Commit 76f17a41 authored by R.W.Majeed's avatar R.W.Majeed
Browse files

allow DataSource in constructors in addition to property configuration

parent dbeaa19e

CHANGELOG.txt

0 → 100644
+2 −0
Original line number Diff line number Diff line 
Changelog

i2b2 integration constructors also accept DataSource for database connections.

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/I2b2Inserter.java

+19 −13
Original line number Diff line number Diff line
@@ -34,6 +34,8 @@ import java.util.Objects; 
import java.util.Set;

import java.util.logging.Logger;



import javax.sql.DataSource;



import de.sekmi.histream.Modifier;

import de.sekmi.histream.Observation;

import de.sekmi.histream.ObservationException;
@@ -84,14 +86,13 @@ public class I2b2Inserter extends AbstractObservationHandler implements Observat 
	private int insertCount;

	

	public I2b2Inserter(Map<String,String> config) throws ClassNotFoundException, SQLException{

		this.nullUnitCd = "@"; // technically, null is allowed, but the demodata uses both '@' and ''

		this.nullLocationCd = "@"; // technically, null is allowed, but the demodata only uses '@'

		this.nullValueFlagCd = "@";// technically, null is allowed, but the demodata uses both '@' and ''

		// TODO nullBlob (technically null allowed, but '' is used in demodata)

		this.nullModifierCd = "@"; // null not allowed, @ is used in demodata

		this.nullValueTypeCd = "@"; // TODO check database

		insertCount = 0;

		open(config);

		db = PostgresExtension.getConnection(config, new String[]{"jdbc.","data.jdbc."});

		initialize(config);

	}

	

	public I2b2Inserter(DataSource ds, Map<String,String> config) throws SQLException{

		db = ds.getConnection();

		initialize(config);

	}
@@ -168,18 +169,23 @@ public class I2b2Inserter extends AbstractObservationHandler implements Observat 
		

	}

	/**

	 * Opens a database connection and prepares statements

	 * Initialize the database connection

	 * @throws SQLException if preparation/initialisation failed

	 * @throws ClassNotFoundException if database driver not found 

	 */

	private void open(Map<String,String> props)throws SQLException, ClassNotFoundException{

		db = PostgresExtension.getConnection(props, new String[]{"jdbc.","data.jdbc."});

		db.setAutoCommit(false);

	private void initialize(Map<String,String> props)throws SQLException{

		this.nullUnitCd = "@"; // technically, null is allowed, but the demodata uses both '@' and ''

		this.nullLocationCd = "@"; // technically, null is allowed, but the demodata only uses '@'

		this.nullValueFlagCd = "@";// technically, null is allowed, but the demodata uses both '@' and ''

		// TODO nullBlob (technically null allowed, but '' is used in demodata)

		this.nullModifierCd = "@"; // null not allowed, @ is used in demodata

		this.nullValueTypeCd = "@"; // TODO check database

		this.nullProviderId = props.get("nullProvider");

		if( this.nullProviderId == null ){

			log.warning("property 'nullProvider' missing, using '@' (may violate foreign keys)");

			this.nullProviderId = "@";

		}

		insertCount = 0;

		db.setAutoCommit(false);

		prepareStatements(props);

	}

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/PostgresExtension.java

+19 −1
Original line number Diff line number Diff line
@@ -27,9 +27,10 @@ import java.sql.DriverManager; 
import java.sql.SQLException;

import java.sql.Timestamp;

import java.util.Map;

import java.util.Objects;

import java.util.Properties;



import javax.sql.DataSource;



import de.sekmi.histream.DateTimeAccuracy;

import de.sekmi.histream.Extension;

import de.sekmi.histream.Plugin;
@@ -97,11 +98,28 @@ public abstract class PostgresExtension<T> implements Extension<T>, Plugin { 
		);

	}



	/**

	 * Open a database connection using configuration properties 

	 * with the given prefixes.

	 * @param propertyPrefixes prefix to the configuration properties

	 * @throws ClassNotFoundException if the database driver could not be loaded

	 * @throws SQLException any SQL exceptions

	 */

	protected void openDatabase(String[] propertyPrefixes) throws ClassNotFoundException, SQLException{

		db = getConnection(config, propertyPrefixes);

		prepareStatements();

	}

	

	/**

	 * Open a database connection using a data source

	 * @param ds data source

	 * @throws SQLException SQL exceptions

	 */

	protected void openDatabase(DataSource ds) throws SQLException{

		db = ds.getConnection();

		prepareStatements();

	}



	@Override

	public void close()throws IOException{

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/PostgresPatientStore.java

+23 −10
Original line number Diff line number Diff line
@@ -36,11 +36,7 @@ import java.util.Map; 
import java.util.logging.Level;

import java.util.logging.Logger;













import javax.sql.DataSource;



import de.sekmi.histream.DateTimeAccuracy;

import de.sekmi.histream.Observation;
@@ -125,19 +121,33 @@ public class PostgresPatientStore extends PostgresExtension<I2b2Patient> impleme 
	public PostgresPatientStore(Map<String,String> configuration) throws ClassNotFoundException, SQLException {

		super(configuration);

		this.projectId = config.get("project");

		if( projectId == null ){

			log.warning("property project is null, some things might fail");

		openDatabase(new String[]{"jdbc.","data.jdbc."});

		initialize();

	}

	



	/**

	 * Create a patient store using a {@link DataSource}.

	 * The project id must be specified with the key {@code project}. 

	 * @param ds data source for the connection

	 * @param configuration configuration settings

	 * @throws SQLException SQL error

	 */

	public PostgresPatientStore(DataSource ds, Map<String,String> configuration) throws SQLException{

		super(configuration);

		this.projectId = config.get("project");

		openDatabase(ds);

		initialize();

	}

	private void initialize() throws SQLException{

		this.idSourceDefault = "HIVE";

		this.idSourceSeparator = ':';

//		this.autoInsertSourceId = "HS.auto";

		patientCache = new Hashtable<>(1000);

		idCache = new Hashtable<>(1000);

		openDatabase(new String[]{"jdbc.","data.jdbc."});

		loadMaxPatientNum();

		batchLoad();

	}

	

	private I2b2Patient getCached(int patient_num){

		return patientCache.get(patient_num);

	}
@@ -167,6 +177,9 @@ public class PostgresPatientStore extends PostgresExtension<I2b2Patient> impleme 
	protected void prepareStatements()throws SQLException{



		db.setAutoCommit(true);

		if( projectId == null ){

			log.warning("property project is null, some things might fail");

		}

		// TODO: use prefix from configuration to specify tablespace

		insert = db.prepareStatement("INSERT INTO patient_dimension(patient_num, import_date, sourcesystem_cd) VALUES(?,current_timestamp,?)");

		insertIde = db.prepareStatement("INSERT INTO patient_mapping(patient_ide, patient_ide_source, patient_num, patient_ide_status, project_id, import_date, download_date, sourcesystem_cd) values (?,?,?,?,'"+projectId+"',current_timestamp,?,?)");

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/PostgresVisitStore.java

+30 −3
Original line number Diff line number Diff line
@@ -36,6 +36,8 @@ import java.util.Map; 
import java.util.logging.Level;

import java.util.logging.Logger;



import javax.sql.DataSource;



import de.sekmi.histream.DateTimeAccuracy;

import de.sekmi.histream.Observation;

import de.sekmi.histream.ext.ExternalSourceType;
@@ -80,21 +82,46 @@ public class PostgresVisitStore extends PostgresExtension<I2b2Visit>{ 
	private PreparedStatement deleteSource;

	private PreparedStatement deleteMapSource;

	

	/**

	 * Create a visit store using configuration settings.

	 * The project id must be specified with the key {@code project}. 

	 * JDBC connection configuration is specified with the key 

	 * prefixes {@code jdbc.*} and {@code data.jdbc.*}

	 * @param configuration key value pairs

	 * @throws ClassNotFoundException database driver not found

	 * @throws SQLException SQL exceptions

	 */

	public PostgresVisitStore(Map<String,String> configuration) throws ClassNotFoundException, SQLException {

		super(configuration);

		this.projectId = config.get("project");

		openDatabase(new String[]{"jdbc.","data.jdbc."});

		initialize();

	}



	/**

	 * Create a visit store using a {@link DataSource}.

	 * The project id must be specified with the key {@code project}. 

	 * @param ds data source for the connection

	 * @param configuration configuration settings

	 * @throws SQLException SQL error

	 */

	public PostgresVisitStore(DataSource ds, Map<String,String> configuration) throws SQLException{

		super(configuration);

		this.projectId = config.get("project");

		openDatabase(ds);

		initialize();

	}

	private void initialize() throws SQLException{

		visitCache = new Hashtable<>();

		idCache = new Hashtable<>();

		projectId = config.get("project");

		idSourceDefault = "HIVE";

		idSourceSeparator = ':';

		

		openDatabase(new String[]{"jdbc.","data.jdbc."});

		db.setAutoCommit(true);



		loadMaxEncounterNum();

		batchLoad();

	}



	@Override

	protected void prepareStatements() throws SQLException {

		// TODO: use prefix from configuration to specify tablespace