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Unified Source and Target View Setting for Every Driver #145

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110 changes: 79 additions & 31 deletions ...n/java/org/texttechnologylab/DockerUnifiedUIMAInterface/driver/DUUIPipelineComponent.java
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Original file line number Diff line number Diff line change
@@ -1,11 +1,13 @@
package org.texttechnologylab.DockerUnifiedUIMAInterface.driver;

import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableMap;
import org.apache.commons.compress.compressors.CompressorException;
import org.apache.commons.compress.compressors.CompressorInputStream;
import org.apache.commons.compress.compressors.CompressorOutputStream;
import org.apache.commons.compress.compressors.CompressorStreamFactory;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.cas.CAS;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.util.InvalidXMLException;
import org.json.JSONArray;
Expand All @@ -28,8 +30,8 @@
* @author Alexander Leonhardt
*/
public class DUUIPipelineComponent {
private HashMap<String, String> _options;
private HashMap<String,String> _parameters;
private Map<String, String> _options;
private Map<String,String> _parameters;

private AnalysisEngineDescription _engine;
private String _finalizedEncoded;
Expand Down Expand Up @@ -65,7 +67,7 @@ public class DUUIPipelineComponent {

private static String versionInformation = "version";
private static String writeToViewName = "uimaViewName";
private static String initialViewFromInitialViewName = "uimaViewInitializeFromInitial";
private static String initializeTargetView = "uimaViewInitializeFromInitial";

private static String componentName = "name";

Expand Down Expand Up @@ -114,6 +116,9 @@ public void finalizeComponent() throws CompressorException, IOException, SAXExce
cos.close();
_finalizedEncoded = Base64.getEncoder().encodeToString(out.toByteArray());
_finalizedEncodedHash = _finalizedEncoded.hashCode();

_options = ImmutableMap.copyOf(_options);
_parameters = ImmutableMap.copyOf(_parameters);
}

public String getFinalizedRepresentation() {
Expand Down Expand Up @@ -466,39 +471,70 @@ public Boolean getDockerImageFetching(Boolean defaultValue) {
return Boolean.parseBoolean(result);
}

/**
* @deprecated Use {@link #withTargetView(String)} instead
*/
@Deprecated
public DUUIPipelineComponent withWriteToView(String viewName) {
return withWriteToView(viewName,false);
System.err.printf("[DEPRECATED] DUUIPipelineComponent.withWriteToView(String) is deprecated, use withTargetView(String) instead.%n");
this.withTargetView(viewName);
return this;
}

public DUUIPipelineComponent withWriteToView(String viewName, boolean createViewFromInitialView) {
if(_finalizedEncoded!=null) {
throw new RuntimeException("DUUIPipelineComponent has already been finalized, it is immutable now!");
/**
* @deprecated Use {@link #withTargetView(String)} and {@link #withInitializeTargetView(boolean)} instead
*/
@Deprecated
public DUUIPipelineComponent withWriteToView(String viewName, boolean initializeTargetView) {
System.err.printf("[DEPRECATED] DUUIPipelineComponent.withWriteToView(String, boolean) is deprecated, use withTargetView(String) and withInitializeTargetView(boolean) instead.%n");
if (viewName == null) {
this.withTargetView(CAS.NAME_DEFAULT_SOFA);
this.withInitializeTargetView(false);
return this;
}
this.withTargetView(viewName);
this.withInitializeTargetView(initializeTargetView);
return this;
}

if(viewName==null) {
_options.remove(writeToViewName);
_options.remove(initialViewFromInitialViewName);
return this;
/**
* If set {@code true} and the configured {@link #withTargetView(String) target view} does not exist,
* the {@code Sofa}s {@link org.apache.uima.jcas.JCas#setDocumentText(String) document text},
* {@link org.apache.uima.jcas.JCas#setDocumentLanguage(String) document language} from the
* {@link org.apache.uima.jcas.tcas.DocumentAnnotation DocumentAnnotation}, and&mdash;if present&mdash;the
* {@link de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData DocumentMetaData}
* will be copied from the {@link #withSourceView(String) source view} ({@code _InitialView} by default).
*/
public DUUIPipelineComponent withInitializeTargetView(boolean bool) {
if(_finalizedEncoded!=null) {
throw new RuntimeException("DUUIPipelineComponent has already been finalized, it is immutable now!");
}
_options.put(writeToViewName,viewName);
_options.put(initialViewFromInitialViewName,String.valueOf(createViewFromInitialView));
_options.put(initializeTargetView, String.valueOf(bool));
return this;
}

public Boolean getCreateViewFromInitialView() {
String value = _options.get(initialViewFromInitialViewName);
if(value == null) return null;
public Boolean getInitializeTargetView() {
String value = _options.get(initializeTargetView);
if (value == null) return false;
return Boolean.valueOf(value);
}

/**
* @deprecated Use {@link #getTargetView()} instead
*/
@Deprecated
public String getViewName() {
return getViewName(null);
System.err.printf("[DEPRECATED] DUUIPipelineComponent.getViewName() is deprecated, use getTargetView() instead.%n");
return this.getTargetView();
}

/**
* @deprecated Use {@link #getTargetView()} instead
*/
@Deprecated
public String getViewName(String defaultValue) {
String value = _options.get(writeToViewName);
if(value==null) return defaultValue;
return value;
System.err.printf("[DEPRECATED] DUUIPipelineComponent.getViewName(String) is deprecated, use getTargetView() instead.%n");
return _options.getOrDefault(targetView, defaultValue);
}

public String toJson() {
Expand Down Expand Up @@ -538,24 +574,44 @@ public DUUIPipelineComponent withParameter(String key, String value) {
return this;
}

/**
* Sets source and target view to {@code viewName}.
*/
public DUUIPipelineComponent withView(String viewName){
if (_finalizedEncoded != null) {
throw new RuntimeException("DUUIPipelineComponent has already been finalized, it is immutable now!");
}
withSourceView(viewName);
withTargetView(viewName);
return this;
}

public DUUIPipelineComponent withSourceView(String viewName) {
if (_finalizedEncoded != null) {
throw new RuntimeException("DUUIPipelineComponent has already been finalized, it is immutable now!");
}
if (viewName == null) {
viewName = CAS.NAME_DEFAULT_SOFA;
}
_options.put(sourceView, viewName);
return this;
}


public DUUIPipelineComponent withTargetView(String viewName) {
if (_finalizedEncoded != null) {
throw new RuntimeException("DUUIPipelineComponent has already been finalized, it is immutable now!");
}
if (viewName == null) {
viewName = CAS.NAME_DEFAULT_SOFA;
}
_options.put(targetView, viewName);
return this;
}

public DUUIPipelineComponent withTimeout(long lLong) {
if (_finalizedEncoded != null) {
throw new RuntimeException("DUUIPipelineComponent has already been finalized, it is immutable now!");
}
_parameters.put(timeout, String.valueOf(lLong));
return this;
}
Expand Down Expand Up @@ -634,19 +690,11 @@ public final Map<String,String> getParameters() {
}

public String getSourceView() {
String result = _options.get(sourceView);
if(result == null) {
return "_InitialView";
}
return result;
return _options.getOrDefault(sourceView, CAS.NAME_DEFAULT_SOFA);
}

public String getTargetView() {
String result = _options.get(targetView);
if(result == null) {
return "_InitialView";
}
return result;
return _options.getOrDefault(targetView, CAS.NAME_DEFAULT_SOFA);
}

public DUUIPipelineComponent clearParameters() {
Expand Down
35 changes: 21 additions & 14 deletions src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/driver/DUUIUIMADriver.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
package org.texttechnologylab.DockerUnifiedUIMAInterface.driver;

import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData;
import org.apache.commons.compress.compressors.CompressorException;
import org.apache.commons.lang3.exception.ExceptionUtils;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CASException;
import org.apache.uima.cas.CASRuntimeException;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
Expand All @@ -16,6 +16,7 @@
import org.apache.uima.resource.metadata.ConfigurationParameter;
import org.apache.uima.resource.metadata.NameValuePair;
import org.apache.uima.resource.metadata.TypeSystemDescription;
import org.apache.uima.util.CasCopier;
import org.apache.uima.util.InvalidXMLException;
import org.texttechnologylab.DockerUnifiedUIMAInterface.DUUIComposer;
import org.texttechnologylab.DockerUnifiedUIMAInterface.exception.PipelineComponentException;
Expand Down Expand Up @@ -374,34 +375,40 @@ public void run(String uuid, JCas aCas, DUUIPipelineDocumentPerformance perf, DU
long mutexEnd = System.nanoTime();
try {
long annotatorStart = mutexEnd;
JCas jc;
String viewName = component.getPipelineComponent().getViewName();
if (viewName == null) {
jc = aCas;
} else {
String sourceViewName = component.getPipelineComponent().getSourceView();
JCas sourceView = aCas.getView(sourceViewName);

JCas targetView = sourceView;
String targetViewName = component.getPipelineComponent().getTargetView();
if (targetViewName != null && !Objects.equals(sourceViewName, targetViewName)) {
try {
jc = aCas.getView(viewName);
targetView = sourceView.getView(targetViewName);
} catch (CASException | CASRuntimeException e) {
if (component.getPipelineComponent().getCreateViewFromInitialView()) {
jc = aCas.createView(viewName);
jc.setDocumentText(aCas.getDocumentText());
jc.setDocumentLanguage(aCas.getDocumentLanguage());
targetView = aCas.createView(targetViewName);
if (component.getPipelineComponent().getInitializeTargetView()) {
targetView.setDocumentText(sourceView.getDocumentText());
targetView.setDocumentLanguage(sourceView.getDocumentLanguage());
try {
DocumentMetaData documentMetaData = DocumentMetaData.get(sourceView);
CasCopier casCopier = new CasCopier(sourceView.getCas(), targetView.getCas());
casCopier.copyFs(documentMetaData).addToIndexes();
} catch (IllegalArgumentException ignored) {}
} else {
throw e;
}
}
}

// if (composer.shouldShutdown()) return;
engine.process(jc);
engine.process(targetView);
long annotatorEnd = System.nanoTime();
ReproducibleAnnotation ann = new ReproducibleAnnotation(jc);
ReproducibleAnnotation ann = new ReproducibleAnnotation(targetView);
ann.setDescription(component.getPipelineComponent().getFinalizedRepresentation());
ann.setCompression(DUUIPipelineComponent.compressionMethod);
ann.setTimestamp(System.nanoTime());
ann.setPipelineName(perf.getRunKey());
ann.addToIndexes();
perf.addData(0, 0, annotatorEnd - annotatorStart, mutexEnd - mutexStart, annotatorEnd - mutexStart, String.valueOf(component.getPipelineComponent().getFinalizedRepresentationHash()), 0, jc, null);
perf.addData(0, 0, annotatorEnd - annotatorStart, mutexEnd - mutexStart, annotatorEnd - mutexStart, String.valueOf(component.getPipelineComponent().getFinalizedRepresentationHash()), 0, targetView, null);
} catch (Exception e) {

// track error docs
Expand Down
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