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  1. Bug Repository
  2. BUG-194

can't access PSL EST alignments from BioViz DAS2

    Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Fixed
    • Labels:
      None
    • Environment:

      IGB 6.7

      Description

      When I attempt to "load data" on any of the BioViz DAS2 EST data sets, I get this error:

      [java] Nov 1, 2011 2:42:07 PM com.affymetrix.genometryImpl.das2.Das2VersionedSource initSegments
      [java] FINE: Das2 Segments Request: http://www.bioviz.org/das2/genome/A_thaliana_Jun_2009/segments
      [java] Nov 1, 2011 2:42:07 PM com.affymetrix.genometryImpl.das2.Das2VersionedSource getInputStream
      [java] INFO: Das2 Segments Request : http://www.bioviz.org/das2/genome/A_thaliana_Jun_2009/segments
      [java] [Fatal Error] :1:50: White spaces are required between publicId and systemId.
      [java] org.xml.sax.SAXParseException: White spaces are required between publicId and systemId.
      [java] at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:249)
      [java] at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:284)
      [java] at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:124)
      [java] at com.affymetrix.genometryImpl.util.XMLUtils.getDocument(XMLUtils.java:102)
      [java] at com.affymetrix.genometryImpl.das2.Das2VersionedSource.initSegments(Das2VersionedSource.java:220)
      [java] at com.affymetrix.genometryImpl.das2.Das2VersionedSource.getSegments(Das2VersionedSource.java:142)
      [java] at com.affymetrix.genometryImpl.das2.Das2VersionedSource.getSegment(Das2VersionedSource.java:152)
      [java] at com.affymetrix.igb.featureloader.Das2.loadFeatures(Das2.java:51)
      [java] at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:877)
      [java] at com.affymetrix.igb.view.load.GeneralLoadUtils.access$200(GeneralLoadUtils.java:89)
      [java] at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:823)
      [java] at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:818)
      [java] at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
      [java] at javax.swing.SwingWorker$1.call(SwingWorker.java:277)
      [java] at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
      [java] at java.util.concurrent.FutureTask.run(FutureTask.java:138)
      [java] at javax.swing.SwingWorker.run(SwingWorker.java:316)
      [java] at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
      [java] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
      [java] at java.lang.Thread.run(Thread.java:680)
      [java] Nov 1, 2011 2:42:36 PM com.affymetrix.igb.view.load.GeneralLoadUtils loadFeaturesForSym
      [java] INFO: All of new query covered by previous queries for feature EST (single map)

      However, I am able to retrieve data using the IGB 6.6.1 release from the Web site.

      (I am trying to check how the Sequence Viewer functions with PSL data.)

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            ann.loraine Ann Loraine created issue -
            hiralv Hiral Vora (Inactive) made changes -
            Field Original Value New Value
            Assignee Hiral Vora [ hiralv ] Jeremy Villalobos [ jfvillal ]
            ann.loraine Ann Loraine made changes -
            Assignee Jeremy Villalobos [ jfvillal ] Hiral Vora [ hiralv ]
            hiralv Hiral Vora (Inactive) made changes -
            Assignee Hiral Vora [ hiralv ] David Norris [ david ]
            hiralv Hiral Vora (Inactive) made changes -
            Assignee David Norris [ david ] Hiral Vora [ hiralv ]
            hiralv Hiral Vora (Inactive) made changes -
            Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Open [ 1 ] Resolved [ 5 ]
            Assignee Alyssa Gulledge [ alyssa ]
            Resolution Fixed [ 1 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Resolved [ 5 ] Closed [ 6 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Project IGB 6.7 [ 10040 ] Bug Repository [ 10030 ]
            Key IGBB-74 BUG-194
            fwang4 Fuquan Wang (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            Assignee Fuquan Wang [ fwang4 ]
            fwang4 Fuquan Wang (Inactive) made changes -
            Status Reopened [ 4 ] Resolved [ 5 ]
            Assignee Fuquan Wang [ fwang4 ]
            Resolution Fixed [ 1 ]
            richard Richard Linchangco (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Resolved [ 5 ] Reopened [ 4 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Link This issue relates to BUG-647 [ BUG-647 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Reopened [ 4 ] Closed [ 6 ]
            Resolution Fixed [ 1 ]

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              • Assignee:
                Unassigned
                Reporter:
                ann.loraine Ann Loraine
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                Dates

                • Created:
                  Updated:
                  Resolved: