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Posted to dev@ctakes.apache.org by "Chen, Pei" <Pe...@childrens.harvard.edu> on 2012/10/10 22:56:22 UTC
Update cTAKES Building and Running page?
I think it would be great if someone who was able to recently successfully check out cTAKES project to update the Building and Running section on the website?
This will help any new developers get started...
Perhaps both as CLI and/or Eclipse IDE (required plugins: m2e plugin, subversive, scm connectors, uima plugin, etc.) import.
I'm probably already so biased and therefore not a good candidate...
http://incubator.apache.org/ctakes/source.html
RE: Update cTAKES Building and Running page?
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
> > I just wanted to be sure that "standard" use of maven install works.
mvn install should work. I don't think it's a big deal for us to handle users running mvn install to install it to their local ~/.m2 repository assuming they understand where it's going; could be useful at times to actually have it there.
> >> All that said, I can confirm that I also see test failures:
Updating of the existing unit tests cases was actually not as trivial as I originally thought and took longer than expected. The paths/references have been updated (/src/test/java and src/test/resources, etc.) but there were a few logical issues where I did not fully understand and did not have enough time to follow to confidently make the logical changes. I am actually not sure how they were passing in the past...
Anyhow, they should be working now-The below have been temporarily commented out and needs to be revisited:
https://issues.apache.org/jira/browse/CTAKES-77
https://issues.apache.org/jira/browse/CTAKES-78
https://issues.apache.org/jira/browse/CTAKES-79
Thanks,
Pei
> -----Original Message-----
> From: Steven Bethard [mailto:steven.bethard@Colorado.EDU]
> Sent: Thursday, October 11, 2012 12:09 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: Update cTAKES Building and Running page?
>
> On Oct 11, 2012, at 9:59 AM, Oleg Tikhonov <ol...@gmail.com>
> wrote:
> > I just wanted to be sure that "standard" use of maven install works.
>
> Yeah, I agree that `mvn install` should not fail, like it does now. =)
>
> But I don't think we should be recommending that anyone actually run `mvn
> install`. Expert Maven users who know the few times where it is appropriate
> to run `mvn install` won't need instructions. And all the remaining users are
> better off never hearing about `mvn install`. ;-)
>
> Steve
>
> > I can
> > tweak this by all options you've mentioned, however, IMO it would be
> > great if we could solve such kind of problems.
> >
> > Any way thank you for quick response.
> >
> > Cheers,
> > Oleg
> >
> >
> >
> > On Thu, Oct 11, 2012 at 4:48 PM, Steven Bethard
> > <steven.bethard@colorado.edu
> >> wrote:
> >
> >> On Oct 11, 2012, at 8:29 AM, Oleg Tikhonov <ol...@apache.org> wrote:
> >>> I've svn'ed the source and tryed to mvn clean install.
> >>
> >> Are you sure you want to run `mvn install`? In my experience you
> >> almost
> >> *never* want to do that.
> >>
> >> If you just want to compile the source, why not use `mvn compile`?
> >>
> >> If you want to run the tests too, run `mvn test`.
> >>
> >> If you want to compile, run tests and build jar files, run `mvn package`.
> >>
> >> If the tests are failing, but you still want to build the jar files,
> >> you can add -DskipTests=true to the command line (
> >> http://maven.apache.org/plugins/maven-surefire-plugin/test-
> mojo.html#skipTests).
> >> (This will also work for `mvn install` if you're really sure that's
> >> what you want to run.)
> >>
> >> All that said, I can confirm that I also see test failures:
> >>
> >> -------------------------------------------------------
> >> T E S T S
> >> -------------------------------------------------------
> >> Running org.apache.ctakes.core.ae.SimpleSegmentAnnotatorTests
> >> ...
> >> Caused by: org.apache.uima.cas.CASRuntimeException: JCas type
> >> "org.apache.ctakes.typesystem.type.textspan.Segment" used in Java
> >> code, but was not declared in the XML type descriptor.
> >> at org.apache.uima.jcas.impl.JCasImpl.getType(JCasImpl.java:412)
> >> at org.apache.uima.jcas.cas.TOP.<init>(TOP.java:92)
> >> at
> >> org.apache.uima.jcas.cas.AnnotationBase.<init>(AnnotationBase.java:53)
> >> at org.apache.uima.jcas.tcas.Annotation.<init>(Annotation.java:54)
> >> at
> >>
> org.apache.ctakes.typesystem.type.textspan.Segment.<init>(Segment.java:
> 46)
> >> at
> >>
> org.apache.ctakes.core.ae.SimpleSegmentAnnotator.process(SimpleSegme
> ntAnnotator.java:54)
> >> at
> >>
> org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCa
> sAnnotator_ImplBase.java:48)
> >> at
> >>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnal
> ysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
> >> ... 34 more
> >> Running org.apache.ctakes.core.ci.HyphenTextModifierImplTests
> >> ...
> >> java.io.FileNotFoundException: resources/tokenizer/hyphenated.txt (No
> >> such file or directory)
> >> at java.io.FileInputStream.open(Native Method)
> >> at java.io.FileInputStream.<init>(FileInputStream.java:120)
> >> at java.io.FileReader.<init>(FileReader.java:55)
> >> at
> >>
> org.apache.ctakes.core.ci.HyphenTextModifierImpl.<init>(HyphenTextMod
> >> ifierImpl.java:66)
> >> ...
> >> Results :
> >>
> >> Failed tests:
> >>
> testTokenizerAnnotatorPTB(org.apache.ctakes.core.ae.TokenizerAnnotator
> PTBTests):
> >> expected:<class org.apache.ctakes.typesystem.type.syntax.NumToken>
> >> but was:<class
> >> org.apache.ctakes.typesystem.type.syntax.PunctuationToken>
> >> testTest(org.apache.ctakes.core.ci.HyphenTextModifierImplTests)
> >>
> >> Tests in error:
> >>
> >>
> testSimpleSegment(org.apache.ctakes.core.ae.SimpleSegmentAnnotatorTes
> ts):
> >> Annotator processing failed.
> >>
> >> Tests run: 3, Failures: 2, Errors: 1, Skipped: 0
> >>
> >> Steve
> >>
> >>
Re: Update cTAKES Building and Running page?
Posted by Steven Bethard <st...@Colorado.EDU>.
On Oct 11, 2012, at 9:59 AM, Oleg Tikhonov <ol...@gmail.com> wrote:
> I just wanted to be sure that "standard" use of maven install works.
Yeah, I agree that `mvn install` should not fail, like it does now. =)
But I don't think we should be recommending that anyone actually run `mvn install`. Expert Maven users who know the few times where it is appropriate to run `mvn install` won't need instructions. And all the remaining users are better off never hearing about `mvn install`. ;-)
Steve
> I can
> tweak this by all options you've mentioned,
> however, IMO it would be great if we could solve such kind of problems.
>
> Any way thank you for quick response.
>
> Cheers,
> Oleg
>
>
>
> On Thu, Oct 11, 2012 at 4:48 PM, Steven Bethard <steven.bethard@colorado.edu
>> wrote:
>
>> On Oct 11, 2012, at 8:29 AM, Oleg Tikhonov <ol...@apache.org> wrote:
>>> I've svn'ed the source and tryed to mvn clean install.
>>
>> Are you sure you want to run `mvn install`? In my experience you almost
>> *never* want to do that.
>>
>> If you just want to compile the source, why not use `mvn compile`?
>>
>> If you want to run the tests too, run `mvn test`.
>>
>> If you want to compile, run tests and build jar files, run `mvn package`.
>>
>> If the tests are failing, but you still want to build the jar files, you
>> can add -DskipTests=true to the command line (
>> http://maven.apache.org/plugins/maven-surefire-plugin/test-mojo.html#skipTests).
>> (This will also work for `mvn install` if you're really sure that's what
>> you want to run.)
>>
>> All that said, I can confirm that I also see test failures:
>>
>> -------------------------------------------------------
>> T E S T S
>> -------------------------------------------------------
>> Running org.apache.ctakes.core.ae.SimpleSegmentAnnotatorTests
>> …
>> Caused by: org.apache.uima.cas.CASRuntimeException: JCas type
>> "org.apache.ctakes.typesystem.type.textspan.Segment" used in Java code,
>> but was not declared in the XML type descriptor.
>> at org.apache.uima.jcas.impl.JCasImpl.getType(JCasImpl.java:412)
>> at org.apache.uima.jcas.cas.TOP.<init>(TOP.java:92)
>> at
>> org.apache.uima.jcas.cas.AnnotationBase.<init>(AnnotationBase.java:53)
>> at org.apache.uima.jcas.tcas.Annotation.<init>(Annotation.java:54)
>> at
>> org.apache.ctakes.typesystem.type.textspan.Segment.<init>(Segment.java:46)
>> at
>> org.apache.ctakes.core.ae.SimpleSegmentAnnotator.process(SimpleSegmentAnnotator.java:54)
>> at
>> org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
>> at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
>> ... 34 more
>> Running org.apache.ctakes.core.ci.HyphenTextModifierImplTests
>> …
>> java.io.FileNotFoundException: resources/tokenizer/hyphenated.txt (No such
>> file or directory)
>> at java.io.FileInputStream.open(Native Method)
>> at java.io.FileInputStream.<init>(FileInputStream.java:120)
>> at java.io.FileReader.<init>(FileReader.java:55)
>> at
>> org.apache.ctakes.core.ci.HyphenTextModifierImpl.<init>(HyphenTextModifierImpl.java:66)
>> ...
>> Results :
>>
>> Failed tests:
>> testTokenizerAnnotatorPTB(org.apache.ctakes.core.ae.TokenizerAnnotatorPTBTests):
>> expected:<class org.apache.ctakes.typesystem.type.syntax.NumToken> but
>> was:<class org.apache.ctakes.typesystem.type.syntax.PunctuationToken>
>> testTest(org.apache.ctakes.core.ci.HyphenTextModifierImplTests)
>>
>> Tests in error:
>>
>> testSimpleSegment(org.apache.ctakes.core.ae.SimpleSegmentAnnotatorTests):
>> Annotator processing failed.
>>
>> Tests run: 3, Failures: 2, Errors: 1, Skipped: 0
>>
>> Steve
>>
>>
Re: Update cTAKES Building and Running page?
Posted by Oleg Tikhonov <ol...@gmail.com>.
Hey Steve,
I just wanted to be sure that "standard" use of maven install works. I can
tweak this by all options you've mentioned,
however, IMO it would be great if we could solve such kind of problems.
Any way thank you for quick response.
Cheers,
Oleg
On Thu, Oct 11, 2012 at 4:48 PM, Steven Bethard <steven.bethard@colorado.edu
> wrote:
> On Oct 11, 2012, at 8:29 AM, Oleg Tikhonov <ol...@apache.org> wrote:
> > I've svn'ed the source and tryed to mvn clean install.
>
> Are you sure you want to run `mvn install`? In my experience you almost
> *never* want to do that.
>
> If you just want to compile the source, why not use `mvn compile`?
>
> If you want to run the tests too, run `mvn test`.
>
> If you want to compile, run tests and build jar files, run `mvn package`.
>
> If the tests are failing, but you still want to build the jar files, you
> can add -DskipTests=true to the command line (
> http://maven.apache.org/plugins/maven-surefire-plugin/test-mojo.html#skipTests).
> (This will also work for `mvn install` if you're really sure that's what
> you want to run.)
>
> All that said, I can confirm that I also see test failures:
>
> -------------------------------------------------------
> T E S T S
> -------------------------------------------------------
> Running org.apache.ctakes.core.ae.SimpleSegmentAnnotatorTests
> …
> Caused by: org.apache.uima.cas.CASRuntimeException: JCas type
> "org.apache.ctakes.typesystem.type.textspan.Segment" used in Java code,
> but was not declared in the XML type descriptor.
> at org.apache.uima.jcas.impl.JCasImpl.getType(JCasImpl.java:412)
> at org.apache.uima.jcas.cas.TOP.<init>(TOP.java:92)
> at
> org.apache.uima.jcas.cas.AnnotationBase.<init>(AnnotationBase.java:53)
> at org.apache.uima.jcas.tcas.Annotation.<init>(Annotation.java:54)
> at
> org.apache.ctakes.typesystem.type.textspan.Segment.<init>(Segment.java:46)
> at
> org.apache.ctakes.core.ae.SimpleSegmentAnnotator.process(SimpleSegmentAnnotator.java:54)
> at
> org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
> ... 34 more
> Running org.apache.ctakes.core.ci.HyphenTextModifierImplTests
> …
> java.io.FileNotFoundException: resources/tokenizer/hyphenated.txt (No such
> file or directory)
> at java.io.FileInputStream.open(Native Method)
> at java.io.FileInputStream.<init>(FileInputStream.java:120)
> at java.io.FileReader.<init>(FileReader.java:55)
> at
> org.apache.ctakes.core.ci.HyphenTextModifierImpl.<init>(HyphenTextModifierImpl.java:66)
> ...
> Results :
>
> Failed tests:
> testTokenizerAnnotatorPTB(org.apache.ctakes.core.ae.TokenizerAnnotatorPTBTests):
> expected:<class org.apache.ctakes.typesystem.type.syntax.NumToken> but
> was:<class org.apache.ctakes.typesystem.type.syntax.PunctuationToken>
> testTest(org.apache.ctakes.core.ci.HyphenTextModifierImplTests)
>
> Tests in error:
>
> testSimpleSegment(org.apache.ctakes.core.ae.SimpleSegmentAnnotatorTests):
> Annotator processing failed.
>
> Tests run: 3, Failures: 2, Errors: 1, Skipped: 0
>
> Steve
>
>
Re: Update cTAKES Building and Running page?
Posted by Steven Bethard <st...@Colorado.EDU>.
On Oct 11, 2012, at 8:29 AM, Oleg Tikhonov <ol...@apache.org> wrote:
> I've svn'ed the source and tryed to mvn clean install.
Are you sure you want to run `mvn install`? In my experience you almost *never* want to do that.
If you just want to compile the source, why not use `mvn compile`?
If you want to run the tests too, run `mvn test`.
If you want to compile, run tests and build jar files, run `mvn package`.
If the tests are failing, but you still want to build the jar files, you can add -DskipTests=true to the command line (http://maven.apache.org/plugins/maven-surefire-plugin/test-mojo.html#skipTests). (This will also work for `mvn install` if you're really sure that's what you want to run.)
All that said, I can confirm that I also see test failures:
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.core.ae.SimpleSegmentAnnotatorTests
…
Caused by: org.apache.uima.cas.CASRuntimeException: JCas type "org.apache.ctakes.typesystem.type.textspan.Segment" used in Java code, but was not declared in the XML type descriptor.
at org.apache.uima.jcas.impl.JCasImpl.getType(JCasImpl.java:412)
at org.apache.uima.jcas.cas.TOP.<init>(TOP.java:92)
at org.apache.uima.jcas.cas.AnnotationBase.<init>(AnnotationBase.java:53)
at org.apache.uima.jcas.tcas.Annotation.<init>(Annotation.java:54)
at org.apache.ctakes.typesystem.type.textspan.Segment.<init>(Segment.java:46)
at org.apache.ctakes.core.ae.SimpleSegmentAnnotator.process(SimpleSegmentAnnotator.java:54)
at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
... 34 more
Running org.apache.ctakes.core.ci.HyphenTextModifierImplTests
…
java.io.FileNotFoundException: resources/tokenizer/hyphenated.txt (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:120)
at java.io.FileReader.<init>(FileReader.java:55)
at org.apache.ctakes.core.ci.HyphenTextModifierImpl.<init>(HyphenTextModifierImpl.java:66)
...
Results :
Failed tests: testTokenizerAnnotatorPTB(org.apache.ctakes.core.ae.TokenizerAnnotatorPTBTests): expected:<class org.apache.ctakes.typesystem.type.syntax.NumToken> but was:<class org.apache.ctakes.typesystem.type.syntax.PunctuationToken>
testTest(org.apache.ctakes.core.ci.HyphenTextModifierImplTests)
Tests in error:
testSimpleSegment(org.apache.ctakes.core.ae.SimpleSegmentAnnotatorTests): Annotator processing failed.
Tests run: 3, Failures: 2, Errors: 1, Skipped: 0
Steve
Re: Update cTAKES Building and Running page?
Posted by Oleg Tikhonov <ol...@apache.org>.
Hey,
I've svn'ed the source and tryed to mvn clean install.
I could not build it successfully, the SimpleSegmentAnnotatorTests's failed
with the following error:
"Oct 11, 2012 4:13:38 PM
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl
callAnalysisComponentProcess(407)
SEVERE: Exception occurred
org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator
processing failed.
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:280)
at org.apache.ctakes.core.TestUtil.processAE(TestUtil.java:125)
at
org.apache.ctakes.core.ae.SimpleSegmentAnnotatorTests.testSimpleSegment(SimpleSegmentAnnotatorTests.java:37)
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.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
at
org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at
org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
at
org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
at
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:76)
at
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:193)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:52)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:191)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:42)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:184)
at org.junit.runners.ParentRunner.run(ParentRunner.java:236)
at
org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:49)
at
org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
at
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:467)
at
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:683)
at
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:390)
at
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:197)
Caused by: org.apache.uima.cas.CASRuntimeException: JCas type
"org.apache.ctakes.typesystem.type.textspan.Segment" used in Java code,
but was not declared in the XML type descriptor.
at org.apache.uima.jcas.impl.JCasImpl.getType(JCasImpl.java:412)
at org.apache.uima.jcas.cas.TOP.<init>(TOP.java:92)
at
org.apache.uima.jcas.cas.AnnotationBase.<init>(AnnotationBase.java:53)
at org.apache.uima.jcas.tcas.Annotation.<init>(Annotation.java:54)
at
org.apache.ctakes.typesystem.type.textspan.Segment.<init>(Segment.java:46)
at
org.apache.ctakes.core.ae.SimpleSegmentAnnotator.process(SimpleSegmentAnnotator.java:54)
at
org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
... 27 more
"
Is there some workaround ???
That's it in the meanwhile.
BR,
Oleg
On Wed, Oct 10, 2012 at 10:56 PM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:
> I think it would be great if someone who was able to recently successfully
> check out cTAKES project to update the Building and Running section on the
> website?
> This will help any new developers get started...
>
> Perhaps both as CLI and/or Eclipse IDE (required plugins: m2e plugin,
> subversive, scm connectors, uima plugin, etc.) import.
> I'm probably already so biased and therefore not a good candidate...
> http://incubator.apache.org/ctakes/source.html
>