Changes in BratWriter #1170
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@@ -19,7 +19,10 @@ | |
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| import static org.apache.uima.fit.util.JCasUtil.selectAll; | ||
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| 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; | ||
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@@ -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; | ||
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@@ -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; | ||
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@@ -102,6 +108,14 @@ public class BratWriter extends JCasFileWriter_ImplBase | |
| @ConfigurationParameter(name = PARAM_FILENAME_EXTENSION, mandatory = true, defaultValue = ".ann") | ||
| private String filenameSuffix; | ||
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| /** | ||
| * Specify the suffix of output files. Default value <code>.ann</code>. 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; | ||
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| /** | ||
| * Types that will not be written to the exported file. | ||
| */ | ||
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@@ -111,12 +125,13 @@ public class BratWriter extends JCasFileWriter_ImplBase | |
| private Set<String> excludeTypes; | ||
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| /** | ||
| * 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 = "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: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", | ||
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@@ -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 String[] spanTypesVals; | ||
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| /** | ||
| * Types that are relations. It is mandatory to provide the type name followed by two feature | ||
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@@ -205,7 +220,7 @@ public class BratWriter extends JCasFileWriter_ImplBase | |
| private int nextAttributeId; | ||
| private int nextPaletteIndex; | ||
| private Map<FeatureStructure, String> spanIdMap; | ||
| private Map<String,LinkedList<String>> spanTypes; | ||
| private BratConfiguration conf; | ||
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| private Set<String> warnings; | ||
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@@ -218,7 +233,22 @@ public void initialize(UimaContext aContext) | |
| conf = new BratConfiguration(); | ||
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| warnings = new LinkedHashSet<String>(); | ||
| spanTypes= new HashMap<>(); | ||
| for (String s: spanTypesVals){ | ||
| String[] parts=s.split(":"); | ||
| LinkedList<String>list; | ||
| 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); | ||
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@@ -306,36 +336,41 @@ private void writeAnnotations(JCas aJCas) | |
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| // 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(typeName) || excludeTypes.contains(superType) ) { | ||
| // it would be logged too much times | ||
| // getLogger().debug("Excluding [" + fs.getType().getName() + "]"); | ||
| continue; | ||
| } | ||
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| if (spanTypes.containsKey(typeName) || spanTypes.containsKey(superType)) { | ||
| // writeTextAnnotation(doc, (AnnotationFS) fs); | ||
| } | ||
| else if (parsedRelationTypes.containsKey(typeName)|| parsedRelationTypes.containsKey(superType)) { | ||
| relationFS.add(fs); | ||
| } | ||
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There was a problem hiding this comment. @joancf why did you entirely drop the support for annotations with multiple non-primitive features? |
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There was a problem hiding this comment. Why did you drop the fall-back handling for other types of annotations and the warning if an annotation could not be handled? There was a problem hiding this comment. Yes, in the same way as before: why should the component export elements the user hasn't ask for? |
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| } | ||
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| // Handle relations now since now we can resolve their targets to IDs. | ||
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@@ -358,7 +393,8 @@ else if (fs instanceof AnnotationFS) { | |
| case ".json": | ||
| String template ; | ||
| if (filenameSuffix.equals(".html")) { | ||
| InputStream it=new FileInputStream(htmlTemplate) ; | ||
| template = IOUtils.toString(it,"UTF-8"); | ||
| } | ||
| else { | ||
| template = "{ \"collData\" : ##COLL-DATA## , \"docData\" : ##DOC-DATA## }"; | ||
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@@ -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()); | ||
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There was a problem hiding this comment. If we reach this function the type or his parent is in parsdRelationTypes |
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| } | ||
| FeatureStructure arg1 = aFS.getFeatureValue(aFS.getType().getFeatureByBaseName( | ||
| rel.getArg1())); | ||
| FeatureStructure arg2 = aFS.getFeatureValue(aFS.getType().getFeatureByBaseName( | ||
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@@ -581,15 +619,25 @@ private void writeRelationAnnotation(BratAnnotationDocument aDoc, FeatureStructu | |
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| String superType = getBratType(aFS.getCAS().getTypeSystem().getParent(aFS.getType())); | ||
| String type = getBratType(aFS.getType()); | ||
| String value=type; | ||
| if (rel.getSubcat()!=""){ | ||
| value=aFS.getFeatureValueAsString(aFS.getType().getFeatureByBaseName(rel.getSubcat())); | ||
| } | ||
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| BratRelationAnnotation anno = new BratRelationAnnotation(nextRelationAnnotationId, | ||
| value, rel.getArg1(), arg1Id, rel.getArg2(), arg2Id); | ||
| nextRelationAnnotationId++; | ||
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| conf.addRelationDecl(superType, value, rel.getArg1(), rel.getArg2()); | ||
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| 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)); | ||
| } | ||
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| aDoc.addAnnotation(anno); | ||
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@@ -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()); | ||
| // 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<String> 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<splits.length-1;f++){ | ||
| currentAnnot = currentAnnot.getFeatureValue(currentAnnot.getType().getFeatureByBaseName(splits[f])); | ||
| } | ||
| value= currentAnnot.getFeatureValueAsString(currentAnnot.getType().getFeatureByBaseName(splits[splits.length-1])); | ||
| } else { | ||
| value=aFS.getFeatureValueAsString(aFS.getType().getFeatureByBaseName(splits[0])); | ||
| } | ||
| } | ||
| } catch (NullPointerException E){ // if the feature is not there, then a null pointer exception raises. | ||
| getLogger().error("Type "+ type + "does not have the fature: "+ spanData + "as defined in PARAM_TEXT_ANNOTATION_TYPES"); | ||
| } | ||
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| BratTextAnnotation anno = new BratTextAnnotation(nextTextAnnotationId, value, | ||
| aFS.getBegin(), aFS.getEnd(), aFS.getCoveredText()); | ||
| nextTextAnnotationId++; | ||
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| conf.addEntityDecl(superType, value); | ||
| 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)); | ||
| } | ||
| if (!conf.hasDrawingDecl(anno.getType())) { | ||
| conf.addDrawingDecl(new BratTextAnnotationDrawingDecl(anno.getType(), "black", | ||
| palette[nextPaletteIndex % palette.length])); | ||
| nextPaletteIndex++; | ||
| } | ||
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| aDoc.addAnnotation(anno); | ||
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| // writeAttributes(anno, aFS); | ||
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There was a problem hiding this comment. Why did you disable the ability to write attributes? There was a problem hiding this comment. They are not displayed, and I could not see any advantage of having them |
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| spanIdMap.put(aFS, anno.getId()); | ||
| } | ||
| } | ||
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| private boolean isInternalFeature(Feature aFeature) | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -44,11 +44,11 @@ public class BratTextAnnotation | |
| private final String text; | ||
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| public BratTextAnnotation(int aId, String aType, int aBegin, int aEnd, String aText) | ||
| { | ||
| this("T" + String.format("%04d", aId), aType, aBegin, aEnd, aText); | ||
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There was a problem hiding this comment. @joancf You mentioned in the previous PR this change is done to permit sorting in the JS (btw. the change to the sorting in the JS code is not included in the present PR anymore). But using the padded numbers is kind of brittle as one needs to pre-suppose the number of annotations. How about instead changing the sorting code so that it strips the annotation type letter and then compares the rest of the ID numerically? There was a problem hiding this comment. Also we could have an ID of the form "layer-id" for sorting, so it will sort by layer (the layer can be a two digits padded number, more than 100 layers would be crazy) |
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| } | ||
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| private BratTextAnnotation(String aId, String aType, int aBegin, int aEnd, String aText) | ||
| { | ||
| super(aId, aType); | ||
| begin = aBegin; | ||
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This code seems to take into account only the type and the direct supertype of the FS. When taking into account the direct supertype, it seems sensible to actually check the entire inheritance hierarchy, no?
org.apache.uima.cas.TypeSystem.subsumes(Type, Type)should be useful here.Comment applies also to other changes further down.
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I just used the same way it was used somewhere else in the module. I understood that it was a method to specify the parent type instead of the all the subsumed types.