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Merge pull request #1444 from jamesagnew/1443-multiaxial-properties-need-to-be-supported-for-code-lookups 

Resolve "Multiaxial properties need to be supported for code lookups."
This commit is contained in:
Diederik Muylwyk 2019-08-26 14:48:59 -04:00 committed by GitHub
parent 5071c62cb9 b01d59d5a0
commit a93d4e9bcd
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GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 124 additions and 1 deletions
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13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincHierarchyHandler.java
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@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.term.loinc;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
@ -52,6 +53,18 @@ public class LoincHierarchyHandler implements IRecordHandler {
TermConcept child = getOrCreate(childCode, childCodeText);
parent.addChild(child, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
parent.addPropertyCoding(
"child",
IHapiTerminologyLoaderSvc.LOINC_URI,
child.getCode(),
child.getDisplay());
child.addPropertyCoding(
"parent",
IHapiTerminologyLoaderSvc.LOINC_URI,
parent.getCode(),
parent.getDisplay());
}
}

108
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
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@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptProperty;
import ca.uhn.fhir.jpa.term.loinc.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@ -19,6 +20,8 @@ import org.mockito.Captor;
import org.mockito.Mock;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import static org.hamcrest.Matchers.*;
@ -336,7 +339,6 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
}
}
public static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UPLOAD_PROPERTIES_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_FILE);
@ -358,6 +360,110 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE);
}
@Test
public void testLoadLoincMultiaxialHierarchySupport() throws Exception {
addLoincMandatoryFilesToZip(myFiles);
// Actually do the load
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
Map<String, ValueSet> valueSets = extractValueSets();
Map<String, ConceptMap> conceptMaps = extractConceptMaps();
ConceptMap conceptMap;
TermConcept code;
ValueSet vs;
ConceptMap.ConceptMapGroupComponent group;
// Normal loinc code
code = concepts.get("10013-1");
assertEquals("10013-1", code.getCode());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, code.getCodingProperties("PROPERTY").get(0).getSystem());
assertEquals("LP6802-5", code.getCodingProperties("PROPERTY").get(0).getCode());
assertEquals("Elpot", code.getCodingProperties("PROPERTY").get(0).getDisplay());
assertEquals("EKG.MEAS", code.getStringProperty("CLASS"));
assertEquals("R' wave amplitude in lead I", code.getDisplay());
// Codes with parent and child properties
code = concepts.get("LP31755-9");
assertEquals("LP31755-9", code.getCode());
List<TermConceptProperty> properties = new ArrayList<>(code.getProperties());
assertEquals(1, properties.size());
assertEquals("child", properties.get(0).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
assertEquals("LP14559-6", properties.get(0).getValue());
assertEquals("Microorganism", properties.get(0).getDisplay());
assertEquals(0, code.getParents().size());
assertEquals(1, code.getChildren().size());
TermConcept childCode = code.getChildren().get(0).getChild();
assertEquals("LP14559-6", childCode.getCode());
assertEquals("Microorganism", childCode.getDisplay());
properties = new ArrayList<>(childCode.getProperties());
assertEquals(2, properties.size());
assertEquals("parent", properties.get(0).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
assertEquals(code.getCode(), properties.get(0).getValue());
assertEquals(code.getDisplay(), properties.get(0).getDisplay());
assertEquals("child", properties.get(1).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(1).getCodeSystem());
assertEquals("LP98185-9", properties.get(1).getValue());
assertEquals("Bacteria", properties.get(1).getDisplay());
assertEquals(1, childCode.getParents().size());
assertEquals(1, childCode.getChildren().size());
assertEquals(code.getCode(), new ArrayList<>(childCode.getParents()).get(0).getParent().getCode());
TermConcept nestedChildCode = childCode.getChildren().get(0).getChild();
assertEquals("LP98185-9", nestedChildCode.getCode());
assertEquals("Bacteria", nestedChildCode.getDisplay());
properties = new ArrayList<>(nestedChildCode.getProperties());
assertEquals(2, properties.size());
assertEquals("parent", properties.get(0).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
assertEquals(childCode.getCode(), properties.get(0).getValue());
assertEquals(childCode.getDisplay(), properties.get(0).getDisplay());
assertEquals("child", properties.get(1).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(1).getCodeSystem());
assertEquals("LP14082-9", properties.get(1).getValue());
assertEquals("Bacteria", properties.get(1).getDisplay());
assertEquals(1, nestedChildCode.getParents().size());
assertEquals(1, nestedChildCode.getChildren().size());
assertEquals(childCode.getCode(), new ArrayList<>(nestedChildCode.getParents()).get(0).getParent().getCode());
TermConcept doublyNestedChildCode = nestedChildCode.getChildren().get(0).getChild();
assertEquals("LP14082-9", doublyNestedChildCode.getCode());
assertEquals("Bacteria", doublyNestedChildCode.getDisplay());
properties = new ArrayList<>(doublyNestedChildCode.getProperties());
assertEquals(4, properties.size());
assertEquals("parent", properties.get(0).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
assertEquals(nestedChildCode.getCode(), properties.get(0).getValue());
assertEquals(nestedChildCode.getDisplay(), properties.get(0).getDisplay());
assertEquals("child", properties.get(1).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(1).getCodeSystem());
assertEquals("LP52258-8", properties.get(1).getValue());
assertEquals("Bacteria | Body Fluid", properties.get(1).getDisplay());
assertEquals("child", properties.get(2).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(2).getCodeSystem());
assertEquals("LP52260-4", properties.get(2).getValue());
assertEquals("Bacteria | Cerebral spinal fluid", properties.get(2).getDisplay());
assertEquals("child", properties.get(3).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(3).getCodeSystem());
assertEquals("LP52960-9", properties.get(3).getValue());
assertEquals("Bacteria | Cervix", properties.get(3).getDisplay());
assertEquals(1, doublyNestedChildCode.getParents().size());
assertEquals(3, doublyNestedChildCode.getChildren().size());
assertEquals(nestedChildCode.getCode(), new ArrayList<>(doublyNestedChildCode.getParents()).get(0).getParent().getCode());
assertEquals("LP52258-8", doublyNestedChildCode.getChildren().get(0).getChild().getCode());
assertEquals("LP52260-4", doublyNestedChildCode.getChildren().get(1).getChild().getCode());
assertEquals("LP52960-9", doublyNestedChildCode.getChildren().get(2).getChild().getCode());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

4
src/changes/changes.xml
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@ -78,6 +78,10 @@
Note that this means that data in any existing installations will need to be
re-uploaded to the new database platform.
</action>
<action type="add" issue="1443">
LOINC concepts now include multiaxial hierarchical properties (e.g. <![CDATA[<code>parent</code>]]> and
<![CDATA[<code>child</code>]]>, which identify parent and child concepts.
</action>
</release>
<release version="4.0.0" date="2019-08-14" description="Igloo">
<action type="add">