[BUG-194] can't access PSL EST alignments from BioViz DAS2 - JIRA UNCC

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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relates to

BUG-647 Server bugs

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Ann Loraine created issue - 01/Nov/11 10:45 AM

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Ann Loraine added a comment - 02/Nov/11 8:26 AM

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)

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Ann Loraine added a comment - 02/Nov/11 8:26 AM 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)

Hiral Vora (Inactive) made changes - 07/Nov/11 6:19 AM

Field	Original Value	New Value
Assignee	Hiral Vora [ hiralv ]	Jeremy Villalobos [ jfvillal ]

Ann Loraine made changes - 09/Dec/11 5:27 AM

Assignee

Jeremy Villalobos [ jfvillal ]

Hiral Vora [ hiralv ]

Hiral Vora (Inactive) made changes - 13/Dec/11 10:31 AM

Assignee

Hiral Vora [ hiralv ]

David Norris [ david ]

Hiral Vora (Inactive) made changes - 15/Dec/11 11:17 AM

Assignee

David Norris [ david ]

Hiral Vora [ hiralv ]

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Hiral Vora (Inactive) added a comment - 15/Dec/11 11:18 AM

Fixed.

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Hiral Vora (Inactive) added a comment - 15/Dec/11 11:18 AM Fixed.

Hiral Vora (Inactive) made changes - 15/Dec/11 11:18 AM

Assignee

Hiral Vora [ hiralv ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 19/Dec/11 9:13 AM

Status	Open [ 1 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 19/Dec/11 9:13 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 19/Dec/11 9:13 AM

Project	IGB 6.7 [ 10040 ]	Bug Repository [ 10030 ]
Key	~~IGBB-74~~	~~BUG-194~~

Fuquan Wang (Inactive) made changes - 12/Jun/12 12:37 PM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Fuquan Wang [ fwang4 ]

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Fuquan Wang (Inactive) added a comment - 12/Jun/12 12:37 PM

Passed on 7.0.0 (11945) Mac.

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Fuquan Wang (Inactive) added a comment - 12/Jun/12 12:37 PM Passed on 7.0.0 (11945) Mac.

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Vineeth Mylapur (Inactive) added a comment - 12/Jun/12 12:42 PM

Passed 7.0 (11953) on windows.

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Vineeth Mylapur (Inactive) added a comment - 12/Jun/12 12:42 PM Passed 7.0 (11953) on windows.

Fuquan Wang (Inactive) made changes - 14/Jun/12 5:02 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Fuquan Wang [ fwang4 ]
Resolution		Fixed [ 1 ]

Richard Linchangco (Inactive) made changes - 13/Nov/12 10:25 AM

Resolution	Fixed [ 1 ]
Status	Resolved [ 5 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 18/Dec/12 6:53 AM

Link

This issue relates to ~~BUG-647~~ [ ~~BUG-647~~ ]

Alyssa Gulledge (Inactive) made changes - 19/Dec/12 6:34 AM

Status	Reopened [ 4 ]	Closed [ 6 ]
Resolution		Fixed [ 1 ]

People

Assignee:

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Reporter:

Ann Loraine

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Dates

Created:

01/Nov/11 10:45 AM

Updated:

19/Dec/12 6:34 AM

Resolved:

19/Dec/12 6:34 AM