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geneontology / paint

This curation tool allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
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Bug with 'colocalizes with' #15

Closed pgaudet closed 7 years ago

pgaudet commented 8 years ago

Hello,

In PAINT2.0-beta 15, trying to propagate a 'colocalizes' annotation crashes PAINT :( For example: In PTHR14625, try to propagate Nucleus.

Thanks, Pascale

selewis commented 8 years ago

I couldn't duplicate this. It would just as you'd expect. Did the dialog box show up? Can you send me the console output too.

pgaudet commented 8 years ago

Hello,

This happened again with PTHR11715. The pop up box does appeear, but then nothing happens when I try to click on continue (or check the 'CONTRIBUTES TO box). I have been waiting for over 3 hours.

Here's the terminal window output, but it didn't seem to have output anything:

M-200278:paint2.0-beta pascalegaudet$ sh launchpaint.sh 2016-06-09 11:15:07,444 INFO (PaintYaml:45) Trying config found at: config/preferences.yaml 2016-06-09 11:15:07,550 INFO (PaintYaml:50) Using config found at: config/preferences.yaml 2016-06-09 11:15:07,838 INFO (PaintStartupTask:203) Loading Paint version 2.0-beta19 2016-06-09 11:15:20,220 INFO (class:571) View #4, Garbage0, is a garbage view--destroying 2016-06-09 11:16:15,648 INFO (LoginUtil:404) Logging in to Panther URL: http://paintcuration.usc.edu 2016-06-09 11:16:26,131 INFO (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go.owl from: http://purl.obolibrary.org/obo/go.owl 2016-06-09 11:25:03,515 INFO (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go.owl from: http://purl.obolibrary.org/obo/go.owl 2016-06-09 11:25:04,630 INFO (Reasoner:117) ELK reasoner was created 2016-06-09 11:25:18,733 INFO (LoggingStageExecutor:70) Loading of Axioms started 2016-06-09 11:25:18,876 INFO (AbstractReasonerStage:161) Loading of Axioms using 2 workers 2016-06-09 11:25:38,600 WARN (ChangeIndexingProcessor:66) ELK does not support InverseObjectProperties. Axiom ignored: InverseObjectProperties(http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000051) 2016-06-09 11:25:51,606 INFO (LoggingStageExecutor:103) Loading of Axioms took 32732 ms 2016-06-09 11:25:51,606 INFO (LoggingStageExecutor:70) Property Saturation Initialization started 2016-06-09 11:25:51,621 INFO (AbstractReasonerStage:161) Property Saturation Initialization using 2 workers 2016-06-09 11:25:51,624 INFO (LoggingStageExecutor:103) Property Saturation Initialization took 6 ms 2016-06-09 11:25:51,624 INFO (LoggingStageExecutor:70) Reflexive Property Computation started 2016-06-09 11:25:51,628 INFO (AbstractReasonerStage:161) Reflexive Property Computation using 2 workers 2016-06-09 11:25:51,632 INFO (LoggingStageExecutor:103) Reflexive Property Computation took 8 ms 2016-06-09 11:25:51,632 INFO (LoggingStageExecutor:70) Object Property Hierarchy and Composition Computation started 2016-06-09 11:25:51,638 INFO (AbstractReasonerStage:161) Object Property Hierarchy and Composition Computation using 2 workers 2016-06-09 11:25:51,658 INFO (LoggingStageExecutor:103) Object Property Hierarchy and Composition Computation took 25 ms 2016-06-09 11:25:52,099 INFO (LoggingStageExecutor:70) Context Initialization started 2016-06-09 11:25:52,100 INFO (AbstractReasonerStage:161) Context Initialization using 2 workers 2016-06-09 11:25:52,103 INFO (LoggingStageExecutor:103) Context Initialization took 3 ms 2016-06-09 11:25:52,103 INFO (LoggingStageExecutor:70) Consistency Checking started 2016-06-09 11:25:52,113 INFO (AbstractReasonerStage:161) Consistency Checking using 2 workers 2016-06-09 11:25:52,229 INFO (LoggingStageExecutor:103) Consistency Checking took 125 ms 2016-06-09 11:25:52,229 INFO (LoggingStageExecutor:70) Class Taxonomy Computation started 2016-06-09 11:25:52,243 INFO (AbstractReasonerStage:161) Class Taxonomy Computation using 2 workers 2016-06-09 11:26:38,711 INFO (LoggingStageExecutor:103) Class Taxonomy Computation took 46481 ms 2016-06-09 11:29:13,040 INFO (IDmap:113) Identical Seq ID (UniProtKB:Q8ZHI7) for 2 different genes: ENSEMBL:YP_3603 ENSEMBL:y3293 2016-06-09 11:29:13,047 INFO (DisplayTree:70) There are 267 nodes in the PTHR11715 tree

Thanks, Pascale

cmungall commented 8 years ago

Thanks for posting the log output.

Most of that is logging from the OWLAPI and is all normal.

This comes from PAINT: 2016-06-09 11:29:13,040 INFO (IDmap:113) Identical Seq ID (UniProtKB:Q8ZHI7) for 2 different genes: ENSEMBL:YP_3603 ENSEMBL:y3293

I very much doubt it is the cause, but that is all I would have to go on without investigating a lot more deeply, I'm sure Suzi could figure it out quickly but she's not back until after next week.

On 10 Jun 2016, at 6:11, pgaudet wrote:

Hello,

This happened again with PTHR11715. The pop up box does appeear, but then nothing happens when I try to click on continue (or check the 'CONTRIBUTES TO box). I have been waiting for over 3 hours.

Here's the terminal window output, but it didn't seem to have output anything:

M-200278:paint2.0-beta pascalegaudet$ sh launchpaint.sh 2016-06-09 11:15:07,444 INFO (PaintYaml:45) Trying config found at: config/preferences.yaml 2016-06-09 11:15:07,550 INFO (PaintYaml:50) Using config found at: config/preferences.yaml 2016-06-09 11:15:07,838 INFO (PaintStartupTask:203) Loading Paint version 2.0-beta19 2016-06-09 11:15:20,220 INFO (class:571) View #4, Garbage0, is a garbage view--destroying 2016-06-09 11:16:15,648 INFO (LoginUtil:404) Logging in to Panther URL: http://paintcuration.usc.edu 2016-06-09 11:16:26,131 INFO (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go.owl from: http://purl.obolibrary.org/obo/go.owl 2016-06-09 11:25:03,515 INFO (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go.owl from: http://purl.obolibrary.org/obo/go.owl 2016-06-09 11:25:04,630 INFO (Reasoner:117) ELK reasoner was created 2016-06-09 11:25:18,733 INFO (LoggingStageExecutor:70) Loading of Axioms started 2016-06-09 11:25:18,876 INFO (AbstractReasonerStage:161) Loading of Axioms using 2 workers 2016-06-09 11:25:38,600 WARN (ChangeIndexingProcessor:66) ELK does not support InverseObjectProperties. Axiom ignored: InverseObjectProperties(http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000051) 2016-06-09 11:25:51,606 INFO (LoggingStageExecutor:103) Loading of Axioms took 32732 ms 2016-06-09 11:25:51,606 INFO (LoggingStageExecutor:70) Property Saturation Initialization started 2016-06-09 11:25:51,621 INFO (AbstractReasonerStage:161) Property Saturation Initialization using 2 workers 2016-06-09 11:25:51,624 INFO (LoggingStageExecutor:103) Property Saturation Initialization took 6 ms 2016-06-09 11:25:51,624 INFO (LoggingStageExecutor:70) Reflexive Property Computation started 2016-06-09 11:25:51,628 INFO (AbstractReasonerStage:161) Reflexive Property Computation using 2 workers 2016-06-09 11:25:51,632 INFO (LoggingStageExecutor:103) Reflexive Property Computation took 8 ms 2016-06-09 11:25:51,632 INFO (LoggingStageExecutor:70) Object Property Hierarchy and Composition Computation started 2016-06-09 11:25:51,638 INFO (AbstractReasonerStage:161) Object Property Hierarchy and Composition Computation using 2 workers 2016-06-09 11:25:51,658 INFO (LoggingStageExecutor:103) Object Property Hierarchy and Composition Computation took 25 ms 2016-06-09 11:25:52,099 INFO (LoggingStageExecutor:70) Context Initialization started 2016-06-09 11:25:52,100 INFO (AbstractReasonerStage:161) Context Initialization using 2 workers 2016-06-09 11:25:52,103 INFO (LoggingStageExecutor:103) Context Initialization took 3 ms 2016-06-09 11:25:52,103 INFO (LoggingStageExecutor:70) Consistency Checking started 2016-06-09 11:25:52,113 INFO (AbstractReasonerStage:161) Consistency Checking using 2 workers 2016-06-09 11:25:52,229 INFO (LoggingStageExecutor:103) Consistency Checking took 125 ms 2016-06-09 11:25:52,229 INFO (LoggingStageExecutor:70) Class Taxonomy Computation started 2016-06-09 11:25:52,243 INFO (AbstractReasonerStage:161) Class Taxonomy Computation using 2 workers 2016-06-09 11:26:38,711 INFO (LoggingStageExecutor:103) Class Taxonomy Computation took 46481 ms 2016-06-09 11:29:13,040 INFO (IDmap:113) Identical Seq ID (UniProtKB:Q8ZHI7) for 2 different genes: ENSEMBL:YP_3603 ENSEMBL:y3293 2016-06-09 11:29:13,047 INFO (DisplayTree:70) There are 267 nodes in the PTHR11715 tree

Thanks, Pascale

You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/geneontology/paint/issues/15#issuecomment-225177951

selewis commented 8 years ago

Yes, messages such as this: 2016-06-09 11:29:13,040 INFO (IDmap:113) Identical Seq ID (UniProtKB:Q8ZHI7) for 2 different genes: ENSEMBL:YP_3603 ENSEMBL:y3293

Are informational only. There are many cases with one uniprot ID mapping to multiple gene IDs, and similarly single gene IDs mapping to multiple UniProt IDs. Just the usual splits and merges of genes being out of phase across project. I output them simply because I was interested in how often this occurs and thinking that at some point it might be useful feedback to the gene annotators.

selewis commented 8 years ago

Also I was unable to duplicate the problem. I was able to annotate "contributes to" for glycine dehydrogenase in family PTHR 11715. You got the dialog, clicked the check box, and hit continue, right?

mystified.

Using PAINT 2.0-beta19

pgaudet commented 7 years ago

I get it ! You need to check *or not check) the 'contributes to' box, and hit 'enter'. For me the 'Continue' button is not working. So for usability, pls remove the button or activate it.

Thanks, Pascale

selewis commented 7 years ago

Do you know what version of Java you are running?

Try typing this on the command line: java -version

krchristie commented 7 years ago

I am seeing this problem also.

For family PTHR21524, I would like to propagate the term "cytoplasmic microtubules" with the colocalizes qualifier. When I drag the term to the root, the dialog box appears. PAINT doesn't seem fully crashed, as I can move this dialog window around, but the dialog box is unresponsive to any of these actions:

Restarting PAINT and reloading this family duplicates the problem.

Below is info on Java version and output in console window.

thanks,

-Karen

Here is the info on my version of Java:

bash-3.2$ java -version
java version "1.8.0_71"
Java(TM) SE Runtime Environment (build 1.8.0_71-b15)
Java HotSpot(TM) 64-Bit Server VM (build 25.71-b15, mixed mode)

Here is a portion of the stuff from the console window from the first time. I included some of the families before this one that I had also opened):

2016-08-26 10:42:38,980 INFO  (DisplayTree:70) There are 15 nodes in the PTHR38608 tree
2016-08-26 10:42:43,376 INFO  (class:135) Retrieving experimental annotations from: http://golr.geneontology.org
2016-08-26 10:44:53,605 INFO  (GafRecorder:81) Wrote updated paint GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR38608/PTHR38608.gaf
2016-08-26 10:44:53,615 INFO  (GafRecorder:121) Wrote experimental evidence GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR38608/PTHR38608.exp
2016-08-26 10:52:20,109 INFO  (DisplayTree:70) There are 9 nodes in the PTHR40661 tree
2016-08-26 10:52:21,633 INFO  (class:135) Retrieving experimental annotations from: http://golr.geneontology.org
2016-08-26 10:59:57,066 INFO  (GafRecorder:81) Wrote updated paint GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR40661/PTHR40661.gaf
2016-08-26 10:59:57,075 INFO  (GafRecorder:121) Wrote experimental evidence GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR40661/PTHR40661.exp
2016-08-26 11:21:43,070 INFO  (IDmap:113) Identical Seq ID (UniProtKB:Q7PSE6) for 2 different genes: Gene:AGAP009389 Gene:AgaP_AGAP009389
2016-08-26 11:21:43,071 INFO  (DisplayTree:70) There are 15 nodes in the PTHR21524 tree
2016-08-26 11:21:46,419 INFO  (class:135) Retrieving experimental annotations from: http://golr.geneontology.org
Exception in thread "AWT-EventQueue-0" java.lang.reflect.UndeclaredThrowableException
          at com.sun.proxy.$Proxy0.handleReOpenApplication(Unknown Source)
          at com.apple.eawt._AppEventLegacyHandler$4.dispatchEvent(_AppEventLegacyHandler.java:126)
          at com.apple.eawt._AppEventLegacyHandler.sendEventToEachListenerUntilHandled(_AppEventLegacyHandler.java:184)
          at com.apple.eawt._AppEventLegacyHandler.appReOpened(_AppEventLegacyHandler.java:124)
          at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:276)
          at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:273)
          at com.apple.eawt._AppEventHandler$_AppEventMultiplexor$1.run(_AppEventHandler.java:439)
          at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
          at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
          at java.awt.EventQueue.access$500(EventQueue.java:97)
          at java.awt.EventQueue$3.run(EventQueue.java:709)
          at java.awt.EventQueue$3.run(EventQueue.java:703)
          at java.security.AccessController.doPrivileged(Native Method)
          at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
          at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
          at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
          at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
          at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.reflect.InvocationTargetException
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
       at java.lang.reflect.Method.invoke(Method.java:497)
       at org.simplericity.macify.eawt.DefaultApplication$ApplicationListenerInvocationHandler.invoke(DefaultApplication.java:400)
       ... 21 more
Caused by: java.lang.AbstractMethodError: org.bbop.framework.AbstractApplicationStartupTask$MacApplicationSupport.handleReOpenApplication(Lorg/simplericity/macify/eawt/ApplicationEvent;)V
       ... 26 more

Here is everything from the console window from killing PAINT with Ctrl-C within the terminal window and then relaunching PAINT onwards:

^Cbash-3.2$ ./launchPAINT.sh 
2016-08-26 14:43:29,558 INFO  (PaintYaml:45) Trying config found at: config/preferences.yaml
2016-08-26 14:43:29,593 INFO  (PaintYaml:50) Using config found at: config/preferences.yaml
2016-08-26 14:43:29,666 INFO  (PaintStartupTask:203) Loading Paint version 2.21
2016-08-26 14:43:32,314 INFO  (class:571) View #4, Garbage0, is a garbage view--destroying
2016-08-26 14:43:53,666 INFO  (LoginUtil:404) Logging in to Panther URL:  http://paintcuration.usc.edu
2016-08-26 14:44:03,965 INFO  (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go.owl from: http://purl.obolibrary.org/obo/go.owl
Exception in thread "AWT-EventQueue-0" java.lang.reflect.UndeclaredThrowableException
    at com.sun.proxy.$Proxy0.handleReOpenApplication(Unknown Source)
    at com.apple.eawt._AppEventLegacyHandler$4.dispatchEvent(_AppEventLegacyHandler.java:126)
    at com.apple.eawt._AppEventLegacyHandler.sendEventToEachListenerUntilHandled(_AppEventLegacyHandler.java:184)
    at com.apple.eawt._AppEventLegacyHandler.appReOpened(_AppEventLegacyHandler.java:124)
    at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:276)
    at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:273)
    at com.apple.eawt._AppEventHandler$_AppEventMultiplexor$1.run(_AppEventHandler.java:439)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:709)
    at java.awt.EventQueue$3.run(EventQueue.java:703)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.simplericity.macify.eawt.DefaultApplication$ApplicationListenerInvocationHandler.invoke(DefaultApplication.java:400)
    ... 21 more
Caused by: java.lang.AbstractMethodError: org.bbop.framework.AbstractApplicationStartupTask$MacApplicationSupport.handleReOpenApplication(Lorg/simplericity/macify/eawt/ApplicationEvent;)V
    ... 26 more
Exception in thread "AWT-EventQueue-0" java.lang.reflect.UndeclaredThrowableException
    at com.sun.proxy.$Proxy0.handleReOpenApplication(Unknown Source)
    at com.apple.eawt._AppEventLegacyHandler$4.dispatchEvent(_AppEventLegacyHandler.java:126)
    at com.apple.eawt._AppEventLegacyHandler.sendEventToEachListenerUntilHandled(_AppEventLegacyHandler.java:184)
    at com.apple.eawt._AppEventLegacyHandler.appReOpened(_AppEventLegacyHandler.java:124)
    at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:276)
    at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:273)
    at com.apple.eawt._AppEventHandler$_AppEventMultiplexor$1.run(_AppEventHandler.java:439)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:709)
    at java.awt.EventQueue$3.run(EventQueue.java:703)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.simplericity.macify.eawt.DefaultApplication$ApplicationListenerInvocationHandler.invoke(DefaultApplication.java:400)
    ... 21 more
Caused by: java.lang.AbstractMethodError: org.bbop.framework.AbstractApplicationStartupTask$MacApplicationSupport.handleReOpenApplication(Lorg/simplericity/macify/eawt/ApplicationEvent;)V
    ... 26 more
2016-08-26 14:51:50,145 INFO  (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go.owl from: http://purl.obolibrary.org/obo/go.owl
2016-08-26 14:51:50,455 INFO  (Reasoner:117) ELK reasoner was created
2016-08-26 14:51:56,833 INFO  (LoggingStageExecutor:70) Loading of Axioms started
2016-08-26 14:51:56,847 INFO  (AbstractReasonerStage:161) Loading of Axioms using 8 workers
2016-08-26 14:51:57,530 WARN  (ChangeIndexingProcessor:66) ELK does not support SymmetricObjectProperty. Axiom ignored:
SymmetricObjectProperty()
2016-08-26 14:51:58,018 WARN  (ChangeIndexingProcessor:66) ELK does not support InverseObjectProperties. Axiom ignored:
InverseObjectProperties( )
2016-08-26 14:52:01,108 INFO  (LoggingStageExecutor:103) Loading of Axioms took 4264 ms
2016-08-26 14:52:01,109 INFO  (LoggingStageExecutor:70) Property Saturation Initialization started
2016-08-26 14:52:01,110 INFO  (AbstractReasonerStage:161) Property Saturation Initialization using 8 workers
2016-08-26 14:52:01,111 INFO  (LoggingStageExecutor:103) Property Saturation Initialization took 1 ms
2016-08-26 14:52:01,111 INFO  (LoggingStageExecutor:70) Reflexive Property Computation started
2016-08-26 14:52:01,114 INFO  (AbstractReasonerStage:161) Reflexive Property Computation using 8 workers
2016-08-26 14:52:01,116 INFO  (LoggingStageExecutor:103) Reflexive Property Computation took 5 ms
2016-08-26 14:52:01,116 INFO  (LoggingStageExecutor:70) Object Property Hierarchy and Composition Computation started
2016-08-26 14:52:01,119 INFO  (AbstractReasonerStage:161) Object Property Hierarchy and Composition Computation using 8 workers
2016-08-26 14:52:01,124 INFO  (LoggingStageExecutor:103) Object Property Hierarchy and Composition Computation took 7 ms
2016-08-26 14:52:01,124 INFO  (LoggingStageExecutor:70) Context Initialization started
2016-08-26 14:52:01,125 INFO  (AbstractReasonerStage:161) Context Initialization using 8 workers
2016-08-26 14:52:01,128 INFO  (LoggingStageExecutor:103) Context Initialization took 2 ms
2016-08-26 14:52:01,128 INFO  (LoggingStageExecutor:70) Consistency Checking started
2016-08-26 14:52:01,132 INFO  (AbstractReasonerStage:161) Consistency Checking using 8 workers
2016-08-26 14:52:01,212 INFO  (LoggingStageExecutor:103) Consistency Checking took 83 ms
2016-08-26 14:52:01,212 INFO  (LoggingStageExecutor:70) Class Taxonomy Computation started
2016-08-26 14:52:01,217 INFO  (AbstractReasonerStage:161) Class Taxonomy Computation using 8 workers
2016-08-26 14:52:08,851 INFO  (LoggingStageExecutor:103) Class Taxonomy Computation took 7639 ms
2016-08-26 14:53:50,637 INFO  (IDmap:113) Identical Seq ID (UniProtKB:Q7PSE6) for 2 different genes: Gene:AGAP009389 Gene:AgaP_AGAP009389
2016-08-26 14:53:50,639 INFO  (DisplayTree:70) There are 15 nodes in the PTHR21524 tree
2016-08-26 14:53:52,878 INFO  (class:135) Retrieving experimental annotations from: http://golr.geneontology.org
selewis commented 7 years ago

We changed/updated the layout manager library (macify) and I'm guessing that is the problem. Will need to either revert or find a third alternative. Not a super quick fix since it takes some research.

On Fri, Aug 26, 2016 at 3:26 PM, Karen R Christie notifications@github.com wrote:

I am seeing this problem also.

For family PTHR21524, I would like to propagate the term "cytoplasmic microtubules" with the colocalizes qualifier. When I drag the term to the root, the dialog box appears. PAINT doesn't seem fully crashed, as I can move this dialog window around, but the dialog box is unresponsive to any of these actions:

  • checking the COLOCOLIZES button
  • pressing the continue button
  • clicking either the red x or green + buttons in the upper left corner to dismiss or expand the window Since I can't do anything to make the box close, I have to quit PAINT.

Restarting PAINT and reloading this family duplicates the problem.

Below is info on Java version and output in console window.

thanks,

-Karen

Here is the info on my version of Java:

bash-3.2$ java -version java version "1.8.0_71" Java(TM) SE Runtime Environment (build 1.8.0_71-b15) Java HotSpot(TM) 64-Bit Server VM (build 25.71-b15, mixed mode)

Here is a portion of the stuff from the console window from the first time. I included some of the families before this one that I had also opened):

2016-08-26 10:42:38,980 INFO (DisplayTree:70) There are 15 nodes in the PTHR38608 tree 2016-08-26 10:42:43,376 INFO (class:135) Retrieving experimental annotations from: http://golr.geneontology.org 2016-08-26 10:44:53,605 INFO (GafRecorder:81) Wrote updated paint GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR38608/PTHR38608.gaf 2016-08-26 10:44:53,615 INFO (GafRecorder:121) Wrote experimental evidence GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR38608/PTHR38608.exp 2016-08-26 10:52:20,109 INFO (DisplayTree:70) There are 9 nodes in the PTHR40661 tree 2016-08-26 10:52:21,633 INFO (class:135) Retrieving experimental annotations from: http://golr.geneontology.org 2016-08-26 10:59:57,066 INFO (GafRecorder:81) Wrote updated paint GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR40661/PTHR40661.gaf 2016-08-26 10:59:57,075 INFO (GafRecorder:121) Wrote experimental evidence GAF to /Users/krc/Documents/PAINTcuration/GO-paint/PTHR40661/PTHR40661.exp 2016-08-26 11:21:43,070 INFO (IDmap:113) Identical Seq ID (UniProtKB:Q7PSE6) for 2 different genes: Gene:AGAP009389 Gene:AgaP_AGAP009389 2016-08-26 11:21:43,071 INFO (DisplayTree:70) There are 15 nodes in the PTHR21524 tree 2016-08-26 11:21:46,419 INFO (class:135) Retrieving experimental annotations from: http://golr.geneontology.org Exception in thread "AWT-EventQueue-0" java.lang.reflect.UndeclaredThrowableException at com.sun.proxy.$Proxy0.handleReOpenApplication(Unknown Source) at com.apple.eawt._AppEventLegacyHandler$4.dispatchEvent(_AppEventLegacyHandler.java:126) at com.apple.eawt._AppEventLegacyHandler.sendEventToEachListenerUntilHandled(_AppEventLegacyHandler.java:184) at com.apple.eawt._AppEventLegacyHandler.appReOpened(_AppEventLegacyHandler.java:124) at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:276) at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:273) at com.apple.eawt._AppEventHandler$_AppEventMultiplexor$1.run(_AppEventHandler.java:439) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at org.simplericity.macify.eawt.DefaultApplication$ApplicationListenerInvocationHandler.invoke(DefaultApplication.java:400) ... 21 more Caused by: java.lang.AbstractMethodError: org.bbop.framework.AbstractApplicationStartupTask$MacApplicationSupport.handleReOpenApplication(Lorg/simplericity/macify/eawt/ApplicationEvent;)V ... 26 more

Here is everything from the console window from killing PAINT with Ctrl-C within the terminal window and then relaunching PAINT onwards:

^Cbash-3.2$ ./launchPAINT.sh 2016-08-26 14:43:29,558 INFO (PaintYaml:45) Trying config found at: config/preferences.yaml 2016-08-26 14:43:29,593 INFO (PaintYaml:50) Using config found at: config/preferences.yaml 2016-08-26 14:43:29,666 INFO (PaintStartupTask:203) Loading Paint version 2.21 2016-08-26 14:43:32,314 INFO (class:571) View #4, Garbage0, is a garbage view--destroying 2016-08-26 14:43:53,666 INFO (LoginUtil:404) Logging in to Panther URL: http://paintcuration.usc.edu 2016-08-26 14:44:03,965 INFO (ParserWrapper:67) Start loading ontology: http://purl.obolibrary.org/obo/go.owl from: http://purl.obolibrary.org/obo/go.owl Exception in thread "AWT-EventQueue-0" java.lang.reflect.UndeclaredThrowableException at com.sun.proxy.$Proxy0.handleReOpenApplication(Unknown Source) at com.apple.eawt._AppEventLegacyHandler$4.dispatchEvent(_AppEventLegacyHandler.java:126) at com.apple.eawt._AppEventLegacyHandler.sendEventToEachListenerUntilHandled(_AppEventLegacyHandler.java:184) at com.apple.eawt._AppEventLegacyHandler.appReOpened(_AppEventLegacyHandler.java:124) at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:276) at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:273) at com.apple.eawt._AppEventHandler$_AppEventMultiplexor$1.run(_AppEventHandler.java:439) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at org.simplericity.macify.eawt.DefaultApplication$ApplicationListenerInvocationHandler.invoke(DefaultApplication.java:400) ... 21 more Caused by: java.lang.AbstractMethodError: org.bbop.framework.AbstractApplicationStartupTask$MacApplicationSupport.handleReOpenApplication(Lorg/simplericity/macify/eawt/ApplicationEvent;)V ... 26 more Exception in thread "AWT-EventQueue-0" java.lang.reflect.UndeclaredThrowableException at com.sun.proxy.$Proxy0.handleReOpenApplication(Unknown Source) at com.apple.eawt._AppEventLegacyHandler$4.dispatchEvent(_AppEventLegacyHandler.java:126) at com.apple.eawt._AppEventLegacyHandler.sendEventToEachListenerUntilHandled(_AppEventLegacyHandler.java:184) at com.apple.eawt._AppEventLegacyHandler.appReOpened(_AppEventLegacyHandler.java:124) at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:276) at com.apple.eawt._AppEventHandler$_AppReOpenedDispatcher.performOnListener(_AppEventHandler.java:273) at com.apple.eawt._AppEventHandler$_AppEventMultiplexor$1.run(_AppEventHandler.java:439) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at org.simplericity.macify.eawt.DefaultApplication$ApplicationListenerInvocationHandler.invoke(DefaultApplication.java:400) ... 21 more Caused by: java.lang.AbstractMethodError: org.bbop.framework.AbstractApplicationStartupTask$MacApplicationSupport.handleReOpenApplication(Lorg/simplericity/macify/eawt/ApplicationEvent;)V ... 26 more 2016-08-26 14:51:50,145 INFO (ParserWrapper:74) Finished loading ontology: http://purl.obolibrary.org/obo/go.owl from: http://purl.obolibrary.org/obo/go.owl 2016-08-26 http://purl.obolibrary.org/obo/go.owl2016-08-26 14:51:50,455 INFO (Reasoner:117) ELK reasoner was created 2016-08-26 14:51:56,833 INFO (LoggingStageExecutor:70) Loading of Axioms started 2016-08-26 14:51:56,847 INFO (AbstractReasonerStage:161) Loading of Axioms using 8 workers 2016-08-26 14:51:57,530 WARN (ChangeIndexingProcessor:66) ELK does not support SymmetricObjectProperty. Axiom ignored: SymmetricObjectProperty() 2016-08-26 14:51:58,018 WARN (ChangeIndexingProcessor:66) ELK does not support InverseObjectProperties. Axiom ignored: InverseObjectProperties( ) 2016-08-26 14:52:01,108 INFO (LoggingStageExecutor:103) Loading of Axioms took 4264 ms 2016-08-26 14:52:01,109 INFO (LoggingStageExecutor:70) Property Saturation Initialization started 2016-08-26 14:52:01,110 INFO (AbstractReasonerStage:161) Property Saturation Initialization using 8 workers 2016-08-26 14:52:01,111 INFO (LoggingStageExecutor:103) Property Saturation Initialization took 1 ms 2016-08-26 14:52:01,111 INFO (LoggingStageExecutor:70) Reflexive Property Computation started 2016-08-26 14:52:01,114 INFO (AbstractReasonerStage:161) Reflexive Property Computation using 8 workers 2016-08-26 14:52:01,116 INFO (LoggingStageExecutor:103) Reflexive Property Computation took 5 ms 2016-08-26 14:52:01,116 INFO (LoggingStageExecutor:70) Object Property Hierarchy and Composition Computation started 2016-08-26 14:52:01,119 INFO (AbstractReasonerStage:161) Object Property Hierarchy and Composition Computation using 8 workers 2016-08-26 14:52:01,124 INFO (LoggingStageExecutor:103) Object Property Hierarchy and Composition Computation took 7 ms 2016-08-26 14:52:01,124 INFO (LoggingStageExecutor:70) Context Initialization started 2016-08-26 14:52:01,125 INFO (AbstractReasonerStage:161) Context Initialization using 8 workers 2016-08-26 14:52:01,128 INFO (LoggingStageExecutor:103) Context Initialization took 2 ms 2016-08-26 14:52:01,128 INFO (LoggingStageExecutor:70) Consistency Checking started 2016-08-26 14:52:01,132 INFO (AbstractReasonerStage:161) Consistency Checking using 8 workers 2016-08-26 14:52:01,212 INFO (LoggingStageExecutor:103) Consistency Checking took 83 ms 2016-08-26 14:52:01,212 INFO (LoggingStageExecutor:70) Class Taxonomy Computation started 2016-08-26 14:52:01,217 INFO (AbstractReasonerStage:161) Class Taxonomy Computation using 8 workers 2016-08-26 14:52:08,851 INFO (LoggingStageExecutor:103) Class Taxonomy Computation took 7639 ms 2016-08-26 14:53:50,637 INFO (IDmap:113) Identical Seq ID (UniProtKB:Q7PSE6) for 2 different genes: Gene:AGAP009389 Gene:AgaP_AGAP009389 2016-08-26 14:53:50,639 INFO (DisplayTree:70) There are 15 nodes in the PTHR21524 tree 2016-08-26 14:53:52,878 INFO (class:135) Retrieving experimental annotations from: http://golr.geneontology.org

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krchristie commented 7 years ago

This problem with the popup menus being non-functional and impossible to dismiss also occurs with the "evolutionary loss" popup.

20161018-evolosspopup

I understand that this isn't a super quick fix, but it is super annoying. I keep losing work because I've done several propagations in quick sucession without saving and get then get one of these popups which effectively renders PAINT non-functional as I have to force quit it and repeat what I've just done.

cmungall commented 7 years ago

I have changed the label on this ticket from 'question' to 'bug'. And because @krchristie was losing work I added a label 'affects usability'.

pgaudet commented 7 years ago

I think there is a work around for this bug: for me when I try to click on continue, then PAINT freezes. However when I hit enter then it works fine.

Pascale

On Thu, Oct 27, 2016 at 10:22 PM, Chris Mungall notifications@github.com wrote:

I have changed the label on this ticket from 'question' to 'bug'. And because @krchristie https://github.com/krchristie was losing work I added a label 'affects usability'.

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krchristie commented 7 years ago

Thanks for that info Pascale. Hitting 'enter' is a work around for at least not losing work.

However, the fact that these pop-ups are non-functional in terms of being able to propagate a qualifier since ticking the box does not work means that there are some propagations that are impossible to make since it is impossible to select the qualifier.

-Karen

selewis commented 7 years ago

I think this is related to this bug report: https://bugs.openjdk.java.net/browse/JDK-8139393 Basically the fact that the dialog is called from the drop function (which means the drop class has control of the mouse) it isn't letting go of mouse control for the dialog box to hear about.

It is java version dependent, but in the meantime I can implement the fix they recommend and see if that works. Can I ask you to test it please when I have it ready.

-S

krchristie commented 7 years ago

I'll be happy to Suzi, just let me know.

-K

selewis commented 7 years ago

I've made another attempt at a fix for this. Give try to v2.28b and see if I've managed to work around it.

krchristie commented 7 years ago

v2.28b did not fix this for me.

v2.28c does fix the dialog box issue for me!

FYI: I notice that this version seems to make my computer run quite loudly, i.e. activates the fan. I also turned on "Activity Monitor" and watched the CPU load, and it is noticeably high in a way that correlates with v2.28c, especially after doing some propagations (launched, did some propagations, and quit 3 times). I didn't see this with v2.28a (only tested 1 time today, though I don't remember hearing the fan kick so regularly with previous versions of PAINT-2. This might not be avoidable based on the way you fixed the dialog box, but I thought I'd mention it.

Also, v2.28c just has 2.28 in the title bar once it's launched. I know you've been trying to turn this around quickly, but it's super helpful to have that when I'm comparing different versions, so just wanted to point it out so it gets on your list to update for the next version.

Thanks!!

-Karen

selewis commented 7 years ago

So happy that the dialog box issue is fixed (whew).

In my memory it's always been 'noisy' when initially loading during the allocation of memory, so I don't think this is new. It should quiet down post-loading.

I'll take a look at the title bar thing and make a v2.29 release.

On Thu, Dec 8, 2016 at 4:31 PM, Karen R Christie notifications@github.com wrote:

v2.28b did not fix this for me.

v2.28c does fix the dialog box issue for me!

FYI: I notice that this version seems to make my computer run quite loudly, i.e. activates the fan. I also turned on "Activity Monitor" and watched the CPU load, and it is noticeably high in a way that correlates with v2.28c, especially after doing some propagations (launched, did some propagations, and quit 3 times). I didn't see this with v2.28a (only tested 1 time today, though I don't remember hearing the fan kick so regularly with previous versions of PAINT-2. This might not be avoidable based on the way you fixed the dialog box, but I thought I'd mention it.

Also, v2.28c just has 2.28 in the title bar once it's launched. I know you've been trying to turn this around quickly, but it's super helpful to have that when I'm comparing different versions, so just wanted to point it out so it gets on your list to update for the next version.

Thanks!!

-Karen

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krchristie commented 7 years ago

2.28c isn't any noisier than previous versions during initial loading. It's after a propagation that popped up the qualifier dialog box. But more of an FYI observation than anything else. Certainly the qualifier box works. I didn't actually check the taxon popup...

Thanks for fixing it!!!