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MedCoDatabase.java
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Fri, Jul 26, 10:18

MedCoDatabase.java
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/*
* Copyright (c) 2006-2007 Massachusetts General Hospital
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the i2b2 Software License v1.0
* which accompanies this distribution.
*
* Contributors:
* Lori Phillips
*/
package ch.epfl.lca1.medco;
import java.util.*;
import javax.sql.DataSource;
import ch.epfl.lca1.medco.util.Logger;
import org.springframework.jdbc.core.support.JdbcDaoSupport;
import ch.epfl.lca1.medco.util.MedCoUtil;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import org.springframework.jdbc.support.rowset.SqlRowSet;
// TODO: migrate the medco_data.enc_observation_fact to the normal i2b2 observation fact
// todo: do not use the bootstrap datasource, use it according to the user (from PM)
public class MedCoDatabase extends JdbcDaoSupport {
public MedCoDatabase() throws I2B2Exception {
DataSource ds = null;
try {
ds = MedCoUtil.getInstance().getDataSource("java:/MedCoBootStrapDS");
Logger.debug(ds.toString());
} catch (I2B2Exception e2) {
throw Logger.fatal(e2);
}
this.setDataSource(ds);
}
/**
* search a concept in the CLINICAL_NON_SENSITIVE TABLE
*/
public String searchConceptClinicalNonSensitive(String concept){
String sql =
"select c_fullname " +
"from shrine_ont.clinical_non_sensitive " +
"where c_fullname like " + "'%"+concept+"%'";
try {
SqlRowSet rowSet = this.getJdbcTemplate().queryForRowSet(sql);
String concept_path = "";
rowSet.next();
concept_path = rowSet.getString("c_fullname");
return concept_path ;
} catch (Exception e) {
return "";
}
}
/**
* search a concept in the CLINICAL_SENSITIVE TABLE
*/
public String searchConceptClinicalSensitive(String concept){
String sql =
"select c_basecode " +
"from shrine_ont.clinical_sensitive " +
"where c_fullname like " + "'%"+concept+"%'";
try {
SqlRowSet rowSet = this.getJdbcTemplate().queryForRowSet(sql);
String concept_path = "";
rowSet.next();
concept_path = rowSet.getString("c_basecode");
return concept_path ;
} catch (Exception e) {
return "";
}
}
/**
* search a concept in the GENOMIC_ANNOTATIONS
*/
public List<String> searchConceptGenomic(String key, String value){
String sql =
"select variant_id " +
"from shrine_ont.genomic_annotations " +
"where variant_annotations ->> '" + key + "' = '" + value + "'";
try {
SqlRowSet rowSet = this.getJdbcTemplate().queryForRowSet(sql);
List<String> genomicIDs = new ArrayList<>(0);
while (rowSet.next()){
genomicIDs.add(rowSet.getString("variant_id"));
}
return genomicIDs;
} catch (Exception e) {
return new ArrayList<>(0);
}
}
}

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