allow DataSource in constructors in addition to property configuration

CHANGELOG.txt

+Changelog
+i2b2 integration constructors also accept DataSource for database connections.

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

@@ -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

@@ -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;
@@ -97,10 +98,27 @@ 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

@@ -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

@@ -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