org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl Maven / Gradle / Ivy
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* 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.ytex.kernel;
import org.apache.commons.cli.*;
import org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao;
import org.apache.ctakes.ytex.kernel.dao.ConceptDao;
import org.apache.ctakes.ytex.kernel.model.ConcRel;
import org.apache.ctakes.ytex.kernel.model.ConceptGraph;
import org.apache.ctakes.ytex.umls.dao.UMLSDao;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
import java.util.*;
public class CytoscapeHelperImpl implements CytoscapeHelper {
/**
* @param args
*/
@SuppressWarnings("static-access")
public static void main(String args[]) throws ParseException, IOException {
Options options = new Options();
options.addOption(OptionBuilder
.withArgName("prop")
.hasArg()
.withDescription(
"property file with queries and other parameters. todo desc")
.create("prop"));
OptionGroup og = new OptionGroup();
og.addOption(OptionBuilder
.withArgName("network")
.hasArg()
.withDescription(
"create network using specified concept graph and corpus. creates prefix.sif with edges and prefix.node.txt with node data in working directory.")
.create("network"));
og.addOption(OptionBuilder
.withArgName("concept id")
.hasArg()
.withDescription(
"get all descendants of specified concept, creates concept_id.tree file in working directory")
.create("subtree"));
og.setRequired(true);
options.addOptionGroup(og);
try {
CommandLineParser parser = new GnuParser();
CommandLine line = parser.parse(options, args);
CytoscapeHelper cytHelper = KernelContextHolder
.getApplicationContext().getBean(CytoscapeHelper.class);
Properties props = new Properties(System.getProperties());
props.putAll(FileUtil.loadProperties(
line.getOptionValue("prop"), true));
if (!cytHelper.validateProps(props)) {
printHelp(options);
} else {
if (line.hasOption("network")) {
cytHelper.exportNetwork(line.getOptionValue("network"),
props);
} else if (line.hasOption("subtree")) {
cytHelper.exportSubtree(line.getOptionValue("subtree"),
props);
} else {
printHelp(options);
}
}
} catch (ParseException pe) {
printHelp(options);
}
}
private static void printHelp(Options options) {
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("java " + CytoscapeHelperImpl.class.getName()
+ " generate graphs and node lists for cytoscape", options);
}
protected ClassifierEvaluationDao classifierEvaluationDao;
protected ConceptDao conceptDao;
protected UMLSDao umlsDao;
private void addConcepts(ConceptGraph cg, String conceptId,
Set nodesToInclude, Set leaves) {
ConcRel cr = cg.getConceptMap().get(conceptId);
// only process this node if it isn't already in the list
if (!nodesToInclude.contains(cr.getConceptID())) {
// add me to the list
nodesToInclude.add(cr.getConceptID());
// iterate over parents and recurse
for (ConcRel crp : cr.getParents()) {
addConcepts(cg, crp.getConceptID(), nodesToInclude, leaves);
// parent is not a leaf - remove it from the list of candidate
// leaves
leaves.remove(crp.getConceptID());
}
}
}
private void addSubtree(Set nodes, ConcRel cr) {
if (!nodes.contains(cr.getConceptID())) {
nodes.add(cr.getConceptID());
for (ConcRel crc : cr.getChildren()) {
addSubtree(nodes, crc);
}
}
}
private void exportEdges(ConceptGraph cg, BufferedWriter network) throws IOException {
for (ConcRel cr : cg.getConceptList()) {
for (ConcRel crc : cr.getChildren()) {
network.write(crc.getConceptID());
network.write("\tisa\t");
network.write(cr.getConceptID());
network.write("\n");
}
}
}
/*
* (non-Javadoc)
*
* @see
* org.apache.ctakes.ytex.kernel.CytoscapeHelper#exportNetwork(org.apache.ctakes.ytex.kernel.model.ConceptGraph,
* java.lang.String, java.lang.String, java.lang.String, int,
* java.io.BufferedWriter, java.io.BufferedWriter)
*/
@Override
public void exportNetwork(ConceptGraph cg, String corpusName,
String conceptGraphName, String conceptSetName,
int leafChildrenDepth, BufferedWriter networkData,
BufferedWriter nodeData) throws IOException {
exportEdges(cg, networkData);
}
@Override
public void exportNetwork(String filePrefix, Properties props)
throws IOException {
BufferedWriter networkData = null;
BufferedWriter nodeData = null;
try {
networkData = new BufferedWriter(
new FileWriter(filePrefix + ".sif"));
nodeData = new BufferedWriter(new FileWriter(filePrefix
+ ".node.txt"));
String conceptGraphName = props
.getProperty("org.apache.ctakes.ytex.conceptGraphName");
exportNetwork(this.conceptDao.getConceptGraph(conceptGraphName),
props.getProperty("org.apache.ctakes.ytex.corpusName"), conceptGraphName,
props.getProperty("org.apache.ctakes.ytex.conceptSetName"), 0, networkData,
nodeData);
} finally {
if (networkData != null) {
networkData.close();
}
if (nodeData != null) {
nodeData.close();
}
}
}
private void exportNodes(List subList, BufferedWriter nodeData,
Map ic) throws IOException {
Map nodeNames = this.umlsDao.getNames(subList);
for (String conceptID : subList) {
nodeData.write(conceptID);
nodeData.write("\t");
nodeData.write(Double.toString(ic.containsKey(conceptID) ? ic
.get(conceptID) : 0.0));
nodeData.write("\t\"");
nodeData.write(nodeNames.containsKey(conceptID) ? nodeNames.get(
conceptID).toString() : "");
nodeData.write("\"\n");
}
}
private void exportNodes(Set exportedNodes,
BufferedWriter nodeData, Map ic) throws IOException {
List exportedNodeList = new ArrayList(exportedNodes);
int size = exportedNodes.size();
int chunks = size / 1000;
if (size % 1000 != 0)
chunks++;
for (int chunk = 0; chunk < chunks; chunk++) {
int start = chunk * 1000;
int end = Math.min(size - 1, (chunk + 1) * 1000 - 1);
List subList = exportedNodeList.subList(start, end);
exportNodes(subList, nodeData, ic);
}
}
@Override
public void exportSubtree(String conceptID, Properties props)
throws IOException {
Set nodes = new HashSet();
ConceptGraph cg = this.conceptDao.getConceptGraph(props
.getProperty("org.apache.ctakes.ytex.conceptGraphName"));
ConcRel cr = cg.getConceptMap().get(conceptID);
if (cr != null) {
addSubtree(nodes, cr);
}
BufferedWriter w = null;
try {
w = new BufferedWriter(new FileWriter(conceptID + ".idlist"));
for (String node : nodes) {
w.write(node);
w.write("\n");
}
} finally {
if (w != null)
w.close();
}
}
public ClassifierEvaluationDao getClassifierEvaluationDao() {
return classifierEvaluationDao;
}
public ConceptDao getConceptDao() {
return conceptDao;
}
public UMLSDao getUmlsDao() {
return umlsDao;
}
public void setClassifierEvaluationDao(
ClassifierEvaluationDao classifierEvaluationDao) {
this.classifierEvaluationDao = classifierEvaluationDao;
}
public void setConceptDao(ConceptDao conceptDao) {
this.conceptDao = conceptDao;
}
public void setUmlsDao(UMLSDao umlsDao) {
this.umlsDao = umlsDao;
}
@Override
public boolean validateProps(Properties props) {
// String corpusName = props.getProperty("org.apache.ctakes.ytex.corpusName");
String conceptGraphName = props.getProperty("org.apache.ctakes.ytex.conceptGraphName");
return conceptGraphName != null;
}
}
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