Commit a9f30afa authored by R.W.Majeed's avatar R.W.Majeed
Browse files

fixed missed duplicate during validation (when first concept for a patient is a duplicate)

parent fb9b3622

histream-import/src/main/java/de/sekmi/histream/etl/validation/Validator.java

+4 −0
Original line number Original line Diff line number Diff line
@@ -75,6 +75,10 @@ public class Validator extends AbstractObservationHandler implements Transformat 




			// clear concepts

			// clear concepts

			concepts.clear();

			concepts.clear();

			// add concept

			if( duplicateConceptCheck ){

				concepts.add(new StartPlusConcept(t));

			}

			

			

			prevPatient = patid; // remember patient to suppress errors for the same patient

			prevPatient = patid; // remember patient to suppress errors for the same patient

histream-import/src/test/java/de/sekmi/histream/etl/validation/TestValidator.java

+18 −0
Original line number Original line Diff line number Diff line
@@ -51,4 +51,22 @@ public class TestValidator { 
			Streams.transfer(os, v);

			Streams.transfer(os, v);

		}

		}

	}

	}

	@Test

	public void validateData4() throws Exception{

		// duplicate concepts

		try( ObservationSupplier os = ETLObservationSupplier.load(getClass().getResource("/data/test-4-datasource.xml")) ){

			Validator v = new Validator(true,true);

			v.setErrorHandler(e -> {throw new RuntimeException(e);});

			Streams.transfer(os, v);

		}catch( RuntimeException e ){

			if( e.getCause() instanceof DuplicateConceptException ){

				// expected behaviour

				return;

			}else{

				// unexpected exceptoin

				throw e;

			}

		}

		Assert.fail("Exception expected");

	}

}
 
}

histream-import/src/test/resources/data/test-4-datasource.xml

0 → 100644
+79 −0
Original line number Original line Diff line number Diff line 
<?xml version="1.0" encoding="UTF-8"?>

<datasource version="1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">

	<!-- Duplicate concept for patient -->

	<meta>

		<id>LTx_PH_ILD_COPD</id>

		<etl-strategy>replace-source</etl-strategy>

	</meta>

	

	 <patient-table>

		<source xsi:type="csv-file">

			<url>test-4-table.csv</url>

			<separator>;</separator>

		</source>

		<idat>

      <!-- Vorname, Nachname, Geschlecht unbekannt -->

			<patient-id column="Pheno-ID"/>

			<given-name column="Pheno-ID"/>

			<surname column="Pheno-ID"/>

		</idat>

		<ignore xsi:type="string" column="*"/>

	</patient-table>

	<visit-table>

		<source xsi:type="csv-file">

			<url>test-4-table.csv</url>

			<type>text/csv</type>

			<separator>;</separator>

		</source>

		<idat>

			<patient-id column="Pheno-ID"/>

			<visit-id column="Zeitpunkt"/>

			<start column="Zeitpunkt" format="d.M.u[ H[:m[:s]]]"/>

		</idat>

	<ignore xsi:type="string" column="*"/>

	</visit-table>

	<eav-table>

		<source xsi:type="csv-file">

			<url>test-4-table.csv</url>

			<type>text/csv</type>

			<separator>;</separator>

		</source>	

		<idat>

			<patient-id column="Pheno-ID"/>

			<visit-id column="Zeitpunkt"/>

		</idat>

		<mdat>

			<concept column="Export-Param"/>

			<start column="Zeitpunkt" format="d.M.u[ H[:m[:s]]]"/>

			<end column="Zeitpunkt" format="d.M.u[ H[:m[:s]]]"/>

			<type constant-value="string"/>

			<value column="Wert" na=""/>

			<unit column="Einheiten" na=""/>

		</mdat>

		<virtual>

			<value column="Diagnose" xsi:type="string" na="">

				<map>					

					<otherwise log-warning="Unexpected value" action="drop-fact" />

				</map>

			</value>

			<value column="Zusatzdiagnose" xsi:type="string" na="">

				<map>

					<case value="IPF" set-concept="B:DP-ID-IPF" set-value=""/>

					<case value="UIP" set-concept="B:DP-ID-IPF" set-value=""/>

					<otherwise log-warning="Unexpected value" action="drop-fact" />

				</map>

			</value>

			<value column="Probenart" xsi:type="string" na="">

				<map>

					<otherwise action="drop-fact"/>

				</map>

			</value>

			<value column="Diesease Area" xsi:type="string" na="">

				<map>

					<otherwise action="drop-fact"/>

				</map>

			</value>

		</virtual>	

		<ignore xsi:type="string" column="*"/>

	</eav-table>

</datasource>

histream-import/src/test/resources/data/test-4-table.csv

0 → 100644
+3 −0
Original line number Original line Diff line number Diff line 
Pheno-ID;Bereich;Zeitpunkt;Export-Param;Wert;Einheiten;

Mmqp212;Biobank-IDs;21.04.2016;Zusatzdiagnose;UIP;;

Mmqp212;Biobank-IDs;21.04.2016;Zusatzdiagnose;IPF;;
 
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