diff --git a/dkpro-core-io-brat-asl/src/main/java/de/tudarmstadt/ukp/dkpro/core/io/brat/BratWriter.java b/dkpro-core-io-brat-asl/src/main/java/de/tudarmstadt/ukp/dkpro/core/io/brat/BratWriter.java
index 0234846f46..5427d880df 100644
--- a/dkpro-core-io-brat-asl/src/main/java/de/tudarmstadt/ukp/dkpro/core/io/brat/BratWriter.java
+++ b/dkpro-core-io-brat-asl/src/main/java/de/tudarmstadt/ukp/dkpro/core/io/brat/BratWriter.java
@@ -19,7 +19,10 @@
import static org.apache.uima.fit.util.JCasUtil.selectAll;
+import java.io.File;
+import java.io.FileInputStream;
import java.io.IOException;
+import java.io.InputStream;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.StringWriter;
@@ -28,6 +31,7 @@
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
+import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -46,7 +50,9 @@
import org.apache.uima.cas.text.AnnotationFS;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import org.apache.uima.fit.descriptor.ResourceMetaData;
+import org.apache.uima.fit.util.CasUtil;
import org.apache.uima.fit.util.FSUtil;
+import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
@@ -102,6 +108,14 @@ public class BratWriter extends JCasFileWriter_ImplBase
@ConfigurationParameter(name = PARAM_FILENAME_EXTENSION, mandatory = true, defaultValue = ".ann")
private String filenameSuffix;
+ /**
+ * Specify the suffix of output files. Default value .ann. If the suffix is not
+ * needed, provide an empty string as value.
+ */
+ public static final String PARAM_HTML_TEMPLANTE = "htmlTemplate";
+ @ConfigurationParameter(name = PARAM_HTML_TEMPLANTE , mandatory = false, defaultValue = "template.html")
+ private String htmlTemplate;
+
/**
* Types that will not be written to the exported file.
*/
@@ -111,12 +125,13 @@ public class BratWriter extends JCasFileWriter_ImplBase
private Set excludeTypes;
/**
- * Types that are text annotations (aka entities or spans).
+ * Types that are text annotations (aka entities or spans). Each of them includes a
+ * type (or parent type) after it ":" and element to extract use pipes to make a chain of elements.
*/
- public static final String PARAM_TEXT_ANNOTATION_TYPES = "spanTypes";
+ public static final String PARAM_TEXT_ANNOTATION_TYPES = "spanTypesVals";
@ConfigurationParameter(name = PARAM_TEXT_ANNOTATION_TYPES, mandatory = true, defaultValue = {
// "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence",
-// "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token",
+// "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token:Lemma|Value",
// "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS",
// "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Lemma",
// "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Stem",
@@ -125,7 +140,7 @@ public class BratWriter extends JCasFileWriter_ImplBase
// "de.tudarmstadt.ukp.dkpro.core.api.semantics.type.SemArg",
// "de.tudarmstadt.ukp.dkpro.core.api.semantics.type.SemPred"
})
- private Set spanTypes;
+ private String[] spanTypesVals;
/**
* Types that are relations. It is mandatory to provide the type name followed by two feature
@@ -205,7 +220,7 @@ public class BratWriter extends JCasFileWriter_ImplBase
private int nextAttributeId;
private int nextPaletteIndex;
private Map spanIdMap;
-
+ private Map> spanTypes;
private BratConfiguration conf;
private Set warnings;
@@ -218,7 +233,22 @@ public void initialize(UimaContext aContext)
conf = new BratConfiguration();
warnings = new LinkedHashSet();
-
+ spanTypes= new HashMap<>();
+ for (String s: spanTypesVals){
+ String[] parts=s.split(":");
+ LinkedListlist;
+ if (spanTypes.containsKey(parts[0])){
+ list=spanTypes.get(parts[0]);
+ } else {
+ list=new LinkedList<>();
+ }
+ if (parts.length>1){
+ list.add(parts[1]);
+ } else {
+ list.add("");
+ }
+ spanTypes.put(parts[0], list);
+ }
parsedRelationTypes = new HashMap<>();
for (String rel : relationTypes) {
RelationParam p = RelationParam.parse(rel);
@@ -306,36 +336,41 @@ private void writeAnnotations(JCas aJCas)
// Go through all the annotations but only handle the ones that have no references to
// other annotations.
+ for (String currentType: spanTypes.keySet()){
+ for (FeatureStructure fs : selectAll(aJCas)) {
+ String typeName=fs.getType().getName();
+ String superType = fs.getCAS().getTypeSystem().getParent(fs.getType()).getName();
+ // Skip excluded types
+ if (excludeTypes.contains(typeName) || excludeTypes.contains(superType) ) {
+ getLogger().debug("Excluding [" + fs.getType().getName() + "]");
+ continue;
+ }
+ if (currentType.equalsIgnoreCase(typeName) || currentType.equalsIgnoreCase(superType)) {
+ writeTextAnnotation(doc, (AnnotationFS) fs);
+ }
+ }
+ }
+ // second loop, only for relationships once spans have been set.
for (FeatureStructure fs : selectAll(aJCas)) {
// Skip document annotation
if (fs == aJCas.getDocumentAnnotationFs()) {
continue;
}
-
+ String typeName=fs.getType().getName();
+ String superType = fs.getCAS().getTypeSystem().getParent(fs.getType()).getName();
// Skip excluded types
- if (excludeTypes.contains(fs.getType().getName())) {
- getLogger().debug("Excluding [" + fs.getType().getName() + "]");
+ if (excludeTypes.contains(typeName) || excludeTypes.contains(superType) ) {
+ // it would be logged too much times
+ // getLogger().debug("Excluding [" + fs.getType().getName() + "]");
continue;
}
- if (spanTypes.contains(fs.getType().getName())) {
- writeTextAnnotation(doc, (AnnotationFS) fs);
+ if (spanTypes.containsKey(typeName) || spanTypes.containsKey(superType)) {
+ // writeTextAnnotation(doc, (AnnotationFS) fs);
}
- else if (parsedRelationTypes.containsKey(fs.getType().getName())) {
+ else if (parsedRelationTypes.containsKey(typeName)|| parsedRelationTypes.containsKey(superType)) {
relationFS.add(fs);
}
- else if (hasNonPrimitiveFeatures(fs) && (fs instanceof AnnotationFS)) {
-// else if (parsedEventTypes.containsKey(fs.getType().getName())) {
- BratEventAnnotation event = writeEventAnnotation(doc, (AnnotationFS) fs);
- eventFS.put(event, fs);
- }
- else if (fs instanceof AnnotationFS) {
- warnings.add("Assuming annotation type ["+fs.getType().getName()+"] is span");
- writeTextAnnotation(doc, (AnnotationFS) fs);
- }
- else {
- warnings.add("Skipping annotation with type ["+fs.getType().getName()+"]");
- }
}
// Handle relations now since now we can resolve their targets to IDs.
@@ -358,7 +393,8 @@ else if (fs instanceof AnnotationFS) {
case ".json":
String template ;
if (filenameSuffix.equals(".html")) {
- template = IOUtils.toString(getClass().getResource("html/template.html"));
+ InputStream it=new FileInputStream(htmlTemplate) ;
+ template = IOUtils.toString(it,"UTF-8");
}
else {
template = "{ \"collData\" : ##COLL-DATA## , \"docData\" : ##DOC-DATA## }";
@@ -562,7 +598,9 @@ private boolean isSlotFeature(FeatureStructure aFS, Feature aFeature)
private void writeRelationAnnotation(BratAnnotationDocument aDoc, FeatureStructure aFS)
{
RelationParam rel = parsedRelationTypes.get(aFS.getType().getName());
-
+ if (rel== null ) {// then is the parent type
+ rel=parsedRelationTypes.get(aFS.getCAS().getTypeSystem().getParent(aFS.getType()).getName());
+ }
FeatureStructure arg1 = aFS.getFeatureValue(aFS.getType().getFeatureByBaseName(
rel.getArg1()));
FeatureStructure arg2 = aFS.getFeatureValue(aFS.getType().getFeatureByBaseName(
@@ -581,15 +619,25 @@ private void writeRelationAnnotation(BratAnnotationDocument aDoc, FeatureStructu
String superType = getBratType(aFS.getCAS().getTypeSystem().getParent(aFS.getType()));
String type = getBratType(aFS.getType());
-
- BratRelationAnnotation anno = new BratRelationAnnotation(nextRelationAnnotationId,
- type, rel.getArg1(), arg1Id, rel.getArg2(), arg2Id);
+ String value=type;
+ if (rel.getSubcat()!=""){
+ value=aFS.getFeatureValueAsString(aFS.getType().getFeatureByBaseName(rel.getSubcat()));
+ }
+
+ BratRelationAnnotation anno = new BratRelationAnnotation(nextRelationAnnotationId,
+ value, rel.getArg1(), arg1Id, rel.getArg2(), arg2Id);
nextRelationAnnotationId++;
- conf.addRelationDecl(superType, type, rel.getArg1(), rel.getArg2());
-
+ conf.addRelationDecl(superType, value, rel.getArg1(), rel.getArg2());
+
+ if (enableTypeMappings){
+// conf.addLabelDecl(type,type,type.substring(0, 2),type.substring(0, 1));
+ conf.addLabelDecl(value,value);
+ }else {
conf.addLabelDecl(anno.getType(), aFS.getType().getShortName(), aFS.getType()
.getShortName().substring(0, 1));
+ }
+
aDoc.addAnnotation(anno);
@@ -604,27 +652,57 @@ private void writeTextAnnotation(BratAnnotationDocument aDoc, AnnotationFS aFS)
{
String superType = getBratType(aFS.getCAS().getTypeSystem().getParent(aFS.getType()));
String type = getBratType(aFS.getType());
-
- BratTextAnnotation anno = new BratTextAnnotation(nextTextAnnotationId, type,
- aFS.getBegin(), aFS.getEnd(), aFS.getCoveredText());
- nextTextAnnotationId++;
-
- conf.addEntityDecl(superType, type);
-
- conf.addLabelDecl(anno.getType(), aFS.getType().getShortName(), aFS.getType()
- .getShortName().substring(0, 1));
-
- if (!conf.hasDrawingDecl(anno.getType())) {
- conf.addDrawingDecl(new BratTextAnnotationDrawingDecl(anno.getType(), "black",
- palette[nextPaletteIndex % palette.length]));
- nextPaletteIndex++;
+ // check if the type has a value to display, replace the the type by the value
+ // do it similar as with declarations that looks for the value
+ LinkedList spanDatas=null;
+ String value=type;
+ if (spanTypes.containsKey(aFS.getType().getName())) {
+ spanDatas=spanTypes.get(aFS.getType().getName());
+ } else if (spanTypes.containsKey(aFS.getCAS().getTypeSystem().getParent(aFS.getType()).getName() )) {
+ spanDatas=spanTypes.get(aFS.getCAS().getTypeSystem().getParent(aFS.getType()).getName() );
+ }
+ for (String spanData : spanDatas){
+ try {
+ if (!spanData.equalsIgnoreCase("")){
+ String [] splits=spanData.split("\\|");
+ if (splits.length>1){
+ FeatureStructure currentAnnot = aFS.getFeatureValue(aFS.getType().getFeatureByBaseName(splits[0]));
+ for (int f=1;f