. The SAXParseException for survey module has been resolved and you are seeing the fatal error because it isn't fixed for update module. A different ticket has been raised for that as well.
The fix has been provided so you can go ahead and move the ticket forward to "submit a PR".

Show

Prutha Kulkarni (Inactive) added a comment - 12/Aug/20 3:48 PM Logan Weidenhammer , the fatal error is because of other module i.e. "update" module to be specific. The SAXParseException for survey module has been resolved and you are seeing the fatal error because it isn't fixed for update module. A different ticket has been raised for that as well. The fix has been provided so you can go ahead and move the ticket forward to "submit a PR".

Hide

Permalink

Prutha Kulkarni (Inactive) added a comment - 13/Aug/20 12:38 PM

PR has been submitted:
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/817/igbf-2475-fix-saxparserexception-in-igb/diff
cc: [~aloraine]

Show

Prutha Kulkarni (Inactive) added a comment - 13/Aug/20 12:38 PM PR has been submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/817/igbf-2475-fix-saxparserexception-in-igb/diff cc: [~aloraine]

Hide

Permalink

Ann Loraine added a comment - 13/Aug/20 6:38 PM

Merged and master branch installers are built. Moving to ready for testing.

Show

Ann Loraine added a comment - 13/Aug/20 6:38 PM Merged and master branch installers are built. Moving to ready for testing.

Hide

Permalink

Shamika Gajanan Kulkarni (Inactive) added a comment - 14/Aug/20 7:33 PM

Tested this ticket. The SAXParseException did not occur after running IGB. Moving to closed.

Show

Shamika Gajanan Kulkarni (Inactive) added a comment - 14/Aug/20 7:33 PM Tested this ticket. The SAXParseException did not occur after running IGB. Moving to closed.

People

Assignee:

Prutha Kulkarni (Inactive)

Reporter:

Prutha Kulkarni (Inactive)

Votes:

0 Vote for this issue

Watchers:

5 Start watching this issue

Dates

Created:

16/Jul/20 6:22 PM

Updated:

14/Aug/20 7:34 PM

Resolved:

14/Aug/20 7:34 PM