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hapi-fhir
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Add equivalency flag to reverse lookup

This commit is contained in:
James Agnew 2018-08-11 09:55:28 -04:00
parent 98d794e30f
commit acfe442cf9
6 changed files with 127 additions and 14 deletions
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4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java
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@ -143,6 +143,10 @@ public class FhirResourceDaoConceptMapR4 extends FhirResourceDaoR4<ConceptMap> i
translationMatch.setSource(new UriType(element.getConceptMapUrl()));
if (element.getConceptMapGroupElementTargets().size() == 1) {
translationMatch.setEquivalence(new CodeType(element.getConceptMapGroupElementTargets().get(0).getEquivalence().toCode()));
}
retVal.addMatch(translationMatch);
}
}

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -1343,14 +1343,18 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
predicates = new ArrayList<>();
coding = translationQuery.getCoding();
String targetCode = null;
String targetCodeSystem = null;
if (coding.hasCode()) {
predicates.add(criteriaBuilder.equal(targetJoin.get("myCode"), coding.getCode()));
targetCode = coding.getCode();
} else {
throw new InvalidRequestException("A code must be provided for translation to occur.");
}
if (coding.hasSystem()) {
predicates.add(criteriaBuilder.equal(groupJoin.get("myTarget"), coding.getSystem()));
targetCodeSystem = coding.getSystem();
}
if (coding.hasVersion()) {
@ -1384,7 +1388,24 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
Iterator<TermConceptMapGroupElement> scrollableResultsIterator = new ScrollableResultsIterator<>(scrollableResults);
while (scrollableResultsIterator.hasNext()) {
elements.add(scrollableResultsIterator.next());
TermConceptMapGroupElement nextElement = scrollableResultsIterator.next();
nextElement.getConceptMapGroupElementTargets().size();
myEntityManager.detach(nextElement);
if (isNotBlank(targetCode) && isNotBlank(targetCodeSystem)) {
for (Iterator<TermConceptMapGroupElementTarget> iter = nextElement.getConceptMapGroupElementTargets().iterator(); iter.hasNext(); ) {
TermConceptMapGroupElementTarget next = iter.next();
if (targetCodeSystem.equals(next.getSystem())) {
if (targetCode.equals(next.getCode())) {
continue;
}
}
iter.remove();
}
}
elements.add(nextElement);
}
ourLastResultsFromTranslationWithReverseCache = false; // For testing.

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -395,6 +395,12 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
target.setDisplay("Target Code 45678");
target.setEquivalence(ConceptMapEquivalence.WIDER);
// Add a duplicate
target = element.addTarget();
target.setCode("45678");
target.setDisplay("Target Code 45678");
target.setEquivalence(ConceptMapEquivalence.WIDER);
group = conceptMap.addGroup();
group.setSource(CS_URL);
group.setSourceVersion("Version 3");

69
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java
View File

@ -613,7 +613,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(1, translationResult.getMatches().size());
TranslationMatch translationMatch = translationResult.getMatches().get(0);
assertNull(translationMatch.getEquivalence());
assertEquals("narrower", translationMatch.getEquivalence().getCode());
Coding concept = translationMatch.getConcept();
assertEquals("78901", concept.getCode());
assertEquals("Source Code 78901", concept.getDisplay());
@ -625,6 +625,49 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
});
}
@Test
public void testTranslateWithReverseHavingEquivalence() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
/*
* Provided:
* source code
* source code system
* target code system
* reverse = true
*/
TranslationRequest translationRequest = new TranslationRequest();
translationRequest.getCodeableConcept().addCoding()
.setSystem(CS_URL_3)
.setCode("67890");
translationRequest.setTargetSystem(new UriType(CS_URL));
translationRequest.setReverse(true);
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
assertTrue(translationResult.getResult().booleanValue());
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
assertEquals(1, translationResult.getMatches().size());
TranslationMatch translationMatch = translationResult.getMatches().get(0);
Coding concept = translationMatch.getConcept();
assertEquals("12345", concept.getCode());
assertEquals("Source Code 12345", concept.getDisplay());
assertEquals(CS_URL, concept.getSystem());
assertEquals("Version 3", concept.getVersion());
assertFalse(concept.getUserSelected());
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
assertEquals("wider", translationMatch.getEquivalence().getCode());
}
});
}
@Test
public void testTranslateWithReverseByCodeSystemsAndSourceCodeUnmapped() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
@ -680,7 +723,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(2, translationResult.getMatches().size());
TranslationMatch translationMatch = translationResult.getMatches().get(0);
assertNull(translationMatch.getEquivalence());
assertEquals("equal", translationMatch.getEquivalence().getCode());
Coding concept = translationMatch.getConcept();
assertEquals("12345", concept.getCode());
assertEquals("Source Code 12345", concept.getDisplay());
@ -690,7 +733,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
translationMatch = translationResult.getMatches().get(1);
assertNull(translationMatch.getEquivalence());
assertEquals("narrower", translationMatch.getEquivalence().getCode());
concept = translationMatch.getConcept();
assertEquals("78901", concept.getCode());
assertEquals("Source Code 78901", concept.getDisplay());
@ -733,7 +776,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(1, translationResult.getMatches().size());
TranslationMatch translationMatch = translationResult.getMatches().get(0);
assertNull(translationMatch.getEquivalence());
assertEquals("equal", translationMatch.getEquivalence().getCode());
Coding concept = translationMatch.getConcept();
assertEquals("12345", concept.getCode());
assertEquals("Source Code 12345", concept.getDisplay());
@ -776,7 +819,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(1, translationResult.getMatches().size());
TranslationMatch translationMatch = translationResult.getMatches().get(0);
assertNull(translationMatch.getEquivalence());
assertEquals("narrower", translationMatch.getEquivalence().getCode());
Coding concept = translationMatch.getConcept();
assertEquals("78901", concept.getCode());
assertEquals("Source Code 78901", concept.getDisplay());
@ -817,7 +860,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(2, translationResult.getMatches().size());
TranslationMatch translationMatch = translationResult.getMatches().get(0);
assertNull(translationMatch.getEquivalence());
assertEquals("equal", translationMatch.getEquivalence().getCode());
Coding concept = translationMatch.getConcept();
assertEquals("12345", concept.getCode());
assertEquals("Source Code 12345", concept.getDisplay());
@ -827,7 +870,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
translationMatch = translationResult.getMatches().get(1);
assertNull(translationMatch.getEquivalence());
assertEquals("narrower", translationMatch.getEquivalence().getCode());
concept = translationMatch.getConcept();
assertEquals("78901", concept.getCode());
assertEquals("Source Code 78901", concept.getDisplay());
@ -870,7 +913,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(2, translationResult.getMatches().size());
TranslationMatch translationMatch = translationResult.getMatches().get(0);
assertNull(translationMatch.getEquivalence());
assertEquals("equal", translationMatch.getEquivalence().getCode());
Coding concept = translationMatch.getConcept();
assertEquals("12345", concept.getCode());
assertEquals("Source Code 12345", concept.getDisplay());
@ -880,7 +923,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
translationMatch = translationResult.getMatches().get(1);
assertNull(translationMatch.getEquivalence());
assertEquals("narrower", translationMatch.getEquivalence().getCode());
concept = translationMatch.getConcept();
assertEquals("78901", concept.getCode());
assertEquals("Source Code 78901", concept.getDisplay());
@ -921,7 +964,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(2, translationResult.getMatches().size());
TranslationMatch translationMatch = translationResult.getMatches().get(0);
assertNull(translationMatch.getEquivalence());
assertEquals("equal", translationMatch.getEquivalence().getCode());
Coding concept = translationMatch.getConcept();
assertEquals("12345", concept.getCode());
assertEquals("Source Code 12345", concept.getDisplay());
@ -931,7 +974,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
translationMatch = translationResult.getMatches().get(1);
assertNull(translationMatch.getEquivalence());
assertEquals("narrower", translationMatch.getEquivalence().getCode());
concept = translationMatch.getConcept();
assertEquals("78901", concept.getCode());
assertEquals("Source Code 78901", concept.getDisplay());
@ -972,7 +1015,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(2, translationResult.getMatches().size());
TranslationMatch translationMatch = translationResult.getMatches().get(0);
assertNull(translationMatch.getEquivalence());
assertEquals("equal", translationMatch.getEquivalence().getCode());
Coding concept = translationMatch.getConcept();
assertEquals("12345", concept.getCode());
assertEquals("Source Code 12345", concept.getDisplay());
@ -982,7 +1025,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
translationMatch = translationResult.getMatches().get(1);
assertNull(translationMatch.getEquivalence());
assertEquals("narrower", translationMatch.getEquivalence().getCode());
concept = translationMatch.getConcept();
assertEquals("78901", concept.getCode());
assertEquals("Source Code 78901", concept.getDisplay());

35
hapi-fhir-jpaserver-uhnfhirtest/derby_maintenance.txt
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@ -195,3 +195,38 @@ drop column SP_ID from table HFJ_RES_PARAM_PRESENT;
drop index IDX_SEARCHPARM_RESTYPE_SPNAME;
drop index IDX_RESPARMPRESENT_SPID_RESID;
drop table HFJ_SEARCH_PARM;
# Delete everything
update hfj_res_ver set forced_id_pid = null where res_id in (select res_id from hfj_resource);
update hfj_resource set forced_id_pid = null where res_id in (select res_id from hfj_resource);
delete from hfj_history_tag where res_id in (select res_id from hfj_resource);
delete from hfj_res_ver where res_id in (select res_id from hfj_resource);
delete from hfj_forced_id where resource_pid in (select res_id from hfj_resource);
delete from hfj_res_link where src_resource_id in (select res_id from hfj_resource);
delete from hfj_res_link where target_resource_id in (select res_id from hfj_resource);
delete from hfj_spidx_coords;
delete from hfj_spidx_date;
delete from hfj_spidx_number;
delete from hfj_spidx_quantity;
delete from hfj_spidx_string;
delete from hfj_spidx_token;
delete from hfj_spidx_uri;
delete from hfj_res_tag;
delete from hfj_search_result;
delete from hfj_res_param_present;
delete from hfj_idx_cmp_string_uniq;
delete from hfj_subscription_stats;
DELETE FROM TRM_CONCEPT_MAP_GRP_ELM_TGT;
DELETE FROM TRM_CONCEPT_MAP_GRP_ELEMENT;
DELETE FROM TRM_CONCEPT_MAP_GROUP;
DELETE FROM TRM_CONCEPT_MAP;
DELETE FROM TRM_CONCEPT_DESIG;
DELETE FROM TRM_CONCEPT_PC_LINK;
DELETE FROM TRM_CONCEPT_PROPERTY;
DELETE FROM TRM_CONCEPT;
DELETE FROM TRM_CODESYSTEM_VER;
DELETE FROM TRM_CODESYSTEM;
delete from hfj_resource;

4
src/changes/changes.xml
View File

@ -249,6 +249,10 @@
queue (only the ID), which should reduce the memory/disk footprint of the queue
when it grows long.
</action>
<action type="add">
When performing a ConceptMap/$translate operation with reverse="true" in the arguments,
the equivalency flag is now set on the response just as it is for a non-reverse lookup.
</action>
</release>
<release version="3.4.0" date="2018-05-28">
<action type="add">