Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
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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.)
Attachments
Issue Links
- relates to
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BUG-647 Server bugs
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- Closed
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Activity
Passed on 7.0.0 (11945) Mac.
Fixed.
I checked the DAS2 data source today under revision 9337.
I cleared the cache, reset preferences to defaults, and ran the program with
$ ant cbc clean run
I then selected genome A_thaliana_Jun_2009.
The BioViz DAS2 data source was not visible.
Relevant text from Console is here:
Nov 2, 2011 12:23:12 PM com.affymetrix.genometryImpl.das2.Das2VersionedSource getInputStream
INFO: Das2 Types Request : http://www.bioviz.org/das2/genome/A_thaliana_Jun_2009/types
[Fatal Error] :1:50: White spaces are required between publicId and systemId.
Nov 2, 2011 12:23:12 PM com.affymetrix.genometryImpl.das2.Das2VersionedSource initTypes
SEVERE: null
org.xml.sax.SAXParseException: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:249)
at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:284)
at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:124)
at com.affymetrix.genometryImpl.util.XMLUtils.getDocument(XMLUtils.java:102)
at com.affymetrix.genometryImpl.das2.Das2VersionedSource.initTypes(Das2VersionedSource.java:300)
at com.affymetrix.genometryImpl.das2.Das2VersionedSource.getTypes(Das2VersionedSource.java:186)
at com.affymetrix.igb.general.FeatureLoading.loadFeatureNames(FeatureLoading.java:45)
at com.affymetrix.igb.view.load.GeneralLoadUtils.initVersionAndSeq(GeneralLoadUtils.java:477)
at com.affymetrix.igb.view.SeqGroupView$InitVersionWorker.doInBackground(SeqGroupView.java:873)
at com.affymetrix.igb.view.SeqGroupView$InitVersionWorker.doInBackground(SeqGroupView.java:860)
at com.jidesoft.utils.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at com.jidesoft.utils.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)
Passed 7.0 (11953) on windows.