honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Fixed ConceptMap $translation without conceptMapVersion issue.

This commit is contained in:
Frank Tao 2020-09-09 22:24:02 -04:00
parent b4a87adc64
commit c873b6d6dd
3 changed files with 346 additions and 84 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

64
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

@ -1937,6 +1937,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
List<TermConceptMapGroupElementTarget> cachedTargets;
ArrayList<Predicate> predicates;
Coding coding;
//-- get the latest ConceptMapVersion if theTranslationRequest has url, but ConceptMapVersion
String latestConceptMapVersion = null;
if (theTranslationRequest.hasUrl() && !theTranslationRequest.hasConceptMapVersion())
latestConceptMapVersion = getLatestConceptMapVersion(theTranslationRequest);
for (TranslationQuery translationQuery : translationQueries) {
cachedTargets = myTranslationCache.getIfPresent(translationQuery);
if (cachedTargets == null) {
@ -1965,10 +1971,21 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
if (translationQuery.hasUrl()) {
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myUrl"), translationQuery.getUrl().getValueAsString()));
}
if (translationQuery.hasConceptMapVersion()) {
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion().getValueAsString()));
if (translationQuery.hasConceptMapVersion()) {
// both url and conceptMapVersion
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion().getValueAsString()));
} else {
if (StringUtils.isNotBlank(latestConceptMapVersion)) {
// only url and use latestConceptMapVersion
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), latestConceptMapVersion));
} else {
predicates.add(criteriaBuilder.isNull(conceptMapJoin.get("myVersion")));
}
}
} else {
if (translationQuery.hasConceptMapVersion()) {
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion().getValueAsString()));
}
}
if (translationQuery.hasSource()) {
@ -2028,6 +2045,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
List<TermConceptMapGroupElement> cachedElements;
ArrayList<Predicate> predicates;
Coding coding;
//-- get the latest ConceptMapVersion if theTranslationRequest has url, but ConceptMapVersion
String latestConceptMapVersion = null;
if (theTranslationRequest.hasUrl() && !theTranslationRequest.hasConceptMapVersion())
latestConceptMapVersion = getLatestConceptMapVersion(theTranslationRequest);
for (TranslationQuery translationQuery : translationQueries) {
cachedElements = myTranslationWithReverseCache.getIfPresent(translationQuery);
if (cachedElements == null) {
@ -2056,10 +2079,21 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
if (translationQuery.hasUrl()) {
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myUrl"), translationQuery.getUrl().getValueAsString()));
}
if (translationQuery.hasConceptMapVersion()) {
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion().getValueAsString()));
if (translationQuery.hasConceptMapVersion()) {
// both url and conceptMapVersion
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion().getValueAsString()));
} else {
if (StringUtils.isNotBlank(latestConceptMapVersion)) {
// only url and use latestConceptMapVersion
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), latestConceptMapVersion));
} else {
predicates.add(criteriaBuilder.isNull(conceptMapJoin.get("myVersion")));
}
}
} else {
if (translationQuery.hasConceptMapVersion()) {
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion().getValueAsString()));
}
}
if (translationQuery.hasTargetSystem()) {
@ -2127,6 +2161,20 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
throw new ResourceNotFoundException("Unknown ValueSet: " + UrlUtil.escapeUrlParam(theValueSet));
}
// Special case for the translate operation with url and without
// conceptMapVersion, find the latest conecptMapVersion
private String getLatestConceptMapVersion(TranslationRequest theTranslationRequest) {
Pageable page = PageRequest.of(0, 1);
List<TermConceptMap> theConceptMapList = myConceptMapDao.findTermConceptMapByUrl(page,
theTranslationRequest.getUrl().asStringValue());
if (!theConceptMapList.isEmpty()) {
return theConceptMapList.get(0).getVersion();
}
return null;
}
@Override
@Transactional
public CodeValidationResult validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, @Nonnull IBaseResource theValueSet) {

200
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ConceptMapTest.java
View File

@ -211,45 +211,12 @@ public class ResourceProviderDstu3ConceptMapTest extends BaseResourceProviderDst
@Test
public void testTranslateWithReverseConcaptMapUrlAndVersion() {
//- conceptMap1 v1
ConceptMap conceptMap1 = new ConceptMap();
conceptMap1.setUrl(CM_URL).setVersion("v1").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group1 = conceptMap1.addGroup();
group1.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element1 = group1.addElement();
element1.setCode("12222").setDisplay("Source Code 12222");
TargetElementComponent target1 = element1.addTarget();
target1.setCode("11111").setDisplay("11111");
IIdType conceptMapId1 = myConceptMapDao.create(conceptMap1, mySrd).getId().toUnqualifiedVersionless();
conceptMap1 = myConceptMapDao.read(conceptMapId1);
ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap1));
//- conceptMap1 v2
ConceptMap conceptMap2 = new ConceptMap();
conceptMap2.setUrl(CM_URL).setVersion("v2").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group2 = conceptMap2.addGroup();
group2.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element2 = group2.addElement();
element2.setCode("13333").setDisplay("Source Code 13333");
TargetElementComponent target2 = element2.addTarget();
target2.setCode("11111").setDisplay("Target Code 11111");
IIdType conceptMapId2 = myConceptMapDao.create(conceptMap2, mySrd).getId().toUnqualifiedVersionless();
conceptMap2 = myConceptMapDao.read(conceptMapId2);
ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap2));
String url = "http://url";
createReverseConceptMap(url, "v1", "12222", "Source Code 12222");
createReverseConceptMap(url, "v2", "13333", "Source Code 13333");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("conceptMapVersion").setValue(new StringType("v2"));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
inParams.addParameter().setName("reverse").setValue(new BooleanType(true));
@ -284,6 +251,163 @@ public class ResourceProviderDstu3ConceptMapTest extends BaseResourceProviderDst
assertEquals(CS_URL, coding.getSystem());
assertEquals("Version 1", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithReverseConcaptMapUrl_NoVersion() {
String url = "http://url";
createReverseConceptMap(url, "v1", "12222", "Source Code 12222");
createReverseConceptMap(url, "v2", "13333", "Source Code 13333");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
inParams.addParameter().setName("reverse").setValue(new BooleanType(true));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(2, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Source Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL, coding.getSystem());
assertEquals("Version 1", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithReverseConcaptMapUrl_NoVersion_null_v1() {
String url = "http://url";
createReverseConceptMap(url, null, "12222", "Source Code 12222");
createReverseConceptMap(url, "v2", "13333", "Source Code 13333");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
inParams.addParameter().setName("reverse").setValue(new BooleanType(true));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(2, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Source Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL, coding.getSystem());
assertEquals("Version 1", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithReverseConcaptMapUrl_NoVersion_null_v2() {
String url = "http://url";
createReverseConceptMap(url, "v1", "12222", "Source Code 12222");
createReverseConceptMap(url, null, "13333", "Source Code 13333");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
inParams.addParameter().setName("reverse").setValue(new BooleanType(true));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(2, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Source Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL, coding.getSystem());
assertEquals("Version 1", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
private void createReverseConceptMap(String url, String version, String sourceCode, String sourceDisplay) {
//- conceptMap1 v1
ConceptMap conceptMap = new ConceptMap();
conceptMap.setUrl(url).setVersion(version).setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group1 = conceptMap.addGroup();
group1.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element1 = group1.addElement();
element1.setCode(sourceCode).setDisplay(sourceDisplay);
TargetElementComponent target1 = element1.addTarget();
target1.setCode("11111").setDisplay("11111");
IIdType conceptMapId = myConceptMapDao.create(conceptMap, mySrd).getId().toUnqualifiedVersionless();
ConceptMap conceptMap1 = myConceptMapDao.read(conceptMapId);
ourLog.info("ConceptMap : \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap1));
}
}

160
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ConceptMap_Ian_Test.java
View File

@ -26,50 +26,19 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
public class ResourceProviderDstu3ConceptMap_Ian_Test extends BaseResourceProviderDstu3Test {
private static final Logger ourLog = LoggerFactory.getLogger(ResourceProviderDstu3ConceptMap_Ian_Test.class);
@BeforeEach
@Transactional
public void before02() {
//- conceptMap v1
ConceptMap conceptMap = new ConceptMap();
conceptMap.setUrl(CM_URL).setVersion("v1").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group1 = conceptMap.addGroup();
group1.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element1 = group1.addElement();
element1.setCode("11111").setDisplay("Source Code 11111");
TargetElementComponent target1 = element1.addTarget();
target1.setCode("12222").setDisplay("Target Code 12222").setEquivalence(ConceptMapEquivalence.EQUAL);
IIdType conceptMapId1 = myConceptMapDao.create(conceptMap, mySrd).getId().toUnqualifiedVersionless();
conceptMap = myConceptMapDao.read(conceptMapId1);
ourLog.info("ConceptMap: v1 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
//- conceptMap v2
conceptMap = new ConceptMap();
conceptMap.setUrl(CM_URL).setVersion("v2").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group2 = conceptMap.addGroup();
group2.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element2 = group2.addElement();
element2.setCode("11111").setDisplay("Source Code 11111");
TargetElementComponent target2 = element2.addTarget();
target2.setCode("13333").setDisplay("Target Code 13333").setEquivalence(ConceptMapEquivalence.EQUAL);
IIdType conceptMapId2 = myConceptMapDao.create(conceptMap, mySrd).getId().toUnqualifiedVersionless();
conceptMap = myConceptMapDao.read(conceptMapId2);
ourLog.info("ConceptMap: v2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
}
@Test
public void testTranslateWithVersionedConcaptMapUrl_v2() {
createConceptMap("v1", "12222", "Target Code 12222");
createConceptMap("v2", "13333", "Target Code 13333");
// Call translate with ConceptMap v2.
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
@ -116,6 +85,9 @@ public class ResourceProviderDstu3ConceptMap_Ian_Test extends BaseResourceProvid
@Test
public void testTranslateWithVersionedConcaptMapUrl_v1() {
createConceptMap("v1", "12222", "Target Code 12222");
createConceptMap("v2", "13333", "Target Code 13333");;
// Call translate with ConceptMap v1.
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
@ -162,6 +134,9 @@ public class ResourceProviderDstu3ConceptMap_Ian_Test extends BaseResourceProvid
@Test
public void testTranslateWithVersionedConcaptMapUrl_NoVersion() {
createConceptMap("v1", "12222", "Target Code 12222");
createConceptMap("v2", "13333", "Target Code 13333");
// Call translate with no ConceptMap version.
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
@ -203,4 +178,119 @@ public class ResourceProviderDstu3ConceptMap_Ian_Test extends BaseResourceProvid
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithVersionedConcaptMapUrl_NoVersion_null_v1() {
createConceptMap(null, "12222", "Target Code 12222"); // first version is null
createConceptMap("v2", "13333", "Target Code 13333");
// Call translate with no ConceptMap version.
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
inParams.addParameter().setName("system").setValue(new UriType(CS_URL));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_2));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
// Should return v2 since v2 is the most recently updated version.
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("equal", ((CodeType) part.getValue()).getValueAsString());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Target Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL_2, coding.getSystem());
assertEquals("Version 2", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithVersionedConcaptMapUrl_NoVersion_null_v2() {
createConceptMap("v1", "12222", "Target Code 12222");
createConceptMap(null, "13333", "Target Code 13333"); // second version is null
// Call translate with no ConceptMap version.
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
inParams.addParameter().setName("system").setValue(new UriType(CS_URL));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_2));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
// Should return v2 since v2 is the most recently updated version.
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("equal", ((CodeType) part.getValue()).getValueAsString());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Target Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL_2, coding.getSystem());
assertEquals("Version 2", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
}
private void createConceptMap(String version, String targetCode, String targetDisplay) {
ConceptMap conceptMap = new ConceptMap();
conceptMap.setUrl(CM_URL).setVersion(version).setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group1 = conceptMap.addGroup();
group1.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element1 = group1.addElement();
element1.setCode("11111").setDisplay("Source Code 11111");
TargetElementComponent target1 = element1.addTarget();
target1.setCode(targetCode).setDisplay(targetDisplay).setEquivalence(ConceptMapEquivalence.EQUAL);
IIdType conceptMapId = myConceptMapDao.create(conceptMap, mySrd).getId().toUnqualifiedVersionless();
conceptMap = myConceptMapDao.read(conceptMapId);
ourLog.info("ConceptMap: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
}
}