/**
* 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.annotators;
import java.io.IOException;
import java.util.Properties;
import javax.sql.DataSource;
import org.apache.ctakes.ytex.uima.ApplicationContextHolder;
import org.apache.ctakes.ytex.uima.TestUtils;
import org.apache.ctakes.ytex.uima.types.DocKey;
import org.apache.ctakes.ytex.uima.types.KeyValuePair;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.springframework.context.ApplicationContext;
import org.springframework.context.ConfigurableApplicationContext;
import org.springframework.jdbc.core.JdbcTemplate;
import com.google.common.base.Strings;
/**
* TODO get rid of hard-coded path to Types.xml - load from classpath
*
* @author vgarla
*
*/
public class DBConsumerTest {
static ApplicationContext ctx = null;
@BeforeClass
public static void setup() {
ctx = ApplicationContextHolder.getApplicationContext();
}
/**
* hsql will not write data unless the connection is explicitly closed. for
* debugging issues helpful to look at data; therefore uncomment this
* method. however, this will cause issues with other tests as they run in
* the same classloader, and the pool will be closed. most elegant solution
* would be for spring to close the connections on shutdown.
*
* alternatively, fork tests.
*/
@AfterClass
public static void cleanup() {
((ConfigurableApplicationContext)ctx).close();
// ApplicationContext ctx = ApplicationContextHolder
// .getApplicationContext();
// DataSource ds = ctx.getBean(DataSource.class);
// try {
// ((BasicDataSource)ds).close();
// } catch (Exception e) {
// e.printStackTrace();
// }
}
// @Test
// public void testGetCols() throws SQLException {
// ApplicationContext ctx = ApplicationContextHolder
// .getApplicationContext();
// DataSource ds = ctx.getBean(DataSource.class);
// Connection conn = ds.getConnection();
// DatabaseMetaData dmd = conn.getMetaData();
// // get columns for corresponding table
// // mssql - add schema prefix
// // oracle - convert table name to upper case
// ResultSet rs = dmd.getColumns(
// null,
// "PUBLIC",
// "ANNO_TOKEN",
// null);
// while(rs.next()) {
// String colName = rs.getString("COLUMN_NAME");
// System.out.println(colName);
// }
// rs.close();
// conn.close();
// }
/**
* Verify that date parsing with a manually created date works
*
* @throws UIMAException
* @throws Exception
*/
@Test
public void testProcessAndSaveDoc() throws UIMAException, IOException {
// JCas jCas =
// JCasFactory.createJCasFromPath("src/main/resources/org/apache/ctakes/ytex/types/TypeSystem.xml");
String text = "Title: US Abdomen\n\nDr. Doolitle asked patient\nto take a deep breath\nand exhale slowly. Patient coughed. Prescribed acetominophen";
AnalysisEngine engine = TestUtils.createTokenizerAE(null);
JCas jCas = engine.newJCas();
jCas.setDocumentText(text);
// create a docKey so we can find the doc
long key = System.currentTimeMillis();
DocKey docKey = new DocKey(jCas);
KeyValuePair kvp = new KeyValuePair(jCas);
kvp.setKey("instance_id");
kvp.setValueLong(key);
FSArray fsa = new FSArray(jCas, 1);
fsa.set(0, kvp);
docKey.setKeyValuePairs(fsa);
docKey.addToIndexes();
// run the analysis engine
engine.process(jCas);
DataSource ds = ctx.getBean(DataSource.class);
Properties ytexProperties = (Properties) ctx.getBean("ytexProperties");
String schema = ytexProperties.getProperty("db.schema");
String schemaPrefix = Strings.isNullOrEmpty(schema) ? "" : schema + ".";
JdbcTemplate jt = new JdbcTemplate(ds);
String query = String.format(
"select count(*) from %sdocument where instance_id=%s",
schemaPrefix, key);
Assert.assertTrue(query, jt.queryForInt(query) == 1);
query = String
.format("select count(*) from %sdocument d inner join %sanno_base ab on ab.document_id = d.document_id inner join %sanno_segment s on s.anno_base_id = ab.anno_base_id where d.instance_id=%s",
schemaPrefix, schemaPrefix, schemaPrefix, key);
Assert.assertTrue(query, jt.queryForInt(query) == 1);
query = String
.format("select count(*) from %sdocument d inner join %sanno_base ab on ab.document_id = d.document_id inner join %sanno_sentence s on s.anno_base_id = ab.anno_base_id where d.instance_id=%s",
schemaPrefix, schemaPrefix, schemaPrefix, key);
Assert.assertTrue(query, jt.queryForInt(query) > 1);
query = String
.format("select count(*) from %sdocument d inner join %sanno_base ab on ab.document_id = d.document_id inner join %sanno_token s on s.anno_base_id = ab.anno_base_id where d.instance_id=%s",
schemaPrefix, schemaPrefix, schemaPrefix, key);
Assert.assertTrue(query, jt.queryForInt(query) > 1);
}
}