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Posted to dev@ctakes.apache.org by "Kaggal, Vinod C." <Ka...@mayo.edu> on 2013/03/14 15:45:32 UTC
relation-extractor - how to include it as a dependency?
Hello!
Quick Background: We have been working on integrating CTAKES with DataNormalization pipeline (as part of SHARPN effort). I have added relation-extractor as a dependency to our Normalization project as the template-filling module/project uses it.
Question: What is the is a recommended way of adding the relation-extraction's resource directory to a project that uses this project? Just adding the project (relation-extractor) to the build-path (projects) results in the following error:
Caused by: org.apache.uima.resource.ResourceInitializationException
at org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:115)
at org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnotator.initialize(RelationExtractorAnnotator.java:121)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 71 more
Caused by: java.io.FileNotFoundException: resources/models/em_pair/model.jar (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:120)
at java.io.FileInputStream.<init>(FileInputStream.java:79)
at org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassifier(GenericJarClassifierFactory.java:67)
at org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarClassifierFactory.java:35)
at org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:113)
Looks like copying the resources directory to the target project (Normalization project in this case) seems to take care of this issue. However, I wanted to see a cleaner way of doing this instead of duplicating the jar (and other resources).
Vinod
Re: relation-extractor - how to include it as a dependency?
Posted by "Kaggal, Vinod C." <Ka...@mayo.edu>.
Thanks Steve.
On Mar 15, 2013, at 3:51 AM, "Steven Bethard" <st...@Colorado.EDU> wrote:
> On Mar 14, 2013, at 3:45 PM, "Kaggal, Vinod C." <Ka...@mayo.edu> wrote:
>> Question: What is the is a recommended way of adding the relation-extraction's resource directory to a project that uses this project? Just adding the project (relation-extractor) to the build-path (projects) results in the following error:
> [snip]
>> Caused by: java.io.FileNotFoundException: resources/models/em_pair/model.jar (No such file or directory)
>> at java.io.FileInputStream.open(Native Method)
>> at java.io.FileInputStream.<init>(FileInputStream.java:120)
>> at java.io.FileInputStream.<init>(FileInputStream.java:79)
>> at org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassifier(GenericJarClassifierFactory.java:67)
>> at org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarClassifierFactory.java:35)
>> at org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:113)
>
> I opened an issue for this:
>
> https://issues.apache.org/jira/browse/CTAKES-177
>
> And I believe it should be fixed in r1456800 - ctakes-relation-extractor should now be looking on the classpath for its models now.
>
> Let me know if that solves the problem for you.
>
> Steve
>
Re: relation-extractor - how to include it as a dependency?
Posted by Steven Bethard <st...@Colorado.EDU>.
On Mar 14, 2013, at 3:45 PM, "Kaggal, Vinod C." <Ka...@mayo.edu> wrote:
> Question: What is the is a recommended way of adding the relation-extraction's resource directory to a project that uses this project? Just adding the project (relation-extractor) to the build-path (projects) results in the following error:
[snip]
> Caused by: java.io.FileNotFoundException: resources/models/em_pair/model.jar (No such file or directory)
> at java.io.FileInputStream.open(Native Method)
> at java.io.FileInputStream.<init>(FileInputStream.java:120)
> at java.io.FileInputStream.<init>(FileInputStream.java:79)
> at org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassifier(GenericJarClassifierFactory.java:67)
> at org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarClassifierFactory.java:35)
> at org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:113)
I opened an issue for this:
https://issues.apache.org/jira/browse/CTAKES-177
And I believe it should be fixed in r1456800 - ctakes-relation-extractor should now be looking on the classpath for its models now.
Let me know if that solves the problem for you.
Steve
RE: relation-extractor - how to include it as a dependency?
Posted by "Masanz, James J." <Ma...@mayo.edu>.
In this theoretical version of things I would suggest we have 2 sets of descriptors and both would live in the cTAKES SVN
- one set for all the real models
- one set for the dummy models.
And 2 sets of tests, also both in cTAKES SVN
-- James
> -----Original Message-----
> From: ctakes-dev-return-1371-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1371-Masanz.James=mayo.edu@incubator.apache.org]
> On Behalf Of Steven Bethard
> Sent: Thursday, March 14, 2013 3:00 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: relation-extractor - how to include it as a dependency?
>
> On Mar 14, 2013, at 8:52 PM, "Masanz, James J." <Ma...@mayo.edu>
> wrote:
> > If we end up unable to keep the (real) models in the apache SVN, I'm
> imagining not having the tests that rely on the real models run
> automatically.
> >
> > We can create some dummy models just for testing and only run those
> tests automatically.
> > And to run the tests using the real models, someone would need to check
> out the project, get the real resources, and run the real tests.
>
> And the descriptors in SVN would also point to the dummy models?
>
> Steve
>
> >
> >
> > Regards,
> > James Masanz
> >
> >
> >> -----Original Message-----
> >> From:
> >> ctakes-dev-return-1369-Masanz.James=mayo.edu@incubator.apache.org
> >> [mailto:ctakes-dev-return-1369-Masanz.James=mayo.edu@incubator.apache
> >> .org]
> >> On Behalf Of Steven Bethard
> >> Sent: Thursday, March 14, 2013 2:46 PM
> >> To: ctakes-dev@incubator.apache.org
> >> Subject: Re: relation-extractor - how to include it as a dependency?
> >>
> >> On Mar 14, 2013, at 8:43 PM, "Masanz, James J."
> >> <Ma...@mayo.edu>
> >> wrote:
> >>> I just posted a comment on LEGAL-157 asking for some movement.
> >>>
> >>> No matter what the answer there about the models, I suggest leaving
> >>> the
> >> descriptors and the tests in Apache cTAKES SVN.
> >>
> >> But if the tests require the models, won't they always fail if
> >> they're in cTAKES SVN?
> >>
> >> Or are you imagining that ctakes-relation-extractor will depend on
> >> ctakes- resources-relationextractor?
> >>
> >> Steve
> >>
> >>>
> >>> -- James
> >>>
> >>>> -----Original Message-----
> >>>> From:
> >>>> ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apache.org
> >>>> [mailto:ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apac
> >>>> he
> >>>> .org]
> >>>> On Behalf Of Steven Bethard
> >>>> Sent: Thursday, March 14, 2013 10:39 AM
> >>>> To: ctakes-dev@incubator.apache.org
> >>>> Subject: Re: relation-extractor - how to include it as a dependency?
> >>>>
> >>>> Yeah, I never saw a conclusion to the discussion of where the
> >>>> relation- extractor models should go. My last impression was that
> >>>> they can't be in the Apache SVN at all, and they need to be in the
> >>>> Sourceforge ctakesresources project. Is that right?
> >>>>
> >>>> If that's the case, we need to update RelationExtractorTrain to
> >>>> deploy the models to that project rather than src/main/resources
> >>>> (where it currently deploys them), and delete all the models in the
> >> cTAKES SVN.
> >>>>
> >>>> And then where would the descriptors go? In the Sourceforge project?
> >>>> Or in the cTAKES SVN? Seems weird to have them in the cTAKES SVN if
> >>>> they can't refer to their models.
> >>>>
> >>>> And if we move the descriptors to Sourceforge, I guess that also
> >>>> means moving the tests to Sourceforge?
> >>>>
> >>>> Steve
> >>>>
> >>>> P.S. In the meantime, you may be able to get things working by
> >>>> making a copy of EntityMentionPairRelationExtractorAnnotator.xml
> >>>> that looks in org/apache/ctakes/relationextractor/models/em_pair
> >>>> instead of resources/models/em_pair, since there are currently
> >>>> still models in src/main/resources.
> >>>>
> >>>>
> >>>> On Mar 14, 2013, at 4:11 PM, "Chen, Pei"
> >>>> <Pe...@childrens.harvard.edu>
> >>>> wrote:
> >>>>
> >>>>> Hi Vinod,
> >>>>> I think that looks like a bug. Feel free to open a Jira.
> >>>>>
> >>>>> Sent from my iPhone
> >>>>>
> >>>>> Sent from my iPhone
> >>>>>
> >>>>> On Mar 14, 2013, at 10:46 AM, "Kaggal, Vinod C."
> >>>>> <Ka...@mayo.edu>
> >>>> wrote:
> >>>>>
> >>>>>> Hello!
> >>>>>>
> >>>>>> Quick Background: We have been working on integrating CTAKES with
> >>>> DataNormalization pipeline (as part of SHARPN effort). I have added
> >>>> relation-extractor as a dependency to our Normalization project as
> >>>> the template-filling module/project uses it.
> >>>>>>
> >>>>>> Question: What is the is a recommended way of adding the
> >>>>>> relation-
> >>>> extraction's resource directory to a project that uses this project?
> >>>> Just adding the project (relation-extractor) to the build-path
> >>>> (projects) results in the following error:
> >>>>>>
> >>>>>>
> >>>>>> Caused by: org.apache.uima.resource.ResourceInitializationException
> >>>>>> at
> >>>> org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator
> >>>> .j
> >>>> ava:1
> >>>> 15)
> >>>>>> at
> >>>> org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnno
> >>>> ta
> >>>> tor.i
> >>>> nitialize(RelationExtractorAnnotator.java:121)
> >>>>>> at
> >>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.i
> >>>> ni
> >>>> tiali
> >>>> zeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> >>>>>> ... 71 more
> >>>>>> Caused by: java.io.FileNotFoundException:
> >>>> resources/models/em_pair/model.jar (No such file or directory)
> >>>>>> at java.io.FileInputStream.open(Native Method)
> >>>>>> at java.io.FileInputStream.<init>(FileInputStream.java:120)
> >>>>>> at java.io.FileInputStream.<init>(FileInputStream.java:79)
> >>>>>> at
> >>>> org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassi
> >>>> fi
> >>>> er(Ge
> >>>> nericJarClassifierFactory.java:67)
> >>>>>> at
> >>>> org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(Ja
> >>>> rC
> >>>> lassi
> >>>> fierFactory.java:35)
> >>>>>> at
> >>>> org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator
> >>>> .j
> >>>> ava:1
> >>>> 13)
> >>>>>>
> >>>>>>
> >>>>>> Looks like copying the resources directory to the target project
> >>>> (Normalization project in this case) seems to take care of this
> issue.
> >>>> However, I wanted to see a cleaner way of doing this instead of
> >>>> duplicating the jar (and other resources).
> >>>>>>
> >>>>>>
> >>>>>> Vinod
> >>>
> >
Re: relation-extractor - how to include it as a dependency?
Posted by Steven Bethard <st...@Colorado.EDU>.
On Mar 14, 2013, at 8:52 PM, "Masanz, James J." <Ma...@mayo.edu> wrote:
> If we end up unable to keep the (real) models in the apache SVN, I'm imagining not having the tests that rely on the real models run automatically.
>
> We can create some dummy models just for testing and only run those tests automatically.
> And to run the tests using the real models, someone would need to check out the project, get the real resources, and run the real tests.
And the descriptors in SVN would also point to the dummy models?
Steve
>
>
> Regards,
> James Masanz
>
>
>> -----Original Message-----
>> From: ctakes-dev-return-1369-Masanz.James=mayo.edu@incubator.apache.org
>> [mailto:ctakes-dev-return-1369-Masanz.James=mayo.edu@incubator.apache.org]
>> On Behalf Of Steven Bethard
>> Sent: Thursday, March 14, 2013 2:46 PM
>> To: ctakes-dev@incubator.apache.org
>> Subject: Re: relation-extractor - how to include it as a dependency?
>>
>> On Mar 14, 2013, at 8:43 PM, "Masanz, James J." <Ma...@mayo.edu>
>> wrote:
>>> I just posted a comment on LEGAL-157 asking for some movement.
>>>
>>> No matter what the answer there about the models, I suggest leaving the
>> descriptors and the tests in Apache cTAKES SVN.
>>
>> But if the tests require the models, won't they always fail if they're in
>> cTAKES SVN?
>>
>> Or are you imagining that ctakes-relation-extractor will depend on ctakes-
>> resources-relationextractor?
>>
>> Steve
>>
>>>
>>> -- James
>>>
>>>> -----Original Message-----
>>>> From:
>>>> ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apache.org
>>>> [mailto:ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apache
>>>> .org]
>>>> On Behalf Of Steven Bethard
>>>> Sent: Thursday, March 14, 2013 10:39 AM
>>>> To: ctakes-dev@incubator.apache.org
>>>> Subject: Re: relation-extractor - how to include it as a dependency?
>>>>
>>>> Yeah, I never saw a conclusion to the discussion of where the
>>>> relation- extractor models should go. My last impression was that
>>>> they can't be in the Apache SVN at all, and they need to be in the
>>>> Sourceforge ctakesresources project. Is that right?
>>>>
>>>> If that's the case, we need to update RelationExtractorTrain to
>>>> deploy the models to that project rather than src/main/resources
>>>> (where it currently deploys them), and delete all the models in the
>> cTAKES SVN.
>>>>
>>>> And then where would the descriptors go? In the Sourceforge project?
>>>> Or in the cTAKES SVN? Seems weird to have them in the cTAKES SVN if
>>>> they can't refer to their models.
>>>>
>>>> And if we move the descriptors to Sourceforge, I guess that also
>>>> means moving the tests to Sourceforge?
>>>>
>>>> Steve
>>>>
>>>> P.S. In the meantime, you may be able to get things working by making
>>>> a copy of EntityMentionPairRelationExtractorAnnotator.xml that looks
>>>> in org/apache/ctakes/relationextractor/models/em_pair instead of
>>>> resources/models/em_pair, since there are currently still models in
>>>> src/main/resources.
>>>>
>>>>
>>>> On Mar 14, 2013, at 4:11 PM, "Chen, Pei"
>>>> <Pe...@childrens.harvard.edu>
>>>> wrote:
>>>>
>>>>> Hi Vinod,
>>>>> I think that looks like a bug. Feel free to open a Jira.
>>>>>
>>>>> Sent from my iPhone
>>>>>
>>>>> Sent from my iPhone
>>>>>
>>>>> On Mar 14, 2013, at 10:46 AM, "Kaggal, Vinod C."
>>>>> <Ka...@mayo.edu>
>>>> wrote:
>>>>>
>>>>>> Hello!
>>>>>>
>>>>>> Quick Background: We have been working on integrating CTAKES with
>>>> DataNormalization pipeline (as part of SHARPN effort). I have added
>>>> relation-extractor as a dependency to our Normalization project as
>>>> the template-filling module/project uses it.
>>>>>>
>>>>>> Question: What is the is a recommended way of adding the relation-
>>>> extraction's resource directory to a project that uses this project?
>>>> Just adding the project (relation-extractor) to the build-path
>>>> (projects) results in the following error:
>>>>>>
>>>>>>
>>>>>> Caused by: org.apache.uima.resource.ResourceInitializationException
>>>>>> at
>>>> org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.j
>>>> ava:1
>>>> 15)
>>>>>> at
>>>> org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnota
>>>> tor.i
>>>> nitialize(RelationExtractorAnnotator.java:121)
>>>>>> at
>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
>>>> tiali
>>>> zeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>>>>> ... 71 more
>>>>>> Caused by: java.io.FileNotFoundException:
>>>> resources/models/em_pair/model.jar (No such file or directory)
>>>>>> at java.io.FileInputStream.open(Native Method)
>>>>>> at java.io.FileInputStream.<init>(FileInputStream.java:120)
>>>>>> at java.io.FileInputStream.<init>(FileInputStream.java:79)
>>>>>> at
>>>> org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassifi
>>>> er(Ge
>>>> nericJarClassifierFactory.java:67)
>>>>>> at
>>>> org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarC
>>>> lassi
>>>> fierFactory.java:35)
>>>>>> at
>>>> org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.j
>>>> ava:1
>>>> 13)
>>>>>>
>>>>>>
>>>>>> Looks like copying the resources directory to the target project
>>>> (Normalization project in this case) seems to take care of this issue.
>>>> However, I wanted to see a cleaner way of doing this instead of
>>>> duplicating the jar (and other resources).
>>>>>>
>>>>>>
>>>>>> Vinod
>>>
>
RE: relation-extractor - how to include it as a dependency?
Posted by "Masanz, James J." <Ma...@mayo.edu>.
If we end up unable to keep the (real) models in the apache SVN, I'm imagining not having the tests that rely on the real models run automatically.
We can create some dummy models just for testing and only run those tests automatically.
And to run the tests using the real models, someone would need to check out the project, get the real resources, and run the real tests.
Regards,
James Masanz
> -----Original Message-----
> From: ctakes-dev-return-1369-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1369-Masanz.James=mayo.edu@incubator.apache.org]
> On Behalf Of Steven Bethard
> Sent: Thursday, March 14, 2013 2:46 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: relation-extractor - how to include it as a dependency?
>
> On Mar 14, 2013, at 8:43 PM, "Masanz, James J." <Ma...@mayo.edu>
> wrote:
> > I just posted a comment on LEGAL-157 asking for some movement.
> >
> > No matter what the answer there about the models, I suggest leaving the
> descriptors and the tests in Apache cTAKES SVN.
>
> But if the tests require the models, won't they always fail if they're in
> cTAKES SVN?
>
> Or are you imagining that ctakes-relation-extractor will depend on ctakes-
> resources-relationextractor?
>
> Steve
>
> >
> > -- James
> >
> >> -----Original Message-----
> >> From:
> >> ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apache.org
> >> [mailto:ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apache
> >> .org]
> >> On Behalf Of Steven Bethard
> >> Sent: Thursday, March 14, 2013 10:39 AM
> >> To: ctakes-dev@incubator.apache.org
> >> Subject: Re: relation-extractor - how to include it as a dependency?
> >>
> >> Yeah, I never saw a conclusion to the discussion of where the
> >> relation- extractor models should go. My last impression was that
> >> they can't be in the Apache SVN at all, and they need to be in the
> >> Sourceforge ctakesresources project. Is that right?
> >>
> >> If that's the case, we need to update RelationExtractorTrain to
> >> deploy the models to that project rather than src/main/resources
> >> (where it currently deploys them), and delete all the models in the
> cTAKES SVN.
> >>
> >> And then where would the descriptors go? In the Sourceforge project?
> >> Or in the cTAKES SVN? Seems weird to have them in the cTAKES SVN if
> >> they can't refer to their models.
> >>
> >> And if we move the descriptors to Sourceforge, I guess that also
> >> means moving the tests to Sourceforge?
> >>
> >> Steve
> >>
> >> P.S. In the meantime, you may be able to get things working by making
> >> a copy of EntityMentionPairRelationExtractorAnnotator.xml that looks
> >> in org/apache/ctakes/relationextractor/models/em_pair instead of
> >> resources/models/em_pair, since there are currently still models in
> >> src/main/resources.
> >>
> >>
> >> On Mar 14, 2013, at 4:11 PM, "Chen, Pei"
> >> <Pe...@childrens.harvard.edu>
> >> wrote:
> >>
> >>> Hi Vinod,
> >>> I think that looks like a bug. Feel free to open a Jira.
> >>>
> >>> Sent from my iPhone
> >>>
> >>> Sent from my iPhone
> >>>
> >>> On Mar 14, 2013, at 10:46 AM, "Kaggal, Vinod C."
> >>> <Ka...@mayo.edu>
> >> wrote:
> >>>
> >>>> Hello!
> >>>>
> >>>> Quick Background: We have been working on integrating CTAKES with
> >> DataNormalization pipeline (as part of SHARPN effort). I have added
> >> relation-extractor as a dependency to our Normalization project as
> >> the template-filling module/project uses it.
> >>>>
> >>>> Question: What is the is a recommended way of adding the relation-
> >> extraction's resource directory to a project that uses this project?
> >> Just adding the project (relation-extractor) to the build-path
> >> (projects) results in the following error:
> >>>>
> >>>>
> >>>> Caused by: org.apache.uima.resource.ResourceInitializationException
> >>>> at
> >> org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.j
> >> ava:1
> >> 15)
> >>>> at
> >> org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnota
> >> tor.i
> >> nitialize(RelationExtractorAnnotator.java:121)
> >>>> at
> >> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
> >> tiali
> >> zeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> >>>> ... 71 more
> >>>> Caused by: java.io.FileNotFoundException:
> >> resources/models/em_pair/model.jar (No such file or directory)
> >>>> at java.io.FileInputStream.open(Native Method)
> >>>> at java.io.FileInputStream.<init>(FileInputStream.java:120)
> >>>> at java.io.FileInputStream.<init>(FileInputStream.java:79)
> >>>> at
> >> org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassifi
> >> er(Ge
> >> nericJarClassifierFactory.java:67)
> >>>> at
> >> org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarC
> >> lassi
> >> fierFactory.java:35)
> >>>> at
> >> org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.j
> >> ava:1
> >> 13)
> >>>>
> >>>>
> >>>> Looks like copying the resources directory to the target project
> >> (Normalization project in this case) seems to take care of this issue.
> >> However, I wanted to see a cleaner way of doing this instead of
> >> duplicating the jar (and other resources).
> >>>>
> >>>>
> >>>> Vinod
> >
Re: relation-extractor - how to include it as a dependency?
Posted by Steven Bethard <st...@Colorado.EDU>.
On Mar 14, 2013, at 8:43 PM, "Masanz, James J." <Ma...@mayo.edu> wrote:
> I just posted a comment on LEGAL-157 asking for some movement.
>
> No matter what the answer there about the models, I suggest leaving the descriptors and the tests in Apache cTAKES SVN.
But if the tests require the models, won't they always fail if they're in cTAKES SVN?
Or are you imagining that ctakes-relation-extractor will depend on ctakes-resources-relationextractor?
Steve
>
> -- James
>
>> -----Original Message-----
>> From: ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apache.org
>> [mailto:ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apache.org]
>> On Behalf Of Steven Bethard
>> Sent: Thursday, March 14, 2013 10:39 AM
>> To: ctakes-dev@incubator.apache.org
>> Subject: Re: relation-extractor - how to include it as a dependency?
>>
>> Yeah, I never saw a conclusion to the discussion of where the relation-
>> extractor models should go. My last impression was that they can't be in
>> the Apache SVN at all, and they need to be in the Sourceforge
>> ctakesresources project. Is that right?
>>
>> If that's the case, we need to update RelationExtractorTrain to deploy the
>> models to that project rather than src/main/resources (where it currently
>> deploys them), and delete all the models in the cTAKES SVN.
>>
>> And then where would the descriptors go? In the Sourceforge project? Or in
>> the cTAKES SVN? Seems weird to have them in the cTAKES SVN if they can't
>> refer to their models.
>>
>> And if we move the descriptors to Sourceforge, I guess that also means
>> moving the tests to Sourceforge?
>>
>> Steve
>>
>> P.S. In the meantime, you may be able to get things working by making a
>> copy of EntityMentionPairRelationExtractorAnnotator.xml that looks in
>> org/apache/ctakes/relationextractor/models/em_pair instead of
>> resources/models/em_pair, since there are currently still models in
>> src/main/resources.
>>
>>
>> On Mar 14, 2013, at 4:11 PM, "Chen, Pei" <Pe...@childrens.harvard.edu>
>> wrote:
>>
>>> Hi Vinod,
>>> I think that looks like a bug. Feel free to open a Jira.
>>>
>>> Sent from my iPhone
>>>
>>> Sent from my iPhone
>>>
>>> On Mar 14, 2013, at 10:46 AM, "Kaggal, Vinod C." <Ka...@mayo.edu>
>> wrote:
>>>
>>>> Hello!
>>>>
>>>> Quick Background: We have been working on integrating CTAKES with
>> DataNormalization pipeline (as part of SHARPN effort). I have added
>> relation-extractor as a dependency to our Normalization project as the
>> template-filling module/project uses it.
>>>>
>>>> Question: What is the is a recommended way of adding the relation-
>> extraction's resource directory to a project that uses this project? Just
>> adding the project (relation-extractor) to the build-path (projects)
>> results in the following error:
>>>>
>>>>
>>>> Caused by: org.apache.uima.resource.ResourceInitializationException
>>>> at
>> org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:1
>> 15)
>>>> at
>> org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnotator.i
>> nitialize(RelationExtractorAnnotator.java:121)
>>>> at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initiali
>> zeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>>> ... 71 more
>>>> Caused by: java.io.FileNotFoundException:
>> resources/models/em_pair/model.jar (No such file or directory)
>>>> at java.io.FileInputStream.open(Native Method)
>>>> at java.io.FileInputStream.<init>(FileInputStream.java:120)
>>>> at java.io.FileInputStream.<init>(FileInputStream.java:79)
>>>> at
>> org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassifier(Ge
>> nericJarClassifierFactory.java:67)
>>>> at
>> org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarClassi
>> fierFactory.java:35)
>>>> at
>> org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:1
>> 13)
>>>>
>>>>
>>>> Looks like copying the resources directory to the target project
>> (Normalization project in this case) seems to take care of this issue.
>> However, I wanted to see a cleaner way of doing this instead of
>> duplicating the jar (and other resources).
>>>>
>>>>
>>>> Vinod
>
RE: relation-extractor - how to include it as a dependency?
Posted by "Masanz, James J." <Ma...@mayo.edu>.
I just posted a comment on LEGAL-157 asking for some movement.
No matter what the answer there about the models, I suggest leaving the descriptors and the tests in Apache cTAKES SVN.
-- James
> -----Original Message-----
> From: ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apache.org]
> On Behalf Of Steven Bethard
> Sent: Thursday, March 14, 2013 10:39 AM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: relation-extractor - how to include it as a dependency?
>
> Yeah, I never saw a conclusion to the discussion of where the relation-
> extractor models should go. My last impression was that they can't be in
> the Apache SVN at all, and they need to be in the Sourceforge
> ctakesresources project. Is that right?
>
> If that's the case, we need to update RelationExtractorTrain to deploy the
> models to that project rather than src/main/resources (where it currently
> deploys them), and delete all the models in the cTAKES SVN.
>
> And then where would the descriptors go? In the Sourceforge project? Or in
> the cTAKES SVN? Seems weird to have them in the cTAKES SVN if they can't
> refer to their models.
>
> And if we move the descriptors to Sourceforge, I guess that also means
> moving the tests to Sourceforge?
>
> Steve
>
> P.S. In the meantime, you may be able to get things working by making a
> copy of EntityMentionPairRelationExtractorAnnotator.xml that looks in
> org/apache/ctakes/relationextractor/models/em_pair instead of
> resources/models/em_pair, since there are currently still models in
> src/main/resources.
>
>
> On Mar 14, 2013, at 4:11 PM, "Chen, Pei" <Pe...@childrens.harvard.edu>
> wrote:
>
> > Hi Vinod,
> > I think that looks like a bug. Feel free to open a Jira.
> >
> > Sent from my iPhone
> >
> > Sent from my iPhone
> >
> > On Mar 14, 2013, at 10:46 AM, "Kaggal, Vinod C." <Ka...@mayo.edu>
> wrote:
> >
> >> Hello!
> >>
> >> Quick Background: We have been working on integrating CTAKES with
> DataNormalization pipeline (as part of SHARPN effort). I have added
> relation-extractor as a dependency to our Normalization project as the
> template-filling module/project uses it.
> >>
> >> Question: What is the is a recommended way of adding the relation-
> extraction's resource directory to a project that uses this project? Just
> adding the project (relation-extractor) to the build-path (projects)
> results in the following error:
> >>
> >>
> >> Caused by: org.apache.uima.resource.ResourceInitializationException
> >> at
> org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:1
> 15)
> >> at
> org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnotator.i
> nitialize(RelationExtractorAnnotator.java:121)
> >> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initiali
> zeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> >> ... 71 more
> >> Caused by: java.io.FileNotFoundException:
> resources/models/em_pair/model.jar (No such file or directory)
> >> at java.io.FileInputStream.open(Native Method)
> >> at java.io.FileInputStream.<init>(FileInputStream.java:120)
> >> at java.io.FileInputStream.<init>(FileInputStream.java:79)
> >> at
> org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassifier(Ge
> nericJarClassifierFactory.java:67)
> >> at
> org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarClassi
> fierFactory.java:35)
> >> at
> org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:1
> 13)
> >>
> >>
> >> Looks like copying the resources directory to the target project
> (Normalization project in this case) seems to take care of this issue.
> However, I wanted to see a cleaner way of doing this instead of
> duplicating the jar (and other resources).
> >>
> >>
> >> Vinod
Re: relation-extractor - how to include it as a dependency?
Posted by Steven Bethard <st...@Colorado.EDU>.
Yeah, I never saw a conclusion to the discussion of where the relation-extractor models should go. My last impression was that they can't be in the Apache SVN at all, and they need to be in the Sourceforge ctakesresources project. Is that right?
If that's the case, we need to update RelationExtractorTrain to deploy the models to that project rather than src/main/resources (where it currently deploys them), and delete all the models in the cTAKES SVN.
And then where would the descriptors go? In the Sourceforge project? Or in the cTAKES SVN? Seems weird to have them in the cTAKES SVN if they can't refer to their models.
And if we move the descriptors to Sourceforge, I guess that also means moving the tests to Sourceforge?
Steve
P.S. In the meantime, you may be able to get things working by making a copy of EntityMentionPairRelationExtractorAnnotator.xml that looks in org/apache/ctakes/relationextractor/models/em_pair instead of resources/models/em_pair, since there are currently still models in src/main/resources.
On Mar 14, 2013, at 4:11 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
> Hi Vinod,
> I think that looks like a bug. Feel free to open a Jira.
>
> Sent from my iPhone
>
> Sent from my iPhone
>
> On Mar 14, 2013, at 10:46 AM, "Kaggal, Vinod C." <Ka...@mayo.edu> wrote:
>
>> Hello!
>>
>> Quick Background: We have been working on integrating CTAKES with DataNormalization pipeline (as part of SHARPN effort). I have added relation-extractor as a dependency to our Normalization project as the template-filling module/project uses it.
>>
>> Question: What is the is a recommended way of adding the relation-extraction's resource directory to a project that uses this project? Just adding the project (relation-extractor) to the build-path (projects) results in the following error:
>>
>>
>> Caused by: org.apache.uima.resource.ResourceInitializationException
>> at org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:115)
>> at org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnotator.initialize(RelationExtractorAnnotator.java:121)
>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>> ... 71 more
>> Caused by: java.io.FileNotFoundException: resources/models/em_pair/model.jar (No such file or directory)
>> at java.io.FileInputStream.open(Native Method)
>> at java.io.FileInputStream.<init>(FileInputStream.java:120)
>> at java.io.FileInputStream.<init>(FileInputStream.java:79)
>> at org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassifier(GenericJarClassifierFactory.java:67)
>> at org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarClassifierFactory.java:35)
>> at org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:113)
>>
>>
>> Looks like copying the resources directory to the target project (Normalization project in this case) seems to take care of this issue. However, I wanted to see a cleaner way of doing this instead of duplicating the jar (and other resources).
>>
>>
>> Vinod
Re: relation-extractor - how to include it as a dependency?
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Hi Vinod,
I think that looks like a bug. Feel free to open a Jira.
Sent from my iPhone
Sent from my iPhone
On Mar 14, 2013, at 10:46 AM, "Kaggal, Vinod C." <Ka...@mayo.edu> wrote:
> Hello!
>
> Quick Background: We have been working on integrating CTAKES with DataNormalization pipeline (as part of SHARPN effort). I have added relation-extractor as a dependency to our Normalization project as the template-filling module/project uses it.
>
> Question: What is the is a recommended way of adding the relation-extraction's resource directory to a project that uses this project? Just adding the project (relation-extractor) to the build-path (projects) results in the following error:
>
>
> Caused by: org.apache.uima.resource.ResourceInitializationException
> at org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:115)
> at org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnotator.initialize(RelationExtractorAnnotator.java:121)
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> ... 71 more
> Caused by: java.io.FileNotFoundException: resources/models/em_pair/model.jar (No such file or directory)
> at java.io.FileInputStream.open(Native Method)
> at java.io.FileInputStream.<init>(FileInputStream.java:120)
> at java.io.FileInputStream.<init>(FileInputStream.java:79)
> at org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassifier(GenericJarClassifierFactory.java:67)
> at org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarClassifierFactory.java:35)
> at org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:113)
>
>
> Looks like copying the resources directory to the target project (Normalization project in this case) seems to take care of this issue. However, I wanted to see a cleaner way of doing this instead of duplicating the jar (and other resources).
>
>
> Vinod