Strange error with example session file

Lars Juhl Jensen

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Aug 6, 2018, 3:48:06 AM8/6/18

to cytoscape-helpdesk

Hi,

I started the latest version of Cytoscape, opened the Ivacaftor_coauthors.cys example session. The result is shown in the attached screenshot — two error popups.

The error is unfortunately not reproducible. I restarted Cytoscape, did the exact same thing, and second time it worked. So I guess it must be some sort of race condition in the code.

Excerpt from framework-cytoscape.log:

2018-08-06 09:36:47,654 [Task-Thread-4-Factory-0x55d5f568] WARN org.cytoscape.application.userlog - Caught exception executing task.

java.lang.IllegalArgumentException: Network view cannot be added, because its network (Ivacaftor_coauthors) is not registered

at org.cytoscape.view.model.internal.CyNetworkViewManagerImpl.addNetworkView(CyNetworkViewManagerImpl.java:180)

at org.cytoscape.session.internal.CySessionManagerImpl.restoreNetworkViews(CySessionManagerImpl.java:377)

at org.cytoscape.session.internal.CySessionManagerImpl.setCurrentSession(CySessionManagerImpl.java:237)

at org.cytoscape.task.internal.session.OpenSessionTask$OpenSessionWithoutWarningTask.changeCurrentSession(OpenSessionTask.java:156)

at org.cytoscape.task.internal.session.OpenSessionTask$OpenSessionWithoutWarningTask.run(OpenSessionTask.java:143)

at org.cytoscape.work.internal.sync.DelegateTask.run(DelegateTask.java:72)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:326)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:355)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)

2018-08-06 09:36:47,708 [Task-Thread-5-Factory-0x55d5f568] WARN org.cytoscape.application.userlog - Caught exception executing task.

java.lang.NullPointerException

at org.cytoscape.io.internal.util.ReadCache.getNetwork(ReadCache.java:168)

at org.cytoscape.io.internal.read.session.Cy3SessionReaderImpl.mergeNetworkTables(Cy3SessionReaderImpl.java:529)

at org.cytoscape.io.internal.read.session.Cy3SessionReaderImpl.complete(Cy3SessionReaderImpl.java:209)

at org.cytoscape.io.internal.read.session.AbstractSessionReader.run(AbstractSessionReader.java:116)

at org.cytoscape.task.internal.session.OpenSessionTask$OpenSessionWithoutWarningTask.run(OpenSessionTask.java:132)

at org.cytoscape.work.internal.sync.DelegateTask.run(DelegateTask.java:72)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:326)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:355)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)

BW

Lars

Screen Shot 2018-08-06 at 09.37.19.png

Scooter Morris

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Aug 9, 2018, 11:48:06 AM8/9/18

to cytoscape-helpdesk

Hi Lars,

Are you using 3.6.1 or a 3.7-SNAPSHOT? I can't reproduce this on 3.7...

-- scooter

Lars Juhl Jensen

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Aug 10, 2018, 5:35:43 AM8/10/18

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I'm using 3.6.1, but as I wrote it is not a reproducible bug. It just happens every once in a blue moon, which is why I suspect a race condition.