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Merge remote-tracking branch 'remotes/origin/im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support

This commit is contained in:
ianmarshall 2020-09-15 16:52:02 -04:00
parent 539ef63fc0 ca0bdc8e4c
commit 3add1320b7
35 changed files with 150 additions and 148 deletions
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4
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
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@ -144,11 +144,13 @@ ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownType=Content in resource of
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrlAndVersion=Can not create multiple CodeSystem resources with CodeSystem.url "{0}" and CodeSystem.version "{1}", already have one with resource ID: {2}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotUpdateVersionForExistingCodeSystemVersion=Updated CodeSystem has wrong version id. Existing CodeSystem resource has CodeSystem.url "{0}" and CodeSystem.version "{1}", already have one with resource ID: {2}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotUpdateUrlOrVersionForCodeSystemResource=Cannot update URL or version for CodeSystem resource. Existing CodeSystem resource with resource ID {0} found with CodeSystem.url "{1}" and CodeSystem.version "{2}"
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateConceptMapUrlAndVersion=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", ConceptMap.version "{1}", already have one with resource ID: {2}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrlAndVersion=Can not create multiple CodeSystem resources with CodeSystem.url "{0}" and CodeSystem.version "{1}", already have one with resource ID: {2}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotUpdateUrlOrVersionForValueSetResource=Cannot update URL or version for ValueSet resource. Existing ValueSet resource with resource ID {0} found with ValueSet.url "{1}" and ValueSet.version "{2}"
ca.uhn.fhir.jpa.patch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}

28
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/HapiFhirResourceDaoCodeSystemUtil.java
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@ -1,28 +0,0 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class HapiFhirResourceDaoCodeSystemUtil {
static public void deleteCodeSystemEntities(ITermCodeSystemDao theCsDao, ITermCodeSystemVersionDao theCsvDao,
ITermDeferredStorageSvc theTermDeferredStorageSvc, String theCodeSystemUrl,
String theCodeSystemVersion) {
if (isNotBlank(theCodeSystemUrl)) {
TermCodeSystem persCs = theCsDao.findByCodeSystemUri(theCodeSystemUrl);
if (persCs != null) {
if (theCodeSystemVersion != null) {
TermCodeSystemVersion persCsVersion = theCsvDao.findByCodeSystemPidAndVersion(persCs.getPid(), theCodeSystemVersion);
theTermDeferredStorageSvc.deleteCodeSystemVersion(persCsVersion);
} else {
theTermDeferredStorageSvc.deleteCodeSystem(persCs);
}
}
}
}
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java
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@ -28,6 +28,7 @@ import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import java.util.List;
import java.util.Optional;
public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
@ -41,4 +42,14 @@ public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
@Query("SELECT vs FROM TermValueSet vs WHERE vs.myExpansionStatus = :expansion_status")
Slice<TermValueSet> findByExpansionStatus(Pageable pageable, @Param("expansion_status") TermValueSetPreExpansionStatusEnum theExpansionStatus);
@Query(value="SELECT vs FROM TermValueSet vs INNER JOIN ResourceTable r ON r.myId = vs.myResourcePid WHERE vs.myUrl = :url ORDER BY r.myUpdated DESC")
List<TermValueSet> findTermValueSetByUrl(Pageable thePage, @Param("url") String theUrl);
@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url AND vs.myVersion IS NULL")
Optional<TermValueSet> findTermValueSetByUrlAndNullVersion(@Param("url") String theUrl);
@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url AND vs.myVersion = :version")
Optional<TermValueSet> findTermValueSetByUrlAndVersion(@Param("url") String theUrl, @Param("version") String theVersion);
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
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@ -25,10 +25,6 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
@ -67,10 +63,6 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
@Autowired
protected ITermDeferredStorageSvc myTermDeferredStorageSvc;
@Autowired
private ITermCodeSystemDao myCsDao;
@Autowired
private ITermCodeSystemVersionDao myCsvDao;
@Autowired
private IValidationSupport myValidationSupport;
@Autowired
private FhirContext myFhirContext;
@ -155,8 +147,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
super.preDelete(theResourceToDelete, theEntityToDelete);
HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
theResourceToDelete.getVersion());
myTermDeferredStorageSvc.deleteCodeSystemForResource(theEntityToDelete);
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
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@ -65,9 +65,6 @@ import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
@Autowired
private ITermReadSvc myHapiTerminologySvc;
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
@ -283,12 +280,12 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
try {
ValueSet valueSet = (ValueSet) theResource;
org.hl7.fhir.r4.model.ValueSet converted = convertValueSet(valueSet);
myHapiTerminologySvc.storeTermValueSet(retVal, converted);
myTerminologySvc.storeTermValueSet(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
}
} else {
myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
myTerminologySvc.deleteValueSetAndChildren(retVal);
}
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
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@ -25,10 +25,6 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
@ -60,10 +56,6 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCodeSystemR4.class);
@Autowired
private ITermCodeSystemDao myCsDao;
@Autowired
private ITermCodeSystemVersionDao myCsvDao;
@Autowired
private IValidationSupport myValidationSupport;
@Autowired
@ -153,8 +145,7 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
super.preDelete(theResourceToDelete, theEntityToDelete);
HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
theResourceToDelete.getVersion());
myTermDeferredStorageSvc.deleteCodeSystemForResource(theEntityToDelete);
}

25
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
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@ -60,9 +60,6 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
@Autowired
private ITermReadSvc myHapiTerminologySvc;
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
@ -113,17 +110,14 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
ValueSet source = new ValueSet();
source.setUrl(theUri);
// source.getCompose().addInclude().addValueSet(theUri);
source.getCompose().addInclude().addValueSet(theUri);
if (isNotBlank(theFilter)) {
// ConceptSetComponent include = source.getCompose().addInclude();
// ConceptSetFilterComponent filter = include.addFilter();
ConceptSetFilterComponent filter = source.getCompose().addInclude().addValueSet(theUri).addFilter();
ConceptSetComponent include = source.getCompose().addInclude();
ConceptSetFilterComponent filter = include.addFilter();
filter.setProperty("display");
filter.setOp(FilterOperator.EQUAL);
filter.setValue(theFilter);
} else {
source.getCompose().addInclude().addValueSet(theUri);
}
ValueSet retVal = doExpand(source);
@ -151,17 +145,14 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
ValueSet source = new ValueSet();
source.setUrl(theUri);
// source.getCompose().addInclude().addValueSet(theUri);
source.getCompose().addInclude().addValueSet(theUri);
if (isNotBlank(theFilter)) {
// ConceptSetComponent include = source.getCompose().addInclude();
// ConceptSetFilterComponent filter = include.addFilter();
ConceptSetFilterComponent filter = source.getCompose().addInclude().addValueSet(theUri).addFilter();
ConceptSetComponent include = source.getCompose().addInclude();
ConceptSetFilterComponent filter = include.addFilter();
filter.setProperty("display");
filter.setOp(FilterOperator.EQUAL);
filter.setValue(theFilter);
} else {
source.getCompose().addInclude().addValueSet(theUri);
}
ValueSet retVal = doExpand(source, theOffset, theCount);
@ -268,9 +259,9 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSet(retVal, valueSet);
myTerminologySvc.storeTermValueSet(retVal, valueSet);
} else {
myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
myTerminologySvc.deleteValueSetAndChildren(retVal);
}
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -25,11 +25,7 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
@ -65,10 +61,6 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
@Autowired
protected IdHelperService myIdHelperService;
@Autowired
private ITermCodeSystemDao myCsDao;
@Autowired
private ITermCodeSystemVersionDao myCsvDao;
@Autowired
private IValidationSupport myValidationSupport;
@Autowired
private FhirContext myFhirContext;
@ -155,8 +147,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
super.preDelete(theResourceToDelete, theEntityToDelete);
HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
theResourceToDelete.getVersion());
myTermDeferredStorageSvc.deleteCodeSystemForResource(theEntityToDelete);
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
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@ -64,9 +64,6 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
@Autowired
private ITermReadSvc myHapiTerminologySvc;
@Autowired
@Qualifier("myDefaultProfileValidationSupport")
private IValidationSupport myDefaultProfileValidationSupport;
@ -267,9 +264,9 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSet));
myTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSet));
} else {
myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
myTerminologySvc.deleteValueSetAndChildren(retVal);
}
}

17
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java
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@ -37,7 +37,7 @@ import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Table(name = "TRM_VALUESET", uniqueConstraints = {
@UniqueConstraint(name = "IDX_VALUESET_URL", columnNames = {"URL"})
@UniqueConstraint(name = "IDX_VALUESET_URL", columnNames = {"URL", "VER"})
})
@Entity()
public class TermValueSet implements Serializable {
@ -46,6 +46,7 @@ public class TermValueSet implements Serializable {
public static final int MAX_EXPANSION_STATUS_LENGTH = 50;
public static final int MAX_NAME_LENGTH = 200;
public static final int MAX_URL_LENGTH = 200;
static final int MAX_VER_LENGTH = 200;
@Id()
@SequenceGenerator(name = "SEQ_VALUESET_PID", sequenceName = "SEQ_VALUESET_PID")
@ -56,6 +57,9 @@ public class TermValueSet implements Serializable {
@Column(name = "URL", nullable = false, length = MAX_URL_LENGTH)
private String myUrl;
@Column(name = "VER", nullable = true, length = MAX_VER_LENGTH)
private String myVersion;
@OneToOne()
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_TRMVALUESET_RES"))
private ResourceTable myResource;
@ -183,6 +187,17 @@ public class TermValueSet implements Serializable {
myExpansionStatus = theExpansionStatus;
}
public String getVersion() {
return myVersion;
}
public TermValueSet setVersion(String theVersion) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theVersion, MAX_VER_LENGTH,
"Version exceeds maximum length (" + MAX_VER_LENGTH + "): " + length(theVersion));
myVersion = theVersion;
return this;
}
@Override
public boolean equals(Object theO) {
if (this == theO) return true;

51
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

@ -332,7 +332,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
deleteConceptMap(theResourceTable);
}
public void deleteValueSet(ResourceTable theResourceTable) {
public void deleteValueSetForResource(ResourceTable theResourceTable) {
// Get existing entity so it can be deleted.
Optional<TermValueSet> optionalExistingTermValueSetById = myValueSetDao.findByResourcePid(theResourceTable.getId());
@ -350,7 +350,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
@Override
@Transactional
public void deleteValueSetAndChildren(ResourceTable theResourceTable) {
deleteValueSet(theResourceTable);
deleteValueSetForResource(theResourceTable);
}
private ValueSet expandValueSetInMemory(ValueSetExpansionOptions theExpansionOptions, ValueSet theValueSetToExpand, VersionIndependentConcept theWantConceptOrNull) {
@ -392,7 +392,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
Optional<TermValueSet> optionalTermValueSet;
if (theValueSetToExpand.hasUrl()) {
optionalTermValueSet = myValueSetDao.findByUrl(theValueSetToExpand.getUrl());
if (theValueSetToExpand.hasVersion()) {
optionalTermValueSet = myValueSetDao.findTermValueSetByUrlAndVersion(theValueSetToExpand.getUrl(), theValueSetToExpand.getVersion());
} else {
List<TermValueSet> termValueSets = myValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 1), theValueSetToExpand.getUrl());
optionalTermValueSet = Optional.of(termValueSets.get(0));
}
} else {
optionalTermValueSet = Optional.empty();
}
@ -1795,38 +1800,52 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theValueSet.getUrl(), "ValueSet has no value for ValueSet.url");
/*
* Get CodeSystem and validate CodeSystemVersion
*/
TermValueSet termValueSet = new TermValueSet();
termValueSet.setResource(theResourceTable);
termValueSet.setUrl(theValueSet.getUrl());
termValueSet.setVersion(theValueSet.getVersion());
termValueSet.setName(theValueSet.hasName() ? theValueSet.getName() : null);
// We delete old versions; we don't support versioned ValueSets.
deleteValueSet(theResourceTable);
// Delete version being replaced
deleteValueSetForResource(theResourceTable);
/*
* Do the upload.
*/
String url = termValueSet.getUrl();
Optional<TermValueSet> optionalExistingTermValueSetByUrl = myValueSetDao.findByUrl(url);
String version = termValueSet.getVersion();
Optional<TermValueSet> optionalExistingTermValueSetByUrl;
if (version != null) {
optionalExistingTermValueSetByUrl = myValueSetDao.findTermValueSetByUrlAndVersion(url, version);
} else {
optionalExistingTermValueSetByUrl = myValueSetDao.findTermValueSetByUrlAndNullVersion(url);
}
if (!optionalExistingTermValueSetByUrl.isPresent()) {
termValueSet = myValueSetDao.save(termValueSet);
myValueSetDao.save(termValueSet);
} else {
TermValueSet existingTermValueSet = optionalExistingTermValueSetByUrl.get();
String msg = myContext.getLocalizer().getMessage(
BaseTermReadSvcImpl.class,
"cannotCreateDuplicateValueSetUrl",
url,
existingTermValueSet.getResource().getIdDt().toUnqualifiedVersionless().getValue());
String msg;
if (version != null) {
msg = myContext.getLocalizer().getMessage(
BaseTermReadSvcImpl.class,
"cannotCreateDuplicateValueSetUrlAndVersion",
url, version, existingTermValueSet.getResource().getIdDt().toUnqualifiedVersionless().getValue());
} else {
msg = myContext.getLocalizer().getMessage(
BaseTermReadSvcImpl.class,
"cannotCreateDuplicateValueSetUrl",
url, existingTermValueSet.getResource().getIdDt().toUnqualifiedVersionless().getValue());
}
throw new UnprocessableEntityException(msg);
}
ourLog.info("Done storing TermValueSet[{}] for {}", termValueSet.getId(), theValueSet.getIdElement().toVersionless().getValueAsString());
}
@Override
public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB,
IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB) {

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
View File

@ -238,17 +238,6 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
ourLog.info(" * Deleting code system version {}", theCodeSystemVersion.getCodeSystemVersionId());
deleteCodeSystemVersion(theCodeSystemVersion.getPid());
// Check if the version deleted is the current version. If so, delete TermCodeSystem as well.
TermCodeSystem termCodeSystem = theCodeSystemVersion.getCodeSystem();
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
txTemplate.executeWithoutResult(t -> {
if (myCodeSystemVersionDao.findByCodeSystemPid(termCodeSystem.getPid()).size() == 0) {
ourLog.info(" * Deleting code system {}", termCodeSystem.getPid());
deleteCodeSystem(termCodeSystem);
}
});
}
/**
@ -709,27 +698,29 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
}
private void checkForCodeSystemVersionDuplicate(TermCodeSystem theCodeSystem, String theSystemUri, String theSystemVersionId, ResourceTable theCodeSystemResourceTable) {
// Check if CodeSystemVersion entity already exists.
TermCodeSystemVersion codeSystemVersionEntity;
String msg = null;
if (theSystemVersionId == null) {
// Check if a non-versioned TermCodeSystemVersion entity already exists for this TermCodeSystem.
codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(theCodeSystem.getPid());
if (codeSystemVersionEntity != null) {
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
}
} else {
// Check if a TermCodeSystemVersion entity already exists for this TermCodeSystem and version.
codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(theCodeSystem.getPid(), theSystemVersionId);
if (codeSystemVersionEntity != null) {
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrlAndVersion", theSystemUri, theSystemVersionId, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
} else {
// Check if a TermCodeSystemVersion entity already exists for this CodeSystem resource (i.e. with a different version or URL)
codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourceTable.getId());
if (codeSystemVersionEntity != null) {
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrlAndVersion", theSystemUri, theSystemVersionId, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotUpdateUrlOrVersionForCodeSystemResource", codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue(), theSystemUri, theSystemVersionId);
throw new UnprocessableEntityException(msg);
}
}
}
// Throw exception if the CodeSystemVersion is being duplicated.
// Throw exception if the TermCodeSystemVersion is being duplicated.
if (codeSystemVersionEntity != null) {
if (!ObjectUtil.equals(codeSystemVersionEntity.getResource().getId(), theCodeSystemResourceTable.getId())) {
throw new UnprocessableEntityException(msg);

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
View File

@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.sched.HapiJob;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
@ -119,8 +120,15 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
@Override
@Transactional
public void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
myDefferedCodeSystemVersionsDeletions.add(theCodeSystemVersion);
public void deleteCodeSystemForResource(ResourceTable theCodeSystemToDelete) {
TermCodeSystemVersion codeSystemVersionToDelete = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemToDelete.getResourceId());
if (codeSystemVersionToDelete != null) {
myDefferedCodeSystemVersionsDeletions.add(codeSystemVersionToDelete);
}
TermCodeSystem codeSystemToDelete = myCodeSystemDao.findByResourcePid(theCodeSystemToDelete.getResourceId());
if (codeSystemToDelete != null) {
deleteCodeSystem(codeSystemToDelete);
}
}
@Override
@ -219,6 +227,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
myDeferredConceptMaps.clear();
myDeferredConcepts.clear();
myDefferedCodeSystemsDeletions.clear();
myConceptLinksToSaveLater.clear();
}
@Transactional(propagation = Propagation.NEVER)

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
View File

@ -381,6 +381,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
String codeSystemVersionId = theUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
if (codeSystemVersionId != null) {
loincCs.setVersion(codeSystemVersionId);
loincCs.setId(loincCs.getId() + "-" + codeSystemVersionId);
}
} catch (IOException e) {
throw new InternalErrorException("Failed to load loinc.xml", e);

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
View File

@ -42,13 +42,12 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValueSetConceptAccumulator.class);
private TermValueSet myTermValueSet;
private ITermValueSetDao myValueSetDao;
private ITermValueSetConceptDao myValueSetConceptDao;
private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
final private ITermValueSetDao myValueSetDao;
final private ITermValueSetConceptDao myValueSetConceptDao;
final private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
private int myConceptsSaved;
private int myDesignationsSaved;
private int myConceptsExcluded;
private int myCount;
public ValueSetConceptAccumulator(@Nonnull TermValueSet theTermValueSet, @Nonnull ITermValueSetDao theValueSetDao, @Nonnull ITermValueSetConceptDao theValueSetConceptDao, @Nonnull ITermValueSetConceptDesignationDao theValueSetConceptDesignationDao) {
myTermValueSet = theTermValueSet;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermDeferredStorageSvc.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
@ -55,7 +56,7 @@ public interface ITermDeferredStorageSvc {
void deleteCodeSystem(TermCodeSystem theCodeSystem);
void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion);
void deleteCodeSystemForResource(ResourceTable theCodeSystemResourceToDelete);
/**
* This is mostly here for unit tests - Saves any and all deferred concepts and links

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -52,7 +52,6 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.io.IOUtils;
import org.hibernate.search.jpa.FullTextEntityManager;

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -80,6 +80,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
private CodeSystem createExternalCs() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
codeSystem.setName("ACME Codes");
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -124,6 +125,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
private void createExternalCsLarge() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -165,6 +167,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
private CodeSystem createExternalCsDogs() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -698,6 +701,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
public void testLookupSnomed() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl("http://snomed.info/sct");
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValueSetTest.java
View File

@ -22,6 +22,7 @@ import org.springframework.transaction.annotation.Transactional;
import java.io.IOException;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
@ -76,6 +77,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
validationOutcome = myValueSetDao.validateCode(vsIdentifier, null, code, system, null, null, null, mySrd);
assertEquals(false, validationOutcome.isOk());
await().until(() -> clearDeferredStorageQueue());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
runInTransaction(() -> {
@ -95,6 +97,16 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
}
private boolean clearDeferredStorageQueue() {
if(!myTerminologyDeferredStorageSvc.isStorageQueueEmpty()) {
myTerminologyDeferredStorageSvc.saveAllDeferred();
return false;
} else {
return true;
}
}
@Test
@Disabled

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -64,7 +64,6 @@ import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc;
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
@ -81,7 +80,6 @@ import ca.uhn.fhir.rest.server.BasePagingProvider;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.test.utilities.ITestDataBuilder;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CodeSystemTest.java
View File

@ -136,10 +136,10 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
// Attempt to delete second version
myCodeSystemDao.delete(id_second, mySrd);
// Only the resource will be deleted initially
// Only the resource will be deleted initially, but the URL for the TermCodeSystem will be cleared and not searchable.
runInTransaction(() -> {
assertEquals(1, myTermCodeSystemDao.count());
assertNotNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
assertNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
assertEquals(1, myTermCodeSystemVersionDao.count());
assertEquals(222, myTermConceptDao.count());
List<ResourceTable> resourceList = myResourceTableDao.findAll();

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java
View File

@ -209,6 +209,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
private CodeSystem createExternalCs() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyElasticsearchIT.java
View File

@ -85,6 +85,7 @@ public class FhirResourceDaoR4TerminologyElasticsearchIT extends BaseJpaTest {
public void testExpandWithIncludeContainingDashesInInclude() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
View File

@ -80,6 +80,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
private CodeSystem createExternalCs() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -129,6 +130,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
private CodeSystem createExternalCsDogs() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -159,6 +161,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
private void createExternalCsLarge() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -473,6 +476,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
public void testExpandWithIncludeContainingDashesInInclude() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -815,6 +819,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
public void testLookupSnomed() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl("http://snomed.info/sct");
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -828,7 +833,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
StringType code = new StringType("ParentA");
StringType system = new StringType("http://snomed.info/sct");
IValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null,null, mySrd);
IValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null, mySrd);
assertEquals(true, outcome.isFound());
}

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
View File

@ -9,8 +9,6 @@ import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcLoincTest;
import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
@ -80,7 +78,6 @@ import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.mock;

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java
View File

@ -69,7 +69,6 @@ import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.BasePagingProvider;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
View File

@ -13,7 +13,6 @@ import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
@ -37,7 +36,6 @@ import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
@ -137,6 +135,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
runInTransaction(() -> {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -823,7 +822,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
codeSystem.setName("ACME Codes");
codeSystem.setVersion("1.2.3.4");
codeSystem.setVersion("SYSTEM VERSION");
IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();
ResourceTable table = theResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4CodeSystemTest.java
View File

@ -25,9 +25,6 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
myCodeSystemDao.create(cs, mySrd);
ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
CodeSystem parentChildCs = new CodeSystem();
parentChildCs.setUrl(SYSTEM_PARENTCHILD);
parentChildCs.setStatus(Enumerations.PublicationStatus.ACTIVE);

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4CodeSystemVersionedTest.java
View File

@ -37,9 +37,6 @@ public class ResourceProviderR4CodeSystemVersionedTest extends BaseResourceProvi
cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs-v2.xml");
myCodeSystemDao.create(cs, mySrd);
ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
CodeSystem parentChildCs = new CodeSystem();
parentChildCs.setUrl(SYSTEM_PARENTCHILD);
parentChildCs.setVersion("1");

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
View File

@ -16,7 +16,6 @@ import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.ParametersUtil;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
@ -1060,6 +1059,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
public static CodeSystem createExternalCs(IFhirResourceDao<CodeSystem> theCodeSystemDao, IResourceTableDao theResourceTableDao, ITermCodeSystemStorageSvc theTermCodeSystemStorageSvc, ServletRequestDetails theRequestDetails) {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();
@ -1093,6 +1093,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
public static CodeSystem createExternalCs(IFhirResourceDao<CodeSystem> theCodeSystemDao, IResourceTableDao theResourceTableDao, ITermCodeSystemStorageSvc theTermCodeSystemStorageSvc, ServletRequestDetails theRequestDetails, String theCodeSystemVersion) {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
codeSystem.setVersion(theCodeSystemVersion);
IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java
View File

@ -106,7 +106,7 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
ourLog.info(resp);
assertThat(((IntegerType) respParam.getParameter().get(1).getValue()).getValue(), greaterThan(1));
assertThat(((Reference) respParam.getParameter().get(2).getValue()).getReference(), matchesPattern("CodeSystem\\/[a-zA-Z0-9]+"));
assertThat(((Reference) respParam.getParameter().get(2).getValue()).getReference(), matchesPattern("CodeSystem\\/[a-zA-Z0-9\\.\\-]+"));
/*
* Try uploading a second time

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ValueSetTest.java
View File

@ -1405,6 +1405,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
public static CodeSystem createExternalCs(IFhirResourceDao<CodeSystem> theCodeSystemDao, IResourceTableDao theResourceTableDao, ITermCodeSystemStorageSvc theTermCodeSystemStorageSvc, ServletRequestDetails theRequestDetails) {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincIntegratedTest.java
View File

@ -41,6 +41,8 @@ public class TerminologyLoaderSvcLoincIntegratedTest extends BaseJpaR4Test {
TermCodeSystemVersion myTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion.getPid());
assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion.getResource().getId());
assertEquals(1, myResourceTableDao.count());
});
// Update LOINC marked as version 2.67
@ -56,6 +58,8 @@ public class TerminologyLoaderSvcLoincIntegratedTest extends BaseJpaR4Test {
TermCodeSystemVersion myTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion.getPid());
assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion.getResource().getId());
assertEquals(1, myResourceTableDao.count());
});
@ -72,6 +76,8 @@ public class TerminologyLoaderSvcLoincIntegratedTest extends BaseJpaR4Test {
TermCodeSystemVersion mySecondTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.68");
assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), mySecondTermCodeSystemVersion.getPid());
assertEquals(myTermCodeSystem.getResource().getId(), mySecondTermCodeSystemVersion.getResource().getId());
assertEquals(2, myResourceTableDao.count());
});
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcDeltaR4Test.java
View File

@ -184,7 +184,7 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
assertEquals(2, outcome.getUpdatedConceptCount());
runInTransaction(() -> {
TermConcept concept = myTermSvc.findCode("http://foo/cs", "ChildAA", null).orElseThrow(() -> new IllegalStateException());
TermConcept concept = myTermSvc.findCode("http://foo/cs", "ChildAA").orElseThrow(() -> new IllegalStateException());
assertEquals(2, concept.getParents().size());
assertThat(concept.getParentPidsAsString(), matchesPattern("^[0-9]+ [0-9]+$"));
});

11
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
View File

@ -63,6 +63,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
codeSystem.setUrl(CS_URL);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
codeSystem.setName("SYSTEM NAME");
codeSystem.setVersion("SYSTEM VERSION");
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
@ -116,6 +117,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
private void createCodeSystem2() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL_2);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -135,6 +137,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
runInTransaction(() -> {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(LOINC_URI);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -204,6 +207,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
public void testCreateDuplicateCodeSystemUri() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -226,12 +230,13 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
// Try to update to a different resource
codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
try {
myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
fail();
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/"));
assertThat(e.getMessage(), containsString("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\" and CodeSystem.version \"SYSTEM VERSION\", already have one with resource ID: CodeSystem/"));
}
}
@ -1813,6 +1818,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
public void testStoreCodeSystemInvalidCyclicLoop() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
codeSystem.setVersion("SYSTEM VERSION");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
@ -1834,7 +1840,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
child.addChild(parent, RelationshipTypeEnum.ISA);
try {
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getPersistentId(), "http://foo", "SYSTEM NAME", "SYSTEM VERSION", cs, table);
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getPersistentId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
fail();
} catch (InvalidRequestException e) {
assertEquals("CodeSystem contains circular reference around code parent", e.getMessage());
@ -1948,6 +1954,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
CodeSystem cs = new CodeSystem();
cs.setUrl("http://codesystems-r-us");
cs.setVersion("SYSTEM VERSION");
cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
IIdType csId = myCodeSystemDao.create(cs).getId().toUnqualifiedVersionless();