V.13758, Mac, Java 1.7.0_09

Tested using IGB Das (DAS2) > affy > AG netaffx consensus and ATH1-121501 netaffx consensus. Opened bookmark with reopened IGB 3 times, and a reset IGB 3 times.

Loaded without issue BUT threw an IOException.

java.io.IOException: stream is closed
at sun.net.www.http.ChunkedInputStream.ensureOpen(ChunkedInputStream.java:169)
at sun.net.www.http.ChunkedInputStream.read(ChunkedInputStream.java:664)
at java.io.FilterInputStream.read(FilterInputStream.java:133)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3035)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3029)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3017)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.close(HttpURLConnection.java:3099)
at com.affymetrix.genometryImpl.util.GeneralUtils.safeClose(GeneralUtils.java:64)
at com.affymetrix.genometryImpl.das2.Das2ServerType.LoadFeaturesFromQuery(Das2ServerType.java:476)
at com.affymetrix.genometryImpl.das2.Das2ServerType.loadSpan(Das2ServerType.java:315)
at com.affymetrix.genometryImpl.das2.Das2ServerType.loadFeatures(Das2ServerType.java:295)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:836)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:777)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:772)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:74)
at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at javax.swing.SwingWorker.run(SwingWorker.java:335)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)

Cannot reproduce, please give more info on how to make a stable reproduction.

What I did:

1. Added bookmark for 'IGB Das (DAS2) > affy > AG netaffx consensus and ATH1-121501 netaffx consensus'
2. Reset, started and loaded the bookmark for several times, it still work without any exceptions.

To reproduce

• Open freshly reset IGB
• Load the A_thaliana_Jun_2009 genome
• Zoom in to chr1: 16,239,257 - 16,293,953
• From 'Available Data' under 'Data Access' Tab click 'IGB Das (DAS2)'
  • Click 'affy' folder and select 'AG netaffx consensus'
• Click 'Load Data'
• The following IOException is displayed on the Java console:

Dec 19, 2012 10:31:50 AM com.affymetrix.genometryImpl.das2.Das2ServerType LoadFeaturesFromQuery
INFO: Parsing LINK.PSL format for DAS2 feature response
java.io.IOException: stream is closed
at sun.net.www.http.ChunkedInputStream.ensureOpen(ChunkedInputStream.java:169)
at sun.net.www.http.ChunkedInputStream.read(ChunkedInputStream.java:664)
at java.io.FilterInputStream.read(FilterInputStream.java:133)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3035)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3029)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3017)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.close(HttpURLConnection.java:3099)
at com.affymetrix.genometryImpl.util.GeneralUtils.safeClose(GeneralUtils.java:64)
at com.affymetrix.genometryImpl.das2.Das2ServerType.LoadFeaturesFromQuery(Das2ServerType.java:476)
at com.affymetrix.genometryImpl.das2.Das2ServerType.loadSpan(Das2ServerType.java:315)
at com.affymetrix.genometryImpl.das2.Das2ServerType.loadFeatures(Das2ServerType.java:295)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:836)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:777)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:772)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:74)
at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at javax.swing.SwingWorker.run(SwingWorker.java:335)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)

Cannot reproduce on my side, assigning to Alyssa to see if that happens.

good for me - closing issue