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From Marshall Schor <...@schor.com>
Subject Re: UIMAv3 & WebAnno
Date Thu, 18 Jan 2018 15:50:34 GMT
Fixed this problem. 

It was due to many places in webAnno where the code fragment:

feature.toString()  was expected to return the fully-qualified feature name.

But v3 augmented the feature "toString" to provide more information about a feature.

Fix was to change all occurrances of feature.toString() to feature.getName().

Now the webanno-io-tsv first test succeeds, although it still is reporting lots
of updating of Annotation "end" values while the annotation is in the index
(UIMA is recovering these, one at a time).

on to the next problem...


On 1/17/2018 4:52 PM, Marshall Schor wrote:
> I changed the testcase for WebAnnoTsv2ReaderWriterTest to turn off the
> exception, to move on to the next issue :-)
>
> Next issue: the first runPipeLine() in that same test now fails, saying:
>
> Caused by: java.io.IOException: Target file
> [target\test-output\WebAnnoTsv2ReaderWriterTest-test\example2.tsv] already
> exists and overwriting not enabled.
>     at
> de.tudarmstadt.ukp.dkpro.core.api.io.JCasFileWriter_ImplBase.getOutputStream(JCasFileWriter_ImplBase.java:230)
>     at
> de.tudarmstadt.ukp.dkpro.core.api.io.JCasFileWriter_ImplBase.getOutputStream(JCasFileWriter_ImplBase.java:155)
>     at
> de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv2Writer.process(WebannoTsv2Writer.java:101)
>     ... 38 more
>
> I got around that by erasing the target/ directory, then doing a
> maven-update-project to cause an Eclispe rebuild of the project. Now when I run
> it I get a beyond the above error.  The next error is:
>
> java.io.IOException: example2.tsv This is not a valid TSV File. check this line:
> 1-1    Ms.    Sofa
>     at
> de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv2Reader.setAnnotations(WebannoTsv2Reader.java:159)
>     at
> de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv2Reader.convertToCas(WebannoTsv2Reader.java:78)
>     at
> de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv2Reader.getNext(WebannoTsv2Reader.java:547)
>     at
> de.tudarmstadt.ukp.dkpro.core.api.io.JCasResourceCollectionReader_ImplBase.getNext(JCasResourceCollectionReader_ImplBase.java:36)
>     at
> de.tudarmstadt.ukp.clarin.webanno.tsv.WebAnnoTsv2ReaderWriterTest.test(WebAnnoTsv2ReaderWriterTest.java:81)
>     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>     at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>     at java.lang.reflect.Method.invoke(Method.java:498)
>     at
> org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
>     at
> org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
>     at
> org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
>     at
> org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
>     at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:55)
>     at org.junit.rules.RunRules.evaluate(RunRules.java:20)
>     at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
>     at
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
>     at
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
>     at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
>     at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
>     at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
>     at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
>     at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
>     at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
>     at
> org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:86)
>     at
> org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
>     at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:538)
>     at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:760)
>     at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:460)
>     at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:206)
>
> The file in question has these as its first few lines:
>
>  # de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity | sofa | begin | end |
> value | identifier # de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS |
> sofa | begin | end | PosValue | coarseValue #
> de.tudarmstadt.ukp.dkpro.core.api.syntax.type.dependency.Dependency | sofa |
> begin | end | DependencyType | flavor |
> AttachTo=de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS
> #id=1
> #text=Ms. Haag plays Elianti .
> 1-1    Ms.    Sofa
>    sofaNum: 1
>    sofaID: "_InitialView"
>    mimeType: "text"
>    sofaArray: <null>
>    sofaString: "Ms. Haag plays Elianti .
> Rolls-Royce Motor Cars Inc. said it expects its U.S. sa..."
>    sofaURI: <null>    0    3    B-PER   
> B-de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity_    NNP   
> de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS_    Sofa
>    sofaNum: 1
>    sofaID: "_InitialView"
>    mimeType: "text"
>    sofaArray: <null>
>    sofaString: "Ms. Haag plays Elianti .
> Rolls-Royce Motor Cars Inc. said it expects its U.S. sa..."
>    sofaURI: <null>    0    14    SUBJ   
> de.tudarmstadt.ukp.dkpro.core.api.syntax.type.dependency.Dependency_    1-3   
> 1-2    Haag    Sofa
>    sofaNum: 1
>    sofaID: "_InitialView"
>    mimeType: "text"
>    sofaArray: <null>
>    sofaString: "Ms. Haag plays Elianti .
> Rolls-Royce Motor Cars Inc. said it expects its U.S. sa..."
>    sofaURI: <null>    4    8    I-PER   
> I-de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity_    NNP   
> de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS_    Sofa
>    sofaNum: 1
>    sofaID: "_InitialView"
>    mimeType: "text"
>    sofaArray: <null>
>    sofaString: "Ms. Haag plays Elianti .
> Rolls-Royce Motor Cars Inc. said it expects its U.S. sa..."
>    sofaURI: <null>    4    14    SBJ   
> de.tudarmstadt.ukp.dkpro.core.api.syntax.type.dependency.Dependency_    1-3   
>
> ( wonder about the sofa string ending in "...")
>
> -Marshall
>
>
> On 1/17/2018 4:12 PM, Marshall Schor wrote:
>> I put in an exclude for the slf4j-log4j12, and went to the next issue:
>>
>> Tests in webanno-io-tsv fail.  The first one is failing here:
>> WebAnnoTsv2ReaderWriterTest, line  65 (runPipeLine(reader, writer).
>>
>> It fails because it's updating an "end" value for an annotation that's already
>> in the index, causing the message which follows.
>> UIMA normally recovers from these things, but a global flag was configured:
>> "uima.exception_when_fs_update_corrupts_index".
>>
>> System.getProperty("uima.exception_when_fs_update_corrupts_index")
>>      (java.lang.String) true
>>
>> I can't see where this is being set, though.  Any ideas?  Is the updating of the
>> annotation:end while the item is indexed, the way it is designed to work?
>>
>> -Marshall
>> === test =====================
>> 2018-01-17 15:52:35 INFO WebannoTsv2Reader - Scanning
>> [file:/C:/au/gitClones/webanno/webanno-io-tsv/src/test/resources/tsv2/]
>> 2018-01-17 15:52:35 INFO WebannoTsv2Reader - Found [1] resources to be read
>> 2018-01-17 15:54:31 INFO WebannoTsv2Reader - 0 of 1:
>> file:/C:/au/gitClones/webanno/webanno-io-tsv/src/test/resources/tsv2/example2.tsv
>> 2018-01-17 15:54:31 WARN uima - While FS was in the index, the feature
>> "uima.tcas.Annotation:end", which is used as a key in one or more indexes, was
>> modified
>>  FS = "NamedEntity
>>    sofa: _InitialView
>>    begin: 0
>>    end: 3
>>    value: "PER"
>>    identifier: <null>"
>> java.lang.Throwable
>>     at org.apache.uima.cas.impl.CASImpl.featModWhileInIndexReport(CASImpl.java:2985)
>>     at org.apache.uima.cas.impl.CASImpl.featModWhileInIndexReport(CASImpl.java:2977)
>>     at
>> org.apache.uima.cas.impl.CASImpl.checkForInvalidFeatureSetting(CASImpl.java:2865)
>>     at org.apache.uima.cas.impl.CASImpl.setWithCheckAndJournal(CASImpl.java:1828)
>>     at
>> org.apache.uima.cas.impl.FeatureStructureImplC._setIntValueNfcCJ(FeatureStructureImplC.java:684)
>>     at
>> org.apache.uima.cas.impl.FeatureStructureImplC._setIntValueNfc(FeatureStructureImplC.java:460)
>>     at org.apache.uima.jcas.tcas.Annotation.setEnd(Annotation.java:123)
>>     at
>> de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv2Reader.createSpanAnnotation(WebannoTsv2Reader.java:506)
>>     at
>> de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv2Reader.setAnnotations(WebannoTsv2Reader.java:176)
>>     at
>> de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv2Reader.convertToCas(WebannoTsv2Reader.java:78)
>>     at
>> de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv2Reader.getNext(WebannoTsv2Reader.java:547)
>>     at
>> de.tudarmstadt.ukp.dkpro.core.api.io.JCasResourceCollectionReader_ImplBase.getNext(JCasResourceCollectionReader_ImplBase.java:36)
>>     at
>> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:100)
>>     at
>> de.tudarmstadt.ukp.clarin.webanno.tsv.WebAnnoTsv2ReaderWriterTest.test(WebAnnoTsv2ReaderWriterTest.java:65)
>>
>


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