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Merge pull request #4837 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 30, 2024
2 parents ab12e22 + 9dc521b commit 73a1f2a
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Showing 26 changed files with 233 additions and 180 deletions.
4 changes: 2 additions & 2 deletions ...src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/rendering/NopRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -48,14 +48,14 @@ protected boolean typeSystemInit(TypeSystem aTypeSystem)

@Override
public void render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
VDocument aResponse, int windowBeginOffset, int windowEndOffset)
VDocument aResponse)
{
// Nothing to do
}

@Override
public List<VObject> render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
VDocument aResponse, int windowBeginOffset, int windowEndOffset, AnnotationFS aFS)
VDocument aResponse, AnnotationFS aFS)

{
return Collections.emptyList();
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5 changes: 2 additions & 3 deletions ...main/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/rendering/PreRendererImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -105,8 +105,7 @@ public void render(VDocument aResponse, RenderRequest aRequest)
var renderBegin = Math.max(0, aRequest.getWindowBeginOffset());
var renderEnd = Math.min(documentText.length(), aRequest.getWindowEndOffset());
aResponse.setText(documentText.substring(renderBegin, renderEnd));
aResponse.setWindowBegin(renderBegin);
aResponse.setWindowEnd(renderEnd);
aResponse.setWindow(renderBegin, renderEnd);

var start = System.currentTimeMillis();
var project = aRequest.getProject();
Expand All @@ -129,7 +128,7 @@ public void render(VDocument aResponse, RenderRequest aRequest)
// the same because otherwise the IDs of armed slots would be inconsistent
LayerSupport<?, ?> layerSupport = layerSupportRegistry.getLayerSupport(layer);
var renderer = layerSupport.createRenderer(layer, () -> layerAllFeatures);
renderer.render(aRequest, layerSupportedFeatures, aResponse, renderBegin, renderEnd);
renderer.render(aRequest, layerSupportedFeatures, aResponse);
}

if (LOG.isTraceEnabled()) {
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15 changes: 9 additions & 6 deletions ...tion/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/chain/ChainRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@ public List<AnnotationFS> selectAnnotationsInWindow(CAS aCas, int aWindowBegin,

@Override
public void render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
VDocument aResponse, int aWindowBegin, int aWindowEnd)
VDocument aResponse)
{
if (!checkTypeSystem(aRequest.getCas())) {
return;
Expand All @@ -125,7 +125,10 @@ public void render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
// Sorted index mapping annotations to the corresponding rendered spans
var annoToSpanIdx = new HashMap<AnnotationFS, VSpan>();

int colorIndex = 0;
var windowBegin = aResponse.getWindowBegin();
var windowEnd = aResponse.getWindowEnd();

var colorIndex = 0;
// Iterate over the chains
var chains = aRequest.getCas().select(typeAdapter.getChainTypeName()).asList();
for (var chainFs : chains) {
Expand All @@ -139,13 +142,13 @@ public void render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
var nextLinkFs = (AnnotationFS) linkFs.getFeatureValue(linkNext);

// Is link after window? If yes, we can skip the rest of the chain
if (linkFs.getBegin() >= aWindowEnd) {
if (linkFs.getBegin() >= windowBegin) {
break; // Go to next chain
}

// Is not overlapping the viewport? We only need links that are actually visible in
// the viewport
if (!overlapping(linkFs, aWindowBegin, aWindowEnd)) {
if (!overlapping(linkFs, windowBegin, windowEnd)) {
// prevLinkFs remains null until we enter the window
linkFs = nextLinkFs;
continue; // Go to next link
Expand Down Expand Up @@ -201,13 +204,13 @@ public void render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
}

for (var behavior : behaviors) {
behavior.onRender(typeAdapter, aResponse, annoToSpanIdx, aWindowBegin, aWindowEnd);
behavior.onRender(typeAdapter, aResponse, annoToSpanIdx);
}
}

@Override
public List<VObject> render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
VDocument aResponse, int windowBeginOffset, int windowEndOffset, AnnotationFS aFS)
VDocument aResponse, AnnotationFS aFS)
{
return Collections.emptyList();
}
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59 changes: 31 additions & 28 deletions ...rc/main/java/de/tudarmstadt/ukp/inception/annotation/layer/relation/RelationRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@
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.adapter.TypeAdapter;
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 @@ -70,13 +71,13 @@ public class RelationRenderer
{
private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());

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

private static final VID VID_AFTER = VID.builder() //
public static final VID VID_AFTER = VID.builder() //
.withExtensionId("rel") //
.withAnnotationId(1) //
.withExtensionPayload("after") //
Expand Down Expand Up @@ -136,7 +137,7 @@ private List<Annotation> selectAnnotationsInWindow(RenderRequest aRequest, int a
{
var cas = aRequest.getCas();

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

Expand All @@ -160,7 +161,7 @@ private List<Annotation> selectAnnotationsInWindow(RenderRequest aRequest, int a

@Override
public void render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
VDocument aResponse, int aWindowBegin, int aWindowEnd)
VDocument aResponse)
{
if (!checkTypeSystem(aRequest.getCas())) {
return;
Expand All @@ -171,10 +172,11 @@ 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, aWindowBegin, aWindowEnd);
var annotations = selectAnnotationsInWindow(aRequest, aResponse.getWindowBegin(),
aResponse.getWindowEnd());

for (var fs : annotations) {
for (var obj : render(aRequest, aFeatures, aResponse, aWindowBegin, aWindowEnd, fs)) {
for (var obj : render(aRequest, aFeatures, aResponse, fs)) {
if (!(obj instanceof VArc)) {
aResponse.add(obj);
continue;
Expand Down Expand Up @@ -219,7 +221,7 @@ Optional<String> renderYield(AnnotationFS fs)

@Override
public List<VObject> render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
VDocument aVDocument, int aWindowBegin, int aWindowEnd, AnnotationFS aFS)
VDocument aVDocument, AnnotationFS aFS)
{
if (!checkTypeSystem(aFS.getCAS())) {
return emptyList();
Expand Down Expand Up @@ -252,11 +254,11 @@ public List<VObject> render(RenderRequest aRequest, List<AnnotationFeature> aFea
switch (traits.getRenderMode()) {
case ALWAYS:
return renderRelationAsArcs(aRequest, aVDocument, aFS, typeAdapter, sourceFs, targetFs,
labelFeatures, aWindowBegin, aWindowEnd);
labelFeatures);
case WHEN_SELECTED:
if (aRequest.getState() == null || isSelected(aRequest, aFS, sourceFs, targetFs)) {
return renderRelationAsArcs(aRequest, aVDocument, aFS, typeAdapter, sourceFs,
targetFs, labelFeatures, aWindowBegin, aWindowEnd);
targetFs, labelFeatures);
}
return renderRelationOnLabel(aVDocument, typeAdapter, sourceFs, targetFs,
labelFeatures);
Expand All @@ -265,7 +267,7 @@ public List<VObject> render(RenderRequest aRequest, List<AnnotationFeature> aFea
labelFeatures);
default:
return renderRelationAsArcs(aRequest, aVDocument, aFS, typeAdapter, sourceFs, targetFs,
labelFeatures, aWindowBegin, aWindowEnd);
labelFeatures);
}
}

Expand Down Expand Up @@ -318,16 +320,13 @@ private List<VObject> renderRelationOnLabel(VDocument aVDocument, RelationAdapte

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

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

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

objects.add(VArc.builder().forAnnotation(aFS) //
.withLayer(typeAdapter.getLayer()) //
Expand All @@ -339,11 +338,14 @@ private List<VObject> renderRelationAsArcs(RenderRequest aRequest, VDocument aVD
return objects;
}

private VID createRelationEndpoint(RenderRequest aRequest, VDocument aVDocument,
AnnotationFS aEndpoint, int aWindowBegin, int aWindowEnd, RelationAdapter aTypeAdapter)
public static VID createEndpoint(RenderRequest aRequest, VDocument aVDocument,
AnnotationFS aEndpoint, TypeAdapter aTypeAdapter)
{
if (aEndpoint.getEnd() < aWindowBegin) {
if (aRequest.isClipRelations()) {
var windowBegin = aVDocument.getWindowBegin();
var windowEnd = aVDocument.getWindowEnd();

if (aEndpoint.getEnd() < windowBegin) {
if (aRequest.isClipArcs()) {
if (aVDocument.getSpan(VID_BEFORE) == null) {
var beforeAnchor = VSpan.builder() //
.withVid(VID_BEFORE) //
Expand All @@ -357,22 +359,22 @@ private VID createRelationEndpoint(RenderRequest aRequest, VDocument aVDocument,

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

if (aEndpoint.getBegin() >= aWindowEnd) {
if (aRequest.isClipRelations()) {
if (aEndpoint.getBegin() >= windowEnd) {
if (aRequest.isClipArcs()) {
if (aVDocument.getSpan(VID_AFTER) == null) {
var afterAnchor = VSpan.builder() //
.withVid(VID_AFTER) //
.withLayer(aTypeAdapter.getLayer()) //
.withRange(new VRange(aWindowEnd - aWindowBegin,
aWindowEnd - aWindowBegin)) //
.withRange(new VRange(windowEnd - windowBegin, windowEnd - windowBegin)) //
.build();
aVDocument.add(afterAnchor);
}
Expand All @@ -381,9 +383,10 @@ private VID createRelationEndpoint(RenderRequest aRequest, VDocument aVDocument,

var placeholder = VSpan.builder() //
.forAnnotation(aEndpoint) //
.placeholder() //
.withLayer(aTypeAdapter.getLayer()) //
.withRange(new VRange(aEndpoint.getBegin() - aWindowBegin,
aEndpoint.getEnd() - aWindowBegin)) //
.withRange(new VRange(aEndpoint.getBegin() - windowBegin,
aEndpoint.getEnd() - windowBegin)) //
.build();
aVDocument.add(placeholder);
return placeholder.getVid();
Expand Down
6 changes: 3 additions & 3 deletions ...in/java/de/tudarmstadt/ukp/inception/annotation/layer/span/SpanCrossSentenceBehavior.java
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,7 @@ private <T extends SpanAnnotationRequest_ImplBase<T>> T onRequest(TypeAdapter aA

@Override
public void onRender(TypeAdapter aAdapter, VDocument aResponse,
Map<AnnotationFS, VSpan> annoToSpanIdx, int aPageBegin, int aPageEnd)
Map<AnnotationFS, VSpan> annoToSpanIdx)
{
if (aAdapter.getLayer().isCrossSentence() || annoToSpanIdx.isEmpty()) {
return;
Expand All @@ -114,8 +114,8 @@ public void onRender(TypeAdapter aAdapter, VDocument aResponse,
// particular offset, even if it is not the start/end offset of a sentence.
NavigableMap<Integer, AnnotationFS> sentBeginIdx = new TreeMap<>();
NavigableMap<Integer, AnnotationFS> sentEndIdx = new TreeMap<>();
for (AnnotationFS sent : selectOverlapping(cas, getType(cas, Sentence.class), aPageBegin,
aPageEnd)) {
for (AnnotationFS sent : selectOverlapping(cas, getType(cas, Sentence.class),
aResponse.getWindowBegin(), aResponse.getWindowEnd())) {
sentBeginIdx.put(sent.getBegin(), sent);
sentEndIdx.put(sent.getEnd(), sent);
}
Expand Down
2 changes: 1 addition & 1 deletion ...n/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/span/SpanLayerBehavior.java
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ public abstract MoveSpanAnnotationRequest onMove(TypeAdapter aAdapter,
throws AnnotationException;

public void onRender(TypeAdapter aAdapter, VDocument aResponse,
Map<AnnotationFS, VSpan> annoToSpanIdx, int aPageBegin, int aPageEnd)
Map<AnnotationFS, VSpan> annoToSpanIdx)
{
// Nothing to do by default
}
Expand Down
2 changes: 1 addition & 1 deletion ...src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/span/SpanOverlapBehavior.java
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Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,7 @@ private <T extends SpanAnnotationRequest_ImplBase<T>> T onRequest(TypeAdapter aA

@Override
public void onRender(TypeAdapter aAdapter, VDocument aResponse,
Map<AnnotationFS, VSpan> aAnnoToSpanIdx, int aPageBegin, int aPageEnd)
Map<AnnotationFS, VSpan> aAnnoToSpanIdx)
{
if (aAnnoToSpanIdx.isEmpty()) {
return;
Expand Down
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