#1381 - Annotations starting/ending in inter-token space cause exception

- Ported fix and unit tests
dkpro · Jun 6, 2019 · 575f18c · 575f18c
1 parent 1aae3ea
commit 575f18c
Show file tree

Hide file tree

Showing 10 changed files with 173 additions and 0 deletions.
diff --git a/...l/src/main/java/org/dkpro/core/io/webanno/tsv/internal/tsv3x/Tsv3XCasDocumentBuilder.java b/...l/src/main/java/org/dkpro/core/io/webanno/tsv/internal/tsv3x/Tsv3XCasDocumentBuilder.java
@@ -135,6 +135,16 @@ public static TsvDocument of(TsvSchema aSchema, JCas aJCas)
                 }
 
                 Entry<Integer, TsvToken> beginTokenEntry = tokenBeginIndex.floorEntry(begin);
+                // If the current annotation has leading whitespace, we have wrongly fetched the
+                // token before the start token using floorEntry(end) - so let's try to correct this
+                if (
+                        // found begin token but found the wrong one
+                        (beginTokenEntry != null && beginTokenEntry.getValue().getEnd() < begin) ||
+                        // didn't find end begin because annotation starts before the first token
+                        beginTokenEntry == null
+                ) {
+                    beginTokenEntry = tokenEndIndex.higherEntry(begin);
+                }
                 if (beginTokenEntry == null) {
                     throw new IllegalStateException(
                             "Unable to find begin token starting at or before " + begin
@@ -144,6 +154,16 @@ public static TsvDocument of(TsvSchema aSchema, JCas aJCas)
                 }
 
                 Entry<Integer, TsvToken> endTokenEntry = tokenEndIndex.ceilingEntry(end);
+                // If the current annotation has trailing whitespace, we have wrongly fetched the
+                // token after the end token using ceilingEntry(end) - so let's try to correct this
+                if (
+                        // found end token but found the wrong one
+                        (endTokenEntry != null && endTokenEntry.getValue().getBegin() > end) ||
+                        // didn't find end token because annotation ends beyond the last token
+                        endTokenEntry == null
+                ) {
+                    endTokenEntry = tokenEndIndex.lowerEntry(end);
+                }
                 if (endTokenEntry == null) {
                     throw new IllegalStateException("Unable to find end token ending at or after "
                             + end + " (last token ends at " + tokenEndIndex.pollLastEntry().getKey()

diff --git a/...io-webanno-asl/src/test/java/org/dkpro/core/io/webanno/tsv/WebAnnoTsv3WriterTestBase.java b/...io-webanno-asl/src/test/java/org/dkpro/core/io/webanno/tsv/WebAnnoTsv3WriterTestBase.java
@@ -60,6 +60,7 @@
 import de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.morph.MorphologicalFeatures;
 import de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS;
 import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData;
+import de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity;
 import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Lemma;
 import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
 import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Stem;
@@ -1666,7 +1667,91 @@ public void testTwoSentencesWithNoSpaceInBetween() throws Exception
 
         writeAndAssertEquals(jcas);
     }
+
+    /*
+     * This is something that cannot be done through the editor UI but can happen when working with
+     * externally created data.
+     */
+    @Test
+    public void testAnnotationWithTrailingWhitespace() throws Exception
+    {
+        JCas jcas = JCasFactory.createJCas();
+
+        DocumentMetaData.create(jcas).setDocumentId("doc");
+        jcas.setDocumentText("one  two");
+        new Token(jcas, 0, 3).addToIndexes();
+        new Token(jcas, 5, 8).addToIndexes();
+        new Sentence(jcas, 0, 8).addToIndexes();
+
+        // NE has trailing whitespace - on export this should be silently dropped
+        new NamedEntity(jcas, 0, 4).addToIndexes();
+
+        writeAndAssertEquals(jcas);
+    }
 
+    /*
+     * This is something that cannot be done through the editor UI but can happen when working with
+     * externally created data.
+     */
+    @Test
+    public void testAnnotationWithTrailingWhitespaceAtEnd() throws Exception
+    {
+        JCas jcas = JCasFactory.createJCas();
+
+        DocumentMetaData.create(jcas).setDocumentId("doc");
+        jcas.setDocumentText("one two ");
+        new Token(jcas, 0, 3).addToIndexes();
+        new Token(jcas, 4, 7).addToIndexes();
+        new Sentence(jcas, 0, 7).addToIndexes();
+
+        // NE has trailing whitespace - on export this should be silently dropped
+        new NamedEntity(jcas, 4, 8).addToIndexes();
+
+        writeAndAssertEquals(jcas);
+    }    
+
+    /*
+     * This is something that cannot be done through the editor UI but can happen when working with
+     * externally created data.
+     */
+    @Test
+    public void testAnnotationWithLeadingWhitespaceAtStart() throws Exception
+    {
+        JCas jcas = JCasFactory.createJCas();
+
+        DocumentMetaData.create(jcas).setDocumentId("doc");
+        jcas.setDocumentText(" one two");
+        new Token(jcas, 1, 4).addToIndexes();
+        new Token(jcas, 5, 8).addToIndexes();
+        new Sentence(jcas, 1, 8).addToIndexes();
+
+        // NE has leading whitespace - on export this should be silently dropped
+        new NamedEntity(jcas, 0, 4).addToIndexes();
+
+        writeAndAssertEquals(jcas);
+    }
+
+    /*
+     * This is something that cannot be done through the editor UI but can happen when working with
+     * externally created data.
+     */
+    @Test
+    public void testAnnotationWithLeadingWhitespace() throws Exception
+    {
+        JCas jcas = JCasFactory.createJCas();
+
+        DocumentMetaData.create(jcas).setDocumentId("doc");
+        jcas.setDocumentText("one  two");
+        new Token(jcas, 0, 3).addToIndexes();
+        new Token(jcas, 5, 8).addToIndexes();
+        new Sentence(jcas, 0, 8).addToIndexes();
+
+        // NE has leading whitespace - on export this should be silently dropped
+        new NamedEntity(jcas, 4, 8).addToIndexes();
+
+        writeAndAssertEquals(jcas);
+    }
+
     private void writeAndAssertEquals(JCas aJCas, Object... aParams)
         throws IOException, ResourceInitializationException, AnalysisEngineProcessException
     {

diff --git a/...banno-asl/src/test/resources/tsv3-suite/testAnnotationWithLeadingWhitespace/reference.tsv b/...banno-asl/src/test/resources/tsv3-suite/testAnnotationWithLeadingWhitespace/reference.tsv
@@ -0,0 +1,7 @@
+#FORMAT=WebAnno TSV 3.2
+#T_SP=de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity|identifier|value
+
+
+#Text=one  two
+1-1	0-3	one	_	_	
+1-2	5-8	two	*	*	
diff --git a/...banno-asl/src/test/resources/tsv3-suite/testAnnotationWithLeadingWhitespace/reference.xmi b/...banno-asl/src/test/resources/tsv3-suite/testAnnotationWithLeadingWhitespace/reference.xmi
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?><xmi:XMI xmlns:pos="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/pos.ecore" xmlns:tcas="http:///uima/tcas.ecore" xmlns:xmi="http://www.omg.org/XMI" xmlns:cas="http:///uima/cas.ecore" xmlns:tweet="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/pos/tweet.ecore" xmlns:morph="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/morph.ecore" xmlns:dependency="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/dependency.ecore" xmlns:type6="http:///de/tudarmstadt/ukp/dkpro/core/api/semantics/type.ecore" xmlns:type="http:///de/tudarmstadt/ukp/dkpro/core/api/anomaly/type.ecore" xmlns:type7="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type.ecore" xmlns:type3="http:///de/tudarmstadt/ukp/dkpro/core/api/metadata/type.ecore" xmlns:type4="http:///de/tudarmstadt/ukp/dkpro/core/api/ner/type.ecore" xmlns:type5="http:///de/tudarmstadt/ukp/dkpro/core/api/segmentation/type.ecore" xmlns:type2="http:///de/tudarmstadt/ukp/dkpro/core/api/coref/type.ecore" xmlns:constituent="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/constituent.ecore" xmlns:chunk="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/chunk.ecore" xmi:version="2.0">
+    <cas:NULL xmi:id="0"/>
+    <type3:DocumentMetaData xmi:id="1" sofa="12" begin="0" end="8" documentId="doc" isLastSegment="false"/>
+    <type5:Token xmi:id="19" sofa="12" begin="0" end="3" order="0"/>
+    <type5:Token xmi:id="32" sofa="12" begin="5" end="8" order="0"/>
+    <type5:Sentence xmi:id="45" sofa="12" begin="0" end="8"/>
+    <type4:NamedEntity xmi:id="50" sofa="12" begin="4" end="8"/>
+    <cas:Sofa xmi:id="12" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="one  two"/>
+    <cas:View sofa="12" members="1 19 32 45 50"/>
+</xmi:XMI>
diff --git a/...sl/src/test/resources/tsv3-suite/testAnnotationWithLeadingWhitespaceAtStart/reference.tsv b/...sl/src/test/resources/tsv3-suite/testAnnotationWithLeadingWhitespaceAtStart/reference.tsv
@@ -0,0 +1,7 @@
+#FORMAT=WebAnno TSV 3.2
+#T_SP=de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity|identifier|value
+
+
+#Text=one two
+1-1	1-4	one	*	*	
+1-2	5-8	two	_	_	
diff --git a/...sl/src/test/resources/tsv3-suite/testAnnotationWithLeadingWhitespaceAtStart/reference.xmi b/...sl/src/test/resources/tsv3-suite/testAnnotationWithLeadingWhitespaceAtStart/reference.xmi
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?><xmi:XMI xmlns:pos="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/pos.ecore" xmlns:tcas="http:///uima/tcas.ecore" xmlns:xmi="http://www.omg.org/XMI" xmlns:cas="http:///uima/cas.ecore" xmlns:tweet="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/pos/tweet.ecore" xmlns:morph="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/morph.ecore" xmlns:dependency="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/dependency.ecore" xmlns:type6="http:///de/tudarmstadt/ukp/dkpro/core/api/semantics/type.ecore" xmlns:type="http:///de/tudarmstadt/ukp/dkpro/core/api/anomaly/type.ecore" xmlns:type7="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type.ecore" xmlns:type3="http:///de/tudarmstadt/ukp/dkpro/core/api/metadata/type.ecore" xmlns:type4="http:///de/tudarmstadt/ukp/dkpro/core/api/ner/type.ecore" xmlns:type5="http:///de/tudarmstadt/ukp/dkpro/core/api/segmentation/type.ecore" xmlns:type2="http:///de/tudarmstadt/ukp/dkpro/core/api/coref/type.ecore" xmlns:constituent="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/constituent.ecore" xmlns:chunk="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/chunk.ecore" xmi:version="2.0">
+    <cas:NULL xmi:id="0"/>
+    <type3:DocumentMetaData xmi:id="1" sofa="12" begin="0" end="8" documentId="doc" isLastSegment="false"/>
+    <type5:Token xmi:id="19" sofa="12" begin="1" end="4" order="0"/>
+    <type5:Token xmi:id="32" sofa="12" begin="5" end="8" order="0"/>
+    <type5:Sentence xmi:id="45" sofa="12" begin="1" end="8"/>
+    <type4:NamedEntity xmi:id="50" sofa="12" begin="0" end="4"/>
+    <cas:Sofa xmi:id="12" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString=" one two"/>
+    <cas:View sofa="12" members="1 19 32 45 50"/>
+</xmi:XMI>
diff --git a/...anno-asl/src/test/resources/tsv3-suite/testAnnotationWithTrailingWhitespace/reference.tsv b/...anno-asl/src/test/resources/tsv3-suite/testAnnotationWithTrailingWhitespace/reference.tsv
@@ -0,0 +1,7 @@
+#FORMAT=WebAnno TSV 3.2
+#T_SP=de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity|identifier|value
+
+
+#Text=one  two
+1-1	0-3	one	*	*	
+1-2	5-8	two	_	_	
diff --git a/...anno-asl/src/test/resources/tsv3-suite/testAnnotationWithTrailingWhitespace/reference.xmi b/...anno-asl/src/test/resources/tsv3-suite/testAnnotationWithTrailingWhitespace/reference.xmi
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?><xmi:XMI xmlns:pos="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/pos.ecore" xmlns:tcas="http:///uima/tcas.ecore" xmlns:xmi="http://www.omg.org/XMI" xmlns:cas="http:///uima/cas.ecore" xmlns:tweet="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/pos/tweet.ecore" xmlns:morph="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/morph.ecore" xmlns:dependency="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/dependency.ecore" xmlns:type6="http:///de/tudarmstadt/ukp/dkpro/core/api/semantics/type.ecore" xmlns:type="http:///de/tudarmstadt/ukp/dkpro/core/api/anomaly/type.ecore" xmlns:type7="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type.ecore" xmlns:type3="http:///de/tudarmstadt/ukp/dkpro/core/api/metadata/type.ecore" xmlns:type4="http:///de/tudarmstadt/ukp/dkpro/core/api/ner/type.ecore" xmlns:type5="http:///de/tudarmstadt/ukp/dkpro/core/api/segmentation/type.ecore" xmlns:type2="http:///de/tudarmstadt/ukp/dkpro/core/api/coref/type.ecore" xmlns:constituent="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/constituent.ecore" xmlns:chunk="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/chunk.ecore" xmi:version="2.0">
+    <cas:NULL xmi:id="0"/>
+    <type3:DocumentMetaData xmi:id="1" sofa="12" begin="0" end="8" documentId="doc" isLastSegment="false"/>
+    <type5:Token xmi:id="19" sofa="12" begin="0" end="3" order="0"/>
+    <type5:Token xmi:id="32" sofa="12" begin="5" end="8" order="0"/>
+    <type5:Sentence xmi:id="45" sofa="12" begin="0" end="8"/>
+    <type4:NamedEntity xmi:id="50" sofa="12" begin="0" end="4"/>
+    <cas:Sofa xmi:id="12" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="one  two"/>
+    <cas:View sofa="12" members="1 19 32 45 50"/>
+</xmi:XMI>
diff --git a/...asl/src/test/resources/tsv3-suite/testAnnotationWithTrailingWhitespaceAtEnd/reference.tsv b/...asl/src/test/resources/tsv3-suite/testAnnotationWithTrailingWhitespaceAtEnd/reference.tsv
@@ -0,0 +1,7 @@
+#FORMAT=WebAnno TSV 3.2
+#T_SP=de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity|identifier|value
+
+
+#Text=one two
+1-1	0-3	one	_	_	
+1-2	4-7	two	*	*	
diff --git a/...asl/src/test/resources/tsv3-suite/testAnnotationWithTrailingWhitespaceAtEnd/reference.xmi b/...asl/src/test/resources/tsv3-suite/testAnnotationWithTrailingWhitespaceAtEnd/reference.xmi
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?><xmi:XMI xmlns:pos="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/pos.ecore" xmlns:tcas="http:///uima/tcas.ecore" xmlns:xmi="http://www.omg.org/XMI" xmlns:cas="http:///uima/cas.ecore" xmlns:tweet="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/pos/tweet.ecore" xmlns:morph="http:///de/tudarmstadt/ukp/dkpro/core/api/lexmorph/type/morph.ecore" xmlns:dependency="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/dependency.ecore" xmlns:type6="http:///de/tudarmstadt/ukp/dkpro/core/api/semantics/type.ecore" xmlns:type="http:///de/tudarmstadt/ukp/dkpro/core/api/anomaly/type.ecore" xmlns:type7="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type.ecore" xmlns:type3="http:///de/tudarmstadt/ukp/dkpro/core/api/metadata/type.ecore" xmlns:type4="http:///de/tudarmstadt/ukp/dkpro/core/api/ner/type.ecore" xmlns:type5="http:///de/tudarmstadt/ukp/dkpro/core/api/segmentation/type.ecore" xmlns:type2="http:///de/tudarmstadt/ukp/dkpro/core/api/coref/type.ecore" xmlns:constituent="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/constituent.ecore" xmlns:chunk="http:///de/tudarmstadt/ukp/dkpro/core/api/syntax/type/chunk.ecore" xmi:version="2.0">
+    <cas:NULL xmi:id="0"/>
+    <type3:DocumentMetaData xmi:id="1" sofa="12" begin="0" end="8" documentId="doc" isLastSegment="false"/>
+    <type5:Token xmi:id="19" sofa="12" begin="0" end="3" order="0"/>
+    <type5:Token xmi:id="32" sofa="12" begin="4" end="7" order="0"/>
+    <type5:Sentence xmi:id="45" sofa="12" begin="0" end="7"/>
+    <type4:NamedEntity xmi:id="50" sofa="12" begin="4" end="8"/>
+    <cas:Sofa xmi:id="12" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="one two "/>
+    <cas:View sofa="12" members="1 19 32 45 50"/>
+</xmi:XMI>