invokingMethods broken in moose or inFamix

> hi guys,
>
> one of my students encountered a case where
> FAMIXMethod#invokingMethods is not correctly set. i wonder whether
> that is a moose problem or an infamix one. anybody knows about this?
> the original message is at the end of this mail.
>
> thanks,
>
> --
> Dr. Mircea Lungu
> Researcher
> Software Composition Group
> University of Bern
>
>
>
> I assumed that FAMIXMethod >> invokingMethods would return all methods
> that invoke the method represented by the FAMIXMethod instance, this
> doesn't seem to be the case.
>
>
> I created an mse file with inFamix from the code in svn at
> http://svn.apache.org/repos/asf/incubator/stanbol/trunk/enhancer/engines/keywordextraction/
>
>
> The class org.apache.stanbol.enhancer.engines.keywordextraction.linking.EntityLinker
> has both private methods with an empty collection of invokingMethod as
> well as with a non-empty one:
>
> - The method getLinkedEntityTypes has an empty collection of invokingMethods
>
> even though the method is in fact invoked:
>
> public void process(){
> ...
> if(linkedEntity == null){
> linkedEntity = new LinkedEntity(selectedText,
> suggestions, getLinkedEntityTypes(suggestions.subList(0, 1)));
> linkedEntities.put(selectedText, linkedEntity);
> }
>
>
> By contrast in the same class
>
> - porcessRedirects has {process} as collection of invokingMethods,
> where processRedirects is invokes as follows:
>
> public void process(){
> ...
> if(config.getRedirectProcessingMode() != RedirectProcessingMode.IGNORE){
> for(Suggestion suggestion : suggestions){
> processRedirects(suggestion);
> }
> }
>
> All the method I've looked at with an empty collection of
> inkingMethods in fact had at least one invokation, I tried to make a
> famix model for just the class EntityLinker as this class has both
> private method with empty as well as with a non-empty set of ivokers
> according to Moose, I hoped that with a small mse file it would be
> easier to analyze the problem.
>
> Unfortunately I didn't manage to create such an mse model, I'm getting
> the following exception message running `inFamix -lang java -path
> source -mse test.mse`:
>
> java.lang.StringIndexOutOfBoundsException: String index out of range: -1
> at java.lang.String.substring(String.java:1931)
> at java.lang.String.substring(String.java:1904)
> at com.intooitus.infusion.batch.JavaBatchModelBuilder.compute(JavaBatchModelBuilder.java:43)
> at com.intooitus.infusion.batch.BatchApplication.run(BatchApplication.java:135)
> at com.intooitus.infusion.batch.BatchApplication.start(BatchApplication.java:43)
> at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
> at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
> at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
> at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
> at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
> at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
> at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
>
> Unfortunately as inFamix is not open source and because of section 2.3
> of the SLA it's hard for me to tackle this problem so I would
> appreciate some help.
> _______________________________________________
> Moose-dev mailing list
> [hidden email]
> https://www.iam.unibe.ch/mailman/listinfo/moose-dev

> hi guys,
>
> one of my students encountered a case where
> FAMIXMethod#invokingMethods is not correctly set. i wonder whether
> that is a moose problem or an infamix one. anybody knows about this?
> the original message is at the end of this mail.
>
> thanks,
>
> --
> Dr. Mircea Lungu
> Researcher
> Software Composition Group
> University of Bern
>
>
>
> I assumed that FAMIXMethod >> invokingMethods would return all methods
> that invoke the method represented by the FAMIXMethod instance, this
> doesn't seem to be the case.
>
>
> I created an mse file with inFamix from the code in svn at
> http://svn.apache.org/repos/asf/incubator/stanbol/trunk/enhancer/engines/keywordextraction/
>
>
> The class org.apache.stanbol.enhancer.engines.keywordextraction.linking.EntityLinker
> has both private methods with an empty collection of invokingMethod as
> well as with a non-empty one:
>
> - The method getLinkedEntityTypes has an empty collection of invokingMethods
>
> even though the method is in fact invoked:
>
> public void process(){
> ...
> if(linkedEntity == null){
> linkedEntity = new LinkedEntity(selectedText,
> suggestions, getLinkedEntityTypes(suggestions.subList(0, 1)));
> linkedEntities.put(selectedText, linkedEntity);
> }
>
>
> By contrast in the same class
>
> - porcessRedirects has {process} as collection of invokingMethods,
> where processRedirects is invokes as follows:
>
> public void process(){
> ...
> if(config.getRedirectProcessingMode() != RedirectProcessingMode.IGNORE){
> for(Suggestion suggestion : suggestions){
> processRedirects(suggestion);
> }
> }
>
> All the method I've looked at with an empty collection of
> inkingMethods in fact had at least one invokation, I tried to make a
> famix model for just the class EntityLinker as this class has both
> private method with empty as well as with a non-empty set of ivokers
> according to Moose, I hoped that with a small mse file it would be
> easier to analyze the problem.
>
> Unfortunately I didn't manage to create such an mse model, I'm getting
> the following exception message running `inFamix -lang java -path
> source -mse test.mse`:
>
> java.lang.StringIndexOutOfBoundsException: String index out of range: -1
> at java.lang.String.substring(String.java:1931)
> at java.lang.String.substring(String.java:1904)
> at com.intooitus.infusion.batch.JavaBatchModelBuilder.compute(JavaBatchModelBuilder.java:43)
> at com.intooitus.infusion.batch.BatchApplication.run(BatchApplication.java:135)
> at com.intooitus.infusion.batch.BatchApplication.start(BatchApplication.java:43)
> at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
> at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
> at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
> at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
> at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
> at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
> at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
>
> Unfortunately as inFamix is not open source and because of section 2.3
> of the SLA it's hard for me to tackle this problem so I would
> appreciate some help.
> _______________________________________________
> Moose-dev mailing list
> [hidden email]
> https://www.iam.unibe.ch/mailman/listinfo/moose-dev

> Hi Mircea,
>
> Thanks for the report. This looks troubling, so it is something we need to double check.
>
> However, I cannot reproduce the problem because something seems to be wrong currently with svn.apache.org.
>
> Regarding the error of running inFamix, it might probably due to a trailing "/" in the path string, or that the path is to a file. The former problem should be fixed in the last release of inFamix. The latter is not supposed to work at all because it expects a folder.
>
> In any case, it would be useful to also try with verveineJ:
> http://www.themoosebook.org/book/externals/import-export/external/verveineJ
>
> Doru
>
>
> On 4 Dec 2011, at 00:02, Mircea Filip Lungu wrote:
>
>> hi guys,
>>
>> one of my students encountered a case where
>> FAMIXMethod#invokingMethods is not correctly set. i wonder whether
>> that is a moose problem or an infamix one. anybody knows about this?
>> the original message is at the end of this mail.
>>
>> thanks,
>>
>> --
>> Dr. Mircea Lungu
>> Researcher
>> Software Composition Group
>> University of Bern
>>
>>
>>
>> I assumed that FAMIXMethod >> invokingMethods would return all methods
>> that invoke the method represented by the FAMIXMethod instance, this
>> doesn't seem to be the case.
>>
>>
>> I created an mse file with inFamix from the code in svn at
>> http://svn.apache.org/repos/asf/incubator/stanbol/trunk/enhancer/engines/keywordextraction/
>>
>>
>> The class org.apache.stanbol.enhancer.engines.keywordextraction.linking.EntityLinker
>> has both private methods with an empty collection of invokingMethod as
>> well as with a non-empty one:
>>
>> - The method getLinkedEntityTypes has an empty collection of invokingMethods
>>
>> even though the method is in fact invoked:
>>
>> public void process(){
>> ...
>> if(linkedEntity == null){
>> linkedEntity = new LinkedEntity(selectedText,
>> suggestions, getLinkedEntityTypes(suggestions.subList(0, 1)));
>> linkedEntities.put(selectedText, linkedEntity);
>> }
>>
>>
>> By contrast in the same class
>>
>> - porcessRedirects has {process} as collection of invokingMethods,
>> where processRedirects is invokes as follows:
>>
>> public void process(){
>> ...
>> if(config.getRedirectProcessingMode() != RedirectProcessingMode.IGNORE){
>> for(Suggestion suggestion : suggestions){
>> processRedirects(suggestion);
>> }
>> }
>>
>> All the method I've looked at with an empty collection of
>> inkingMethods in fact had at least one invokation, I tried to make a
>> famix model for just the class EntityLinker as this class has both
>> private method with empty as well as with a non-empty set of ivokers
>> according to Moose, I hoped that with a small mse file it would be
>> easier to analyze the problem.
>>
>> Unfortunately I didn't manage to create such an mse model, I'm getting
>> the following exception message running `inFamix -lang java -path
>> source -mse test.mse`:
>>
>> java.lang.StringIndexOutOfBoundsException: String index out of range: -1
>> at java.lang.String.substring(String.java:1931)
>> at java.lang.String.substring(String.java:1904)
>> at com.intooitus.infusion.batch.JavaBatchModelBuilder.compute(JavaBatchModelBuilder.java:43)
>> at com.intooitus.infusion.batch.BatchApplication.run(BatchApplication.java:135)
>> at com.intooitus.infusion.batch.BatchApplication.start(BatchApplication.java:43)
>> at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
>> at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
>> at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
>> at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
>> at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>> at java.lang.reflect.Method.invoke(Method.java:597)
>> at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
>> at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
>> at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
>>
>> Unfortunately as inFamix is not open source and because of section 2.3
>> of the SLA it's hard for me to tackle this problem so I would
>> appreciate some help.
>> _______________________________________________
>> Moose-dev mailing list
>> [hidden email]
>> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>
> --
> www.tudorgirba.com
>
> "We can create beautiful models in a vacuum.
> But, to get them effective we have to deal with the inconvenience of reality."
>
>
> _______________________________________________
> Moose-dev mailing list
> [hidden email]
> https://www.iam.unibe.ch/mailman/listinfo/moose-dev

> Hi guys and thanks for the prompt responses!
>
> Alex, I tried to use the Chef methods but nothing changes.
>
> Then I tried to use inFusion instead of inFamix. It generates a model file
> which is larger than inFamix but still this particular invocation is not in it.
> Then Fabrizio had the great idea of trying an older version of inFusion and
> that one works: the invocation from process to getLinkedEntityTypes is in
> the model now.
>
> This means that the lastest version of the inFamix still needs improvements.
> (by the way, where should I report this? i don't see any mailinglist or forum
> related to intooitus tools).
>
> I also tried verveinej and I get an error that I will attach to the
> end of this mail.
>
> Cheers,
> M.
>
> The following is what I obtain if I run VerveineJ on the aforementioned project
>
> feivel:verveine.extractor.java mircea$ ./verveinej.sh
> ~/Teaching/SDE-Project/case-studies/keywordextraction/src/
> ~/Desktop/vj-kwx.mse
> ./lib/akuhn-util-r28011.jar:./lib/fame-good.jar:./lib/fame.jar:./lib/famix.jar:./lib/junit.jar:./lib/org.eclipse.core.contenttype_3.4.100.v20110423-0524.jar:./lib/org.eclipse.core.jobs_3.5.100.v20110404.jar:./lib/org.eclipse.core.resources_3.7.100.v20110510-0712.jar:./lib/org.eclipse.core.runtime_3.7.0.v20110110.jar:./lib/org.eclipse.equinox.common_3.6.0.v20110523.jar:./lib/org.eclipse.equinox.preferences_3.4.1.R37x_v20110725.jar:./lib/org.eclipse.jdt.core_3.7.1.v_B76_R37x.jar:./lib/org.eclipse.osgi_3.7.1.R37x_v20110808-1106.jar:./lib/org.eclipse.text_3.5.0.v20100601-1300.jar:./lib/org.hamcrest.core_1.1.0.v20090501071000.jar:./lib/verveine.core.jar:./lib/verveine.extractor.java.jar
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/engine/KeywordLinkingEngine.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/ProcessingState.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/AnalysedContent.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntityLinker.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntityLinkerConfig.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntitySearcher.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntityhubSearcher.java
> *** VerveineJ visitor got exception:
> 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
> fr.inria.verveine.core.gen.famix.Class' while processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntityhubSearcher.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntitySearcherUtils.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/OpenNlpAnalysedContentFactory.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/ReferencedSiteSearcher.java
> *** VerveineJ visitor got exception:
> 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
> fr.inria.verveine.core.gen.famix.Class' while processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/ReferencedSiteSearcher.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/TrackingEntitySearcher.java
> *** VerveineJ visitor got exception:
> 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
> fr.inria.verveine.core.gen.famix.Class' while processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/TrackingEntitySearcher.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/LinkedEntity.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/Suggestion.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/ClasspathDataFileProvider.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/MockComponentContext.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/TestSearcherImpl.java
> VerveineJ processing file:
> /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/TestTaxonomyLinker.java
>
>
>
> On Mon, Dec 5, 2011 at 7:42 AM, Tudor Girba <[hidden email]> wrote:
>> Hi Mircea,
>>
>> Thanks for the report. This looks troubling, so it is something we need to double check.
>>
>> However, I cannot reproduce the problem because something seems to be wrong currently with svn.apache.org.
>>
>> Regarding the error of running inFamix, it might probably due to a trailing "/" in the path string, or that the path is to a file. The former problem should be fixed in the last release of inFamix. The latter is not supposed to work at all because it expects a folder.
>>
>> In any case, it would be useful to also try with verveineJ:
>> http://www.themoosebook.org/book/externals/import-export/external/verveineJ
>>
>> Doru
>>
>>
>> On 4 Dec 2011, at 00:02, Mircea Filip Lungu wrote:
>>
>>> hi guys,
>>>
>>> one of my students encountered a case where
>>> FAMIXMethod#invokingMethods is not correctly set. i wonder whether
>>> that is a moose problem or an infamix one. anybody knows about this?
>>> the original message is at the end of this mail.
>>>
>>> thanks,
>>>
>>> --
>>> Dr. Mircea Lungu
>>> Researcher
>>> Software Composition Group
>>> University of Bern
>>>
>>>
>>>
>>> I assumed that FAMIXMethod >> invokingMethods would return all methods
>>> that invoke the method represented by the FAMIXMethod instance, this
>>> doesn't seem to be the case.
>>>
>>>
>>> I created an mse file with inFamix from the code in svn at
>>> http://svn.apache.org/repos/asf/incubator/stanbol/trunk/enhancer/engines/keywordextraction/
>>>
>>>
>>> The class org.apache.stanbol.enhancer.engines.keywordextraction.linking.EntityLinker
>>> has both private methods with an empty collection of invokingMethod as
>>> well as with a non-empty one:
>>>
>>> - The method getLinkedEntityTypes has an empty collection of invokingMethods
>>>
>>> even though the method is in fact invoked:
>>>
>>> public void process(){
>>> ...
>>> if(linkedEntity == null){
>>> linkedEntity = new LinkedEntity(selectedText,
>>> suggestions, getLinkedEntityTypes(suggestions.subList(0, 1)));
>>> linkedEntities.put(selectedText, linkedEntity);
>>> }
>>>
>>>
>>> By contrast in the same class
>>>
>>> - porcessRedirects has {process} as collection of invokingMethods,
>>> where processRedirects is invokes as follows:
>>>
>>> public void process(){
>>> ...
>>> if(config.getRedirectProcessingMode() != RedirectProcessingMode.IGNORE){
>>> for(Suggestion suggestion : suggestions){
>>> processRedirects(suggestion);
>>> }
>>> }
>>>
>>> All the method I've looked at with an empty collection of
>>> inkingMethods in fact had at least one invokation, I tried to make a
>>> famix model for just the class EntityLinker as this class has both
>>> private method with empty as well as with a non-empty set of ivokers
>>> according to Moose, I hoped that with a small mse file it would be
>>> easier to analyze the problem.
>>>
>>> Unfortunately I didn't manage to create such an mse model, I'm getting
>>> the following exception message running `inFamix -lang java -path
>>> source -mse test.mse`:
>>>
>>> java.lang.StringIndexOutOfBoundsException: String index out of range: -1
>>> at java.lang.String.substring(String.java:1931)
>>> at java.lang.String.substring(String.java:1904)
>>> at com.intooitus.infusion.batch.JavaBatchModelBuilder.compute(JavaBatchModelBuilder.java:43)
>>> at com.intooitus.infusion.batch.BatchApplication.run(BatchApplication.java:135)
>>> at com.intooitus.infusion.batch.BatchApplication.start(BatchApplication.java:43)
>>> at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
>>> at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
>>> at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
>>> at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
>>> at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>> at java.lang.reflect.Method.invoke(Method.java:597)
>>> at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
>>> at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
>>> at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
>>>
>>> Unfortunately as inFamix is not open source and because of section 2.3
>>> of the SLA it's hard for me to tackle this problem so I would
>>> appreciate some help.
>>> _______________________________________________
>>> Moose-dev mailing list
>>> [hidden email]
>>> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>>
>> --
>> www.tudorgirba.com
>>
>> "We can create beautiful models in a vacuum.
>> But, to get them effective we have to deal with the inconvenience of reality."
>>
>>
>> _______________________________________________
>> Moose-dev mailing list
>> [hidden email]
>> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>
> _______________________________________________
> Moose-dev mailing list
> [hidden email]
> https://www.iam.unibe.ch/mailman/listinfo/moose-dev

> De: "Tudor Girba" <[hidden email]>
> À: "Moose-related development" <[hidden email]>
> Envoyé: Mardi 6 Décembre 2011 10:26:02
> Objet: [Moose-dev] Re: invokingMethods broken in moose or inFamix
> Hi Mircea,
>
> I do not understand where the VerveineJ error is.
>
> One thing however is that the mse will always be output.mse. Anyway, I
> still cannot access the case study sources. Could you make them
> available somewhere?
>
> Cheers,
> Doru
>
>
> On 5 Dec 2011, at 15:34, Mircea Filip Lungu wrote:
>
> > Hi guys and thanks for the prompt responses!
> >
> > Alex, I tried to use the Chef methods but nothing changes.
> >
> > Then I tried to use inFusion instead of inFamix. It generates a
> > model file
> > which is larger than inFamix but still this particular invocation is
> > not in it.
> > Then Fabrizio had the great idea of trying an older version of
> > inFusion and
> > that one works: the invocation from process to getLinkedEntityTypes
> > is in
> > the model now.
> >
> > This means that the lastest version of the inFamix still needs
> > improvements.
> > (by the way, where should I report this? i don't see any mailinglist
> > or forum
> > related to intooitus tools).
> >
> > I also tried verveinej and I get an error that I will attach to the
> > end of this mail.
> >
> > Cheers,
> > M.
> >
> > The following is what I obtain if I run VerveineJ on the
> > aforementioned project
> >
> > feivel:verveine.extractor.java mircea$ ./verveinej.sh
> > ~/Teaching/SDE-Project/case-studies/keywordextraction/src/
> > ~/Desktop/vj-kwx.mse
> > ./lib/akuhn-util-r28011.jar:./lib/fame-good.jar:./lib/fame.jar:./lib/famix.jar:./lib/junit.jar:./lib/org.eclipse.core.contenttype_3.4.100.v20110423-0524.jar:./lib/org.eclipse.core.jobs_3.5.100.v20110404.jar:./lib/org.eclipse.core.resources_3.7.100.v20110510-0712.jar:./lib/org.eclipse.core.runtime_3.7.0.v20110110.jar:./lib/org.eclipse.equinox.common_3.6.0.v20110523.jar:./lib/org.eclipse.equinox.preferences_3.4.1.R37x_v20110725.jar:./lib/org.eclipse.jdt.core_3.7.1.v_B76_R37x.jar:./lib/org.eclipse.osgi_3.7.1.R37x_v20110808-1106.jar:./lib/org.eclipse.text_3.5.0.v20100601-1300.jar:./lib/org.hamcrest.core_1.1.0.v20090501071000.jar:./lib/verveine.core.jar:./lib/verveine.extractor.java.jar
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/engine/KeywordLinkingEngine.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/ProcessingState.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/AnalysedContent.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntityLinker.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntityLinkerConfig.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntitySearcher.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntityhubSearcher.java
> > *** VerveineJ visitor got exception:
> > 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
> > fr.inria.verveine.core.gen.famix.Class' while processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntityhubSearcher.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntitySearcherUtils.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/OpenNlpAnalysedContentFactory.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/ReferencedSiteSearcher.java
> > *** VerveineJ visitor got exception:
> > 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
> > fr.inria.verveine.core.gen.famix.Class' while processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/ReferencedSiteSearcher.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/TrackingEntitySearcher.java
> > *** VerveineJ visitor got exception:
> > 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
> > fr.inria.verveine.core.gen.famix.Class' while processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/TrackingEntitySearcher.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/LinkedEntity.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/Suggestion.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/ClasspathDataFileProvider.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/MockComponentContext.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/TestSearcherImpl.java
> > VerveineJ processing file:
> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/TestTaxonomyLinker.java
> >
> >
> >
> > On Mon, Dec 5, 2011 at 7:42 AM, Tudor Girba <[hidden email]>
> > wrote:
> >> Hi Mircea,
> >>
> >> Thanks for the report. This looks troubling, so it is something we
> >> need to double check.
> >>
> >> However, I cannot reproduce the problem because something seems to
> >> be wrong currently with svn.apache.org.
> >>
> >> Regarding the error of running inFamix, it might probably due to a
> >> trailing "/" in the path string, or that the path is to a file. The
> >> former problem should be fixed in the last release of inFamix. The
> >> latter is not supposed to work at all because it expects a folder.
> >>
> >> In any case, it would be useful to also try with verveineJ:
> >> http://www.themoosebook.org/book/externals/import-export/external/verveineJ
> >>
> >> Doru
> >>
> >>
> >> On 4 Dec 2011, at 00:02, Mircea Filip Lungu wrote:
> >>
> >>> hi guys,
> >>>
> >>> one of my students encountered a case where
> >>> FAMIXMethod#invokingMethods is not correctly set. i wonder whether
> >>> that is a moose problem or an infamix one. anybody knows about
> >>> this?
> >>> the original message is at the end of this mail.
> >>>
> >>> thanks,
> >>>
> >>> --
> >>> Dr. Mircea Lungu
> >>> Researcher
> >>> Software Composition Group
> >>> University of Bern
> >>>
> >>>
> >>>
> >>> I assumed that FAMIXMethod >> invokingMethods would return all
> >>> methods
> >>> that invoke the method represented by the FAMIXMethod instance,
> >>> this
> >>> doesn't seem to be the case.
> >>>
> >>>
> >>> I created an mse file with inFamix from the code in svn at
> >>> http://svn.apache.org/repos/asf/incubator/stanbol/trunk/enhancer/engines/keywordextraction/
> >>>
> >>>
> >>> The class
> >>> org.apache.stanbol.enhancer.engines.keywordextraction.linking.EntityLinker
> >>> has both private methods with an empty collection of
> >>> invokingMethod as
> >>> well as with a non-empty one:
> >>>
> >>> - The method getLinkedEntityTypes has an empty collection of
> >>> invokingMethods
> >>>
> >>> even though the method is in fact invoked:
> >>>
> >>> public void process(){
> >>> ...
> >>> if(linkedEntity == null){
> >>> linkedEntity = new LinkedEntity(selectedText,
> >>> suggestions, getLinkedEntityTypes(suggestions.subList(0, 1)));
> >>> linkedEntities.put(selectedText, linkedEntity);
> >>> }
> >>>
> >>>
> >>> By contrast in the same class
> >>>
> >>> - porcessRedirects has {process} as collection of invokingMethods,
> >>> where processRedirects is invokes as follows:
> >>>
> >>> public void process(){
> >>> ...
> >>> if(config.getRedirectProcessingMode() !=
> >>> RedirectProcessingMode.IGNORE){
> >>> for(Suggestion suggestion : suggestions){
> >>> processRedirects(suggestion);
> >>> }
> >>> }
> >>>
> >>> All the method I've looked at with an empty collection of
> >>> inkingMethods in fact had at least one invokation, I tried to make
> >>> a
> >>> famix model for just the class EntityLinker as this class has both
> >>> private method with empty as well as with a non-empty set of
> >>> ivokers
> >>> according to Moose, I hoped that with a small mse file it would be
> >>> easier to analyze the problem.
> >>>
> >>> Unfortunately I didn't manage to create such an mse model, I'm
> >>> getting
> >>> the following exception message running `inFamix -lang java -path
> >>> source -mse test.mse`:
> >>>
> >>> java.lang.StringIndexOutOfBoundsException: String index out of
> >>> range: -1
> >>> at java.lang.String.substring(String.java:1931)
> >>> at java.lang.String.substring(String.java:1904)
> >>> at
> >>> com.intooitus.infusion.batch.JavaBatchModelBuilder.compute(JavaBatchModelBuilder.java:43)
> >>> at
> >>> com.intooitus.infusion.batch.BatchApplication.run(BatchApplication.java:135)
> >>> at
> >>> com.intooitus.infusion.batch.BatchApplication.start(BatchApplication.java:43)
> >>> at
> >>> org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
> >>> at
> >>> org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
> >>> at
> >>> org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
> >>> at
> >>> org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
> >>> at
> >>> org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
> >>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >>> at
> >>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> >>> at
> >>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> >>> at java.lang.reflect.Method.invoke(Method.java:597)
> >>> at
> >>> org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
> >>> at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
> >>> at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
> >>>
> >>> Unfortunately as inFamix is not open source and because of section
> >>> 2.3
> >>> of the SLA it's hard for me to tackle this problem so I would
> >>> appreciate some help.
> >>> _______________________________________________
> >>> Moose-dev mailing list
> >>> [hidden email]
> >>> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
> >>
> >> --
> >> www.tudorgirba.com
> >>
> >> "We can create beautiful models in a vacuum.
> >> But, to get them effective we have to deal with the inconvenience
> >> of reality."
> >>
> >>
> >> _______________________________________________
> >> Moose-dev mailing list
> >> [hidden email]
> >> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
> >
> > _______________________________________________
> > Moose-dev mailing list
> > [hidden email]
> > https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>
> --
> www.tudorgirba.com
>
> "From an abstract enough point of view, any two things are similar."
>
>
>
>
> _______________________________________________
> Moose-dev mailing list
> [hidden email]
> https://www.iam.unibe.ch/mailman/listinfo/moose-dev

> Hi
>
> Thank for taking the time to report and insvestigate the error.
>
> I have downloaded the sources and ran verveinej.
> I have the same problem of missing invoking method.
>
> The bug will be investigated.
> I understand you have a temprorary solution for now, so I will ask for some time to look into that.
> Is that ok ?
>
> nicolas
>
> ----- Mail original -----
>> De: "Tudor Girba" <[hidden email]>
>> À: "Moose-related development" <[hidden email]>
>> Envoyé: Mardi 6 Décembre 2011 10:26:02
>> Objet: [Moose-dev] Re: invokingMethods broken in moose or inFamix
>> Hi Mircea,
>>
>> I do not understand where the VerveineJ error is.
>>
>> One thing however is that the mse will always be output.mse. Anyway, I
>> still cannot access the case study sources. Could you make them
>> available somewhere?
>>
>> Cheers,
>> Doru
>>
>>
>> On 5 Dec 2011, at 15:34, Mircea Filip Lungu wrote:
>>
>> > Hi guys and thanks for the prompt responses!
>> >
>> > Alex, I tried to use the Chef methods but nothing changes.
>> >
>> > Then I tried to use inFusion instead of inFamix. It generates a
>> > model file
>> > which is larger than inFamix but still this particular invocation is
>> > not in it.
>> > Then Fabrizio had the great idea of trying an older version of
>> > inFusion and
>> > that one works: the invocation from process to getLinkedEntityTypes
>> > is in
>> > the model now.
>> >
>> > This means that the lastest version of the inFamix still needs
>> > improvements.
>> > (by the way, where should I report this? i don't see any mailinglist
>> > or forum
>> > related to intooitus tools).
>> >
>> > I also tried verveinej and I get an error that I will attach to the
>> > end of this mail.
>> >
>> > Cheers,
>> > M.
>> >
>> > The following is what I obtain if I run VerveineJ on the
>> > aforementioned project
>> >
>> > feivel:verveine.extractor.java mircea$ ./verveinej.sh
>> > ~/Teaching/SDE-Project/case-studies/keywordextraction/src/
>> > ~/Desktop/vj-kwx.mse
>> > ./lib/akuhn-util-r28011.jar:./lib/fame-good.jar:./lib/fame.jar:./lib/famix.jar:./lib/junit.jar:./lib/org.eclipse.core.contenttype_3.4.100.v20110423-0524.jar:./lib/org.eclipse.core.jobs_3.5.100.v20110404.jar:./lib/org.eclipse.core.resources_3.7.100.v20110510-0712.jar:./lib/org.eclipse.core.runtime_3.7.0.v20110110.jar:./lib/org.eclipse.equinox.common_3.6.0.v20110523.jar:./lib/org.eclipse.equinox.preferences_3.4.1.R37x_v20110725.jar:./lib/org.eclipse.jdt.core_3.7.1.v_B76_R37x.jar:./lib/org.eclipse.osgi_3.7.1.R37x_v20110808-1106.jar:./lib/org.eclipse.text_3.5.0.v20100601-1300.jar:./lib/org.hamcrest.core_1.1.0.v20090501071000.jar:./lib/verveine.core.jar:./lib/verveine.extractor.java.jar
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/engine/KeywordLinkingEngine.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/ProcessingState.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/AnalysedContent.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntityLinker.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntityLinkerConfig.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntitySearcher.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntityhubSearcher.java
>> > *** VerveineJ visitor got exception:
>> > 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
>> > fr.inria.verveine.core.gen.famix.Class' while processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntityhubSearcher.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntitySearcherUtils.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/OpenNlpAnalysedContentFactory.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/ReferencedSiteSearcher.java
>> > *** VerveineJ visitor got exception:
>> > 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
>> > fr.inria.verveine.core.gen.famix.Class' while processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/ReferencedSiteSearcher.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/TrackingEntitySearcher.java
>> > *** VerveineJ visitor got exception:
>> > 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
>> > fr.inria.verveine.core.gen.famix.Class' while processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/TrackingEntitySearcher.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/LinkedEntity.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/Suggestion.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/ClasspathDataFileProvider.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/MockComponentContext.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/TestSearcherImpl.java
>> > VerveineJ processing file:
>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/TestTaxonomyLinker.java
>> >
>> >
>> >
>> > On Mon, Dec 5, 2011 at 7:42 AM, Tudor Girba <[hidden email]>
>> > wrote:
>> >> Hi Mircea,
>> >>
>> >> Thanks for the report. This looks troubling, so it is something we
>> >> need to double check.
>> >>
>> >> However, I cannot reproduce the problem because something seems to
>> >> be wrong currently with svn.apache.org.
>> >>
>> >> Regarding the error of running inFamix, it might probably due to a
>> >> trailing "/" in the path string, or that the path is to a file. The
>> >> former problem should be fixed in the last release of inFamix. The
>> >> latter is not supposed to work at all because it expects a folder.
>> >>
>> >> In any case, it would be useful to also try with verveineJ:
>> >> http://www.themoosebook.org/book/externals/import-export/external/verveineJ
>> >>
>> >> Doru
>> >>
>> >>
>> >> On 4 Dec 2011, at 00:02, Mircea Filip Lungu wrote:
>> >>
>> >>> hi guys,
>> >>>
>> >>> one of my students encountered a case where
>> >>> FAMIXMethod#invokingMethods is not correctly set. i wonder whether
>> >>> that is a moose problem or an infamix one. anybody knows about
>> >>> this?
>> >>> the original message is at the end of this mail.
>> >>>
>> >>> thanks,
>> >>>
>> >>> --
>> >>> Dr. Mircea Lungu
>> >>> Researcher
>> >>> Software Composition Group
>> >>> University of Bern
>> >>>
>> >>>
>> >>>
>> >>> I assumed that FAMIXMethod >> invokingMethods would return all
>> >>> methods
>> >>> that invoke the method represented by the FAMIXMethod instance,
>> >>> this
>> >>> doesn't seem to be the case.
>> >>>
>> >>>
>> >>> I created an mse file with inFamix from the code in svn at
>> >>> http://svn.apache.org/repos/asf/incubator/stanbol/trunk/enhancer/engines/keywordextraction/
>> >>>
>> >>>
>> >>> The class
>> >>> org.apache.stanbol.enhancer.engines.keywordextraction.linking.EntityLinker
>> >>> has both private methods with an empty collection of
>> >>> invokingMethod as
>> >>> well as with a non-empty one:
>> >>>
>> >>> - The method getLinkedEntityTypes has an empty collection of
>> >>> invokingMethods
>> >>>
>> >>> even though the method is in fact invoked:
>> >>>
>> >>> public void process(){
>> >>> ...
>> >>> if(linkedEntity == null){
>> >>> linkedEntity = new LinkedEntity(selectedText,
>> >>> suggestions, getLinkedEntityTypes(suggestions.subList(0, 1)));
>> >>> linkedEntities.put(selectedText, linkedEntity);
>> >>> }
>> >>>
>> >>>
>> >>> By contrast in the same class
>> >>>
>> >>> - porcessRedirects has {process} as collection of invokingMethods,
>> >>> where processRedirects is invokes as follows:
>> >>>
>> >>> public void process(){
>> >>> ...
>> >>> if(config.getRedirectProcessingMode() !=
>> >>> RedirectProcessingMode.IGNORE){
>> >>> for(Suggestion suggestion : suggestions){
>> >>> processRedirects(suggestion);
>> >>> }
>> >>> }
>> >>>
>> >>> All the method I've looked at with an empty collection of
>> >>> inkingMethods in fact had at least one invokation, I tried to make
>> >>> a
>> >>> famix model for just the class EntityLinker as this class has both
>> >>> private method with empty as well as with a non-empty set of
>> >>> ivokers
>> >>> according to Moose, I hoped that with a small mse file it would be
>> >>> easier to analyze the problem.
>> >>>
>> >>> Unfortunately I didn't manage to create such an mse model, I'm
>> >>> getting
>> >>> the following exception message running `inFamix -lang java -path
>> >>> source -mse test.mse`:
>> >>>
>> >>> java.lang.StringIndexOutOfBoundsException: String index out of
>> >>> range: -1
>> >>> at java.lang.String.substring(String.java:1931)
>> >>> at java.lang.String.substring(String.java:1904)
>> >>> at
>> >>> com.intooitus.infusion.batch.JavaBatchModelBuilder.compute(JavaBatchModelBuilder.java:43)
>> >>> at
>> >>> com.intooitus.infusion.batch.BatchApplication.run(BatchApplication.java:135)
>> >>> at
>> >>> com.intooitus.infusion.batch.BatchApplication.start(BatchApplication.java:43)
>> >>> at
>> >>> org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
>> >>> at
>> >>> org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
>> >>> at
>> >>> org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
>> >>> at
>> >>> org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
>> >>> at
>> >>> org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
>> >>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> >>> at
>> >>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>> >>> at
>> >>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>> >>> at java.lang.reflect.Method.invoke(Method.java:597)
>> >>> at
>> >>> org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
>> >>> at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
>> >>> at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
>> >>>
>> >>> Unfortunately as inFamix is not open source and because of section
>> >>> 2.3
>> >>> of the SLA it's hard for me to tackle this problem so I would
>> >>> appreciate some help.
>> >>> _______________________________________________
>> >>> Moose-dev mailing list
>> >>> [hidden email]
>> >>> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>> >>
>> >> --
>> >> www.tudorgirba.com
>> >>
>> >> "We can create beautiful models in a vacuum.
>> >> But, to get them effective we have to deal with the inconvenience
>> >> of reality."
>> >>
>> >>
>> >> _______________________________________________
>> >> Moose-dev mailing list
>> >> [hidden email]
>> >> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>> >
>> > _______________________________________________
>> > Moose-dev mailing list
>> > [hidden email]
>> > https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>>
>> --
>> www.tudorgirba.com
>>
>> "From an abstract enough point of view, any two things are similar."
>>
>>
>>
>>
>> _______________________________________________
>> Moose-dev mailing list
>> [hidden email]
>> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>
> _______________________________________________
> Moose-dev mailing list
> [hidden email]
> https://www.iam.unibe.ch/mailman/listinfo/moose-dev

> Interesting. Please open a bug report.
>
> Doru
>
>
> On Tue, Dec 6, 2011 at 10:51 AM, Nicolas Anquetil
> <[hidden email]> wrote:
>> Hi
>>
>> Thank for taking the time to report and insvestigate the error.
>>
>> I have downloaded the sources and ran verveinej.
>> I have the same problem of missing invoking method.
>>
>> The bug will be investigated.
>> I understand you have a temprorary solution for now, so I will ask for some time to look into that.
>> Is that ok ?
>>
>> nicolas
>>
>> ----- Mail original -----
>>> De: "Tudor Girba" <[hidden email]>
>>> À: "Moose-related development" <[hidden email]>
>>> Envoyé: Mardi 6 Décembre 2011 10:26:02
>>> Objet: [Moose-dev] Re: invokingMethods broken in moose or inFamix
>>> Hi Mircea,
>>>
>>> I do not understand where the VerveineJ error is.
>>>
>>> One thing however is that the mse will always be output.mse. Anyway, I
>>> still cannot access the case study sources. Could you make them
>>> available somewhere?
>>>
>>> Cheers,
>>> Doru
>>>
>>>
>>> On 5 Dec 2011, at 15:34, Mircea Filip Lungu wrote:
>>>
>>> > Hi guys and thanks for the prompt responses!
>>> >
>>> > Alex, I tried to use the Chef methods but nothing changes.
>>> >
>>> > Then I tried to use inFusion instead of inFamix. It generates a
>>> > model file
>>> > which is larger than inFamix but still this particular invocation is
>>> > not in it.
>>> > Then Fabrizio had the great idea of trying an older version of
>>> > inFusion and
>>> > that one works: the invocation from process to getLinkedEntityTypes
>>> > is in
>>> > the model now.
>>> >
>>> > This means that the lastest version of the inFamix still needs
>>> > improvements.
>>> > (by the way, where should I report this? i don't see any mailinglist
>>> > or forum
>>> > related to intooitus tools).
>>> >
>>> > I also tried verveinej and I get an error that I will attach to the
>>> > end of this mail.
>>> >
>>> > Cheers,
>>> > M.
>>> >
>>> > The following is what I obtain if I run VerveineJ on the
>>> > aforementioned project
>>> >
>>> > feivel:verveine.extractor.java mircea$ ./verveinej.sh
>>> > ~/Teaching/SDE-Project/case-studies/keywordextraction/src/
>>> > ~/Desktop/vj-kwx.mse
>>> > ./lib/akuhn-util-r28011.jar:./lib/fame-good.jar:./lib/fame.jar:./lib/famix.jar:./lib/junit.jar:./lib/org.eclipse.core.contenttype_3.4.100.v20110423-0524.jar:./lib/org.eclipse.core.jobs_3.5.100.v20110404.jar:./lib/org.eclipse.core.resources_3.7.100.v20110510-0712.jar:./lib/org.eclipse.core.runtime_3.7.0.v20110110.jar:./lib/org.eclipse.equinox.common_3.6.0.v20110523.jar:./lib/org.eclipse.equinox.preferences_3.4.1.R37x_v20110725.jar:./lib/org.eclipse.jdt.core_3.7.1.v_B76_R37x.jar:./lib/org.eclipse.osgi_3.7.1.R37x_v20110808-1106.jar:./lib/org.eclipse.text_3.5.0.v20100601-1300.jar:./lib/org.hamcrest.core_1.1.0.v20090501071000.jar:./lib/verveine.core.jar:./lib/verveine.extractor.java.jar
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/engine/KeywordLinkingEngine.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/ProcessingState.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/AnalysedContent.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntityLinker.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntityLinkerConfig.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/EntitySearcher.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntityhubSearcher.java
>>> > *** VerveineJ visitor got exception:
>>> > 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
>>> > fr.inria.verveine.core.gen.famix.Class' while processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntityhubSearcher.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/EntitySearcherUtils.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/OpenNlpAnalysedContentFactory.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/ReferencedSiteSearcher.java
>>> > *** VerveineJ visitor got exception:
>>> > 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
>>> > fr.inria.verveine.core.gen.famix.Class' while processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/ReferencedSiteSearcher.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/TrackingEntitySearcher.java
>>> > *** VerveineJ visitor got exception:
>>> > 'fr.inria.verveine.core.gen.famix.Type cannot be cast to
>>> > fr.inria.verveine.core.gen.famix.Class' while processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/impl/TrackingEntitySearcher.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/LinkedEntity.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/main/java/org/apache/stanbol/enhancer/engines/keywordextraction/linking/Suggestion.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/ClasspathDataFileProvider.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/MockComponentContext.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/impl/TestSearcherImpl.java
>>> > VerveineJ processing file:
>>> > /Users/mircea/Teaching/SDE-Project/case-studies/keywordextraction/src/test/java/org/apache/stanbol/enhancer/engines/keywordextraction/TestTaxonomyLinker.java
>>> >
>>> >
>>> >
>>> > On Mon, Dec 5, 2011 at 7:42 AM, Tudor Girba <[hidden email]>
>>> > wrote:
>>> >> Hi Mircea,
>>> >>
>>> >> Thanks for the report. This looks troubling, so it is something we
>>> >> need to double check.
>>> >>
>>> >> However, I cannot reproduce the problem because something seems to
>>> >> be wrong currently with svn.apache.org.
>>> >>
>>> >> Regarding the error of running inFamix, it might probably due to a
>>> >> trailing "/" in the path string, or that the path is to a file. The
>>> >> former problem should be fixed in the last release of inFamix. The
>>> >> latter is not supposed to work at all because it expects a folder.
>>> >>
>>> >> In any case, it would be useful to also try with verveineJ:
>>> >> http://www.themoosebook.org/book/externals/import-export/external/verveineJ
>>> >>
>>> >> Doru
>>> >>
>>> >>
>>> >> On 4 Dec 2011, at 00:02, Mircea Filip Lungu wrote:
>>> >>
>>> >>> hi guys,
>>> >>>
>>> >>> one of my students encountered a case where
>>> >>> FAMIXMethod#invokingMethods is not correctly set. i wonder whether
>>> >>> that is a moose problem or an infamix one. anybody knows about
>>> >>> this?
>>> >>> the original message is at the end of this mail.
>>> >>>
>>> >>> thanks,
>>> >>>
>>> >>> --
>>> >>> Dr. Mircea Lungu
>>> >>> Researcher
>>> >>> Software Composition Group
>>> >>> University of Bern
>>> >>>
>>> >>>
>>> >>>
>>> >>> I assumed that FAMIXMethod >> invokingMethods would return all
>>> >>> methods
>>> >>> that invoke the method represented by the FAMIXMethod instance,
>>> >>> this
>>> >>> doesn't seem to be the case.
>>> >>>
>>> >>>
>>> >>> I created an mse file with inFamix from the code in svn at
>>> >>> http://svn.apache.org/repos/asf/incubator/stanbol/trunk/enhancer/engines/keywordextraction/
>>> >>>
>>> >>>
>>> >>> The class
>>> >>> org.apache.stanbol.enhancer.engines.keywordextraction.linking.EntityLinker
>>> >>> has both private methods with an empty collection of
>>> >>> invokingMethod as
>>> >>> well as with a non-empty one:
>>> >>>
>>> >>> - The method getLinkedEntityTypes has an empty collection of
>>> >>> invokingMethods
>>> >>>
>>> >>> even though the method is in fact invoked:
>>> >>>
>>> >>> public void process(){
>>> >>> ...
>>> >>> if(linkedEntity == null){
>>> >>> linkedEntity = new LinkedEntity(selectedText,
>>> >>> suggestions, getLinkedEntityTypes(suggestions.subList(0, 1)));
>>> >>> linkedEntities.put(selectedText, linkedEntity);
>>> >>> }
>>> >>>
>>> >>>
>>> >>> By contrast in the same class
>>> >>>
>>> >>> - porcessRedirects has {process} as collection of invokingMethods,
>>> >>> where processRedirects is invokes as follows:
>>> >>>
>>> >>> public void process(){
>>> >>> ...
>>> >>> if(config.getRedirectProcessingMode() !=
>>> >>> RedirectProcessingMode.IGNORE){
>>> >>> for(Suggestion suggestion : suggestions){
>>> >>> processRedirects(suggestion);
>>> >>> }
>>> >>> }
>>> >>>
>>> >>> All the method I've looked at with an empty collection of
>>> >>> inkingMethods in fact had at least one invokation, I tried to make
>>> >>> a
>>> >>> famix model for just the class EntityLinker as this class has both
>>> >>> private method with empty as well as with a non-empty set of
>>> >>> ivokers
>>> >>> according to Moose, I hoped that with a small mse file it would be
>>> >>> easier to analyze the problem.
>>> >>>
>>> >>> Unfortunately I didn't manage to create such an mse model, I'm
>>> >>> getting
>>> >>> the following exception message running `inFamix -lang java -path
>>> >>> source -mse test.mse`:
>>> >>>
>>> >>> java.lang.StringIndexOutOfBoundsException: String index out of
>>> >>> range: -1
>>> >>> at java.lang.String.substring(String.java:1931)
>>> >>> at java.lang.String.substring(String.java:1904)
>>> >>> at
>>> >>> com.intooitus.infusion.batch.JavaBatchModelBuilder.compute(JavaBatchModelBuilder.java:43)
>>> >>> at
>>> >>> com.intooitus.infusion.batch.BatchApplication.run(BatchApplication.java:135)
>>> >>> at
>>> >>> com.intooitus.infusion.batch.BatchApplication.start(BatchApplication.java:43)
>>> >>> at
>>> >>> org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
>>> >>> at
>>> >>> org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
>>> >>> at
>>> >>> org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
>>> >>> at
>>> >>> org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
>>> >>> at
>>> >>> org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
>>> >>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>> >>> at
>>> >>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>> >>> at
>>> >>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>> >>> at java.lang.reflect.Method.invoke(Method.java:597)
>>> >>> at
>>> >>> org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
>>> >>> at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
>>> >>> at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
>>> >>>
>>> >>> Unfortunately as inFamix is not open source and because of section
>>> >>> 2.3
>>> >>> of the SLA it's hard for me to tackle this problem so I would
>>> >>> appreciate some help.
>>> >>> _______________________________________________
>>> >>> Moose-dev mailing list
>>> >>> [hidden email]
>>> >>> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>>> >>
>>> >> --
>>> >> www.tudorgirba.com
>>> >>
>>> >> "We can create beautiful models in a vacuum.
>>> >> But, to get them effective we have to deal with the inconvenience
>>> >> of reality."
>>> >>
>>> >>
>>> >> _______________________________________________
>>> >> Moose-dev mailing list
>>> >> [hidden email]
>>> >> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>>> >
>>> > _______________________________________________
>>> > Moose-dev mailing list
>>> > [hidden email]
>>> > https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>>>
>>> --
>>> www.tudorgirba.com
>>>
>>> "From an abstract enough point of view, any two things are similar."
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Moose-dev mailing list
>>> [hidden email]
>>> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>>
>> _______________________________________________
>> Moose-dev mailing list
>> [hidden email]
>> https://www.iam.unibe.ch/mailman/listinfo/moose-dev
>
>
>
> --
> www.tudorgirba.com
>
> "Every thing has its own flow"
>
> _______________________________________________
> Moose-dev mailing list
> [hidden email]
> https://www.iam.unibe.ch/mailman/listinfo/moose-dev