/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the
* specific language governing permissions and limitations
* under the License.
*/
package org.apache.ctakes.drugner.ae;
import java.lang.reflect.Constructor;
import java.lang.reflect.Method;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import java.util.Set;
import org.apache.ctakes.core.util.FSUtil;
import org.apache.ctakes.core.util.JCasUtil;
import org.apache.ctakes.core.util.ParamUtil;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.analysis_engine.ResultSpecification;
import org.apache.uima.analysis_engine.annotator.AnnotatorConfigurationException;
import org.apache.uima.analysis_engine.annotator.AnnotatorContext;
import org.apache.uima.analysis_engine.annotator.AnnotatorInitializationException;
import org.apache.uima.analysis_engine.annotator.AnnotatorProcessException;
import org.apache.uima.analysis_engine.annotator.JTextAnnotator_ImplBase;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.JFSIndexRepository;
import org.apache.uima.jcas.cas.TOP;
import org.apache.uima.resource.ResourceInitializationException;
/**
* Utility annotator that copy's data from an existing JCas object into a new
* JCas object.
*
* @author duffp
*
*/
public class CopyDrugAnnotator extends JCasAnnotator_ImplBase
{
private int iv_srcType;
private int iv_segmentType=0;
/**
* Value is "sectionOverrideSet". This parameter specifies which segments to skip.
* The resulting range of tokens will include the entire contents of the span within
* the section(s) specified in the sectionOverrideSet parameters of the SegmentLookupWindow
* annotator. The parameter should be of type String, should be multi-valued and optional.
*/
public static final String PARAM_SEGMENTS_TO_SKIP = "sectionOverrideSet";
private Set iv_skipSegmentsSet;
// constructor used to create a new instance of the destination
// JCas object
private Constructor iv_destContr;
// key = source getter method (java.lang.reflect.Method)
// val = destination setter method (java.lang.reflect.Method)
private Map iv_getSetMap;
public void initialize(UimaContext annotCtx)
throws ResourceInitializationException
{
super.initialize(annotCtx);
try
{
String className;
className = (String) annotCtx.getConfigParameterValue("srcDrugObjClass");
Class srcClass = Class.forName(className);
iv_srcType = JCasUtil.getType(className);
className = (String) annotCtx.getConfigParameterValue("destDrugObjClass");
Class destClass = Class.forName(className);
Class[] constrArgs = { JCas.class };
iv_destContr = destClass.getConstructor(constrArgs);
iv_skipSegmentsSet = ParamUtil.getStringParameterValuesSet(PARAM_SEGMENTS_TO_SKIP, annotCtx);
Map m = ParamUtil.getStringParameterValuesMap(
"dataDrugBindMap",
annotCtx,
"|");
iv_getSetMap = new HashMap();
Iterator getterItr = m.keySet().iterator();
while (getterItr.hasNext())
{
String getterMethName = (String) getterItr.next();
String setterMethName = (String) m.get(getterMethName);
Method getterMeth = srcClass.getMethod(getterMethName, (Class []) null);
// get corresponding setter that has compatible args
Class[] setterArgs = { getterMeth.getReturnType() };
Method setterMeth = destClass.getMethod(
setterMethName,
setterArgs);
iv_getSetMap.put(getterMeth, setterMeth);
}
}
catch (Exception e)
{
throw new ResourceInitializationException(e);
}
}
public void process(JCas jcas)
throws AnalysisEngineProcessException
{
// iterate over source objects in JCas
JFSIndexRepository indexes = jcas.getJFSIndexRepository();
Iterator srcObjItr = indexes.getAnnotationIndex(org.apache.ctakes.typesystem.type.textspan.Segment.type).iterator();
org.apache.ctakes.typesystem.type.textspan.Segment segment = null;
while (srcObjItr.hasNext())
{
TOP srcObj = (TOP) srcObjItr.next();
Object[] constrArgVals = { jcas };
try
{
// create new destination object
TOP destObj = (TOP) iv_destContr.newInstance(constrArgVals);
// Find the segments that are to be handled as complete sections
boolean okayToSkip = false;
boolean segmentMissing = iv_skipSegmentsSet.isEmpty();
if (!segmentMissing){
Iterator getSkipSegs = iv_skipSegmentsSet.iterator();
segment = (org.apache.ctakes.typesystem.type.textspan.Segment) srcObj;
while (getSkipSegs.hasNext() && !okayToSkip){
if (getSkipSegs.next().equals(segment.getId())){
okayToSkip = true;
}
}
}
// copy data from source to destination
Iterator getterItr = iv_getSetMap.keySet().iterator();
while (getterItr.hasNext() && (okayToSkip || segmentMissing))
{
Method getterMeth = (Method) getterItr.next();
Method setterMeth = (Method) iv_getSetMap.get(getterMeth);
Object val = getterMeth.invoke(srcObj, (Object []) null);
Object[] setterArgs = { val };
setterMeth.invoke(destObj, setterArgs);
}
// add new destination object to JCas
if (okayToSkip) {
destObj.addToIndexes();
} else {
Iterator lookupWindows = FSUtil.getAnnotationsInSpanIterator(jcas, org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation.type, segment.getBegin(), segment.getEnd());
while (lookupWindows.hasNext()){
org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation lookup = (org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation) lookupWindows.next();
org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation drugLookup = new org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation(jcas, lookup.getBegin(), lookup.getEnd()); //Reorganized paths in 3.0 SPM
drugLookup.addToIndexes();
}
}
}
catch (Exception e)
{
throw new AnalysisEngineProcessException(e);
}
}
}
}