/**
* 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.uima;
import java.io.File;
import java.io.IOException;
import java.util.Date;
import org.apache.ctakes.ytex.dao.DBUtil;
import org.apache.ctakes.ytex.uima.annotators.DBConsumer;
import org.apache.uima.UIMAFramework;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.util.InvalidXMLException;
import org.apache.uima.util.XMLInputSource;
import org.apache.uima.util.XMLParser;
import org.uimafit.factory.AggregateBuilder;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.factory.CollectionReaderFactory;
import com.google.common.base.Strings;
public class TestUtils {
static final String queryGetDocumentKeys = "select note_id instance_id from %s%s";
static final String queryGetDocument = "select note_text from %s%s where note_id = :instance_id";
public static void addDescriptor(AggregateBuilder builder, String path)
throws IOException, InvalidXMLException {
File fileCtakes = new File(path);
XMLParser parser = UIMAFramework.getXMLParser();
XMLInputSource source = new XMLInputSource(fileCtakes);
builder.add(parser.parseAnalysisEngineDescription(source));
}
/**
* Create a simple aggregate ae that does sentence splitting, tokenization,
* and stores results in database. runs the following AEs: <li>
* SegmentRegexAnnotator <li>SentenceDetectorAnnotator <li>
* TokenizerAnnotator <li>DBConsumer
*
* @param analysisBatch
* name of analysis batch for dbconsumer. If null will be set to
* test-[current time millis].
* @return
* @throws IOException
* @throws InvalidXMLException
* @throws ResourceInitializationException
*/
public static AnalysisEngine createTokenizerAE(String analysisBatch)
throws IOException, InvalidXMLException,
ResourceInitializationException {
String dbAnalysisBatch = analysisBatch;
if (Strings.isNullOrEmpty(dbAnalysisBatch))
dbAnalysisBatch = "test-" + System.currentTimeMillis();
AggregateBuilder builder = new AggregateBuilder();
addDescriptor(builder, "desc/analysis_engine/SegmentRegexAnnotator.xml");
addDescriptor(builder,
"desc/analysis_engine/SentenceDetectorAnnotator.xml");
addDescriptor(builder,
"../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml");
builder.add(AnalysisEngineFactory.createPrimitiveDescription(
DBConsumer.class, "analysisBatch", dbAnalysisBatch,
"storeDocText", false, "storeCAS", true));
AnalysisEngine engine = builder.createAggregate();
return engine;
}
public static CollectionReader getFractureDemoCollectionReader()
throws ResourceInitializationException {
CollectionReader colReader = CollectionReaderFactory
.createCollectionReader(
DBCollectionReader.class,
"queryGetDocumentKeys",
String.format(queryGetDocumentKeys,
DBUtil.getYTEXTablePrefix(),
DBUtil.formatTableName("fracture_demo")),
"queryGetDocument",
String.format(queryGetDocument,
DBUtil.getYTEXTablePrefix(),
DBUtil.formatTableName("fracture_demo")));
return colReader;
}
}