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Concept properties are not being saved while using the operation apply-codesystem-delta-add (#2577) 

* fix issue #2280

* revert the indentation back.

* revert-back untouched changes.

* saving concept properties using the operation apply-codesystem-delta-add

* fix test cases; add check for null properties

* fix test; expected file descriptors
This commit is contained in:
Hanan Awwad 2021-05-03 15:02:20 +03:00 committed by GitHub
parent 91fa23b11a
commit 871914bd3b
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10 changed files with 267 additions and 19 deletions
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2
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java
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@ -116,7 +116,7 @@ public class UploadTerminologyCommandTest extends BaseTest {
verify(myTermLoaderSvc, times(1)).loadDeltaAdd(eq("http://foo"), myDescriptorListCaptor.capture(), any());
List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
assertEquals(1, listOfDescriptors.size());
assertEquals(2, listOfDescriptors.size());
assertEquals("concepts.csv", listOfDescriptors.get(0).getFilename());
String uploadFile = IOUtils.toString(listOfDescriptors.get(0).getInputStream(), Charsets.UTF_8);
assertThat(uploadFile, uploadFile, containsString("\"CODE\",\"Display\""));

42
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java
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@ -28,6 +28,7 @@ import ca.uhn.fhir.jpa.term.UploadStatistics;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.custom.ConceptHandler;
import ca.uhn.fhir.jpa.term.custom.HierarchyHandler;
import ca.uhn.fhir.jpa.term.custom.PropertyHandler;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
@ -214,12 +215,14 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
private void convertCodeSystemsToFileDescriptors(List<ITermLoaderSvc.FileDescriptor> theFiles, List<IBaseResource> theCodeSystems) {
Map<String, String> codes = new LinkedHashMap<>();
Map<String, List<CodeSystem.ConceptPropertyComponent>> codeToProperties = new LinkedHashMap<>();
Multimap<String, String> codeToParentCodes = ArrayListMultimap.create();
if (theCodeSystems != null) {
for (IBaseResource nextCodeSystemUncast : theCodeSystems) {
CodeSystem nextCodeSystem = canonicalizeCodeSystem(nextCodeSystemUncast);
convertCodeSystemCodesToCsv(nextCodeSystem.getConcept(), codes, null, codeToParentCodes);
convertCodeSystemCodesToCsv(nextCodeSystem.getConcept(), codes, codeToProperties, null, codeToParentCodes);
}
}
@ -260,6 +263,36 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
ITermLoaderSvc.ByteArrayFileDescriptor fileDescriptor = new ITermLoaderSvc.ByteArrayFileDescriptor(fileName, bytes);
theFiles.add(fileDescriptor);
}
// Create codeToProperties file
if (codeToProperties.size() > 0) {
StringBuilder b = new StringBuilder();
b.append(PropertyHandler.CODE);
b.append(",");
b.append(PropertyHandler.KEY);
b.append(",");
b.append(PropertyHandler.VALUE);
b.append(",");
b.append(PropertyHandler.TYPE);
b.append("\n");
for (Map.Entry<String, List<CodeSystem.ConceptPropertyComponent>> nextEntry : codeToProperties.entrySet()) {
for (CodeSystem.ConceptPropertyComponent propertyComponent : nextEntry.getValue()) {
b.append(csvEscape(nextEntry.getKey()));
b.append(",");
b.append(csvEscape(propertyComponent.getCode()));
b.append(",");
//TODO: check this for different types, other types should be added once TermConceptPropertyTypeEnum contain different types
b.append(csvEscape(propertyComponent.getValueStringType().getValue()));
b.append(",");
b.append(csvEscape(propertyComponent.getValue().primitiveValue()));
b.append("\n");
}
}
byte[] bytes = b.toString().getBytes(Charsets.UTF_8);
String fileName = TermLoaderSvcImpl.CUSTOM_PROPERTIES_FILE;
ITermLoaderSvc.ByteArrayFileDescriptor fileDescriptor = new ITermLoaderSvc.ByteArrayFileDescriptor(fileName, bytes);
theFiles.add(fileDescriptor);
}
}
@ -283,14 +316,17 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
return nextCodeSystem;
}
private void convertCodeSystemCodesToCsv(List<CodeSystem.ConceptDefinitionComponent> theConcept, Map<String, String> theCodes, String theParentCode, Multimap<String, String> theCodeToParentCodes) {
private void convertCodeSystemCodesToCsv(List<CodeSystem.ConceptDefinitionComponent> theConcept, Map<String, String> theCodes, Map<String, List<CodeSystem.ConceptPropertyComponent>> theProperties, String theParentCode, Multimap<String, String> theCodeToParentCodes) {
for (CodeSystem.ConceptDefinitionComponent nextConcept : theConcept) {
if (isNotBlank(nextConcept.getCode())) {
theCodes.put(nextConcept.getCode(), nextConcept.getDisplay());
if (isNotBlank(theParentCode)) {
theCodeToParentCodes.put(nextConcept.getCode(), theParentCode);
}
convertCodeSystemCodesToCsv(nextConcept.getConcept(), theCodes, nextConcept.getCode(), theCodeToParentCodes);
if (nextConcept.getProperty() != null) {
theProperties.put(nextConcept.getCode(), nextConcept.getProperty());
}
convertCodeSystemCodesToCsv(nextConcept.getConcept(), theCodes, theProperties, nextConcept.getCode(), theCodeToParentCodes);
}
}
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
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@ -580,6 +580,11 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
conceptToAdd.setParentPids(null);
conceptToAdd.setCodeSystemVersion(theCsv);
if (conceptToAdd.getProperties() !=null)
conceptToAdd.getProperties().forEach(termConceptProperty -> {
termConceptProperty.setConcept(theConceptToAdd);
termConceptProperty.setCodeSystemVersion(theCsv);
});
if (theStatisticsTracker.getUpdatedConceptCount() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
saveConcept(conceptToAdd);
Long nextConceptPid = conceptToAdd.getId();

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
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@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
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.entity.TermConceptProperty;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
@ -140,6 +141,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class TermLoaderSvcImpl implements ITermLoaderSvc {
public static final String CUSTOM_CONCEPTS_FILE = "concepts.csv";
public static final String CUSTOM_HIERARCHY_FILE = "hierarchy.csv";
public static final String CUSTOM_PROPERTIES_FILE = "properties.csv";
static final String IMGTHLA_HLA_NOM_TXT = "hla_nom.txt";
static final String IMGTHLA_HLA_XML = "hla.xml";
static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
@ -789,4 +791,12 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
}
return concept;
}
public static TermConceptProperty getOrCreateConceptProperty(Map<String, List<TermConceptProperty>> code2Properties, String code, String key) {
List<TermConceptProperty> termConceptProperties = code2Properties.get(code);
if (termConceptProperties == null)
return new TermConceptProperty();
Optional<TermConceptProperty> termConceptProperty = termConceptProperties.stream().filter(property -> key.equals(property.getKey())).findFirst();
return termConceptProperty.isPresent() ? termConceptProperty.get() : new TermConceptProperty();
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/CustomTerminologySet.java
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@ -22,18 +22,16 @@ package ca.uhn.fhir.jpa.term.custom;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptProperty;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.jpa.term.LoadedFileDescriptors;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import org.apache.commons.csv.QuoteMode;
import org.apache.commons.lang3.Validate;
import javax.annotation.Nonnull;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
@ -134,10 +132,24 @@ public class CustomTerminologySet {
public static CustomTerminologySet load(LoadedFileDescriptors theDescriptors, boolean theFlat) {
final Map<String, TermConcept> code2concept = new LinkedHashMap<>();
// Concepts
IRecordHandler conceptHandler = new ConceptHandler(code2concept);
TermLoaderSvcImpl.iterateOverZipFile(theDescriptors, TermLoaderSvcImpl.CUSTOM_CONCEPTS_FILE, conceptHandler, ',', QuoteMode.NON_NUMERIC, false);
if (theDescriptors.hasFile(TermLoaderSvcImpl.CUSTOM_PROPERTIES_FILE)) {
Map<String, List<TermConceptProperty>> theCode2property = new LinkedHashMap<>();
IRecordHandler propertyHandler = new PropertyHandler(theCode2property);
TermLoaderSvcImpl.iterateOverZipFile(theDescriptors, TermLoaderSvcImpl.CUSTOM_PROPERTIES_FILE, propertyHandler, ',', QuoteMode.NON_NUMERIC, false);
for (TermConcept termConcept : code2concept.values()) {
if (!theCode2property.isEmpty() && theCode2property.get(termConcept.getCode()) != null) {
theCode2property.get(termConcept.getCode()).forEach(property -> {
termConcept.getProperties().add(property);
});
}
}
}
if (theFlat) {
return new CustomTerminologySet(code2concept.size(), new ArrayList<>(code2concept.values()));

53
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/PropertyHandler.java Normal file
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@ -0,0 +1,53 @@
package ca.uhn.fhir.jpa.term.custom;
import ca.uhn.fhir.jpa.entity.TermConceptProperty;
import ca.uhn.fhir.jpa.entity.TermConceptPropertyTypeEnum;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.csv.CSVRecord;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
public class PropertyHandler implements IRecordHandler {
public static final String CODE = "CODE";
public static final String KEY = "KEY";
public static final String VALUE = "VALUE";
public static final String TYPE = "TYPE";
private final Map<String, List<TermConceptProperty>> myCode2Properties;
public PropertyHandler(Map<String, List<TermConceptProperty>> theCode2concept) {
myCode2Properties = theCode2concept;
}
@Override
public void accept(CSVRecord theRecord) {
String code = trim(theRecord.get(CODE));
String key = trim(theRecord.get(KEY));
if (isNotBlank(code) && isNotBlank(KEY)) {
String value = trim(theRecord.get(VALUE));
String type = trim(theRecord.get(TYPE));
List<TermConceptProperty> conceptProperties = myCode2Properties.get(code);
if (conceptProperties == null)
conceptProperties = new ArrayList<>();
TermConceptProperty conceptProperty = TermLoaderSvcImpl.getOrCreateConceptProperty(myCode2Properties, code, key);
ValidateUtil.isNotNullOrThrowUnprocessableEntity(conceptProperty, "Concept property %s not found in file", conceptProperty);
conceptProperty.setKey(key);
conceptProperty.setValue(value);
//TODO: check this for different types, other types should be added once TermConceptPropertyTypeEnum contain different types
conceptProperty.setType(TermConceptPropertyTypeEnum.STRING);
conceptProperties.add(conceptProperty);
myCode2Properties.put(code, conceptProperties);
}
}
}

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
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@ -48,6 +48,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptMapDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptMapGroupElementTargetDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptPropertyDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
@ -282,6 +283,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
@Autowired
protected ITermConceptDesignationDao myTermConceptDesignationDao;
@Autowired
protected ITermConceptPropertyDao myTermConceptPropertyDao;
@Autowired
@Qualifier("myConditionDaoR4")
protected IFhirResourceDao<Condition> myConditionDao;
@Autowired
@ -644,6 +647,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
List<TermConcept> children = nextCode.getChildCodes();
flattenExpansionHierarchy(theFlattenedHierarchy, children, thePrefix + " ");
}
}
@ -815,6 +819,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
return first.get();
}
}
public List<String> getExpandedConceptsByValueSetUrl(String theValuesetUrl) {
return runInTransaction(() -> {
List<TermValueSet> valueSets = myTermValueSetDao.findTermValueSetByUrl(Pageable.unpaged(), theValuesetUrl);

118
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java
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@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptProperty;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
@ -12,9 +13,11 @@ import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.r4.model.Attachment;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.junit.jupiter.api.Test;
@ -24,6 +27,7 @@ import java.io.FileOutputStream;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
@ -236,6 +240,62 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
));
}
@Test
public void testApplyDeltaAdd_UsingCsv_withPropertiesCsv() throws IOException {
String conceptsCsv = loadResource("/custom_term/concepts.csv");
Attachment conceptsAttachment = new Attachment()
.setData(conceptsCsv.getBytes(Charsets.UTF_8))
.setContentType("text/csv")
.setUrl("file:/foo/concepts.csv");
String hierarchyCsv = loadResource("/custom_term/hierarchy.csv");
Attachment hierarchyAttachment = new Attachment()
.setData(hierarchyCsv.getBytes(Charsets.UTF_8))
.setContentType("text/csv")
.setUrl("file:/foo/hierarchy.csv");
String propertiesCsv = loadResource("/custom_term/properties.csv");
Attachment propertiesAttachment = new Attachment()
.setData(propertiesCsv.getBytes(Charsets.UTF_8))
.setContentType("text/csv")
.setUrl("file:/foo/properties.csv");
LoggingInterceptor interceptor = new LoggingInterceptor(true);
myClient.registerInterceptor(interceptor);
Parameters outcome = myClient
.operation()
.onType(CodeSystem.class)
.named(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD)
.withParameter(Parameters.class, TerminologyUploaderProvider.PARAM_SYSTEM, new UriType("http://foo/cs"))
.andParameter(TerminologyUploaderProvider.PARAM_FILE, conceptsAttachment)
.andParameter(TerminologyUploaderProvider.PARAM_FILE, hierarchyAttachment)
.andParameter(TerminologyUploaderProvider.PARAM_FILE, propertiesAttachment)
.prettyPrint()
.execute();
myClient.unregisterInterceptor(interceptor);
String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ourLog.info(encoded);
assertThat(encoded, stringContainsInOrder(
"\"name\": \"conceptCount\"",
"\"valueInteger\": 5",
"\"name\": \"target\"",
"\"reference\": \"CodeSystem/"
));
runInTransaction(() -> {
TermCodeSystem cs = myTermCodeSystemDao.findByCodeSystemUri("http://foo/cs");
TermCodeSystemVersion version = cs.getCurrentVersion();
TermConcept microCode = myTermConceptDao.findByCodeSystemAndCode(version, "NEUT").get();
assertEquals(2, microCode.getProperties().size());
TermConcept code = myTermConceptDao.findByCodeSystemAndCode(version, "HB").get();
assertEquals(1, code.getProperties().size());
Integer codeProperties = myTermConceptPropertyDao.countByCodeSystemVersion(version.getPid());
assertEquals(6, codeProperties);
Optional<TermConceptProperty> first = code.getProperties().stream().filter(property -> "color".equalsIgnoreCase(property.getKey()) && "red".equalsIgnoreCase(property.getValue())).findFirst();
if (!first.isPresent()) {
String failureMessage = String.format("Concept %s did not contain property with key %s and value %s ", code.getCode(), "property1", "property1Value");
fail(failureMessage);
}
});
}
@Test
public void testApplyDeltaAdd_UsingCodeSystem() {
CodeSystem codeSystem = new CodeSystem();
@ -276,6 +336,64 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
);
}
@Test
public void testApplyDeltaAdd_UsingCodeSystemWithConceptProprieties() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl("http://foo/cs");
CodeSystem.ConceptDefinitionComponent chem = codeSystem.addConcept().setCode("CHEM").setDisplay("Chemistry").addProperty(new CodeSystem.ConceptPropertyComponent(new CodeType("color"), new StringType("green")));
chem.addConcept().setCode("HB").setDisplay("Hemoglobin").addProperty(new CodeSystem.ConceptPropertyComponent(new CodeType("color"), new StringType("red")));
chem.addConcept().setCode("NEUT").setDisplay("Neutrophils").addProperty(new CodeSystem.ConceptPropertyComponent(new CodeType("color"), new StringType("pink"))).addProperty(new CodeSystem.ConceptPropertyComponent(new CodeType("shape"), new StringType("spherical")));
CodeSystem.ConceptDefinitionComponent micro = codeSystem.addConcept().setCode("MICRO").setDisplay("Microbiology").addProperty(new CodeSystem.ConceptPropertyComponent(new CodeType("color"), new StringType("yellow")));
micro.addConcept().setCode("C&S").setDisplay("Culture And Sensitivity").addProperty(new CodeSystem.ConceptPropertyComponent(new CodeType("color"), new StringType("bellow")));
LoggingInterceptor interceptor = new LoggingInterceptor(true);
myClient.registerInterceptor(interceptor);
Parameters outcome = myClient
.operation()
.onType(CodeSystem.class)
.named(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD)
.withParameter(Parameters.class, TerminologyUploaderProvider.PARAM_SYSTEM, new UriType("http://foo/cs"))
.andParameter(TerminologyUploaderProvider.PARAM_CODESYSTEM, codeSystem)
.prettyPrint()
.execute();
myClient.unregisterInterceptor(interceptor);
String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ourLog.info(encoded);
assertThat(encoded, stringContainsInOrder(
"\"name\": \"conceptCount\"",
"\"valueInteger\": 5",
"\"name\": \"target\"",
"\"reference\": \"CodeSystem/"
));
assertHierarchyContains(
"CHEM seq=0",
" HB seq=0",
" NEUT seq=1",
"MICRO seq=0",
" C&S seq=0"
);
runInTransaction(() -> {
TermCodeSystem cs = myTermCodeSystemDao.findByCodeSystemUri("http://foo/cs");
TermCodeSystemVersion version = cs.getCurrentVersion();
TermConcept microCode = myTermConceptDao.findByCodeSystemAndCode(version, "NEUT").get();
assertEquals(2, microCode.getProperties().size());
TermConcept code = myTermConceptDao.findByCodeSystemAndCode(version, "HB").get();
assertEquals(1, code.getProperties().size());
Integer codeProperties = myTermConceptPropertyDao.countByCodeSystemVersion(version.getPid());
assertEquals(6, codeProperties);
Optional<TermConceptProperty> first = code.getProperties().stream().filter(property -> "color".equalsIgnoreCase(property.getKey()) && "red".equalsIgnoreCase(property.getValue())).findFirst();
if (!first.isPresent()) {
String failureMessage = String.format("Concept %s did not contain property with key %s and value %s ", code.getCode(), "property1", "property1Value");
fail(failureMessage);
}
});
}
@Test
public void testApplyDeltaAdd_UsingCodeSystemWithComma() throws IOException {

9
hapi-fhir-jpaserver-base/src/test/resources/custom_term/properties.csv Normal file
View File

@ -0,0 +1,9 @@
CODE,KEY, VALUE, TYPE
CHEM,color,green,String
HB,color,red,String
NEUT,color,pink,String
NEUT,shape,spherical,String
MICRO,color,yellow,String
C&S,color,blue,String
1 CODE KEY VALUE TYPE
2 CHEM color green String
3 HB color red String
4 NEUT color pink String
5 NEUT shape spherical String
6 MICRO color yellow String
7 C&S color blue String