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)
>>
>
