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#4360 - Clean up code #4365

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merged 7 commits into from
Dec 7, 2023
Merged

#4360 - Clean up code #4365

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7fc536c
#4360 - Clean up code
reckart Dec 7, 2023
a497944
#4360 - Clean up code
reckart Dec 7, 2023
fd2dd06
#4360 - Clean up code
reckart Dec 7, 2023
e741d0b
#4360 - Clean up code
reckart Dec 7, 2023
c9b1eff
#4360 - Clean up code
reckart Dec 7, 2023
9b3cd04
#4360 - Clean up code
reckart Dec 7, 2023
6891907
#4360 - Clean up code
reckart Dec 7, 2023
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4 changes: 2 additions & 2 deletions ...c/main/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/page/AnnotationPageBase.java
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Expand Up @@ -318,9 +318,9 @@ public void actionShowSelectedDocument(AjaxRequestTarget aTarget, SourceDocument

protected void handleException(AjaxRequestTarget aTarget, Exception aException)
{
if (aException instanceof ReplaceHandlerException) {
if (aException instanceof ReplaceHandlerException replaceHandlerException) {
// Let Wicket redirects still work
throw (ReplaceHandlerException) aException;
throw replaceHandlerException;
}

LoggerFactory.getLogger(getClass()).error("Error: " + aException.getMessage(), aException);
Expand Down
4 changes: 2 additions & 2 deletions ...rc/main/java/de/tudarmstadt/ukp/inception/annotation/feature/link/LinkFeatureSupport.java
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Expand Up @@ -262,8 +262,8 @@ public ArrayList<LinkWithRoleModel> wrapFeatureValue(AnnotationFeature aFeature,
}

FeatureStructure[] values = null;
if (aValue instanceof ArrayFS) {
values = ((ArrayFS<?>) aValue).toArray();
if (aValue instanceof ArrayFS array) {
values = array.toArray();
}

if (aValue instanceof Collection) {
Expand Down
12 changes: 6 additions & 6 deletions ...de/tudarmstadt/ukp/inception/annotation/feature/misc/ReorderableTagAutoCompleteField.java
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Expand Up @@ -113,14 +113,14 @@ public <C> IConverter<C> getConverter(Class<C> aType)
public Object convertToObject(String aValue, Locale aLocale) throws ConversionException
{
Object value = originalConverter.convertToObject(aValue, aLocale);
if (value instanceof String) {
return value;
if (value instanceof String stringValue) {
return stringValue;
}
else if (value instanceof Tag) {
return ((Tag) value).getName();
else if (value instanceof Tag tag) {
return tag.getName();
}
else if (value instanceof ReorderableTag) {
return ((ReorderableTag) value).getName();
else if (value instanceof ReorderableTag reorderableTag) {
return reorderableTag.getName();
}
else {
return null;
Expand Down
7 changes: 5 additions & 2 deletions .../src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/chain/ChainLayerSupport.java
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Expand Up @@ -57,6 +57,9 @@ public class ChainLayerSupport
{
private final static Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());

@SuppressWarnings("deprecation")
public static final String TYPE = WebAnnoConst.CHAIN_TYPE;

private final ApplicationEventPublisher eventPublisher;
private final LayerBehaviorRegistry layerBehaviorsRegistry;

Expand Down Expand Up @@ -88,7 +91,7 @@ public void setBeanName(String aBeanName)
@Override
public void afterPropertiesSet() throws Exception
{
types = asList(new LayerType(WebAnnoConst.CHAIN_TYPE, "Chain", layerSupportId));
types = asList(new LayerType(TYPE, "Chain", layerSupportId));
}

@Override
Expand All @@ -100,7 +103,7 @@ public List<LayerType> getSupportedLayerTypes()
@Override
public boolean accepts(AnnotationLayer aLayer)
{
return WebAnnoConst.CHAIN_TYPE.equals(aLayer.getType());
return TYPE.equals(aLayer.getType());
}

@Override
Expand Down
37 changes: 16 additions & 21 deletions ...de/tudarmstadt/ukp/inception/annotation/layer/relation/RelationCrossSentenceBehavior.java
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Expand Up @@ -22,21 +22,17 @@
import static de.tudarmstadt.ukp.inception.rendering.vmodel.VCommentType.ERROR;
import static java.util.Collections.emptyList;
import static org.apache.uima.fit.util.CasUtil.getType;
import static org.apache.uima.fit.util.CasUtil.select;

import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.NavigableMap;
import java.util.TreeMap;

import org.apache.commons.lang3.tuple.Pair;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.Feature;
import org.apache.uima.cas.Type;
import org.apache.uima.cas.text.AnnotationFS;
import org.apache.uima.jcas.tcas.Annotation;

import de.tudarmstadt.ukp.clarin.webanno.api.annotation.exception.MultipleSentenceCoveredException;
import de.tudarmstadt.ukp.clarin.webanno.api.annotation.util.WebAnnoCasUtil;
Expand Down Expand Up @@ -85,15 +81,15 @@ public void onRender(TypeAdapter aAdapter, VDocument aResponse,
return;
}

for (Entry<AnnotationFS, VArc> e : aAnnoToArcIdx.entrySet()) {
CAS cas = e.getKey().getCAS();
for (var e : aAnnoToArcIdx.entrySet()) {
var cas = e.getKey().getCAS();

if (!isBeginInSameSentence(cas,
ICasUtil.selectAnnotationByAddr(cas, e.getValue().getSource().getId())
.getBegin(),
ICasUtil.selectAnnotationByAddr(cas, e.getValue().getTarget().getId())
.getBegin())) {
aResponse.add(new VComment(new VID(e.getKey()), ERROR,
aResponse.add(new VComment(VID.of(e.getKey()), ERROR,
"Crossing sentence boundaries is not permitted."));
}
}
Expand All @@ -107,33 +103,33 @@ public List<Pair<LogMessage, AnnotationFS>> onValidate(TypeAdapter aAdapter, CAS
return emptyList();
}

RelationAdapter adapter = (RelationAdapter) aAdapter;
Type type = getType(aCas, aAdapter.getAnnotationTypeName());
Feature targetFeature = type.getFeatureByBaseName(adapter.getTargetFeatureName());
Feature sourceFeature = type.getFeatureByBaseName(adapter.getSourceFeatureName());
var adapter = (RelationAdapter) aAdapter;
var type = getType(aCas, aAdapter.getAnnotationTypeName());
var targetFeature = type.getFeatureByBaseName(adapter.getTargetFeatureName());
var sourceFeature = type.getFeatureByBaseName(adapter.getSourceFeatureName());

// If there are no annotations on this layer, nothing to do
Collection<AnnotationFS> annotations = select(aCas, type);
var annotations = aCas.<Annotation> select(type);
if (annotations.isEmpty()) {
return emptyList();
}

// Prepare feedback message list
List<Pair<LogMessage, AnnotationFS>> messages = new ArrayList<>();
var messages = new ArrayList<Pair<LogMessage, AnnotationFS>>();

// Build indexes to allow quickly looking up the sentence by its begin/end offsets. Since
// The indexes are navigable, we can also find the sentences starting/ending closes to a
// 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 : select(aCas, getType(aCas, Sentence.class))) {
var sentBeginIdx = new TreeMap<Integer, AnnotationFS>();
var sentEndIdx = new TreeMap<Integer, AnnotationFS>();
for (var sent : aCas.select(Sentence.class).asList()) {
sentBeginIdx.put(sent.getBegin(), sent);
sentEndIdx.put(sent.getEnd(), sent);
}

for (AnnotationFS fs : annotations) {
AnnotationFS sourceFs = (AnnotationFS) fs.getFeatureValue(sourceFeature);
AnnotationFS targetFs = (AnnotationFS) fs.getFeatureValue(targetFeature);
for (var fs : annotations) {
var sourceFs = (AnnotationFS) fs.getFeatureValue(sourceFeature);
var targetFs = (AnnotationFS) fs.getFeatureValue(targetFeature);

Entry<Integer, AnnotationFS> s1 = sentBeginIdx.floorEntry(sourceFs.getBegin());
Entry<Integer, AnnotationFS> s2 = sentEndIdx.ceilingEntry(targetFs.getEnd());
Expand All @@ -153,6 +149,5 @@ public List<Pair<LogMessage, AnnotationFS>> onValidate(TypeAdapter aAdapter, CAS
}

return messages;

}
}
9 changes: 6 additions & 3 deletions ...ain/java/de/tudarmstadt/ukp/inception/annotation/layer/relation/RelationLayerSupport.java
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Expand Up @@ -19,7 +19,6 @@

import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.FEAT_REL_SOURCE;
import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.FEAT_REL_TARGET;
import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.RELATION_TYPE;
import static java.util.Arrays.asList;
import static java.util.stream.Collectors.toList;
import static org.apache.uima.cas.CAS.TYPE_NAME_ANNOTATION;
Expand All @@ -43,6 +42,7 @@
import de.tudarmstadt.ukp.inception.schema.api.feature.FeatureSupportRegistry;
import de.tudarmstadt.ukp.inception.schema.api.layer.LayerSupport_ImplBase;
import de.tudarmstadt.ukp.inception.schema.api.layer.LayerType;
import de.tudarmstadt.ukp.inception.support.WebAnnoConst;

/**
* <p>
Expand All @@ -54,6 +54,9 @@ public class RelationLayerSupport
extends LayerSupport_ImplBase<RelationAdapter, RelationLayerTraits>
implements InitializingBean
{
@SuppressWarnings("deprecation")
public static final String TYPE = WebAnnoConst.RELATION_TYPE;

private final ApplicationEventPublisher eventPublisher;
private final LayerBehaviorRegistry layerBehaviorsRegistry;

Expand Down Expand Up @@ -85,7 +88,7 @@ public void setBeanName(String aBeanName)
@Override
public void afterPropertiesSet() throws Exception
{
types = asList(new LayerType(RELATION_TYPE, "Relation", layerSupportId));
types = asList(new LayerType(TYPE, "Relation", layerSupportId));
}

@Override
Expand All @@ -97,7 +100,7 @@ public List<LayerType> getSupportedLayerTypes()
@Override
public boolean accepts(AnnotationLayer aLayer)
{
return RELATION_TYPE.equals(aLayer.getType());
return TYPE.equals(aLayer.getType());
}

@Override
Expand Down
57 changes: 28 additions & 29 deletions .../java/de/tudarmstadt/ukp/inception/annotation/layer/relation/RelationOverlapBehavior.java
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Expand Up @@ -48,11 +48,10 @@
import de.tudarmstadt.ukp.inception.schema.api.adapter.AnnotationComparator;
import de.tudarmstadt.ukp.inception.schema.api.adapter.AnnotationException;
import de.tudarmstadt.ukp.inception.schema.api.adapter.TypeAdapter;
import de.tudarmstadt.ukp.inception.support.WebAnnoConst;
import de.tudarmstadt.ukp.inception.support.logging.LogMessage;

/**
* Handles the {@link OverlapMode} setting for {@link WebAnnoConst#RELATION_TYPE relation layers}.
* Handles the {@link OverlapMode} setting for {@link RelationLayerSupport relation layers}.
* <p>
* This class is exposed as a Spring Component via
* {@code AnnotationServiceAutoConfiguration#relationOverlapBehavior}.
Expand Down Expand Up @@ -151,17 +150,17 @@ public void onRender(TypeAdapter aAdapter, VDocument aResponse,
overlapping);

overlapping.forEach(fs -> aResponse
.add(new VComment(new VID(fs), ERROR, "Overlap is not permitted.")));
.add(new VComment(VID.of(fs), ERROR, "Overlap is not permitted.")));

stacking.forEach(fs -> aResponse
.add(new VComment(new VID(fs), ERROR, "Stacking is not permitted.")));
.add(new VComment(VID.of(fs), ERROR, "Stacking is not permitted.")));
break;
}
case STACKING_ONLY: {
// Here, we must find all overlapping relations because they are not permitted
overlappingNonStackingRelations(sortedRelations, sourceFeature, targetFeature)
.forEach(fs -> aResponse
.add(new VComment(new VID(fs), ERROR, "Only stacking is permitted.")));
.add(new VComment(VID.of(fs), ERROR, "Only stacking is permitted.")));
break;
}
case OVERLAP_ONLY:
Expand All @@ -172,37 +171,37 @@ public void onRender(TypeAdapter aAdapter, VDocument aResponse,
// can be multiple relations going out from the same sourceFS, we need to consider all
// of them for potential stacking.
stackingRelations(sortedRelations, sourceFeature, targetFeature).forEach(fs -> aResponse
.add(new VComment(new VID(fs), ERROR, "Stacking is not permitted.")));
.add(new VComment(VID.of(fs), ERROR, "Stacking is not permitted.")));
break;
}
}

@Override
public List<Pair<LogMessage, AnnotationFS>> onValidate(TypeAdapter aAdapter, CAS aCas)
{
final AnnotationLayer layer = aAdapter.getLayer();
final RelationAdapter adapter = (RelationAdapter) aAdapter;
final Type type = getType(aCas, adapter.getAnnotationTypeName());
final Feature sourceFeature = type.getFeatureByBaseName(adapter.getSourceFeatureName());
final Feature targetFeature = type.getFeatureByBaseName(adapter.getTargetFeatureName());
final var layer = aAdapter.getLayer();
final var adapter = (RelationAdapter) aAdapter;
final var type = getType(aCas, adapter.getAnnotationTypeName());
final var sourceFeature = type.getFeatureByBaseName(adapter.getSourceFeatureName());
final var targetFeature = type.getFeatureByBaseName(adapter.getTargetFeatureName());

List<Pair<LogMessage, AnnotationFS>> messages = new ArrayList<>();
var messages = new ArrayList<Pair<LogMessage, AnnotationFS>>();

switch (layer.getOverlapMode()) {
case ANY_OVERLAP:
return emptyList();
case NO_OVERLAP: {
Set<AnnotationFS> overlapping = new HashSet<>();
Set<AnnotationFS> stacking = new HashSet<>();
var overlapping = new HashSet<AnnotationFS>();
var stacking = new HashSet<AnnotationFS>();

overlappingOrStackingRelations(select(aCas, type), sourceFeature, targetFeature,
stacking, overlapping);

for (AnnotationFS fs : overlapping) {
for (var fs : overlapping) {
messages.add(Pair.of(LogMessage.error(this, "Overlapping relation at [%d-%d]",
fs.getBegin(), fs.getEnd()), fs));
}
for (AnnotationFS fs : stacking) {
for (var fs : stacking) {
messages.add(Pair.of(LogMessage.error(this, "Stacked relation at [%d-%d]",
fs.getBegin(), fs.getEnd()), fs));
}
Expand Down Expand Up @@ -234,8 +233,8 @@ private void overlappingOrStackingRelations(Collection<AnnotationFS> aRelations,
Feature sourceFeature, Feature targetFeature, Collection<AnnotationFS> aStacking,
Collection<AnnotationFS> aOverlapping)
{
for (AnnotationFS rel1 : aRelations) {
for (AnnotationFS rel2 : aRelations) {
for (var rel1 : aRelations) {
for (var rel2 : aRelations) {
if (rel1.equals(rel2)) {
continue;
}
Expand All @@ -255,9 +254,9 @@ else if (overlapping(rel1, rel2, sourceFeature, targetFeature)) {
private Set<AnnotationFS> overlappingNonStackingRelations(Collection<AnnotationFS> aRelations,
Feature sourceFeature, Feature targetFeature)
{
Set<AnnotationFS> overlapping = new HashSet<>();
for (AnnotationFS rel1 : aRelations) {
for (AnnotationFS rel2 : aRelations) {
var overlapping = new HashSet<AnnotationFS>();
for (var rel1 : aRelations) {
for (var rel2 : aRelations) {
if (rel1.equals(rel2)) {
continue;
}
Expand All @@ -281,11 +280,11 @@ private Set<AnnotationFS> stackingRelations(Collection<AnnotationFS> aRelations,
// that a relation A->B does not count as stacked on a relation B->A). But since there
// can be multiple relations going out from the same sourceFS, we need to consider all
// of them for potential stacking.
Set<AnnotationFS> stacking = new HashSet<>();
List<AnnotationFS> candidates = new ArrayList<>();
for (AnnotationFS fs : aRelations) {
AnnotationFS sourceFs = (AnnotationFS) fs.getFeatureValue(sourceFeature);
AnnotationFS targetFs = (AnnotationFS) fs.getFeatureValue(targetFeature);
var stacking = new HashSet<AnnotationFS>();
var candidates = new ArrayList<AnnotationFS>();
for (var fs : aRelations) {
var sourceFs = (AnnotationFS) fs.getFeatureValue(sourceFeature);
var targetFs = (AnnotationFS) fs.getFeatureValue(targetFeature);

// If there are no stacking candidates at the current position yet, collect the
// first
Expand All @@ -302,9 +301,9 @@ else if (candidates.get(0).getBegin() != fs.getBegin()
// If there are already stacking candidates, check if the current FS is stacking on
// any of them. If yes, generate an error message
else {
for (AnnotationFS cand : candidates) {
FeatureStructure candidateOriginFS = cand.getFeatureValue(sourceFeature);
FeatureStructure candidateTargetFS = cand.getFeatureValue(targetFeature);
for (var cand : candidates) {
var candidateOriginFS = cand.getFeatureValue(sourceFeature);
var candidateTargetFS = cand.getFeatureValue(targetFeature);

if (stacking(candidateOriginFS, candidateTargetFS, sourceFs, targetFs)) {
stacking.add(fs);
Expand Down
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