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Merge pull request #4810 from inception-project/feature/4809-Connecti…
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…ng-annotation-and-entity-with-arc-over-different-pages

#4809 - Connecting annotation and entity with arc over different pages
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@reckart
reckart authored May 28, 2024
2 parents 7c743ed + 1abab77 commit 7136d0b
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Showing 23 changed files with 551 additions and 245 deletions.
7 changes: 0 additions & 7 deletions ...src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/rendering/NopRenderer.java
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Expand Up @@ -20,7 +20,6 @@
import java.util.Collections;
import java.util.List;

import org.apache.uima.cas.CAS;
import org.apache.uima.cas.TypeSystem;
import org.apache.uima.cas.text.AnnotationFS;

Expand All @@ -47,12 +46,6 @@ protected boolean typeSystemInit(TypeSystem aTypeSystem)
return false;
}

@Override
public List<AnnotationFS> selectAnnotationsInWindow(CAS aCas, int aWindowBegin, int aWindowEnd)
{
return Collections.emptyList();
}

@Override
public void render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
VDocument aResponse, int windowBeginOffset, int windowEndOffset)
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5 changes: 0 additions & 5 deletions ...in/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/rendering/Renderer_ImplBase.java
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Expand Up @@ -18,13 +18,11 @@
package de.tudarmstadt.ukp.clarin.webanno.api.annotation.rendering;

import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;

import org.apache.uima.cas.CAS;
import org.apache.uima.cas.TypeSystem;
import org.apache.uima.cas.text.AnnotationFS;

import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
Expand Down Expand Up @@ -142,7 +140,4 @@ public <T> Optional<T> getTraits(AnnotationLayer aLayer, Class<T> aInterface)

return Optional.empty();
}

public abstract List<AnnotationFS> selectAnnotationsInWindow(CAS aCas, int aWindowBegin,
int aWindowEnd);
}
1 change: 0 additions & 1 deletion ...tion/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/chain/ChainRenderer.java
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Expand Up @@ -89,7 +89,6 @@ protected boolean typeSystemInit(TypeSystem aTypeSystem)
return true;
}

@Override
public List<AnnotationFS> selectAnnotationsInWindow(CAS aCas, int aWindowBegin, int aWindowEnd)
{
var typeAdapter = getTypeAdapter();
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141 changes: 121 additions & 20 deletions ...rc/main/java/de/tudarmstadt/ukp/inception/annotation/layer/relation/RelationRenderer.java
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Expand Up @@ -17,11 +17,10 @@
*/
package de.tudarmstadt.ukp.inception.annotation.layer.relation;

import static java.util.Arrays.asList;
import static java.util.Collections.emptyList;
import static java.util.stream.Collectors.groupingBy;
import static org.apache.commons.lang3.StringUtils.abbreviate;
import static org.apache.uima.fit.util.CasUtil.selectCovered;
import static org.apache.uima.cas.text.AnnotationPredicates.overlapping;

import java.lang.invoke.MethodHandles;
import java.util.ArrayDeque;
Expand Down Expand Up @@ -56,6 +55,8 @@
import de.tudarmstadt.ukp.inception.rendering.vmodel.VLazyDetail;
import de.tudarmstadt.ukp.inception.rendering.vmodel.VLazyDetailGroup;
import de.tudarmstadt.ukp.inception.rendering.vmodel.VObject;
import de.tudarmstadt.ukp.inception.rendering.vmodel.VRange;
import de.tudarmstadt.ukp.inception.rendering.vmodel.VSpan;
import de.tudarmstadt.ukp.inception.schema.api.feature.FeatureSupportRegistry;
import de.tudarmstadt.ukp.inception.schema.api.layer.LayerSupportRegistry;
import de.tudarmstadt.ukp.inception.support.uima.ICasUtil;
Expand All @@ -69,6 +70,18 @@ public class RelationRenderer
{
private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());

private static final VID VID_BEFORE = VID.builder() //
.withExtensionId("rel") //
.withAnnotationId(0) //
.withExtensionPayload("before") //
.build();

private static final VID VID_AFTER = VID.builder() //
.withExtensionId("rel") //
.withAnnotationId(1) //
.withExtensionPayload("after") //
.build();

private final List<RelationLayerBehavior> behaviors;
private final RelationLayerTraits traits;

Expand Down Expand Up @@ -118,10 +131,31 @@ protected boolean typeSystemInit(TypeSystem aTypeSystem)
return true;
}

@Override
public List<AnnotationFS> selectAnnotationsInWindow(CAS aCas, int aWindowBegin, int aWindowEnd)
private List<Annotation> selectAnnotationsInWindow(RenderRequest aRequest, int aWindowBegin,
int aWindowEnd)
{
return selectCovered(aCas, type, aWindowBegin, aWindowEnd);
var cas = aRequest.getCas();

if (!aRequest.isOutOfRangeRelations()) {
return cas.<Annotation> select(type).coveredBy(aWindowBegin, aWindowEnd).toList();
}

var result = new ArrayList<Annotation>();
for (var rel : cas.<Annotation> select(type)) {
var sourceFs = getSourceFs(rel);
var targetFs = getTargetFs(rel);

if (sourceFs instanceof Annotation source && targetFs instanceof Annotation target) {
var relBegin = Math.min(source.getBegin(), target.getBegin());
var relEnd = Math.max(source.getEnd(), target.getEnd());

if (overlapping(relBegin, relEnd, aWindowBegin, aWindowEnd)) {
result.add(rel);
}
}
}

return result;
}

@Override
Expand All @@ -137,16 +171,17 @@ public void render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
// Index mapping annotations to the corresponding rendered arcs
var annoToArcIdx = new HashMap<AnnotationFS, VArc>();

var annotations = selectAnnotationsInWindow(aRequest.getCas(), aWindowBegin, aWindowEnd);
var annotations = selectAnnotationsInWindow(aRequest, aWindowBegin, aWindowEnd);

for (var fs : annotations) {
for (var arc : render(aRequest, aFeatures, aResponse, aWindowBegin, aWindowEnd, fs)) {
if (!(arc instanceof VArc)) {
for (var obj : render(aRequest, aFeatures, aResponse, aWindowBegin, aWindowEnd, fs)) {
if (!(obj instanceof VArc)) {
aResponse.add(obj);
continue;
}

aResponse.add(arc);
annoToArcIdx.put(fs, (VArc) arc);
aResponse.add(obj);
annoToArcIdx.put(fs, (VArc) obj);

renderRequiredFeatureErrors(aRequest, aFeatures, fs, aResponse);
}
Expand Down Expand Up @@ -216,18 +251,21 @@ public List<VObject> render(RenderRequest aRequest, List<AnnotationFeature> aFea

switch (traits.getRenderMode()) {
case ALWAYS:
return renderRelationAsArcs(aFS, typeAdapter, sourceFs, targetFs, labelFeatures);
return renderRelationAsArcs(aRequest, aVDocument, aFS, typeAdapter, sourceFs, targetFs,
labelFeatures, aWindowBegin, aWindowEnd);
case WHEN_SELECTED:
if (aRequest.getState() == null || isSelected(aRequest, aFS, sourceFs, targetFs)) {
return renderRelationAsArcs(aFS, typeAdapter, sourceFs, targetFs, labelFeatures);
return renderRelationAsArcs(aRequest, aVDocument, aFS, typeAdapter, sourceFs,
targetFs, labelFeatures, aWindowBegin, aWindowEnd);
}
return renderRelationOnLabel(aVDocument, typeAdapter, sourceFs, targetFs,
labelFeatures);
case NEVER:
return renderRelationOnLabel(aVDocument, typeAdapter, sourceFs, targetFs,
labelFeatures);
default:
return renderRelationAsArcs(aFS, typeAdapter, sourceFs, targetFs, labelFeatures);
return renderRelationAsArcs(aRequest, aVDocument, aFS, typeAdapter, sourceFs, targetFs,
labelFeatures, aWindowBegin, aWindowEnd);
}
}

Expand Down Expand Up @@ -278,17 +316,80 @@ private List<VObject> renderRelationOnLabel(VDocument aVDocument, RelationAdapte
return emptyList();
}

private List<VObject> renderRelationAsArcs(AnnotationFS aFS, RelationAdapter typeAdapter,
FeatureStructure sourceFs, FeatureStructure targetFs, Map<String, String> labelFeatures)
private List<VObject> renderRelationAsArcs(RenderRequest aRequest, VDocument aVDocument,
AnnotationFS aFS, RelationAdapter typeAdapter, FeatureStructure sourceFs,
FeatureStructure targetFs, Map<String, String> labelFeatures, int aWindowBegin,
int aWindowEnd)
{
var arc = VArc.builder().forAnnotation(aFS) //
var objects = new ArrayList<VObject>();

var source = createRelationEndpoint(aRequest, aVDocument, (AnnotationFS) sourceFs,
aWindowBegin, aWindowEnd, typeAdapter);

var target = createRelationEndpoint(aRequest, aVDocument, (AnnotationFS) targetFs,
aWindowBegin, aWindowEnd, typeAdapter);

objects.add(VArc.builder().forAnnotation(aFS) //
.withLayer(typeAdapter.getLayer()) //
.withSource(sourceFs) //
.withTarget(targetFs) //
.withSource(source) //
.withTarget(target) //
.withFeatures(labelFeatures) //
.build();
.build());

return objects;
}

private VID createRelationEndpoint(RenderRequest aRequest, VDocument aVDocument,
AnnotationFS aEndpoint, int aWindowBegin, int aWindowEnd, RelationAdapter aTypeAdapter)
{
if (aEndpoint.getEnd() < aWindowBegin) {
if (aRequest.isClipRelations()) {
if (aVDocument.getSpan(VID_BEFORE) == null) {
var beforeAnchor = VSpan.builder() //
.withVid(VID_BEFORE) //
.withLayer(aTypeAdapter.getLayer()) //
.withRange(new VRange(0, 0)) //
.build();
aVDocument.add(beforeAnchor);
}
return VID_BEFORE;
}

var placeholder = VSpan.builder() //
.forAnnotation(aEndpoint) //
.withLayer(aTypeAdapter.getLayer()) //
.withRange(new VRange(aEndpoint.getBegin() - aWindowBegin,
aEndpoint.getEnd() - aWindowBegin)) //
.build();
aVDocument.add(placeholder);
return placeholder.getVid();
}

if (aEndpoint.getBegin() >= aWindowEnd) {
if (aRequest.isClipRelations()) {
if (aVDocument.getSpan(VID_AFTER) == null) {
var afterAnchor = VSpan.builder() //
.withVid(VID_AFTER) //
.withLayer(aTypeAdapter.getLayer()) //
.withRange(new VRange(aWindowEnd - aWindowBegin,
aWindowEnd - aWindowBegin)) //
.build();
aVDocument.add(afterAnchor);
}
return VID_AFTER;
}

var placeholder = VSpan.builder() //
.forAnnotation(aEndpoint) //
.withLayer(aTypeAdapter.getLayer()) //
.withRange(new VRange(aEndpoint.getBegin() - aWindowBegin,
aEndpoint.getEnd() - aWindowBegin)) //
.build();
aVDocument.add(placeholder);
return placeholder.getVid();
}

return asList(arc);
return VID.of(aEndpoint);
}

@Override
Expand Down
12 changes: 6 additions & 6 deletions ...tation/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/span/SpanRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ public SpanRenderer(SpanAdapter aTypeAdapter, LayerSupportRegistry aLayerSupport
behaviors = emptyList();
}
else {
List<SpanLayerBehavior> temp = new ArrayList<>(aBehaviors);
var temp = new ArrayList<SpanLayerBehavior>(aBehaviors);
AnnotationAwareOrderComparator.sort(temp);
behaviors = temp;
}
Expand All @@ -78,7 +78,7 @@ public SpanRenderer(SpanAdapter aTypeAdapter, LayerSupportRegistry aLayerSupport
@Override
protected boolean typeSystemInit(TypeSystem aTypeSystem)
{
SpanAdapter typeAdapter = getTypeAdapter();
var typeAdapter = getTypeAdapter();

type = aTypeSystem.getType(typeAdapter.getAnnotationTypeName());
if (type == null) {
Expand All @@ -90,10 +90,10 @@ protected boolean typeSystemInit(TypeSystem aTypeSystem)
return true;
}

@Override
public List<AnnotationFS> selectAnnotationsInWindow(CAS aCas, int aWindowBegin, int aWindowEnd)
{
return aCas.select(type).coveredBy(0, aWindowEnd).includeAnnotationsWithEndBeyondBounds()
return aCas.select(type).coveredBy(0, aWindowEnd) //
.includeAnnotationsWithEndBeyondBounds() //
.map(fs -> (AnnotationFS) fs)
.filter(ann -> AnnotationPredicates.overlapping(ann, aWindowBegin, aWindowEnd))
.toList();
Expand Down Expand Up @@ -188,9 +188,9 @@ private void renderSlots(AnnotationFS aFS, List<VObject> aSpansAndSlots)
continue nextFeature;
}

if (ARRAY.equals(feat.getMultiValueMode()) && WITH_ROLE.equals(feat.getLinkMode())) {
if (feat.getMultiValueMode() == ARRAY && feat.getLinkMode() == WITH_ROLE) {
List<LinkWithRoleModel> links = typeAdapter.getFeatureValue(feat, aFS);
for (int li = 0; li < links.size(); li++) {
for (var li = 0; li < links.size(); li++) {
var link = links.get(li);
var targetFS = selectFsByAddr(aFS.getCAS(), link.targetAddr);

Expand Down
8 changes: 4 additions & 4 deletions ...on-api-editor/src/main/java/de/tudarmstadt/ukp/inception/editor/AnnotationEditorBase.java
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,6 @@
import de.tudarmstadt.ukp.inception.rendering.pipeline.RenderingPipeline;
import de.tudarmstadt.ukp.inception.rendering.request.RenderRequest;
import de.tudarmstadt.ukp.inception.rendering.request.RenderRequestedEvent;
import de.tudarmstadt.ukp.inception.rendering.vmodel.VDocument;
import de.tudarmstadt.ukp.inception.rendering.vmodel.serialization.VDocumentSerializer;
import de.tudarmstadt.ukp.inception.schema.api.adapter.AnnotationException;
import de.tudarmstadt.ukp.inception.schema.api.config.AnnotationSchemaProperties;
Expand Down Expand Up @@ -189,19 +188,20 @@ public void requestRender(AjaxRequestTarget aTarget)
protected <T> T render(CAS aCas, int aWindowBeginOffset, int aWindowEndOffset,
VDocumentSerializer<T> aTerminalStep)
{
RenderRequest request = RenderRequest.builder() //
var request = RenderRequest.builder() //
.withState(getModelObject()) //
.withWindow(aWindowBeginOffset, aWindowEndOffset) //
.withCas(aCas) //
.withSessionOwner(userService.getCurrentUser()) //
.withVisibleLayers(getLayersToRender(getModelObject())) //
.withOutOfRangeRelations(true) //
.build();

VDocument vdoc = renderingPipeline.render(request);
var vdoc = renderingPipeline.render(request);
return aTerminalStep.render(vdoc, request);
}

private List<AnnotationLayer> getLayersToRender(AnnotatorState state)
protected List<AnnotationLayer> getLayersToRender(AnnotatorState state)
{
List<AnnotationLayer> layersToRender = new ArrayList<>();
for (AnnotationLayer layer : state.getAnnotationLayers()) {
Expand Down
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