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Add version to ValueSet.compose.include when uploading terminology

This commit is contained in:
juan.marchionatto 2021-09-15 10:29:30 -04:00
parent bd456dfff2
commit 7900230431
6 changed files with 47 additions and 31 deletions
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9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
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@ -158,6 +158,7 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
@ -2417,10 +2418,16 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
predicates.add(criteriaBuilder.equal(systemJoin.get("myCodeSystemUri"), theCodeSystemUrl));
}
// for loinc CodeSystem last version is not necessarily the current anymore, so if no version is present
// we need to query for the current, which is that which version is null
if (isNoneBlank(theCodeSystemVersion)) {
predicates.add(criteriaBuilder.equal(systemVersionJoin.get("myCodeSystemVersionId"), theCodeSystemVersion));
} else {
query.orderBy(criteriaBuilder.desc(root.get("myUpdated")));
if (theCodeSystemUrl.toLowerCase(Locale.ROOT).contains("loinc")) {
predicates.add(criteriaBuilder.isNull(systemVersionJoin.get("myCodeSystemVersionId")));
} else {
query.orderBy(criteriaBuilder.desc(root.get("myUpdated")));
}
}
Predicate outerPredicate = criteriaBuilder.and(predicates.toArray(new Predicate[0]));

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
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@ -722,7 +722,7 @@ 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
View File

@ -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
View File

@ -120,6 +120,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IZipCo
.getCompose()
.getIncludeFirstRep()
.setSystem(ITermLoaderSvc.LOINC_URI)
.setVersion(codeSystemVersionId)
.addConcept()
.setCode(loincNumber)
.setDisplay(longCommonName);

61
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplCurrentVersionR4Test.java
View File

@ -22,6 +22,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.BeforeEach;
@ -187,13 +188,13 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
private void validateValidateCodeForVersion(String theVersion) {
IValidationSupport.CodeValidationResult resultNoVersioned = myCodeSystemDao.validateCode(null,
new UriType(BASE_LOINC_URL), null, new CodeType(VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE),
new UriType(BASE_LOINC_URL), new StringType(theVersion), new CodeType(VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE),
null, null, null, null);
assertNotNull(resultNoVersioned);
assertEquals(prefixWithVersion(theVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultNoVersioned.getDisplay());
IValidationSupport.CodeValidationResult resultVersioned = myCodeSystemDao.validateCode(null,
new UriType(BASE_LOINC_URL), null, new CodeType(VS_VERSIONED_ON_UPLOAD_FIRST_CODE),
new UriType(BASE_LOINC_URL), new StringType(theVersion), new CodeType(VS_VERSIONED_ON_UPLOAD_FIRST_CODE),
null, null, null, null);
assertNotNull(resultVersioned);
assertEquals(prefixWithVersion(theVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultVersioned.getDisplay());
@ -245,10 +246,11 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
ValueSet vs = myValueSetDao.expandByIdentifier(VS_NO_VERSIONED_ON_UPLOAD, null);
assertEquals(1, vs.getExpansion().getContains().size());
// version was added before code display to validate
// version was added prefixing code display to validate
assertEquals(prefixWithVersion(currentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY),
vs.getExpansion().getContains().iterator().next().getDisplay());
// for CS ver = null, VS ver != null
ValueSet vs1 = myValueSetDao.expandByIdentifier(VS_VERSIONED_ON_UPLOAD + "|" + VS_ANSWER_LIST_VERSION, null);
assertEquals(3, vs1.getExpansion().getContains().size());
@ -256,6 +258,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
assertEquals(prefixWithVersion(currentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY),
vs1.getExpansion().getContains().iterator().next().getDisplay());
validateExpandedTermConcepts(currentVersion, theAllVersions);
// now for each uploaded version
@ -269,29 +272,33 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
"select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId is null").getSingleResult();
assertNotNull(termConceptNoVerCsvNoVer);
assertEquals(VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY, termConceptNoVerCsvNoVer.getDisplay());
// data should have version because it was loaded with a version
assertEquals(prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptNoVerCsvNoVer.getDisplay());
@SuppressWarnings("unchecked")
TermConcept termConceptVerCsvNoVer = (TermConcept) myEntityManager.createQuery(
"select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
VS_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId is null").getSingleResult();
assertNotNull(termConceptVerCsvNoVer);
assertEquals(VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY, termConceptVerCsvNoVer.getDisplay());
// data should have version because it was loaded with a version
assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptVerCsvNoVer.getDisplay());
if (theCurrentVersion != null) {
@SuppressWarnings("unchecked")
TermConcept termConceptNoVerCsvVer = (TermConcept) myEntityManager.createQuery(
"select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId is null").getSingleResult();
VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId = '" + theCurrentVersion + "'").getSingleResult();
assertNotNull(termConceptNoVerCsvVer);
assertEquals(VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY, termConceptNoVerCsvVer.getDisplay());
// data should have version because it was loaded with a version
assertEquals(prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptNoVerCsvVer.getDisplay());
@SuppressWarnings("unchecked")
TermConcept termConceptVerCsvVer = (TermConcept) myEntityManager.createQuery(
"select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
VS_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId is null").getSingleResult();
VS_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId = '" + theCurrentVersion + "'").getSingleResult();
assertNotNull(termConceptVerCsvVer);
assertEquals(VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY, termConceptVerCsvVer.getDisplay());
// data should have version because it was loaded with a version
assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptVerCsvVer.getDisplay());
}
@ -443,7 +450,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
* _ current TVSs with upload version have upload-version with no version append
* _ current TVSs with no upload version have null version
*/
private void runCommonValidations(String theVersion) {
private void runCommonValidations(List<String> theAllVersions) {
// for CodeSystem:
// _ current CS is present and has no version
@ -452,8 +459,9 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
ourLog.info("CodeSystem:\n" + csString);
HashSet<String> shouldNotBePresentVersions = new HashSet<>(possibleVersions);
shouldNotBePresentVersions.remove(theVersion);
shouldNotBePresentVersions.stream().forEach(vv -> assertFalse(csString.contains(vv)));
shouldNotBePresentVersions.removeAll(theAllVersions);
shouldNotBePresentVersions.stream().forEach(vv -> assertFalse(csString.contains(vv),
"Found version string: '" + vv + "' in CodeSystem: " + csString));
// same reading it from term service
CodeSystem cs = myITermReadSvc.fetchCanonicalCodeSystemFromCompleteContext(BASE_LOINC_URL);
@ -489,7 +497,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
public void uploadCurrentNoVersion() throws Exception {
IIdType csId = uploadLoincCodeSystem(null, true);
runCommonValidations(null);
runCommonValidations(Collections.emptyList());
// validate operation for current (no version parameter)
validateOperations(null, Collections.emptySet());
@ -497,11 +505,11 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Test()
public void uploadCurrentWithVersion() throws Exception {
public void uploadWithVersion() throws Exception {
String ver = "2.67";
IIdType csId = uploadLoincCodeSystem(ver, true);
runCommonValidations(ver);
runCommonValidations(Collections.singletonList(ver));
// validate operation for specific version
validateOperations(ver, Collections.singleton(ver));
@ -509,15 +517,14 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Test
public void uploadCurrentNoVersionThenNoCurrent() throws Exception {
public void uploadNoVersionThenNoCurrent() throws Exception {
uploadLoincCodeSystem(null, true);
String ver = "2.67";
uploadLoincCodeSystem(ver, false);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
runCommonValidations(ver);
// myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
runCommonValidations(Collections.singletonList(ver));
// validate operation for specific version
validateOperations(null, Collections.singleton(ver));
@ -525,15 +532,14 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Test
public void uploadFirstCurrentWithVersionThenNoCurrent() throws Exception {
public void uploadWithVersionThenNoCurrent() throws Exception {
String firstVer = "2.67";
uploadLoincCodeSystem(firstVer, true);
String secondVer = "2.68";
uploadLoincCodeSystem(secondVer, false);
runCommonValidations(firstVer);
runCommonValidations(secondVer);
runCommonValidations(Lists.newArrayList(firstVer, secondVer));
// validate operation for specific version
validateOperations(null, Lists.newArrayList(firstVer, secondVer));
@ -541,7 +547,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Test
public void uploadFirstCurrentNoVersionThenNoCurrentThenCurrent() throws Exception {
public void uploadNoVersionThenNoCurrentThenCurrent() throws Exception {
uploadLoincCodeSystem(null, true);
String firstVer = "2.67";
@ -550,8 +556,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
String secondVer = "2.68";
uploadLoincCodeSystem(secondVer, true);
runCommonValidations(firstVer);
runCommonValidations(secondVer);
runCommonValidations(Lists.newArrayList(firstVer, secondVer));
// validate operation for specific version
validateOperations(secondVer, Lists.newArrayList(firstVer, secondVer));
@ -559,7 +564,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Test
public void uploadFirstCurrentWithVersionThenNoCurrentThenCurrent() throws Exception {
public void uploadWithVersionThenNoCurrentThenCurrent() throws Exception {
String firstVer = "2.67";
uploadLoincCodeSystem(firstVer, true);
@ -569,9 +574,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
String thirdVer = "2.68";
uploadLoincCodeSystem(thirdVer, true);
runCommonValidations(firstVer);
runCommonValidations(secondVer);
runCommonValidations(thirdVer);
runCommonValidations(Lists.newArrayList(firstVer, secondVer, thirdVer));
// validate operation for specific version
validateOperations(thirdVer, Lists.newArrayList(firstVer, secondVer, thirdVer));