org.apache.ctakes.smokingstatus.ae.ClassifiableEntries Maven / Gradle / Ivy
/**
* 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.smokingstatus.ae;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.StringTokenizer;
import org.apache.log4j.Logger;
import org.apache.uima.pear.tools.PackageInstaller;
import org.apache.uima.UIMAFramework;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.annotator.AnnotatorProcessException;
import org.apache.uima.cas.FSIterator;
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;
import org.apache.uima.resource.ResourceManager;
import org.apache.uima.resource.ResourceProcessException;
import org.apache.uima.resource.ResourceSpecifier;
import org.apache.uima.util.CasCreationUtils;
import org.apache.uima.util.XMLInputSource;
import org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence;
import org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification;
import org.apache.ctakes.core.resource.FileResource;
import org.apache.ctakes.smokingstatus.Const;
import org.apache.ctakes.smokingstatus.util.ClassifiableEntry;
import org.apache.ctakes.smokingstatus.util.TruthValue;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue;
/**
* @author Mayo Clinic Intended as an annotator to generate ClassifiableEntries
* for SmokingStatus pipeline
*/
public class ClassifiableEntries extends JCasAnnotator_ImplBase {
/**
* Name of configuration parameter that must be set to the filepath of the
* UIMA descriptor ProductionPostSentenceAggregate.xml
*/
// public static final String PARAM_SMOKING_STATUS_DESC_STEP1 = "UimaDescriptorStep1";
// public static final String PARAM_SMOKING_STATUS_DESC_STEP2 = "UimaDescriptorStep2";
public static final String PARAM_SMOKING_STATUS_DESC_STEP1KEY = "UimaDescriptorStep1Key";
public static final String PARAM_SMOKING_STATUS_DESC_STEP2KEY = "UimaDescriptorStep2Key";
/**
* Name of configuration parameter that must be set to the filepath of the
* delimited truth file. This is optional.
*/
public static final String PARAM_TRUTH_FILE = "TruthFile";
/**
* Name of configuration parameter that describes the character delimiter
* used in the delimited truth file. This is optional.
*/
public static final String PARAM_TRUTH_FILE_DELIMITER = "TruthFileDelimiter";
/**
* Name of configuration parameter that determines the allowed
* Classification values. This is optional and only gets used if a Truth
* file is specified.
*/
public static final String PARAM_ALLOWED_CLASSES = "AllowedClassifications";
/**
* Name of configuration parameter that determines whether section headers
* will be parsed out and Segments made to cover the section text.
*/
public static final String PARAM_PARSE_SECTIONS = "ParseSections";
/**
* Sections NOT to be entered in ClassifiableEntries
*/
public static final String PARAM_IGNORE_SECTIONS = "SectionsToIgnore";
public void initialize(UimaContext aContext)
throws ResourceInitializationException {
boolean windowsSystem = true;
try {
super.initialize(aContext);
ResMgr = UIMAFramework.newDefaultResourceManager();
iv_procEntryList = new ArrayList();
iv_entryIndexMap = new HashMap>();
iv_segList = new ArrayList();
// load (optional) truth data
initTruthData();
// What type of operating system type are we running on? Unix or Windows
if (System.getProperty("file.separator").matches("/"))
windowsSystem = false;
// load TAE from XML descriptor
FileResource fResrc = (FileResource) aContext.getResourceObject(PARAM_SMOKING_STATUS_DESC_STEP1KEY);
File descFile = fResrc.getFile();
taeSpecifierStep1 = UIMAFramework.getXMLParser().parseResourceSpecifier(
new XMLInputSource(fResrc.getFile()));
fResrc = (FileResource) aContext.getResourceObject(PARAM_SMOKING_STATUS_DESC_STEP2KEY);
descFile = fResrc.getFile();
taeSpecifierStep2 = UIMAFramework.getXMLParser().parseResourceSpecifier(
new XMLInputSource(fResrc.getFile()));
ra = new ResolutionAnnotator();
ra.initialize(aContext);
String dataPath = aContext.getDataPath();
System.out.println("descFile "+descFile.getAbsolutePath());
// if (!descFile.getAbsolutePath().contains(apiMacroHome)) {
// ClassLoader thisBundle = this.getClass().getClassLoader();
// iv_logger.info("Using data path : "+dataPath);
// if (!windowsSystem) {
// //thisBundle.getSystemResources(dataPath);
// dataPath = "\""+dataPath+"\"";
// // This bundle is needed for Linux issues w/ embedded blanks in path names
// //this.getClass().getClassLoader().getResource(dataPath);
// ResMgr.setExtensionClassPath(thisBundle, dataPath, true);
// } else {
// ResMgr.setExtensionClassPath(dataPath, true);
// }
// }
// else if (iv_logger.isInfoEnabled()) {
// iv_logger.warn("Shouldn't need to set the classpath "+descFile.getAbsolutePath());
// }
taeStep1 = UIMAFramework.produceAnalysisEngine(taeSpecifierStep1, ResMgr, null);
taeStep2 = UIMAFramework.produceAnalysisEngine(taeSpecifierStep2, ResMgr, null);
jcas_local = CasCreationUtils.createCas(taeStep1.getAnalysisEngineMetaData()).getJCas();
// if (iv_logger.isInfoEnabled())
// iv_logger.info("Loaded UIMA TAE from descriptor: "
// + descFile.getAbsolutePath().replaceAll(apiMacroHome, "."));
// get sections to ignore
String[] sections = (String[]) getContext().getConfigParameterValue(PARAM_IGNORE_SECTIONS);
sectionsToIgnore = new HashSet();
for (int i = 0; i < sections.length; i++)
sectionsToIgnore.add(sections[i]);
} catch (Exception e) {
throw new ResourceInitializationException(e);
}
}
private void initTruthData() throws Exception {
String truthFilePath = (String) getContext().getConfigParameterValue(
PARAM_TRUTH_FILE);
if (truthFilePath != null && truthFilePath.length() > 0) {
String delimiter = "\t";
File truthFile = new File(truthFilePath);
loadTruthData(truthFile, delimiter);
String[] allowedArr = (String[]) getContext()
.getConfigParameterValue(PARAM_ALLOWED_CLASSES);
iv_allowedClassifications = new HashSet();
for (int i = 0; i < allowedArr.length; i++) {
String classification = allowedArr[i];
if (classification.equals(Const.CLASS_CURR_SMOKER)
|| classification.equals(Const.CLASS_NON_SMOKER)
|| classification.equals(Const.CLASS_PAST_SMOKER)
|| classification.equals(Const.CLASS_SMOKER)
|| classification.equals(Const.CLASS_UNKNOWN)) {
iv_allowedClassifications.add(classification);
} else {
throw new Exception(
"Invalid classification value for param "
+ PARAM_ALLOWED_CLASSES + ":"
+ classification);
}
}
}
}
/**
* Parses the TRUTH file in delimited format. Stores data in maps.
*
* @param truthFile
* @param delimiter
* @throws Exception
*/
private void loadTruthData(File truthFile, String delimiter)
throws Exception {
iv_truthMap = new HashMap();
BufferedReader br = new BufferedReader(new FileReader(truthFile));
int lineNum = 1;
String line = br.readLine();
while (line != null) {
StringTokenizer st = new StringTokenizer(line, delimiter);
if (st.countTokens() == 4) {
Integer recordID = new Integer(st.nextToken().trim());
String truthVal = st.nextToken().trim();
String sentence = st.nextToken().trim();
// String section = st.nextToken().trim();
String ssClass = null;
if (truthVal.equals("CURRENT SMOKER")) {
ssClass = Const.CLASS_CURR_SMOKER;
} else if (truthVal.equals("PAST SMOKER")) {
ssClass = Const.CLASS_PAST_SMOKER;
} else if (truthVal.equals("SMOKER")) {
ssClass = Const.CLASS_SMOKER;
} else if (truthVal.equals("NON-SMOKER")) {
ssClass = Const.CLASS_NON_SMOKER;
} else if (truthVal.equals("UNKNOWN")) {
ssClass = Const.CLASS_UNKNOWN;
} else {
throw new Exception("Invalid truth value for line:" + line);
}
TruthValue tVal = (TruthValue) iv_truthMap.get(recordID);
if (tVal == null) {
tVal = new TruthValue();
tVal.iv_sentenceList = new ArrayList();
tVal.iv_classification = ssClass;
}
tVal.iv_sentenceList.add(sentence);
iv_truthMap.put(recordID, tVal);
} else {
iv_logger.warn("Malformed line " + lineNum + ": " + line);
}
line = br.readLine();
lineNum++;
}
br.close();
if (iv_logger.isInfoEnabled())
iv_logger.info("Truth data loaded for "
+ iv_truthMap.keySet().size() + " records");
}
/*
* (non-Javadoc)
*
* @see
* org.apache.uima.analysis_engine.annotator.JTextAnnotator#process(org.
* apache.uima.jcas.impl.JCas,
* org.apache.uima.analysis_engine.ResultSpecification)
*/
public void process(JCas jcas) {
// cleanup
iv_entryIndexMap.clear();
iv_procEntryList.clear();
iv_segList.clear();
List entryList = new ArrayList();
String recordID = null;
if (iv_logger.isInfoEnabled()) {
JFSIndexRepository indexes = jcas.getJFSIndexRepository();
FSIterator documentIDIterator = indexes.getAllIndexedFS(DocumentID.type);
if (documentIDIterator.hasNext()) {
DocumentID didAnn = (DocumentID) documentIDIterator.next();
recordID = didAnn.getDocumentID();
if (iv_logger.isInfoEnabled())
iv_logger.info("Processing record [" + recordID + "]");
}
}
Iterator sentItr = jcas.getJFSIndexRepository().getAnnotationIndex(
Sentence.type).iterator();
while (sentItr.hasNext()) {
Sentence sentAnn = (Sentence) sentItr.next();
/**
* This is not to use the specified section.
* 2-23-2009
* The sentence adjuster has a separate means to check for skipped segments, so
* this needs to be tested here as well.
* 9-8-2011
*/
// ---
// if (sectionsToIgnore.contains(sentAnn.getSegmentId())) {
// // System.out.println("---"+sentAnn.getSegmentId()+"|"+sentAnn.getCoveredText());
// continue;
// }
Iterator segItr = jcas.getJFSIndexRepository().getAnnotationIndex(Segment.type).iterator();
Boolean skip = false;
while (segItr.hasNext() && !skip) {
Segment segment = (Segment) segItr.next();
if (segment.getBegin() <= sentAnn.getBegin() && segment.getEnd() >= sentAnn.getEnd()
&& sectionsToIgnore.contains(segment.getId()))
skip = true;
}
// ---
if (!skip) {
ClassifiableEntry entry = new ClassifiableEntry();
entry.iv_recordID = recordID;
entry.iv_begin = sentAnn.getBegin();
entry.iv_end = sentAnn.getEnd();
entry.iv_text = sentAnn.getCoveredText();
entryList.add(entry);
}
}
// collect segment annotations
Iterator segItr = jcas.getJFSIndexRepository().getAnnotationIndex(
Segment.type).iterator();
while (segItr.hasNext()) {
Segment segAnn = (Segment) segItr.next();
iv_segList.add(segAnn);
}
iv_entryIndexMap.put(recordID, entryList);
buildProcEntryList();
/**
* cycle through the procEntryList to process one sentence at a time
*/
try {
for (iv_classifiableIdx = 0; iv_classifiableIdx < iv_procEntryList
.size(); iv_classifiableIdx++) {
jcas_local.reset();
// create a new JCas object
// jcas_local.setDocumentText(jcas.getDocumentText());
// all sentences should be added to one list in iv_entryIndexMap
ClassifiableEntry entry = (ClassifiableEntry) iv_procEntryList
.get(iv_classifiableIdx);
// add object to CAS that captures entry data
RecordSentence rs = new RecordSentence(jcas_local);
rs.setRecordID(entry.iv_recordID);
/**
* To optimize processing, pcs classifier step will process just
* the sentence that was classified as "Known" by
* KURuleBasedClassifier. Document Text is thus restricted to
* contain Sentence Text and NOT the complete document text.
* Thus, begin and end cannot be directly copied from
* entry.iv_begin and entry.iv_end
*/
rs.setBegin(0);
rs.setRecordTextBegin(0);
rs.setEnd(entry.iv_text.length());
rs.setRecordTextEnd(entry.iv_text.length());
// No CAS Initiliazer
jcas_local.setDocumentText(entry.iv_text);
// get segment for the sentence, assume boundaries to be that of
// the sentence
Segment sa = getSegment(entry);
if (sa != null) {
Segment copy_sa = new Segment(jcas_local);
copy_sa.setBegin(rs.getBegin());
copy_sa.setEnd(rs.getEnd());
copy_sa.setId(sa.getId());
copy_sa.addToIndexes();
} else {
if (iv_logger.isDebugEnabled())
iv_logger.error("Invalid Segment for sentence ["
+ rs.getCoveredText() + "]");
}
// assign classification value if applicable
// this only happens when a Truth data file was specified
if (entry.iv_classification != null) {
rs.setClassification(entry.iv_classification);
}
rs.addToIndexes();
taeStep1.process(jcas_local);
if (isSmokingStatusKnown(jcas_local))
taeStep2.process(jcas_local);
ra.process(jcas_local);
performRecordResolution(jcas_local);
}
// final doc classification needs to be added to the original cas
collectionProcessComplete(jcas);
} catch (Exception aep) {
try {
throw new AnnotatorProcessException(aep);
} catch (AnnotatorProcessException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
public void destroy() {
super.destroy();
taeStep1.destroy();
taeStep2.destroy();
}
/**
* determines of value set by KUClassifier
*
* @param jcas_local
* @return
*/
private boolean isSmokingStatusKnown(JCas jcas_local) {
boolean known = true;
Iterator nominalAttrItr = jcas_local.getJFSIndexRepository()
.getAnnotationIndex(NominalAttributeValue.type).iterator();
while (nominalAttrItr.hasNext()) {
NominalAttributeValue nav = (NominalAttributeValue) nominalAttrItr
.next();
if (nav.getAttributeName().equalsIgnoreCase("smoking_status")
&& nav.getNominalValue().equalsIgnoreCase("UNKNOWN"))
known = false;
// System.err.println("attr name:"+nav.getAttributeName()+" val:"+nav.getNominalValue());
}
return known;
}
private Segment getSegment(ClassifiableEntry rs) {
Segment sa;
for (int i = 0; i < iv_segList.size(); i++) {
sa = (Segment) iv_segList.get(i);
if (rs.iv_begin >= sa.getBegin() && rs.iv_end <= sa.getEnd())
return sa;
}
return null;
}
private void performRecordResolution(JCas jcas_local)
throws AnnotatorProcessException {
// CAS represents a single sentence
try {
// should be only one RecordSentence object produced by
// the I2B2XmlReader collection reader
Iterator rsItr = jcas_local.getJFSIndexRepository()
.getAnnotationIndex(RecordSentence.type).iterator();
if (rsItr.hasNext()) {
// should be only one final NominalAttributeValue object
// produced by
// the ResolutionAnnotator.
Iterator navItr = jcas_local.getJFSIndexRepository()
.getAnnotationIndex(NominalAttributeValue.type)
.iterator();
while (navItr.hasNext()) {
NominalAttributeValue nav = (NominalAttributeValue) navItr
.next();
String classification = nav.getNominalValue();
storeAssignedClasses(classification);
}
}
} catch (Exception e) {
e.printStackTrace();
throw new AnnotatorProcessException(e);
}
}
public void collectionProcessComplete(JCas jcas)
throws ResourceProcessException, IOException {
try {
/**
* sort record IDs ascending For production environment, we must
* have just one record in the collection
*/
String finalClassification = resolveClassification();
SmokingDocumentClassification docClass = new SmokingDocumentClassification(
jcas);
docClass.addToIndexes();
docClass.setClassification(finalClassification);
resetCounts();
} catch (Exception e) {
throw new ResourceProcessException(e);
}
}
/**
* Given all the unique classifications for a given record, resolve it down
* to a single final classifcation.
*
* @param cList
* @return
*/
private String resolveClassification() {
// If (all sentences in a report are classified as UNKNOWN)
// then mark that report as UNKNOWN;
//
if (iUnknownCtr > 0 && iSmokerCtr == 0 && iPastSmokerCtr == 0
&& iCurrentCtr == 0 && iNonSmokerCtr == 0)
return Const.CLASS_UNKNOWN;
else if (iNonSmokerCtr >= 1 && iUnknownCtr >= 0 && iPastSmokerCtr == 0
&& iCurrentCtr == 0 && iSmokerCtr == 0)
return Const.CLASS_NON_SMOKER;
else if (iCurrentCtr >= 1)
return Const.CLASS_CURR_SMOKER;
else if (iPastSmokerCtr >= 1 && iCurrentCtr <= 0)
return Const.CLASS_PAST_SMOKER;
else if (iSmokerCtr >= 1 && iCurrentCtr <= 0 && iPastSmokerCtr <= 0)
return Const.CLASS_SMOKER;
else
return null;
}
private void storeAssignedClasses(String smokClass) {
if (smokClass.equals(Const.CLASS_CURR_SMOKER))
iCurrentCtr++;
else if (smokClass.equals(Const.CLASS_NON_SMOKER))
iNonSmokerCtr++;
else if (smokClass.equals(Const.CLASS_PAST_SMOKER))
iPastSmokerCtr++;
else if (smokClass.equals(Const.CLASS_SMOKER))
iSmokerCtr++;
else if (smokClass.equals(Const.CLASS_UNKNOWN))
iUnknownCtr++;
}
private void resetCounts() {
iSmokerCtr = 0;
iPastSmokerCtr = 0;
iCurrentCtr = 0;
iNonSmokerCtr = 0;
iUnknownCtr = 0;
}
private void buildProcEntryList() {
// assemble the final list of entries that will be considered
// part of the collection to process
int allowedCnt = 0;
int disallowedCnt = 0;
Iterator recItr = iv_entryIndexMap.keySet().iterator();
while (recItr.hasNext()) {
String recordID = (String) recItr.next();
Iterator entryItr = ((List) iv_entryIndexMap.get(recordID))
.iterator();
while (entryItr.hasNext()) {
ClassifiableEntry entry = (ClassifiableEntry) entryItr.next();
if ((iv_allowedClassifications == null)
|| (iv_allowedClassifications
.contains(entry.iv_classification))) {
iv_procEntryList.add(entry);
allowedCnt++;
} else {
if (iv_logger.isInfoEnabled())
iv_logger.info("disallowed value:"
+ entry.iv_classification);
disallowedCnt++;
}
// System.out.println("****Sentence: " +entry.iv_text);
}
}
int totalCnt = allowedCnt + disallowedCnt;
if (iv_logger.isInfoEnabled()) {
iv_logger.info("# total sentences: " + totalCnt);
iv_logger.info("# allowed sentences: " + allowedCnt);
iv_logger.info("# disallowed sentences: " + disallowedCnt);
}
}
// index into the annotations contained in a file, value increments as
// the CollectionReader consumes objects
private int iv_classifiableIdx;
// list of ClassifiableEntry objects to be processed
private List iv_procEntryList;
// list of segments
private List iv_segList;
// Map used to index ALL ClassifiableEntry objects by their record ID
// key = record ID (java.lang.Integer)
// val = list of ClassifiableEntry objects
private Map> iv_entryIndexMap;
// key = record ID (java.lang.Integer)
// val = list of TruthValue objects
private Map iv_truthMap;
// set of classification values of type java.lang.String
// see org.apache.ctakes.smokingstatus.Const for proper String values
private Set iv_allowedClassifications;
private AnalysisEngine taeStep1;
private AnalysisEngine taeStep2;
private ResourceSpecifier taeSpecifierStep1;
private ResourceSpecifier taeSpecifierStep2;
// LOG4J logger based on class name
protected Logger iv_logger = Logger.getLogger(getClass().getName());
// counters to track sentence classification
private int iSmokerCtr;
private int iPastSmokerCtr;
private int iCurrentCtr;
private int iNonSmokerCtr;
private int iUnknownCtr;
//private String apiMacroHome = "\\$main_root";
private JCas jcas_local;
private ResolutionAnnotator ra;
private ResourceManager ResMgr;
private Set sectionsToIgnore;
}
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