support for eav tables (cee90da4) · Commits · Raphael Majeed / histream

histream-import/TODO.txt

+5 −0

Original line number	Original line	Diff line number	Diff line
	@@ -3,3 +3,8 @@ Validate exceptions
	test for specific errors in data files,		test for specific errors in data files,
	e.g. missing visit start timestamps in rows.		e.g. missing visit start timestamps in rows.
	To do so, add data files with errors to test/resources		To do so, add data files with errors to test/resources

			Import configuration
			--------------------
			Allow multiple visit tables with different IDs. Fact tables
			can choose which visit table to reference. e.g. <visit-id table="1">fallnr</visit-id>
			No newline at end of file

histream-import/src/main/java/de/sekmi/histream/etl/ETLObservationSupplier.java

+13 −5

Original line number	Original line	Diff line number	Diff line
	@@ -13,6 +13,7 @@ import de.sekmi.histream.Observation;
	import de.sekmi.histream.ObservationFactory;		import de.sekmi.histream.ObservationFactory;
	import de.sekmi.histream.ObservationSupplier;		import de.sekmi.histream.ObservationSupplier;
	import de.sekmi.histream.etl.config.DataSource;		import de.sekmi.histream.etl.config.DataSource;
			import de.sekmi.histream.etl.config.EavTable;
	import de.sekmi.histream.etl.config.Meta;		import de.sekmi.histream.etl.config.Meta;
	import de.sekmi.histream.etl.config.PatientTable;		import de.sekmi.histream.etl.config.PatientTable;
	import de.sekmi.histream.etl.config.VisitTable;		import de.sekmi.histream.etl.config.VisitTable;
	@@ -62,10 +63,11 @@ public class ETLObservationSupplier implements ObservationSupplier{
	private PatientTable pt;		private PatientTable pt;
	private VisitTable vt;		private VisitTable vt;
	private List<WideTable> wt;		private List<WideTable> wt;
			private List<EavTable> et;

	private RecordSupplier<PatientRow> pr;		private RecordSupplier<PatientRow> pr;
	private RecordSupplier<VisitRow> vr;		private RecordSupplier<VisitRow> vr;
	private List<RecordSupplier<WideRow>> wr;		private List<RecordSupplier<? extends FactRow>> fr;

	private FactGroupingQueue queue;		private FactGroupingQueue queue;

	@@ -118,6 +120,7 @@ public class ETLObservationSupplier implements ObservationSupplier{
	pt = ds.getPatientTable();		pt = ds.getPatientTable();
	vt = ds.getVisitTable();		vt = ds.getVisitTable();
	wt = ds.getWideTables();		wt = ds.getWideTables();
			et = ds.getEavTables();
	// TODO long tables		// TODO long tables

	Meta meta = ds.getMeta();		Meta meta = ds.getMeta();
	@@ -131,12 +134,17 @@ public class ETLObservationSupplier implements ObservationSupplier{
	factory.getExtensionAccessor(Visit.class));		factory.getExtensionAccessor(Visit.class));

	// open all tables		// open all tables
	wr = new ArrayList<>(wt.size());		fr = new ArrayList<>(wt.size());
	for( WideTable t : wt ){		for( WideTable t : wt ){
	//@SuppressWarnings("resource")		//@SuppressWarnings("resource")
	RecordSupplier<WideRow> s = t.open(factory, meta);		RecordSupplier<WideRow> s = t.open(factory, meta);
	queue.addFactTable(s);		queue.addFactTable(s);
	wr.add(s);		fr.add(s);
			}
			for( EavTable t : et ){
			RecordSupplier<EavRow> s = t.open(factory, meta);
			queue.addFactTable(s);
			fr.add(s);
	}		}
	queue.prepare();		queue.prepare();

	@@ -184,8 +192,8 @@ public class ETLObservationSupplier implements ObservationSupplier{
	}		}
	vr=null;		vr=null;
	}		}
	if( wr != null ){		if( fr != null ){
	Iterator<RecordSupplier<WideRow>> i = wr.iterator();		Iterator<RecordSupplier<? extends FactRow>> i = fr.iterator();
	while( i.hasNext() ){		while( i.hasNext() ){
	try{ i.next().close(); }		try{ i.next().close(); }
	catch( IOException e ){		catch( IOException e ){

histream-import/src/main/java/de/sekmi/histream/etl/EavRow.java

0 → 100644

+32 −0

Original line number	Original line	Diff line number	Diff line
			package de.sekmi.histream.etl;

			import java.util.Arrays;
			import java.util.List;

			import de.sekmi.histream.Observation;

			/**
			* Row from EAV table. Per definition, only
			* a single fact per row is contained.
			*
			* @author R.W.Majeed
			*
			*/
			public class EavRow implements FactRow {
			private Observation fact;

			public EavRow(Observation fact){
			this.fact = fact;
			}
			@Override
			public List<Observation> getFacts() {
			return Arrays.asList(fact);
			}

			@Override
			public String getPatientId() {return fact.getPatientId();}

			@Override
			public String getVisitId() {return fact.getEncounterId();}

			}

histream-import/src/main/java/de/sekmi/histream/etl/WideRow.java

+7 −0

Original line number	Original line	Diff line number	Diff line
	@@ -5,6 +5,13 @@ import java.util.List;

	import de.sekmi.histream.Observation;		import de.sekmi.histream.Observation;

			/**
			* Wide fact row which. A single wide row
			* may contain multiple facts.
			*
			* @author R.W.Majeed
			*
			*/
	public class WideRow implements FactRow{		public class WideRow implements FactRow{
	private String patid;		private String patid;
	private String visit;		private String visit;

histream-import/src/main/java/de/sekmi/histream/etl/config/DataSource.java

+7 −0

Original line number	Original line	Diff line number	Diff line
	@@ -44,6 +44,9 @@ public class DataSource {
	@XmlElement(name="wide-table")		@XmlElement(name="wide-table")
	WideTable[] wideTables;		WideTable[] wideTables;

			@XmlElement(name="eav-table")
			EavTable[] eavTables;

	public Meta getMeta(){return meta;}		public Meta getMeta(){return meta;}

	public PatientTable getPatientTable(){		public PatientTable getPatientTable(){
	@@ -58,4 +61,8 @@ public class DataSource {
	return Arrays.asList(wideTables);		return Arrays.asList(wideTables);
	}		}

			public List<EavTable> getEavTables(){
			return Arrays.asList(eavTables);
			}

	}		}