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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;
import org.apache.commons.cli.*;
import org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilder;
import org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo;
import org.springframework.context.ApplicationContext;
import org.springframework.context.support.ClassPathXmlApplicationContext;
import org.springframework.context.support.FileSystemXmlApplicationContext;
public class KernelLauncher {
private static Options initOptions() {
Option oStoreInstanceMap = OptionBuilder
.withArgName("instanceMap.obj")
.hasArg()
.withDescription(
"store the instanceMap. Use prior to running the kernel evaluations in parallel.")
.create("storeInstanceMap");
Option oEvaluateKernel = OptionBuilder
.withDescription(
"evaluate kernel specified in application context on the instances. If instanceMap is specified, load instance from file system, else from db.")
.create("evalKernel");
Option exportBagOfWords = OptionBuilder
.withDescription(
"exportBagOfWords. Must specify property file")
.hasArg().create("exportBagOfWords");
Option exportType = OptionBuilder
.withDescription("exportType. either libsvm or weka").hasArg()
.create("exportType");
Option oLoadInstanceMap = OptionBuilder
.withArgName("instanceMap.obj")
.hasArg()
.withDescription(
"load instanceMap from file system instead of from db. Use after storing instance map.")
.create("loadInstanceMap");
Option oEvalMod = OptionBuilder
.withDescription(
"for parallelization, split the instances into mod slices")
.hasArg().create("mod");
Option oEvalSlice = OptionBuilder
.withDescription(
"for parallelization, parameter that determines which slice we work on. If this is not specified, nMod threads will be started to evaluate all slices in parallel.")
.hasArg().create("slice");
Option oBeanref = OptionBuilder
.withArgName("classpath*:simSvcBeanRefContext.xml")
.hasArg()
.withDescription(
"use specified beanRefContext.xml, default classpath*:simSvcBeanRefContext.xml")
.create("beanref");
Option oAppctx = OptionBuilder
.withArgName("kernelApplicationContext")
.hasArg()
.withDescription(
"use specified applicationContext, default kernelApplicationContext")
.create("appctx");
Option oBeans = OptionBuilder
.withArgName("beans-corpus.xml")
.hasArg()
.withDescription(
"use specified beans.xml, no default. This file is typically required.")
.create("beans");
Option oHelp = new Option("help", "print this message");
Options options = new Options();
OptionGroup og = new OptionGroup();
og.addOption(oStoreInstanceMap);
og.addOption(oEvaluateKernel);
og.addOption(exportBagOfWords);
options.addOptionGroup(og);
// options.addOption(oStoreInstanceMap);
options.addOption(oEvaluateKernel);
// options.addOption(exportBagOfWords);
options.addOption(exportType);
options.addOption(oLoadInstanceMap);
options.addOption(oEvalMod);
options.addOption(oEvalSlice);
options.addOption(oBeanref);
options.addOption(oAppctx);
options.addOption(oBeans);
options.addOption(oHelp);
return options;
}
private static void printHelp(Options options) {
HelpFormatter formatter = new HelpFormatter();
formatter
.printHelp(
"java org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl\n Main Options: -storeInstanceMap or -evalKernel",
options);
}
/**
* @param args
*/
public static void main(String[] args) throws Exception {
Options options = initOptions();
if (args.length == 0) {
printHelp(options);
} else {
CommandLineParser parser = new GnuParser();
try {
// parse the command line arguments
CommandLine line = parser.parse(options, args);
String storeInstanceMap = line
.getOptionValue("storeInstanceMap");
boolean evalKernel = line.hasOption("evalKernel");
String exportBagOfWords = line
.getOptionValue("exportBagOfWords");
if (!evalKernel && storeInstanceMap == null
&& exportBagOfWords == null) {
System.out
.println("specify either -evalKernel, -storeInstanceMap, or -exportBagOfWords");
printHelp(options);
} else {
// parse the command line arguments
// by default use the kernelBeanRefContext
// when evaluating kernel, by default use the
// simSvcBeanRefContext.xml
// don't want to load that for other tasks as the simSvc
// loads the UMLS object graph which needs lots of memory
String beanRefContext = line.getOptionValue("beanref",
evalKernel ? "classpath*:org/apache/ctakes/ytex/simSvcBeanRefContext.xml"
: "classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml");
String contextName = line.getOptionValue("appctx",
"kernelApplicationContext");
String beans = line.getOptionValue("beans");
// ApplicationContext appCtx = (ApplicationContext) ContextSingletonBeanFactoryLocator
// .getInstance(beanRefContext)
// .useBeanFactory(contextName).getFactory();
ApplicationContext appCtx
= (ApplicationContext)SpringContextUtil.INSTANCE.getApplicationContext( beanRefContext )
.getBean( contextName );
ApplicationContext appCtxSource = appCtx;
if (beans != null) {
appCtxSource = new FileSystemXmlApplicationContext(
new String[] { beans }, appCtx);
}
if (storeInstanceMap != null) {
storeInstanceMap(appCtxSource, storeInstanceMap, line);
// } else if (evalKernel) {
// evalKernel(appCtxSource, line);
// } else if (exportBagOfWords != null) {
// exportBagOfWords(appCtxSource, exportBagOfWords, line);
}
}
} catch (ParseException e) {
printHelp(options);
throw e;
}
}
}
// private static void exportBagOfWords(ApplicationContext appCtxSource,
// String exportBagOfWords, CommandLine line) throws IOException {
// String beanName = "wekaBagOfWordsExporter";
// if ("libsvm".equals(line.getOptionValue("exportType"))) {
// beanName = "libsvmBagOfWordsExporter";
// }
// BagOfWordsExporter exporter = (BagOfWordsExporter) appCtxSource
// .getBean(beanName);
// exporter.exportBagOfWords(exportBagOfWords);
// }
// private static void evalKernel(ApplicationContext appCtxSource,
// CommandLine line) throws Exception {
// InstanceTreeBuilder builder = appCtxSource.getBean(
// "instanceTreeBuilder", InstanceTreeBuilder.class);
// CorpusKernelEvaluator corpusEvaluator = appCtxSource.getBean(
// "corpusKernelEvaluator", CorpusKernelEvaluator.class);
// String loadInstanceMap = line.getOptionValue("loadInstanceMap");
// String strMod = line.getOptionValue("mod");
// String strSlice = line.getOptionValue("slice");
// int nMod = strMod != null ? Integer.parseInt(strMod) : 0;
// Integer nSlice = null;
// if (nMod == 0) {
// nSlice = 0;
// } else if (strSlice != null) {
// nSlice = Integer.parseInt(strSlice);
// }
// Map instanceMap = null;
// if (loadInstanceMap != null) {
// instanceMap = builder.loadInstanceTrees(loadInstanceMap);
// } else {
// instanceMap = builder.loadInstanceTrees(appCtxSource.getBean(
// "treeMappingInfo", TreeMappingInfo.class));
// }
// if (nSlice != null) {
// corpusEvaluator.evaluateKernelOnCorpus(instanceMap, nMod, nSlice, false);
// } else {
// corpusEvaluator.evaluateKernelOnCorpus(instanceMap, nMod, false);
// }
// }
private static void storeInstanceMap(ApplicationContext appCtxSource,
String storeInstanceMap, CommandLine line) throws Exception {
InstanceTreeBuilder builder = appCtxSource.getBean(
"instanceTreeBuilder", InstanceTreeBuilder.class);
builder.serializeInstanceTrees(
appCtxSource.getBean("treeMappingInfo", TreeMappingInfo.class),
storeInstanceMap);
}
public enum SpringContextUtil {
INSTANCE;
private ApplicationContext _context;
public ApplicationContext getApplicationContext( final String contextPath ) {
if ( _context == null ) {
_context = new ClassPathXmlApplicationContext( contextPath );
}
return _context;
}
}
}
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