Commit 2145a3b4 authored by R.W.Majeed's avatar R.W.Majeed
Browse files

#feature facts with missing/na start timestamps will use the visit start timestamp

parent f3fc3461

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

+6 −0
Original line number Diff line number Diff line
@@ -187,6 +187,12 @@ public class FactGroupingQueue implements Supplier<Observation>{ 
			// set patient extension

			patientLookup.assignPatient(f, currentPatientInstance);

			visitLookup.assignVisit(f, currentVisitInstance);

			// use visit start date if there is no start date in the observation

			if( f.getStartTime() == null && currentVisitInstance != null ){

				f.setStartTime(currentVisitInstance.getStartTime());

			}

			// TODO throw error/warning for facts without start date???



			workQueue.add(f);

		}

	}

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

+7 −0
Original line number Diff line number Diff line
@@ -96,6 +96,13 @@ public class Concept{ 
		if( mf.isActionDrop() ){

			return null; // ignore this fact

		}



		// if start is null/na, use visit start timestamp

		if( start == null ){

			// start may be null at this point and will be filled later with the visit timestamp

			// see FactGroupingQueue#addFactsToWorkQueue(FactRow)

		}



		Observation o = factory.createObservation(patid, concept, start);

		if( visit != null ){

			o.setEncounterId(visit);

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

+5 −0
Original line number Diff line number Diff line
@@ -168,6 +168,11 @@ public class EavTable extends Table<EavRow> { 
			vval = null;

		}



		if( start == null ){

			// start may be null at this point and will be filled later with the visit timestamp

			// see FactGroupingQueue#addFactsToWorkQueue(FactRow)

		}



		Observation fact = factory.createObservation(patid, concept, start);

		String visit = idat.visitId.valueOf(colMap, row);

		if( visit != null ){

histream-import/src/test/java/de/sekmi/histream/etl/TestETLSupplier.java

+9 −0
Original line number Diff line number Diff line
@@ -133,4 +133,13 @@ public class TestETLSupplier { 
		Assert.assertEquals("v1", v.getId());

		Assert.assertEquals(null, v.getLocationId());

	}

	@Test

	public void missingStartTimestampUsesVisitTimestamp() throws IOException, java.text.ParseException{

		List<Observation> all = new ArrayList<>();

		os.stream().filter( o -> o.getConceptId().equals("natrium") ).forEach(all::add);

		for( Observation o : all ){

			System.out.println("Natrium-start: "+o.getStartTime());

		}

	}



}

histream-import/src/test/resources/data/test-1-datasource.xml

+1 −1
Original line number Diff line number Diff line
@@ -109,7 +109,7 @@ 
		</idat>

		<mdat>

			<concept column="param"/>

			<start column="start_ts" format="u-M-d"/>

			<start column="start_ts" format="u-M-d" na="@"/>

			<end column="end" format="u-M-d" na="@"/>

			<!-- location -->