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From Marshall Schor <...@schor.com>
Subject Re: UIMAv3 & WebAnno
Date Wed, 17 Jan 2018 21:12:56 GMT
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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