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E-CURD-3 fails to create networks #44

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AlexanderPico opened this issue Jan 12, 2022 · 0 comments
Open

E-CURD-3 fails to create networks #44

AlexanderPico opened this issue Jan 12, 2022 · 0 comments
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bug Something isn't working

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@AlexanderPico
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Stack trace below. I looks like Plasmodium falciparum might not be recognized by STRING? If confirmed, we should either fix the mapping or filter/label problematic datasets that won't work with STRING prior to the user attempting to create networks.

10:12:39.084 ERROR [Task-Thread-8-Factory-0x3c1c6df1] Unknown or missing species or NCBI taxon ID
java.lang.NullPointerException: null
at edu.ucsf.rbvi.scNetViz.internal.utils.ModelUtils.rename(ModelUtils.java:73) ~[?:?]
at edu.ucsf.rbvi.scNetViz.internal.tasks.CreateNetworkTask$RenameNetwork.taskFinished(CreateNetworkTask.java:204) ~[?:?]
at org.cytoscape.command.internal.TFExecutor.execute(TFExecutor.java:91) ~[?:?]
at org.cytoscape.command.internal.CommandExecutorImpl.executeCommand(CommandExecutorImpl.java:175) ~[?:?]
at org.cytoscape.command.internal.CommandExecutorTask.run(CommandExecutorTask.java:54) ~[?:?]
at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:83) [!/:?]
at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:99) [!/:?]
at edu.ucsf.rbvi.scNetViz.internal.model.ScNVManager.executeCommand(ScNVManager.java:196) [!/:?]
at edu.ucsf.rbvi.scNetViz.internal.tasks.CreateNetworkTask.createStringNetwork(CreateNetworkTask.java:134) [!/:?]
at edu.ucsf.rbvi.scNetViz.internal.tasks.CreateNetworkTask.run(CreateNetworkTask.java:107) [!/:?]
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321) [!/:?]
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:352) [!/:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) [?:?]
at java.util.concurrent.FutureTask.run(FutureTask.java:264) [?:?]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
at java.lang.Thread.run(Thread.java:829) [?:?]
10:12:39.111 ERROR [Task-Thread-8-Factory-0x3c1c6df1] Error executing task: null
java.lang.NullPointerException
at edu.ucsf.rbvi.scNetViz.internal.utils.ModelUtils.rename(ModelUtils.java:73)
at edu.ucsf.rbvi.scNetViz.internal.tasks.CreateNetworkTask$RenameNetwork.taskFinished(CreateNetworkTask.java:204)
at org.cytoscape.command.internal.TFExecutor.execute(TFExecutor.java:91)
at org.cytoscape.command.internal.CommandExecutorImpl.executeCommand(CommandExecutorImpl.java:175)
at org.cytoscape.command.internal.CommandExecutorTask.run(CommandExecutorTask.java:54)
at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:83)
at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:99)
at edu.ucsf.rbvi.scNetViz.internal.model.ScNVManager.executeCommand(ScNVManager.java:196)
at edu.ucsf.rbvi.scNetViz.internal.tasks.CreateNetworkTask.createStringNetwork(CreateNetworkTask.java:134)
at edu.ucsf.rbvi.scNetViz.internal.tasks.CreateNetworkTask.run(CreateNetworkTask.java:107)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:352)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
java.lang.NullPointerException
at edu.ucsf.rbvi.scNetViz.internal.tasks.CreateNetworkTask.createSubNetwork(CreateNetworkTask.java:145)
at edu.ucsf.rbvi.scNetViz.internal.tasks.CreateNetworkTask.run(CreateNetworkTask.java:111)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:352)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)

@AlexanderPico AlexanderPico added the bug Something isn't working label Jan 12, 2022
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