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Jr 20240325 concept map unmatched codes (#5809)

Browse Source 
* update model

* convert results

* migration

* extend test coverage in cli

* fix broken test

* change log

* code review feedback

* spotless
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JasonRoberts-smile 2024-04-02 16:46:03 -04:00 committed by GitHub
parent e39ee7f47d
commit 1736dadfcf
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18 changed files with 1139 additions and 1043 deletions
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1
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -155,6 +155,7 @@ ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder.invalidCodeMissin
ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl.matchesFound=Matches found
ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl.noMatchesFound=No Matches found
ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl.onlyNegativeMatchesFound=Only negative matches found
ca.uhn.fhir.jpa.dao.JpaResourceDaoSearchParameter.invalidSearchParamExpression=The expression "{0}" can not be evaluated and may be invalid: {1}

13
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ExportConceptMapToCsvCommandR4Test.java
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@ -93,7 +93,8 @@ public class ExportConceptMapToCsvCommandR4Test {
"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2a\",\"Display 2a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2b\",\"Display 2b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2c\",\"Display 2c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2d\",\"Display 2d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n";
"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2d\",\"Display 2d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n" +
"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2e\",\"Display 2e\",\"\",\"\",\"unmatched\",\"3e This is a comment.\"\n";
String result = IOUtils.toString(new FileInputStream(FILE), Charsets.UTF_8);
assertEquals(expected, result);
@ -272,6 +273,16 @@ public class ExportConceptMapToCsvCommandR4Test {
.setEquivalence(ConceptMapEquivalence.EQUAL)
.setComment("3d This is a comment.");
element = group.addElement();
element
.setCode("Code 2e")
.setDisplay("Display 2e");
target = element.addTarget();
target
.setEquivalence(ConceptMapEquivalence.UNMATCHED)
.setComment("3e This is a comment.");
return conceptMap;
}
}

15
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommandDstu3Test.java
View File

@ -273,7 +273,7 @@ public class ImportCsvToConceptMapCommandDstu3Test {
assertEquals(CS_URL_3, group.getTarget());
assertEquals("Version 3t", group.getTargetVersion());
assertEquals(4, group.getElement().size());
assertEquals(5, group.getElement().size());
source = group.getElement().get(0);
assertEquals("Code 2a", source.getCode());
@ -323,6 +323,19 @@ public class ImportCsvToConceptMapCommandDstu3Test {
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
assertEquals("3d This is a comment.", target.getComment());
// ensure unmatched codes are handled correctly
source = group.getElement().get(4);
assertEquals("Code 2e", source.getCode());
assertEquals("Display 2e", source.getDisplay());
assertEquals(1, source.getTarget().size());
target = source.getTarget().get(0);
assertNull(target.getCode());
assertNull(target.getDisplay());
assertEquals(ConceptMapEquivalence.UNMATCHED, target.getEquivalence());
assertEquals("3e This is a comment.", target.getComment());
App.main(myTlsAuthenticationTestHelper.createBaseRequestGeneratingCommandArgs(
new String[]{
ImportCsvToConceptMapCommand.COMMAND,

15
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommandR4Test.java
View File

@ -284,7 +284,7 @@ public class ImportCsvToConceptMapCommandR4Test {
assertEquals(CS_URL_3, group.getTarget());
assertEquals("Version 3t", group.getTargetVersion());
assertEquals(4, group.getElement().size());
assertEquals(5, group.getElement().size());
source = group.getElement().get(0);
assertEquals("Code 2a", source.getCode());
@ -334,6 +334,19 @@ public class ImportCsvToConceptMapCommandR4Test {
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
assertEquals("3d This is a comment.", target.getComment());
// ensure unmatched codes are handled correctly
source = group.getElement().get(4);
assertEquals("Code 2e", source.getCode());
assertEquals("Display 2e", source.getDisplay());
assertEquals(1, source.getTarget().size());
target = source.getTarget().get(0);
assertNull(target.getCode());
assertNull(target.getDisplay());
assertEquals(ConceptMapEquivalence.UNMATCHED, target.getEquivalence());
assertEquals("3e This is a comment.", target.getComment());
App.main(myTlsAuthenticationTestHelper.createBaseRequestGeneratingCommandArgs(
new String[]{
ImportCsvToConceptMapCommand.COMMAND,

1
hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/import-csv-to-conceptmap-command-test-input.csv
View File

@ -11,3 +11,4 @@
"http://example.com/codesystem/2","Version 2s","http://example.com/codesystem/3","Version 3t","Code 2b","Display 2b","Code 3b","Display 3b","equal","3b This is a comment."
"http://example.com/codesystem/2","Version 2s","http://example.com/codesystem/3","Version 3t","Code 2c","Display 2c","Code 3c","Display 3c","equal","3c This is a comment."
"http://example.com/codesystem/2","Version 2s","http://example.com/codesystem/3","Version 3t","Code 2d","Display 2d","Code 3d","Display 3d","equal","3d This is a comment."
"http://example.com/codesystem/2","Version 2s","http://example.com/codesystem/3","Version 3t","Code 2e","Display 2e","","","unmatched","3e This is a comment."

1 SOURCE_CODE_SYSTEM SOURCE_CODE_SYSTEM_VERSION TARGET_CODE_SYSTEM TARGET_CODE_SYSTEM_VERSION SOURCE_CODE SOURCE_DISPLAY TARGET_CODE TARGET_DISPLAY EQUIVALENCE COMMENT
11 http://example.com/codesystem/2 Version 2s http://example.com/codesystem/3 Version 3t Code 2b Display 2b Code 3b Display 3b equal 3b This is a comment.
12 http://example.com/codesystem/2 Version 2s http://example.com/codesystem/3 Version 3t Code 2c Display 2c Code 3c Display 3c equal 3c This is a comment.
13 http://example.com/codesystem/2 Version 2s http://example.com/codesystem/3 Version 3t Code 2d Display 2d Code 3d Display 3d equal 3d This is a comment.
14 http://example.com/codesystem/2 Version 2s http://example.com/codesystem/3 Version 3t Code 2e Display 2e unmatched 3e This is a comment.

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5816-unmatched-translate-target.yaml Normal file
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@ -0,0 +1,5 @@
---
type: add
issue: 5816
title: "The ConceptMap/$translate operation will include targets with an equivalence code of `unmatched` in the response
regardless of whether the target has a code."

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroupElementTarget.java
View File

@ -58,7 +58,7 @@ public class TermConceptMapGroupElementTarget implements Serializable {
foreignKey = @ForeignKey(name = "FK_TCMGETARGET_ELEMENT"))
private TermConceptMapGroupElement myConceptMapGroupElement;
@Column(name = "TARGET_CODE", nullable = false, length = TermConcept.MAX_CODE_LENGTH)
@Column(name = "TARGET_CODE", nullable = true, length = TermConcept.MAX_CODE_LENGTH)
private String myCode;
@Column(name = "TARGET_DISPLAY", nullable = true, length = TermConcept.MAX_DISP_LENGTH)

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -119,6 +119,19 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
init680();
init680_Part2();
init700();
init720();
}
protected void init720() {
// Start of migrations from 7.0 to 7.2
Builder version = forVersion(VersionEnum.V7_2_0);
// allow null codes in concept map targets
version.onTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
.modifyColumn("20240327.1", "TARGET_CODE")
.nullable()
.withType(ColumnTypeEnum.STRING, 500);
}
protected void init700() {

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermConceptClientMappingSvcImpl.java
View File

@ -51,6 +51,7 @@ import org.hibernate.ScrollMode;
import org.hibernate.ScrollableResults;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Enumerations;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -416,6 +417,10 @@ public class TermConceptClientMappingSvcImpl implements ITermConceptClientMappin
theTranslationResult.setResult(false);
msg = myContext.getLocalizer().getMessage(TermConceptMappingSvcImpl.class, "noMatchesFound");
theTranslationResult.setMessage(msg);
} else if (isOnlyNegativeMatches(theTranslationResult)) {
theTranslationResult.setResult(false);
msg = myContext.getLocalizer().getMessage(TermConceptMappingSvcImpl.class, "onlyNegativeMatchesFound");
theTranslationResult.setMessage(msg);
} else {
theTranslationResult.setResult(true);
msg = myContext.getLocalizer().getMessage(TermConceptMappingSvcImpl.class, "matchesFound");
@ -423,6 +428,21 @@ public class TermConceptClientMappingSvcImpl implements ITermConceptClientMappin
}
}
/**
* Evaluates whether a translation result contains any positive matches or only negative ones. This is required
* because the <a href="https://hl7.org/fhir/R4/conceptmap-operation-translate.html">FHIR specification</a> states
* that the result field "can only be true if at least one returned match has an equivalence which is not unmatched
* or disjoint".
* @param theTranslationResult the translation result to be evaluated
* @return true if all the potential matches in the result have a negative valence (i.e., "unmatched" and "disjoint")
*/
private boolean isOnlyNegativeMatches(TranslateConceptResults theTranslationResult) {
return theTranslationResult.getResults().stream()
.map(TranslateConceptResult::getEquivalence)
.allMatch(t -> StringUtils.equals(Enumerations.ConceptMapEquivalence.UNMATCHED.toCode(), t)
|| StringUtils.equals(Enumerations.ConceptMapEquivalence.DISJOINT.toCode(), t));
}
private boolean alreadyContainsMapping(
List<TranslateConceptResult> elements, TranslateConceptResult translationMatch) {
for (TranslateConceptResult nextExistingElement : elements) {

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermConceptMappingSvcImpl.java
View File

@ -41,6 +41,7 @@ import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
@ -218,13 +219,17 @@ public class TermConceptMappingSvcImpl extends TermConceptClientMappingSvcImpl i
if (element.hasTarget()) {
TermConceptMapGroupElementTarget termConceptMapGroupElementTarget;
for (ConceptMap.TargetElementComponent elementTarget : element.getTarget()) {
if (isBlank(elementTarget.getCode())) {
if (isBlank(elementTarget.getCode())
&& elementTarget.getEquivalence()
!= Enumerations.ConceptMapEquivalence.UNMATCHED) {
continue;
}
termConceptMapGroupElementTarget = new TermConceptMapGroupElementTarget();
termConceptMapGroupElementTarget.setConceptMapGroupElement(termConceptMapGroupElement);
termConceptMapGroupElementTarget.setCode(elementTarget.getCode());
termConceptMapGroupElementTarget.setDisplay(elementTarget.getDisplay());
if (isNotBlank(elementTarget.getCode())) {
termConceptMapGroupElementTarget.setCode(elementTarget.getCode());
termConceptMapGroupElementTarget.setDisplay(elementTarget.getDisplay());
}
termConceptMapGroupElementTarget.setEquivalence(elementTarget.getEquivalence());
termConceptMapGroupElement
.getConceptMapGroupElementTargets()

80
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ConceptMapTest.java
View File

@ -307,6 +307,86 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
assertFalse(hasParameterByName(respParams, "match"));
}
@Test
public void testTranslateByCodeSystemsAndSourceCodeMappedToCodelessTarget() {
// ensure that the current behaviour when a target does not have a code is preserved, and no matches returned
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId, mySrd);
ourLog.debug("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
Parameters inParams = new Parameters();
inParams.addParameter().setName("system").setValue(new UriType(CS_URL_4));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_3));
inParams.addParameter().setName("code").setValue(new CodeType("89012"));
ourLog.debug("Request Parameters:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = myClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.debug("Response Parameters\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertFalse(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("No Matches found", ((StringType) param.getValue()).getValueAsString());
assertFalse(hasParameterByName(respParams, "match"));
}
@Test
public void testTranslateByCodeSystemsAndSourceCodeWithEquivalenceUnmatched() {
// the equivalence code 'unmatched' is an exception - it does not normally have a target code,
// so it will be included in the collection of matches even if there is no code present
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId, mySrd);
ourLog.debug("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
Parameters inParams = new Parameters();
inParams.addParameter().setName("system").setValue(new UriType(CS_URL_4));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_3));
inParams.addParameter().setName("code").setValue(new CodeType("89123"));
ourLog.debug("Request Parameters:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = myClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.debug("Response Parameters\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertFalse(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Only negative matches found", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParameterByName(respParams, "match");
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("unmatched", ((CodeType) part.getValue()).getCode());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertNull(coding.getCode());
assertNull(coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL_3, coding.getSystem());
assertEquals("Version 1", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateUsingPredicatesWithCodeOnly() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);

1976
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/TermConceptMappingSvcImplTest.java
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File diff suppressed because it is too large Load Diff

22
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java
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@ -935,6 +935,28 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
target.setDisplay("Target Code 34567");
target.setEquivalence(ConceptMapEquivalence.NARROWER);
group = conceptMap.addGroup();
group.setSource(CS_URL_4);
group.setSourceVersion("Version 1");
group.setTarget(CS_URL_3);
group.setTargetVersion("Version 1");
// This one should not show up in the results because it doesn't have a code
element = group.addElement();
element.setCode("89012");
element.setDisplay("Source Code 89012");
target = element.addTarget();
target.setEquivalence(ConceptMapEquivalence.DISJOINT);
// This one should show up in the results because unmatched targets are allowed to be codeless
element = group.addElement();
element.setCode("89123");
element.setDisplay("Source Code 89123");
target = element.addTarget();
target.setEquivalence(ConceptMapEquivalence.UNMATCHED);
return conceptMap;
}

1
hapi-fhir-jpaserver-test-utilities/src/main/resources/migration/releases/V7_2_0/data/H2_EMBEDDED.sql Normal file
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@ -0,0 +1 @@
INSERT INTO TRM_CONCEPT_MAP_GRP_ELM_TGT (PID, TARGET_CODE, CONCEPT_MAP_URL, TARGET_DISPLAY, TARGET_EQUIVALENCE, SYSTEM_URL, SYSTEM_VERSION, VALUESET_URL, CONCEPT_MAP_GRP_ELM_PID) VALUES (61, NULL, NULL, 'PYRIDOXINE', 'UNMATCHED', NULL, NULL, NULL, 60);

1
hapi-fhir-jpaserver-test-utilities/src/main/resources/migration/releases/V7_2_0/data/MSSQL_2012.sql Normal file
View File

@ -0,0 +1 @@
INSERT INTO TRM_CONCEPT_MAP_GRP_ELM_TGT (PID, TARGET_CODE, CONCEPT_MAP_URL, TARGET_DISPLAY, TARGET_EQUIVALENCE, SYSTEM_URL, SYSTEM_VERSION, VALUESET_URL, CONCEPT_MAP_GRP_ELM_PID) VALUES (61, NULL, NULL, 'PYRIDOXINE', 'UNMATCHED', NULL, NULL, NULL, 60);

1
hapi-fhir-jpaserver-test-utilities/src/main/resources/migration/releases/V7_2_0/data/ORACLE_12C.sql Normal file
View File

@ -0,0 +1 @@
INSERT INTO TRM_CONCEPT_MAP_GRP_ELM_TGT (PID, TARGET_CODE, CONCEPT_MAP_URL, TARGET_DISPLAY, TARGET_EQUIVALENCE, SYSTEM_URL, SYSTEM_VERSION, VALUESET_URL, CONCEPT_MAP_GRP_ELM_PID) VALUES (61, NULL, NULL, 'PYRIDOXINE', 'UNMATCHED', NULL, NULL, NULL, 60);

1
hapi-fhir-jpaserver-test-utilities/src/main/resources/migration/releases/V7_2_0/data/POSTGRES_9_4.sql Normal file
View File

@ -0,0 +1 @@
INSERT INTO TRM_CONCEPT_MAP_GRP_ELM_TGT (PID, TARGET_CODE, CONCEPT_MAP_URL, TARGET_DISPLAY, TARGET_EQUIVALENCE, SYSTEM_URL, SYSTEM_VERSION, VALUESET_URL, CONCEPT_MAP_GRP_ELM_PID) VALUES (61, NULL, NULL, 'PYRIDOXINE', 'UNMATCHED', NULL, NULL, NULL, 60);

4
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/embedded/HapiSchemaMigrationTest.java
View File

@ -83,7 +83,8 @@ public class HapiSchemaMigrationTest {
VersionEnum.V5_4_0,
VersionEnum.V5_5_0,
VersionEnum.V6_0_0,
VersionEnum.V6_6_0
VersionEnum.V6_6_0,
VersionEnum.V7_2_0
);
int fromVersion = 0;
@ -92,6 +93,7 @@ public class HapiSchemaMigrationTest {
for (int i = 0; i < allVersions.length; i++) {
toVersion = allVersions[i];
ourLog.info("Applying migrations for {}", toVersion);
migrate(theDriverType, dataSource, hapiMigrationStorageSvc, toVersion);
if (dataVersions.contains(toVersion)) {
myEmbeddedServersExtension.insertPersistenceTestData(theDriverType, toVersion);