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Merge pull request #3001 from hapifhir/issue-2995-valuesetcomposeincludeversion-is-not-set-when-uploading-terminology

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Issue 2995 valueset.compose.include.version is not set when uploading terminology
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jmarchionatto 2021-09-17 12:40:26 -04:00 committed by GitHub
commit e7cc0335d8
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6 changed files with 316 additions and 1 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2995-valueset-compose-include-version-is-not-set-when-uploading-terminology.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 2995
title: "CodeSystem version is copied to ValueSet.compose.include.version on loinc terminology upload
to support versioned ValueSet expansion."

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
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@ -723,7 +723,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
retVal.setPublisher("Regenstrief Institute, Inc.");
retVal.setDescription("A value set that includes all LOINC codes");
retVal.setCopyright("This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/");
retVal.getCompose().addInclude().setSystem(ITermLoaderSvc.LOINC_URI);
retVal.getCompose().addInclude().setSystem(ITermLoaderSvc.LOINC_URI).setVersion(codeSystemVersionId);
return retVal;
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
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@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.term.loinc;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IZipContentsHandlerCsv;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ContactPoint;
import org.hl7.fhir.r4.model.Enumerations;
@ -74,6 +75,9 @@ public abstract class BaseLoincHandler implements IZipContentsHandlerCsv {
if (include == null) {
include = theVs.getCompose().addInclude();
include.setSystem(theCodeSystemUrl);
if (StringUtils.isNotBlank(theVs.getVersion())) {
include.setVersion(theVs.getVersion());
}
}
boolean found = false;

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
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@ -104,6 +104,7 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
.getCompose()
.getIncludeFirstRep()
.setSystem(ITermLoaderSvc.LOINC_URI)
.setVersion(codeSystemVersionId)
.addConcept()
.setCode(answerString)
.setDisplay(displayText);

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincRsnaPlaybookHandler.java
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@ -120,6 +120,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IZipCo
.getCompose()
.getIncludeFirstRep()
.setSystem(ITermLoaderSvc.LOINC_URI)
.setVersion(codeSystemVersionId)
.addConcept()
.setCode(loincNumber)
.setDisplay(longCommonName);

304
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandlerTest.java Normal file
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@ -0,0 +1,304 @@
package ca.uhn.fhir.jpa.term.loinc;
import com.google.common.collect.Maps;
import org.apache.commons.compress.utils.Lists;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Answers;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension;
import java.io.StringReader;
import java.util.Map;
import java.util.Properties;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.never;
import static org.mockito.Mockito.spy;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
class BaseLoincHandlerTest {
public static final String LOINC_NUMBER = "test-loinc-number";
public static final String DISPLAY_NAME = "test-display-name";
public static final String TEST_VERSION = "2.69";
@Mock(answer = Answers.RETURNS_DEEP_STUBS)
private ValueSet myValueSet;
@Mock
private ValueSet.ConceptSetComponent myInclude;
@Mock
private ValueSet.ConceptReferenceComponent myConceptReferenceComponent;
private Map<String, Integer> headerMap;
private CSVRecord recordWithHeader;
/**
* Need to setup a real parser because we can't mock final classes (without PowerMockito)
*/
private void setupCSVParser(Map<String, String> headerValues) throws Exception {
final String[] headers = headerValues.keySet().toArray(new String[0]);
final String[] values = headerValues.values().toArray(new String[0]);
final String rowData = StringUtils.join(values, ',');
try (final CSVParser parser = CSVFormat.DEFAULT.parse(new StringReader(rowData))) {
parser.iterator().next();
}
try (final CSVParser parser = CSVFormat.DEFAULT.withHeader(headers).parse(new StringReader(rowData))) {
recordWithHeader = parser.iterator().next();
headerMap = parser.getHeaderMap();
}
}
@Nested
public class WithVersion {
@Test
void Top2000LabResultsHandlerTest() throws Exception {
Map<String, String> recordDataMap = Maps.newHashMap();
recordDataMap.put("LOINC #", "test-loinc-number");
recordDataMap.put("Long Common Name", "test-Long-Common-Names");
setupCSVParser(recordDataMap);
BaseLoincHandler loincHandler = new BaseLoincTop2000LabResultsHandler(
null, Lists.newArrayList(), null, null, null, Lists.newArrayList(), new Properties());
BaseLoincHandler spiedLoincHandler = spy(loincHandler);
when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
when(myValueSet.getVersion()).thenReturn(TEST_VERSION);
when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
spiedLoincHandler.accept(recordWithHeader);
Mockito.verify(myInclude).setVersion(Mockito.notNull());
}
@Test
void LoincDocumentOntologyHandlerTest() throws Exception {
Map<String, String> recordDataMap = Maps.newHashMap();
recordDataMap.put("LoincNumber", "test-LoincNumber");
recordDataMap.put("PartNumber", "test-PartNumber");
recordDataMap.put("PartTypeName", "Document.Role");
recordDataMap.put("PartSequenceOrder", "test-PartSequenceOrder");
recordDataMap.put("PartName", "test-PartName");
setupCSVParser(recordDataMap);
BaseLoincHandler loincHandler = new LoincDocumentOntologyHandler(
Maps.newHashMap(), null, Lists.newArrayList(), Lists.newArrayList(), new Properties());
BaseLoincHandler spiedLoincHandler = spy(loincHandler);
when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
when(myValueSet.getVersion()).thenReturn(TEST_VERSION);
when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
spiedLoincHandler.accept(recordWithHeader);
Mockito.verify(myInclude).setVersion(Mockito.notNull());
}
@Test
void LoincGroupTermsFileHandlerTest() throws Exception {
Map<String, String> recordDataMap = Maps.newHashMap();
recordDataMap.put("LoincNumber", "test-LoincNumber");
recordDataMap.put("GroupId", "test-GroupId");
setupCSVParser(recordDataMap);
BaseLoincHandler loincHandler = new LoincGroupTermsFileHandler(
Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
BaseLoincHandler spiedLoincHandler = spy(loincHandler);
when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
when(myValueSet.getVersion()).thenReturn(TEST_VERSION);
when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
spiedLoincHandler.accept(recordWithHeader);
Mockito.verify(myInclude).setVersion(Mockito.notNull());
}
@Test
void LoincImagingDocumentCodeHandlerTest() throws Exception {
Map<String, String> recordDataMap = Maps.newHashMap();
recordDataMap.put("LOINC_NUM", "test-loinc-number");
recordDataMap.put("LONG_COMMON_NAME", "test-Long-Common-Names");
setupCSVParser(recordDataMap);
BaseLoincHandler loincHandler = new LoincImagingDocumentCodeHandler(
Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
BaseLoincHandler spiedLoincHandler = spy(loincHandler);
when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
when(myValueSet.getVersion()).thenReturn(TEST_VERSION);
when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
spiedLoincHandler.accept(recordWithHeader);
Mockito.verify(myInclude).setVersion(Mockito.notNull());
}
@Test
void LoincUniversalOrderSetHandlerTest() throws Exception {
Map<String, String> recordDataMap = Maps.newHashMap();
recordDataMap.put("LOINC_NUM", "test-loinc-number");
recordDataMap.put("LONG_COMMON_NAME", "test-Long-Common-Names");
recordDataMap.put("ORDER_OBS", "test-ORDER_OBS");
setupCSVParser(recordDataMap);
BaseLoincHandler loincHandler = new LoincUniversalOrderSetHandler(
Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
BaseLoincHandler spiedLoincHandler = spy(loincHandler);
when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
when(myValueSet.getVersion()).thenReturn(TEST_VERSION);
when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
spiedLoincHandler.accept(recordWithHeader);
Mockito.verify(myInclude).setVersion(Mockito.notNull());
} }
@Nested
public class WithoutVersion {
@Test
void Top2000LabResultsHandlerTest() throws Exception {
Map<String, String> recordDataMap = Maps.newHashMap();
recordDataMap.put("LOINC #", "test-loinc-number");
recordDataMap.put("Long Common Name", "test-Long-Common-Names");
setupCSVParser(recordDataMap);
BaseLoincHandler loincHandler = new BaseLoincTop2000LabResultsHandler(
Maps.newHashMap(), Lists.newArrayList(), null, null, null, Lists.newArrayList(), new Properties());
BaseLoincHandler spiedLoincHandler = spy(loincHandler);
when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
spiedLoincHandler.accept(recordWithHeader);
Mockito.verify(myInclude, never()).setVersion(any());
}
@Test
void LoincDocumentOntologyHandlerTest() throws Exception {
Map<String, String> recordDataMap = Maps.newHashMap();
recordDataMap.put("LoincNumber", "test-LoincNumber");
recordDataMap.put("PartNumber", "test-PartNumber");
recordDataMap.put("PartTypeName", "Document.Role");
recordDataMap.put("PartSequenceOrder", "test-PartSequenceOrder");
recordDataMap.put("PartName", "test-PartName");
setupCSVParser(recordDataMap);
BaseLoincHandler loincHandler = new LoincDocumentOntologyHandler(
Maps.newHashMap(), null, Lists.newArrayList(), Lists.newArrayList(), new Properties());
BaseLoincHandler spiedLoincHandler = spy(loincHandler);
when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
spiedLoincHandler.accept(recordWithHeader);
Mockito.verify(myInclude, never()).setVersion(any());
}
@Test
void LoincGroupTermsFileHandlerTest() throws Exception {
Map<String, String> recordDataMap = Maps.newHashMap();
recordDataMap.put("LoincNumber", "test-LoincNumber");
recordDataMap.put("GroupId", "test-GroupId");
setupCSVParser(recordDataMap);
BaseLoincHandler loincHandler = new LoincGroupTermsFileHandler(
Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
BaseLoincHandler spiedLoincHandler = spy(loincHandler);
when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
spiedLoincHandler.accept(recordWithHeader);
Mockito.verify(myInclude, never()).setVersion(any());
}
@Test
void LoincImagingDocumentCodeHandlerTest() throws Exception {
Map<String, String> recordDataMap = Maps.newHashMap();
recordDataMap.put("LOINC_NUM", "test-loinc-number");
recordDataMap.put("LONG_COMMON_NAME", "test-Long-Common-Names");
setupCSVParser(recordDataMap);
BaseLoincHandler loincHandler = new LoincImagingDocumentCodeHandler(
Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
BaseLoincHandler spiedLoincHandler = spy(loincHandler);
when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
spiedLoincHandler.accept(recordWithHeader);
Mockito.verify(myInclude, never()).setVersion(any());
}
@Test
void LoincUniversalOrderSetHandlerTest() throws Exception {
Map<String, String> recordDataMap = Maps.newHashMap();
recordDataMap.put("LOINC_NUM", "test-loinc-number");
recordDataMap.put("LONG_COMMON_NAME", "test-Long-Common-Names");
recordDataMap.put("ORDER_OBS", "test-ORDER_OBS");
setupCSVParser(recordDataMap);
BaseLoincHandler loincHandler = new LoincUniversalOrderSetHandler(
Maps.newHashMap(), Lists.newArrayList(), Lists.newArrayList(), new Properties());
BaseLoincHandler spiedLoincHandler = spy(loincHandler);
when(spiedLoincHandler.getValueSet(any(), any(), any(), any())).thenReturn(myValueSet);
when(myValueSet.getCompose().addInclude()).thenReturn(myInclude);
when(myInclude.addConcept()).thenReturn(myConceptReferenceComponent);
when(myConceptReferenceComponent.setCode(any())).thenReturn(myConceptReferenceComponent);
spiedLoincHandler.accept(recordWithHeader);
Mockito.verify(myInclude, never()).setVersion(any());
}
}
}