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Narrow version check scope to fix intermittency produced because argu… (#6279) 

* Narrow version check scope to fix intermittency produced because argument was present in CodeSystem field different from version

* Remove duplication

* Remove code duplication

* fix comment syntax

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
This commit is contained in:
jmarchionatto 2024-09-11 14:48:54 -04:00 committed by GitHub
parent c00292767d
commit ab2ba05fb5
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1 changed files with 42 additions and 90 deletions
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hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplCurrentVersionR4Test.java
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@ -1,9 +1,8 @@
package ca.uhn.fhir.jpa.term; package ca.uhn.fhir.jpa.term;
import static org.junit.jupiter.api.Assertions.assertNull;
import ca.uhn.fhir.context.support.IValidationSupport; import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.LookupCodeRequest; import ca.uhn.fhir.context.support.LookupCodeRequest;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao; import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.config.JpaConfig; import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.entity.TermCodeSystem; import ca.uhn.fhir.jpa.entity.TermCodeSystem;
@ -20,9 +19,10 @@ import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails; import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import com.google.common.collect.Lists; import com.google.common.collect.Lists;
import com.google.common.collect.Sets; import com.google.common.collect.Sets;
import jakarta.persistence.EntityManager;
import jakarta.servlet.http.HttpServletResponse;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem; import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType; import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.IdType; import org.hl7.fhir.r4.model.IdType;
@ -40,8 +40,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.core.io.ClassPathResource; import org.springframework.core.io.ClassPathResource;
import jakarta.persistence.EntityManager;
import jakarta.servlet.http.HttpServletResponse;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.util.ArrayList; import java.util.ArrayList;
@ -82,14 +80,12 @@ import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UPLOAD_
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_XML_FILE; import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_XML_FILE;
import static java.util.stream.Collectors.joining; import static java.util.stream.Collectors.joining;
import static org.assertj.core.api.Assertions.assertThat; import static org.assertj.core.api.Assertions.assertThat;
import static org.junit.jupiter.api.Assertions.fail;
import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_ALL_VALUESET_ID; import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_ALL_VALUESET_ID;
import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW; import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.fail; import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.Mockito.when; import static org.mockito.Mockito.when;
/** /**
@ -141,9 +137,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Autowired @Autowired
private Batch2JobHelper myBatchJobHelper; private Batch2JobHelper myBatchJobHelper;
private final ServletRequestDetails myRequestDetails = new ServletRequestDetails();
private ZipCollectionBuilder myFiles;
private ServletRequestDetails myRequestDetails = new ServletRequestDetails();
private Properties uploadProperties; private Properties uploadProperties;
private IFhirResourceDao<ValueSet> myValueSetIFhirResourceDao; private IFhirResourceDao<ValueSet> myValueSetIFhirResourceDao;
@ -182,17 +176,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
private void validateValidateCode(String theCurrentVersion, Collection<String> allVersions) { private void validateValidateCode(String theCurrentVersion, Collection<String> allVersions) {
IValidationSupport.CodeValidationResult resultNoVersioned = myCodeSystemDao.validateCode(null, validateValidateCodeForVersion(theCurrentVersion);
new UriType(BASE_LOINC_URL), null, new CodeType(VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE),
null, null, null, null);
assertNotNull(resultNoVersioned);
assertEquals(prefixWithVersion(theCurrentVersion, 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),
null, null, null, null);
assertNotNull(resultVersioned);
assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultVersioned.getDisplay());
allVersions.forEach(this::validateValidateCodeForVersion); allVersions.forEach(this::validateValidateCodeForVersion);
} }
@ -215,13 +199,15 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
private void validateValueLookup(String theCurrentVersion, Collection<String> allVersions) { private void validateValueLookup(String theCurrentVersion, Collection<String> allVersions) {
IValidationSupport.LookupCodeResult resultNoVer = myValidationSupport.lookupCode( IValidationSupport.LookupCodeResult resultNoVer = myValidationSupport.lookupCode(
new ValidationSupportContext(myValidationSupport), new LookupCodeRequest(BASE_LOINC_URL, VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE)); new ValidationSupportContext(myValidationSupport),
new LookupCodeRequest(BASE_LOINC_URL, VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE));
assertNotNull(resultNoVer); assertNotNull(resultNoVer);
String expectedNoVer = prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY); String expectedNoVer = prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY);
assertEquals(expectedNoVer, resultNoVer.getCodeDisplay()); assertEquals(expectedNoVer, resultNoVer.getCodeDisplay());
IValidationSupport.LookupCodeResult resultWithVer = myValidationSupport.lookupCode( IValidationSupport.LookupCodeResult resultWithVer = myValidationSupport.lookupCode(
new ValidationSupportContext(myValidationSupport), new LookupCodeRequest(BASE_LOINC_URL, VS_VERSIONED_ON_UPLOAD_FIRST_CODE)); new ValidationSupportContext(myValidationSupport),
new LookupCodeRequest(BASE_LOINC_URL, VS_VERSIONED_ON_UPLOAD_FIRST_CODE));
assertNotNull(resultWithVer); assertNotNull(resultWithVer);
String expectedWithVer = prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY); String expectedWithVer = prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY);
assertEquals(expectedWithVer, resultWithVer.getCodeDisplay()); assertEquals(expectedWithVer, resultWithVer.getCodeDisplay());
@ -293,27 +279,13 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptVerCsvNoVer.getDisplay()); assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptVerCsvNoVer.getDisplay());
if (theCurrentVersion != null) { if (theCurrentVersion != null) {
TermConcept termConceptNoVerCsvVer = (TermConcept) myEntityManager.createQuery( validateExpandedTermConceptsForVersion(theCurrentVersion);
"select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId = '" + theCurrentVersion + "'").getSingleResult();
assertNotNull(termConceptNoVerCsvVer);
// data should have version because it was loaded with a version
assertEquals(prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptNoVerCsvVer.getDisplay());
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 = '" + theCurrentVersion + "'").getSingleResult();
assertNotNull(termConceptVerCsvVer);
// data should have version because it was loaded with a version
assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptVerCsvVer.getDisplay());
} }
theAllVersions.forEach(this::validateExpandedTermConceptsForVersion); theAllVersions.forEach(this::validateExpandedTermConceptsForVersion);
}); });
} }
private void validateExpandedTermConceptsForVersion(String theVersion) { private void validateExpandedTermConceptsForVersion(String theVersion) {
TermConcept termConceptNoVer = (TermConcept) myEntityManager.createQuery( TermConcept termConceptNoVer = (TermConcept) myEntityManager.createQuery(
"select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" + "select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
@ -384,7 +356,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
* no the CodeSystem version. * no the CodeSystem version.
*/ */
private void validateValueSetSearchForVersion(String theVersion) { private void validateValueSetSearchForVersion(String theVersion) {
// for no versioned VS (VS version, different than CS version) // for no versioned VS (VS version, different from CS version)
SearchParameterMap paramsUploadNoVer = new SearchParameterMap("url", new UriParam(VS_NO_VERSIONED_ON_UPLOAD)); SearchParameterMap paramsUploadNoVer = new SearchParameterMap("url", new UriParam(VS_NO_VERSIONED_ON_UPLOAD));
paramsUploadNoVer.add("version", new TokenParam(theVersion)); paramsUploadNoVer.add("version", new TokenParam(theVersion));
@ -398,7 +370,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
assertEquals(expectedLoadNoVersionUnqualifiedId, loadNoVersionValueSet.getIdElement().getIdPart()); assertEquals(expectedLoadNoVersionUnqualifiedId, loadNoVersionValueSet.getIdElement().getIdPart());
// versioned VS (VS version, different than CS version) // versioned VS (VS version, different from CS version)
SearchParameterMap paramsUploadVer = new SearchParameterMap("url", new UriParam(VS_VERSIONED_ON_UPLOAD)); SearchParameterMap paramsUploadVer = new SearchParameterMap("url", new UriParam(VS_VERSIONED_ON_UPLOAD));
paramsUploadVer.add("version", new TokenParam(VS_ANSWER_LIST_VERSION + "-" + theVersion)); paramsUploadVer.add("version", new TokenParam(VS_ANSWER_LIST_VERSION + "-" + theVersion));
@ -437,8 +409,8 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
Set<String> theExpectedIdVersionsPlusNull = Sets.newHashSet(theExpectedIdVersions); Set<String> theExpectedIdVersionsPlusNull = Sets.newHashSet(theExpectedIdVersions);
theExpectedIdVersionsPlusNull.add(null); theExpectedIdVersionsPlusNull.add(null);
assertThat(theExpectedIdVersionsPlusNull).containsExactlyInAnyOrderElementsOf(theValueSets.stream().map(r -> ((ValueSet) r).getVersion()).toList()); List<String> valueSetVersions = theValueSets.stream().map(r -> ((ValueSet) r).getVersion()).toList();
assertThat(valueSetVersions).containsExactlyInAnyOrderElementsOf(theExpectedIdVersionsPlusNull);
} }
@ -455,14 +427,13 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
// for CodeSystem: // for CodeSystem:
// _ current CS is present and has no version // _ current CS is present and has no version
CodeSystem codeSystem = myCodeSystemDao.read(new IdType(LOINC_LOW)); CodeSystem codeSystem = myCodeSystemDao.read(new IdType(LOINC_LOW), myRequestDetails);
String csString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem); String csString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem);
ourLog.info("CodeSystem:\n" + csString); ourLog.info("CodeSystem:\n {}", csString);
HashSet<String> shouldNotBePresentVersions = new HashSet<>(possibleVersions); HashSet<String> shouldNotBePresentVersions = new HashSet<>(possibleVersions);
theAllVersions.forEach(shouldNotBePresentVersions::remove); theAllVersions.forEach(shouldNotBePresentVersions::remove);
shouldNotBePresentVersions.forEach(vv -> assertFalse(csString.contains(vv), assertThat(shouldNotBePresentVersions).noneSatisfy(vv -> assertThat(vv).isEqualTo(codeSystem.getVersion()));
"Found version string: '" + vv + "' in CodeSystem: " + csString));
// same reading it from term service // same reading it from term service
CodeSystem cs = myITermReadSvc.fetchCanonicalCodeSystemFromCompleteContext(BASE_LOINC_URL); CodeSystem cs = myITermReadSvc.fetchCanonicalCodeSystemFromCompleteContext(BASE_LOINC_URL);
@ -501,7 +472,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Test() @Test()
public void uploadCurrentNoVersion() throws Exception { public void uploadCurrentNoVersion() throws Exception {
IIdType csId = uploadLoincCodeSystem(null, true); uploadLoincCodeSystem(null, true);
runCommonValidations(Collections.emptyList()); runCommonValidations(Collections.emptyList());
@ -516,7 +487,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Test() @Test()
public void uploadWithVersion() throws Exception { public void uploadWithVersion() throws Exception {
String ver = "2.67"; String ver = "2.67";
IIdType csId = uploadLoincCodeSystem(ver, true); uploadLoincCodeSystem(ver, true);
runCommonValidations(Collections.singletonList(ver)); runCommonValidations(Collections.singletonList(ver));
@ -637,25 +608,6 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
assertThat(vsContainsDisplay).contains(expectedDisplay); assertThat(vsContainsDisplay).contains(expectedDisplay);
} }
private void validateValidateCodeLoincAllVS(String theCurrentVersion, Collection<String> allVersions) {
IValidationSupport.CodeValidationResult resultNoVersioned = myCodeSystemDao.validateCode(null,
new UriType(BASE_LOINC_URL), null, new CodeType(VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE),
null, null, null, null);
assertNotNull(resultNoVersioned);
assertEquals(prefixWithVersion(theCurrentVersion, 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),
null, null, null, null);
assertNotNull(resultVersioned);
assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultVersioned.getDisplay());
allVersions.forEach(this::validateValidateCodeForVersion);
}
private void validateValueExpandLoincAllVsForVersion(String theVersion) { private void validateValueExpandLoincAllVsForVersion(String theVersion) {
ValueSet vs = myValueSetDao.expandByIdentifier(LOINC_ALL_VS_URL + "|" + theVersion, null); ValueSet vs = myValueSetDao.expandByIdentifier(LOINC_ALL_VS_URL + "|" + theVersion, null);
assertThat(vs.getExpansion().getContains()).hasSize(ALL_VS_QTY); assertThat(vs.getExpansion().getContains()).hasSize(ALL_VS_QTY);
@ -664,7 +616,6 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
checkContainsElementVersion(vs, theVersion); checkContainsElementVersion(vs, theVersion);
} }
/** /**
* Validates TermConcepts were created in the sequence indicated by the parameters * Validates TermConcepts were created in the sequence indicated by the parameters
* and their displays match the expected versions * and their displays match the expected versions
@ -735,8 +686,8 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
} }
private IIdType uploadLoincCodeSystem(String theVersion, boolean theMakeItCurrent) throws Exception { private void uploadLoincCodeSystem(String theVersion, boolean theMakeItCurrent) throws Exception {
myFiles = new ZipCollectionBuilder(); ZipCollectionBuilder files = new ZipCollectionBuilder();
myRequestDetails.getUserData().put(LOINC_CODESYSTEM_MAKE_CURRENT, theMakeItCurrent); myRequestDetails.getUserData().put(LOINC_CODESYSTEM_MAKE_CURRENT, theMakeItCurrent);
uploadProperties.put(LOINC_CODESYSTEM_MAKE_CURRENT.getCode(), Boolean.toString(theMakeItCurrent)); uploadProperties.put(LOINC_CODESYSTEM_MAKE_CURRENT.getCode(), Boolean.toString(theMakeItCurrent));
@ -749,12 +700,10 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
uploadProperties.put(LOINC_CODESYSTEM_VERSION.getCode(), theVersion); uploadProperties.put(LOINC_CODESYSTEM_VERSION.getCode(), theVersion);
} }
addLoincMandatoryFilesToZip(myFiles, theVersion); addLoincMandatoryFilesToZip(files, theVersion);
UploadStatistics stats = myTermLoaderSvc.loadLoinc(myFiles.getFiles(), mySrd); myTermLoaderSvc.loadLoinc(files.getFiles(), mySrd);
myTerminologyDeferredStorageSvc.saveAllDeferred(); myTerminologyDeferredStorageSvc.saveAllDeferred();
return stats.getTarget();
} }
@ -787,10 +736,12 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
private TermCodeSystemVersion fetchCurrentCodeSystemVersion() { private TermCodeSystemVersion fetchCurrentCodeSystemVersion() {
runInTransaction(() -> { runInTransaction(() -> {
@SuppressWarnings("unchecked")
List<TermCodeSystem> tcsList = myEntityManager.createQuery("from TermCodeSystem").getResultList(); List<TermCodeSystem> tcsList = myEntityManager.createQuery("from TermCodeSystem").getResultList();
@SuppressWarnings("unchecked")
List<TermCodeSystemVersion> tcsvList = myEntityManager.createQuery("from TermCodeSystemVersion").getResultList(); List<TermCodeSystemVersion> tcsvList = myEntityManager.createQuery("from TermCodeSystemVersion").getResultList();
ourLog.error("tcslist: {}", tcsList.stream().map(tcs -> tcs.toString()).collect(joining("\n", "\n", ""))); ourLog.error("tcslist: {}", tcsList.stream().map(TermCodeSystem::toString).collect(joining("\n", "\n", "")));
ourLog.error("tcsvlist: {}", tcsvList.stream().map(v -> v.toString()).collect(joining("\n", "\n", ""))); ourLog.error("tcsvlist: {}", tcsvList.stream().map(TermCodeSystemVersion::toString).collect(joining("\n", "\n", "")));
if (tcsList.size() != 1) { if (tcsList.size() != 1) {
throw new IllegalStateException("More than one TCS: " + throw new IllegalStateException("More than one TCS: " +
@ -807,8 +758,9 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
} }
private static void addBaseLoincMandatoryFilesToZip( private static void addBaseLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles,
ZipCollectionBuilder theFiles, Boolean theIncludeTop2000, String theClassPathPrefix) throws IOException { @SuppressWarnings("SameParameterValue") Boolean theIncludeTop2000,
String theClassPathPrefix) throws IOException {
theFiles.addFileZip(theClassPathPrefix, LOINC_XML_FILE.getCode()); theFiles.addFileZip(theClassPathPrefix, LOINC_XML_FILE.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_FILE_DEFAULT.getCode()); theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_TERMS_FILE_DEFAULT.getCode()); theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());