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Merge branch 'master' into ng_20201218_survivorship_poc

This commit is contained in:
Nick 2021-01-21 09:00:28 -05:00
parent f8c1591d21 656dd33ba8
commit 82e52750e7
34 changed files with 351 additions and 279 deletions
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106
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java
View File

@ -32,9 +32,11 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Set;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -77,9 +79,9 @@ public interface IValidationSupport {
* Expands the given portion of a ValueSet
*
* @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theExpansionOptions If provided (may be <code>null</code>), contains options controlling the expansion
* @param theValueSetToExpand The valueset that should be expanded
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theExpansionOptions If provided (may be <code>null</code>), contains options controlling the expansion
* @param theValueSetToExpand The valueset that should be expanded
* @return The expansion, or null
*/
default ValueSetExpansionOutcome expandValueSet(ValidationSupportContext theValidationSupportContext, @Nullable ValueSetExpansionOptions theExpansionOptions, @Nonnull IBaseResource theValueSetToExpand) {
@ -116,15 +118,33 @@ public interface IValidationSupport {
* Loads a resource needed by the validation (a StructureDefinition, or a
* ValueSet)
*
* @param theClass The type of the resource to load
* <p>
* Note: Since 5.3.0, {@literal theClass} can be {@literal null}
* </p>
*
* @param theClass The type of the resource to load, or <code>null</code> to return any resource with the given canonical URI
* @param theUri The resource URI
* @return Returns the resource, or <code>null</code> if no resource with the
* given URI can be found
*/
default <T extends IBaseResource> T fetchResource(Class<T> theClass, String theUri) {
Validate.notNull(theClass, "theClass must not be null or blank");
@SuppressWarnings("unchecked")
default <T extends IBaseResource> T fetchResource(@Nullable Class<T> theClass, String theUri) {
Validate.notBlank(theUri, "theUri must not be null or blank");
if (theClass == null) {
Supplier<IBaseResource>[] sources = new Supplier[]{
() -> fetchStructureDefinition(theUri),
() -> fetchValueSet(theUri),
() -> fetchCodeSystem(theUri)
};
return (T) Arrays
.stream(sources)
.map(t -> t.get())
.filter(t -> t != null)
.findFirst()
.orElse(null);
}
switch (getFhirContext().getResourceType(theClass)) {
case "StructureDefinition":
return theClass.cast(fetchStructureDefinition(theUri));
@ -150,8 +170,8 @@ public interface IValidationSupport {
* or validated
*
* @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theSystem The URI for the code system, e.g. <code>"http://loinc.org"</code>
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theSystem The URI for the code system, e.g. <code>"http://loinc.org"</code>
* @return Returns <code>true</code> if codes in the given code system can be
* validated
*/
@ -172,11 +192,11 @@ public interface IValidationSupport {
* binding fields (e.g. <code>Observation.code</code> in the default profile.
*
* @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theOptions Provides options controlling the validation
* @param theCodeSystem The code system, e.g. "<code>http://loinc.org</code>"
* @param theCode The code, e.g. "<code>1234-5</code>"
* @param theDisplay The display name, if it should also be validated
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theOptions Provides options controlling the validation
* @param theCodeSystem The code system, e.g. "<code>http://loinc.org</code>"
* @param theCode The code, e.g. "<code>1234-5</code>"
* @param theDisplay The display name, if it should also be validated
* @return Returns a validation result object
*/
default CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
@ -189,11 +209,11 @@ public interface IValidationSupport {
* binding fields (e.g. <code>Observation.code</code> in the default profile.
*
* @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theCodeSystem The code system, e.g. "<code>http://loinc.org</code>"
* @param theCode The code, e.g. "<code>1234-5</code>"
* @param theDisplay The display name, if it should also be validated
* @param theValueSet The ValueSet to validate against. Must not be null, and must be a ValueSet resource.
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theCodeSystem The code system, e.g. "<code>http://loinc.org</code>"
* @param theCode The code, e.g. "<code>1234-5</code>"
* @param theDisplay The display name, if it should also be validated
* @param theValueSet The ValueSet to validate against. Must not be null, and must be a ValueSet resource.
* @return Returns a validation result object, or <code>null</code> if this validation support module can not handle this kind of request
*/
default CodeValidationResult validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, @Nonnull IBaseResource theValueSet) {
@ -204,9 +224,9 @@ public interface IValidationSupport {
* Look up a code using the system and code value
*
* @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theSystem The CodeSystem URL
* @param theCode The code
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theSystem The CodeSystem URL
* @param theCode The code
*/
default LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return null;
@ -217,8 +237,8 @@ public interface IValidationSupport {
* validation support module
*
* @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theValueSetUrl The ValueSet canonical URL
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theValueSetUrl The ValueSet canonical URL
*/
default boolean isValueSetSupported(ValidationSupportContext theValidationSupportContext, String theValueSetUrl) {
return false;
@ -228,7 +248,7 @@ public interface IValidationSupport {
* Generate a snapshot from the given differential profile.
*
* @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @return Returns null if this module does not know how to handle this request
*/
default IBaseResource generateSnapshot(ValidationSupportContext theValidationSupportContext, IBaseResource theInput, String theUrl, String theWebUrl, String theProfileName) {
@ -249,6 +269,25 @@ public interface IValidationSupport {
}
enum IssueSeverity {
/**
* The issue caused the action to fail, and no further checking could be performed.
*/
FATAL,
/**
* The issue is sufficiently important to cause the action to fail.
*/
ERROR,
/**
* The issue is not important enough to cause the action to fail, but may cause it to be performed suboptimally or in a way that is not as desired.
*/
WARNING,
/**
* The issue has no relation to the degree of success of the action.
*/
INFORMATION
}
class ConceptDesignation {
private String myLanguage;
private String myUseSystem;
@ -365,25 +404,6 @@ public interface IValidationSupport {
}
}
enum IssueSeverity {
/**
* The issue caused the action to fail, and no further checking could be performed.
*/
FATAL,
/**
* The issue is sufficiently important to cause the action to fail.
*/
ERROR,
/**
* The issue is not important enough to cause the action to fail, but may cause it to be performed suboptimally or in a way that is not as desired.
*/
WARNING,
/**
* The issue has no relation to the degree of success of the action.
*/
INFORMATION
}
class CodeValidationResult {
private String myCode;
private String myMessage;

3
hapi-fhir-docs/src/test/java/ca/uhn/hapi/fhir/docs/ChangelogFilesTest.java
View File

@ -66,6 +66,9 @@ public class ChangelogFilesTest {
// this one is optional
boolean haveIssue = fieldNames.remove("issue");
// this one is optional
fieldNames.remove("backport");
assertThat("Invalid element in " + next + ": " + fieldNames, fieldNames, empty());
if (haveIssue) {

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

@ -32,11 +32,11 @@ import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.CountingInputStream;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IIdType;
import org.jetbrains.annotations.Nullable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
import java.io.*;
import java.util.Date;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -103,8 +103,6 @@ import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Required;
import org.springframework.data.domain.SliceImpl;
@ -539,7 +537,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return myDeleteExpungeService.expungeByResourcePids(theUrl, myResourceName, new SliceImpl<>(ResourcePersistentId.toLongList(theResourceIds)), theTheRequest);
}
@NotNull
@Nonnull
@Override
public DeleteMethodOutcome deletePidList(String theUrl, Collection<ResourcePersistentId> theResourceIds, DeleteConflictList theDeleteConflicts, RequestDetails theRequest) {
StopWatch w = new StopWatch();

74
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java
View File

@ -20,54 +20,34 @@ package ca.uhn.fhir.jpa.dao;
* #L%
*/
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.lucene.analysis.Analyzer;
import org.apache.lucene.analysis.TokenStream;
import org.apache.lucene.search.highlight.Formatter;
import org.apache.lucene.search.highlight.Highlighter;
import org.apache.lucene.search.highlight.Scorer;
import org.apache.lucene.search.highlight.TextFragment;
import org.apache.lucene.search.highlight.TokenGroup;
import org.hibernate.search.backend.lucene.index.LuceneIndexManager;
import org.hibernate.search.engine.search.predicate.dsl.BooleanPredicateClausesStep;
import org.hibernate.search.engine.search.predicate.dsl.SearchPredicateFactory;
import org.hibernate.search.engine.search.query.SearchQuery;
import org.hibernate.search.mapper.orm.Search;
import org.hibernate.search.mapper.orm.mapping.SearchMapping;
import org.hibernate.search.mapper.orm.session.SearchSession;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.jetbrains.annotations.NotNull;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
@ -76,20 +56,20 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FulltextSearchSvcImpl.class);
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
private EntityManager myEntityManager;
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
protected IForcedIdDao myForcedIdDao;
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
private EntityManager myEntityManager;
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
private IdHelperService myIdHelperService;
private Boolean ourDisabled;
@Autowired
private IRequestPartitionHelperSvc myRequestPartitionHelperService;
@Autowired
private PartitionSettings myPartitionSettings;
/**
* Constructor
@ -98,28 +78,28 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
super();
}
private void addTextSearch(SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, List<List<IQueryParameterType>> theTerms, String theFieldName, String theFieldNameEdgeNGram, String theFieldNameTextNGram){
private void addTextSearch(SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, List<List<IQueryParameterType>> theTerms, String theFieldName, String theFieldNameEdgeNGram, String theFieldNameTextNGram) {
if (theTerms == null) {
return;
}
for (List<? extends IQueryParameterType> nextAnd : theTerms) {
Set<String> terms = extractOrStringParams(nextAnd);
if (terms.size() == 1) {
b.must(f.phrase()
.field(theFieldName)
.boost(4.0f)
.matching(terms.iterator().next().toLowerCase())
.slop(2));
} else if (terms.size() > 1){
String joinedTerms = StringUtils.join(terms, ' ');
b.must(f.match().field(theFieldName).matching(joinedTerms));
} else {
ourLog.debug("No Terms found in query parameter {}", nextAnd);
}
if (terms.size() == 1) {
b.must(f.phrase()
.field(theFieldName)
.boost(4.0f)
.matching(terms.iterator().next().toLowerCase())
.slop(2));
} else if (terms.size() > 1) {
String joinedTerms = StringUtils.join(terms, ' ');
b.must(f.match().field(theFieldName).matching(joinedTerms));
} else {
ourLog.debug("No Terms found in query parameter {}", nextAnd);
}
}
}
@NotNull
@Nonnull
private Set<String> extractOrStringParams(List<? extends IQueryParameterType> nextAnd) {
Set<String> terms = new HashSet<>();
for (IQueryParameterType nextOr : nextAnd) {
@ -229,10 +209,4 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
return doSearch(theResourceName, theParams, null);
}
@Autowired
private IRequestPartitionHelperSvc myRequestPartitionHelperService;
@Autowired
private PartitionSettings myPartitionSettings;
}

219
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupport.java
View File

@ -46,9 +46,12 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
import javax.transaction.Transactional;
import java.util.Arrays;
import java.util.concurrent.TimeUnit;
import java.util.function.Supplier;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -104,110 +107,13 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
@Override
@SuppressWarnings({"unchecked", "unused"})
public <T extends IBaseResource> T fetchResource(Class<T> theClass, String theUri) {
public <T extends IBaseResource> T fetchResource(@Nullable Class<T> theClass, String theUri) {
if (isBlank(theUri)) {
return null;
}
String key = theClass.getSimpleName() + " " + theUri;
IBaseResource fetched = myLoadCache.get(key, t -> {
IdType id = new IdType(theUri);
boolean localReference = false;
if (id.hasBaseUrl() == false && id.hasIdPart() == true) {
localReference = true;
}
String resourceName = myFhirContext.getResourceType(theClass);
IBundleProvider search;
switch (resourceName) {
case "ValueSet":
if (localReference) {
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
params.add(IAnyResource.SP_RES_ID, new StringParam(theUri));
search = myDaoRegistry.getResourceDao(resourceName).search(params);
if (search.size() == 0) {
params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
params.add(ValueSet.SP_URL, new UriParam(theUri));
search = myDaoRegistry.getResourceDao(resourceName).search(params);
}
} else {
int versionSeparator = theUri.lastIndexOf('|');
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
if (versionSeparator != -1) {
params.add(ValueSet.SP_VERSION, new TokenParam(theUri.substring(versionSeparator + 1)));
params.add(ValueSet.SP_URL, new UriParam(theUri.substring(0, versionSeparator)));
} else {
params.add(ValueSet.SP_URL, new UriParam(theUri));
}
params.setSort(new SortSpec("_lastUpdated").setOrder(SortOrderEnum.DESC));
search = myDaoRegistry.getResourceDao(resourceName).search(params);
}
break;
case "StructureDefinition": {
// Don't allow the core FHIR definitions to be overwritten
if (theUri.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
String typeName = theUri.substring("http://hl7.org/fhir/StructureDefinition/".length());
if (myFhirContext.getElementDefinition(typeName) != null) {
return myNoMatch;
}
}
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
params.add(StructureDefinition.SP_URL, new UriParam(theUri));
search = myDaoRegistry.getResourceDao("StructureDefinition").search(params);
break;
}
case "Questionnaire": {
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
if (localReference || myFhirContext.getVersion().getVersion().isEquivalentTo(FhirVersionEnum.DSTU2)) {
params.add(IAnyResource.SP_RES_ID, new StringParam(id.getIdPart()));
} else {
params.add(Questionnaire.SP_URL, new UriParam(id.getValue()));
}
search = myDaoRegistry.getResourceDao("Questionnaire").search(params);
break;
}
case "CodeSystem": {
int versionSeparator = theUri.lastIndexOf('|');
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
if (versionSeparator != -1) {
params.add(CodeSystem.SP_VERSION, new TokenParam(theUri.substring(versionSeparator + 1)));
params.add(CodeSystem.SP_URL, new UriParam(theUri.substring(0, versionSeparator)));
} else {
params.add(CodeSystem.SP_URL, new UriParam(theUri));
}
params.setSort(new SortSpec("_lastUpdated").setOrder(SortOrderEnum.DESC));
search = myDaoRegistry.getResourceDao(resourceName).search(params);
break;
}
case "ImplementationGuide":
case "SearchParameter": {
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
params.add(ImplementationGuide.SP_URL, new UriParam(theUri));
search = myDaoRegistry.getResourceDao(resourceName).search(params);
break;
}
default:
throw new IllegalArgumentException("Can't fetch resource type: " + resourceName);
}
Integer size = search.size();
if (size == null || size == 0) {
return myNoMatch;
}
if (size > 1) {
ourLog.warn("Found multiple {} instances with URL search value of: {}", resourceName, theUri);
}
return search.getResources(0, 1).get(0);
});
String key = theClass + " " + theUri;
IBaseResource fetched = myLoadCache.get(key, t -> doFetchResource(theClass, theUri));
if (fetched == myNoMatch) {
return null;
@ -216,6 +122,119 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
return (T) fetched;
}
private <T extends IBaseResource> IBaseResource doFetchResource(@Nullable Class<T> theClass, String theUri) {
if (theClass == null) {
Supplier<IBaseResource>[] fetchers = new Supplier[]{
() -> doFetchResource(ValueSet.class, theUri),
() -> doFetchResource(CodeSystem.class, theUri),
() -> doFetchResource(StructureDefinition.class, theUri)
};
return Arrays
.stream(fetchers)
.map(t -> t.get())
.filter(t -> t != myNoMatch)
.findFirst()
.orElse(myNoMatch);
}
IdType id = new IdType(theUri);
boolean localReference = false;
if (id.hasBaseUrl() == false && id.hasIdPart() == true) {
localReference = true;
}
String resourceName = myFhirContext.getResourceType(theClass);
IBundleProvider search;
switch (resourceName) {
case "ValueSet":
if (localReference) {
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
params.add(IAnyResource.SP_RES_ID, new StringParam(theUri));
search = myDaoRegistry.getResourceDao(resourceName).search(params);
if (search.size() == 0) {
params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
params.add(ValueSet.SP_URL, new UriParam(theUri));
search = myDaoRegistry.getResourceDao(resourceName).search(params);
}
} else {
int versionSeparator = theUri.lastIndexOf('|');
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
if (versionSeparator != -1) {
params.add(ValueSet.SP_VERSION, new TokenParam(theUri.substring(versionSeparator + 1)));
params.add(ValueSet.SP_URL, new UriParam(theUri.substring(0, versionSeparator)));
} else {
params.add(ValueSet.SP_URL, new UriParam(theUri));
}
params.setSort(new SortSpec("_lastUpdated").setOrder(SortOrderEnum.DESC));
search = myDaoRegistry.getResourceDao(resourceName).search(params);
}
break;
case "StructureDefinition": {
// Don't allow the core FHIR definitions to be overwritten
if (theUri.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
String typeName = theUri.substring("http://hl7.org/fhir/StructureDefinition/".length());
if (myFhirContext.getElementDefinition(typeName) != null) {
return myNoMatch;
}
}
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
params.add(StructureDefinition.SP_URL, new UriParam(theUri));
search = myDaoRegistry.getResourceDao("StructureDefinition").search(params);
break;
}
case "Questionnaire": {
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
if (localReference || myFhirContext.getVersion().getVersion().isEquivalentTo(FhirVersionEnum.DSTU2)) {
params.add(IAnyResource.SP_RES_ID, new StringParam(id.getIdPart()));
} else {
params.add(Questionnaire.SP_URL, new UriParam(id.getValue()));
}
search = myDaoRegistry.getResourceDao("Questionnaire").search(params);
break;
}
case "CodeSystem": {
int versionSeparator = theUri.lastIndexOf('|');
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
if (versionSeparator != -1) {
params.add(CodeSystem.SP_VERSION, new TokenParam(theUri.substring(versionSeparator + 1)));
params.add(CodeSystem.SP_URL, new UriParam(theUri.substring(0, versionSeparator)));
} else {
params.add(CodeSystem.SP_URL, new UriParam(theUri));
}
params.setSort(new SortSpec("_lastUpdated").setOrder(SortOrderEnum.DESC));
search = myDaoRegistry.getResourceDao(resourceName).search(params);
break;
}
case "ImplementationGuide":
case "SearchParameter": {
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
params.add(ImplementationGuide.SP_URL, new UriParam(theUri));
search = myDaoRegistry.getResourceDao(resourceName).search(params);
break;
}
default:
throw new IllegalArgumentException("Can't fetch resource type: " + resourceName);
}
Integer size = search.size();
if (size == null || size == 0) {
return myNoMatch;
}
if (size > 1) {
ourLog.warn("Found multiple {} instances with URL search value of: {}", resourceName, theUri);
}
return search.getResources(0, 1).get(0);
}
@Override
public FhirContext getFhirContext() {
return myFhirContext;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/PartitionManagementProvider.java
View File

@ -29,9 +29,10 @@ import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.util.ParametersUtil;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.jetbrains.annotations.NotNull;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
import static ca.uhn.fhir.jpa.partition.PartitionLookupSvcImpl.validatePartitionIdSupplied;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.instance.model.api.IPrimitiveType.toValueOrNull;
@ -151,7 +152,7 @@ public class PartitionManagementProvider {
return retVal;
}
@NotNull
@Nonnull
private PartitionEntity parseInput(@OperationParam(name = ProviderConstants.PARTITION_MANAGEMENT_PARTITION_ID, min = 1, max = 1, typeName = "integer") IPrimitiveType<Integer> thePartitionId, @OperationParam(name = ProviderConstants.PARTITION_MANAGEMENT_PARTITION_NAME, min = 1, max = 1, typeName = "code") IPrimitiveType<String> thePartitionName, @OperationParam(name = ProviderConstants.PARTITION_MANAGEMENT_PARTITION_DESC, min = 0, max = 1, typeName = "string") IPrimitiveType<String> thePartitionDescription) {
PartitionEntity input = new PartitionEntity();
if (thePartitionId != null) {

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java
View File

@ -52,7 +52,6 @@ import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -191,7 +190,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
return retVal;
}
@NotNull
@Nonnull
private RequestPartitionId getRequestPartitionId() {
if (myRequestPartitionId == null) {
if (mySearchEntity.getResourceId() != null) {

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

@ -576,7 +576,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
return null;
}
@org.jetbrains.annotations.Nullable
@Nullable
private Integer getLoadSynchronousUpToOrNull(CacheControlDirective theCacheControlDirective) {
final Integer loadSynchronousUpTo;
if (theCacheControlDirective != null && theCacheControlDirective.isNoStore()) {

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

@ -32,13 +32,13 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.JsonParser;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.PostConstruct;
import java.io.IOException;
import java.util.Locale;
public class ValidatorResourceFetcher implements IResourceValidator.IValidatorResourceFetcher {
@ -61,7 +61,6 @@ public class ValidatorResourceFetcher implements IResourceValidator.IValidatorRe
}
@SuppressWarnings("ConstantConditions")
@Override
public Element fetch(Object appContext, String theUrl) throws FHIRException {
@ -94,13 +93,13 @@ public class ValidatorResourceFetcher implements IResourceValidator.IValidatorRe
}
@Override
public boolean resolveURL(Object appContext, String path, String url) throws IOException, FHIRException {
public boolean resolveURL(Object appContext, String path, String url, String type) throws FHIRException {
return true;
}
@Override
public byte[] fetchRaw(String url) throws IOException {
return new byte[0];
public byte[] fetchRaw(String url) {
throw new UnsupportedOperationException();
}
@Override
@ -108,4 +107,14 @@ public class ValidatorResourceFetcher implements IResourceValidator.IValidatorRe
// ignore
}
@Override
public CanonicalResource fetchCanonicalResource(String url) {
throw new UnsupportedOperationException();
}
@Override
public boolean fetchesCanonicalResource(String url) {
return false;
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2ValidateTest.java
View File

@ -144,7 +144,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
} catch (PreconditionFailedException e) {
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome());
ourLog.info(ooString);
assertThat(ooString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
assertThat(ooString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' has not been checked because it is unknown"));
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java
View File

@ -333,7 +333,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
ourLog.info(outputString);
assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' has not been checked because it is unknown"));
}
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
View File

@ -1138,7 +1138,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
org.hl7.fhir.r4.model.OperationOutcome oo = (org.hl7.fhir.r4.model.OperationOutcome) e.getOperationOutcome();
String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
ourLog.info(outputString);
assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' has not been checked because it is unknown"));
}
}
@ -1174,7 +1174,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
org.hl7.fhir.r4.model.OperationOutcome oo = (org.hl7.fhir.r4.model.OperationOutcome) e.getOperationOutcome();
String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
ourLog.info(outputString);
assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' has not been checked because it is unknown"));
}
}

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/partition/PartitionManagementProviderTest.java
View File

@ -12,7 +12,6 @@ import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.jetbrains.annotations.NotNull;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
@ -28,6 +27,8 @@ import org.springframework.context.annotation.Configuration;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import javax.annotation.Nonnull;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any;
@ -87,7 +88,7 @@ public class PartitionManagementProviderTest {
assertEquals("a description", ((StringType) response.getParameter(ProviderConstants.PARTITION_MANAGEMENT_PARTITION_DESC)).getValue());
}
@NotNull
@Nonnull
private Parameters createInputPartition() {
Parameters input = new Parameters();
input.addParameter(ProviderConstants.PARTITION_MANAGEMENT_PARTITION_ID, new IntegerType(123));
@ -248,7 +249,7 @@ public class PartitionManagementProviderTest {
}
@NotNull
@Nonnull
private static Answer<Object> createAnswer() {
return t -> t.getArgument(0, PartitionEntity.class);
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
View File

@ -2403,7 +2403,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
String respString = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
ourLog.info(respString);
assertEquals(412, resp.getStatusLine().getStatusCode());
assertThat(respString, containsString("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked"));
assertThat(respString, containsString("Profile reference 'http://foo/structuredefinition/myprofile' has not been checked because it is unknown"));
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/config/TestElasticsearchContainerHelper.java
View File

@ -14,7 +14,7 @@ import static java.time.temporal.ChronoUnit.SECONDS;
public class TestElasticsearchContainerHelper {
public static final String ELASTICSEARCH_VERSION = "7.10.0";
public static final String ELASTICSEARCH_VERSION = "7.10.2";
public static final String ELASTICSEARCH_IMAGE = "docker.elastic.co/elasticsearch/elasticsearch:" + ELASTICSEARCH_VERSION;
public static ElasticsearchContainer getEmbeddedElasticSearch() {

10
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmControllerSvcImpl.java
View File

@ -20,23 +20,23 @@ package ca.uhn.fhir.jpa.mdm.svc;
* #L%
*/
import ca.uhn.fhir.mdm.api.MdmLinkJson;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.api.IGoldenResourceMergerSvc;
import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
import ca.uhn.fhir.mdm.api.IMdmLinkQuerySvc;
import ca.uhn.fhir.mdm.api.IMdmLinkUpdaterSvc;
import ca.uhn.fhir.mdm.api.IGoldenResourceMergerSvc;
import ca.uhn.fhir.mdm.api.MdmLinkJson;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.provider.MdmControllerHelper;
import ca.uhn.fhir.mdm.provider.MdmControllerUtil;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.jetbrains.annotations.Nullable;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import javax.annotation.Nullable;
import java.util.stream.Stream;
/**

17
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmResourceDaoSvc.java
View File

@ -20,23 +20,23 @@ package ca.uhn.fhir.jpa.mdm.svc;
* #L%
*/
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.jetbrains.annotations.NotNull;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import javax.annotation.Nonnull;
import java.util.List;
import java.util.Optional;
@ -60,10 +60,11 @@ public class MdmResourceDaoSvc {
}
/**
* Given a resource, remove its Golden Resource tag.
* @param theGoldenResource the {@link IAnyResource} to remove the tag from.
* @param theResourcetype the type of that resource
*/
* Given a resource, remove its Golden Resource tag.
*
* @param theGoldenResource the {@link IAnyResource} to remove the tag from.
* @param theResourcetype the type of that resource
*/
public void removeGoldenResourceTag(IAnyResource theGoldenResource, String theResourcetype) {
IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theResourcetype);
resourceDao.removeTag(theGoldenResource.getIdElement(), TagTypeEnum.TAG, MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS, MdmConstants.CODE_GOLDEN_RECORD);
@ -99,7 +100,7 @@ public class MdmResourceDaoSvc {
}
}
@NotNull
@Nonnull
private SearchParameterMap buildEidSearchParameterMap(String theTheEid) {
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);

3
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java
View File

@ -48,7 +48,6 @@ import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Reference;
import org.jetbrains.annotations.NotNull;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.extension.ExtendWith;
@ -431,7 +430,7 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
return getPatientsByTag(MdmConstants.CODE_GOLDEN_RECORD_REDIRECTED);
}
@NotNull
@Nonnull
private List<IBaseResource> getPatientsByTag(String theCode) {
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);

3
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableColumnTypeTask.java
View File

@ -23,7 +23,8 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.jetbrains.annotations.Nullable;
import javax.annotation.Nullable;
public abstract class BaseTableColumnTypeTask extends BaseTableColumnTask {
private ColumnTypeEnum myColumnType;

19
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/interceptor/FhirPathFilterInterceptorTest.java
View File

@ -13,6 +13,7 @@ import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
@ -95,6 +96,19 @@ public class FhirPathFilterInterceptorTest {
}
@Test
public void testFilteredResponse_ExpressionReturnsExtension() throws IOException {
createPatient();
HttpGet request = new HttpGet(myPatientId + "?_fhirpath=Patient.extension('http://hl7.org/fhir/us/core/StructureDefinition/us-core-race')&_pretty=true");
try (CloseableHttpResponse response = myHttpClient.execute(request)) {
String responseText = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
ourLog.info("Response:\n{}", responseText);
assertThat(responseText, containsString("\"url\": \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-race\""));
}
}
@Test
public void testFilteredResponse_ExpressionReturnsResource() throws IOException {
createPatient();
@ -159,6 +173,11 @@ public class FhirPathFilterInterceptorTest {
private void createPatient() {
Patient p = new Patient();
p.addExtension()
.setUrl("http://hl7.org/fhir/us/core/StructureDefinition/us-core-race")
.addExtension()
.setUrl("ombCategory")
.setValue(new Coding("urn:oid:2.16.840.1.113883.6.238", "2106-3", "White"));
p.setActive(true);
p.addIdentifier().setSystem("http://identifiers/1").setValue("value-1");
p.addIdentifier().setSystem("http://identifiers/2").setValue("value-2");

43
hapi-fhir-structures-r5/pom.xml
View File

@ -107,7 +107,7 @@
</dependency>
<!--
Optional dependencies used by org.hl7.fhir.r4
Optional dependencies used by org.hl7.fhir.r5
We include these here to get the aggregate JavaDoc to work
-->
<dependency>
@ -133,6 +133,11 @@
<artifactId>gson</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.jetbrains</groupId>
<artifactId>annotations</artifactId>
<optional>true</optional>
</dependency>
<!-- Testing -->
<dependency>
@ -181,12 +186,12 @@
<artifactId>thymeleaf</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<!-- Dependencies for Schematron -->
<dependency>
@ -209,16 +214,6 @@
<artifactId>jaxb-api</artifactId>
<scope>test</scope>
</dependency>
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-core</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<!--<dependency>-->
<!--<groupId>com.sun.xml.bind</groupId>-->
<!--<artifactId>jaxb-impl</artifactId>-->
<!--<scope>test</scope>-->
<!--</dependency>-->
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
@ -344,13 +339,13 @@
<extensions>true</extensions>
<configuration>
<instructions>
<_nouses>true</_nouses>
<_removeheaders>Built-By, Include-Resource, Private-Package, Require-Capability</_removeheaders>
<!-- No need to disable normal OSGi class loading
<Fragment-Host>
ca.uhn.hapi.fhir.hapi-fhir-base
</Fragment-Host>
-->
<_nouses>true</_nouses>
<_removeheaders>Built-By, Include-Resource, Private-Package, Require-Capability</_removeheaders>
<!-- No need to disable normal OSGi class loading
<Fragment-Host>
ca.uhn.hapi.fhir.hapi-fhir-base
</Fragment-Host>
-->
</instructions>
</configuration>
</plugin>

10
hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/ctx/HapiWorkerContext.java
View File

@ -287,6 +287,11 @@ public final class HapiWorkerContext extends I18nBase implements IWorkerContext
return myCtx.getVersion().getVersion().getFhirVersionString();
}
@Override
public String getSpecUrl() {
throw new UnsupportedOperationException();
}
@Override
public UcumService getUcumService() {
throw new UnsupportedOperationException();
@ -302,6 +307,11 @@ public final class HapiWorkerContext extends I18nBase implements IWorkerContext
return false;
}
@Override
public Set<String> getCodeSystemsUsed() {
throw new UnsupportedOperationException();
}
@Override
public TranslationServices translator() {
throw new UnsupportedOperationException();

4
hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/fhirpath/FhirPathR5.java
View File

@ -30,9 +30,9 @@ public class FhirPathR5 implements IFhirPath {
result = myEngine.evaluate((Base) theInput, thePath);
} catch (FHIRException e) {
throw new FhirPathExecutionException(e);
}
}
for (Base next : result) {
for (Base next : result) {
if (!theReturnType.isAssignableFrom(next.getClass())) {
throw new FhirPathExecutionException("FluentPath expression \"" + thePath + "\" returned unexpected type " + next.getClass().getSimpleName() + " - Expected " + theReturnType.getName());
}

7
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CachingValidationSupport.java
View File

@ -6,14 +6,13 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import com.github.benmanes.caffeine.cache.Cache;
import com.github.benmanes.caffeine.cache.Caffeine;
import org.checkerframework.checker.nullness.qual.Nullable;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.List;
import java.util.Optional;
import java.util.concurrent.TimeUnit;
@ -64,8 +63,8 @@ public class CachingValidationSupport extends BaseValidationSupportWrapper imple
}
@Override
public <T extends IBaseResource> T fetchResource(Class<T> theClass, String theUri) {
return loadFromCache(myCache, "fetchResource " + theClass.getName() + " " + theUri,
public <T extends IBaseResource> T fetchResource(@Nullable Class<T> theClass, String theUri) {
return loadFromCache(myCache, "fetchResource " + theClass + " " + theUri,
t -> super.fetchResource(theClass, theUri));
}

2
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/FhirInstanceValidator.java
View File

@ -32,7 +32,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
private boolean noExtensibleWarnings = false;
private boolean noBindingMsgSuppressed = false;
private volatile VersionSpecificWorkerContextWrapper myWrappedWorkerContext;
private boolean errorForUnknownProfiles;
private boolean errorForUnknownProfiles = true;
private boolean assumeValidRestReferences;
private List<String> myExtensionDomains = Collections.emptyList();
private IResourceValidator.IValidatorResourceFetcher validatorResourceFetcher;

3
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/HapiToHl7OrgDstu2ValidatingSupportWrapper.java
View File

@ -61,6 +61,9 @@ public class HapiToHl7OrgDstu2ValidatingSupportWrapper extends BaseValidationSup
}
private Class<? extends IBaseResource> translateTypeToHapi(Class<? extends IBaseResource> theCodeSystemType) {
if (theCodeSystemType == null) {
return null;
}
String resName = getFhirContext().getResourceType(theCodeSystemType);
return myHapiCtx.getResourceDefinition(resName).getImplementingClass();
}

11
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/ValidatorWrapper.java
View File

@ -17,6 +17,7 @@ import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.slf4j.Logger;
@ -103,8 +104,9 @@ class ValidatorWrapper {
public List<ValidationMessage> validate(IWorkerContext theWorkerContext, IValidationContext<?> theValidationContext) {
InstanceValidator v;
FHIRPathEngine.IEvaluationContext evaluationCtx = new FhirInstanceValidator.NullEvaluationContext();
XVerExtensionManager xverManager = new XVerExtensionManager(theWorkerContext);
try {
v = new InstanceValidator(theWorkerContext, evaluationCtx);
v = new InstanceValidator(theWorkerContext, evaluationCtx, xverManager);
} catch (Exception e) {
throw new ConfigurationException(e);
}
@ -193,7 +195,12 @@ class ValidatorWrapper {
i--;
}
if (message.endsWith("' could not be resolved, so has not been checked") && next.getLevel() == ValidationMessage.IssueSeverity.WARNING) {
if (
myErrorForUnknownProfiles &&
next.getLevel() == ValidationMessage.IssueSeverity.WARNING &&
message.contains("Profile reference '") &&
message.contains("' has not been checked because it is unknown")
) {
next.setLevel(ValidationMessage.IssueSeverity.ERROR);
}

20
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/VersionSpecificWorkerContextWrapper.java
View File

@ -81,13 +81,15 @@ public class VersionSpecificWorkerContextWrapper extends I18nBase implements IWo
fetchResourceName = "ValueSet";
}
}
Class<? extends IBaseResource> fetchResourceType = myValidationSupportContext.getRootValidationSupport().getFhirContext().getResourceDefinition(fetchResourceName).getImplementingClass();
IBaseResource fetched = myValidationSupportContext.getRootValidationSupport().fetchResource(fetchResourceType, key.getUri());
if (fetched == null) {
return null;
Class<? extends IBaseResource> fetchResourceType;
if (fetchResourceName.equals("Resource")) {
fetchResourceType = null;
} else {
fetchResourceType = myValidationSupportContext.getRootValidationSupport().getFhirContext().getResourceDefinition(fetchResourceName).getImplementingClass();
}
IBaseResource fetched = myValidationSupportContext.getRootValidationSupport().fetchResource(fetchResourceType, key.getUri());
Resource canonical = myModelConverter.toCanonical(fetched);
@ -425,6 +427,11 @@ public class VersionSpecificWorkerContextWrapper extends I18nBase implements IWo
return myValidationSupportContext.getRootValidationSupport().getFhirContext().getVersion().getVersion().getFhirVersionString();
}
@Override
public String getSpecUrl() {
throw new UnsupportedOperationException();
}
@Override
public boolean hasCache() {
throw new UnsupportedOperationException();
@ -440,6 +447,11 @@ public class VersionSpecificWorkerContextWrapper extends I18nBase implements IWo
return false;
}
@Override
public Set<String> getCodeSystemsUsed() {
throw new UnsupportedOperationException();
}
@Override
public List<org.hl7.fhir.r5.model.StructureMap> listTransforms() {
throw new UnsupportedOperationException();

6
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidatorDstu3Test.java
View File

@ -664,6 +664,8 @@ public class FhirInstanceValidatorDstu3Test {
} else if (t.getMessage().contains("ValueSet as a URI SHALL start with http:// or https:// or urn:")) {
// Some DSTU3 structures have missing binding information
return false;
} else if (t.getMessage().contains("The valueSet reference http://www.rfc-editor.org/bcp/bcp13.txt on element")) {
return false;
} else {
return true;
}
@ -1135,7 +1137,7 @@ public class FhirInstanceValidatorDstu3Test {
myInstanceVal.setValidationSupport(myValidationSupport);
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertThat(errors.toString(), containsString("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked"));
assertThat(errors.toString(), containsString("Profile reference 'http://foo/structuredefinition/myprofile' has not been checked because it is unknown"));
}
@Test
@ -1314,7 +1316,7 @@ public class FhirInstanceValidatorDstu3Test {
myInstanceVal.setValidatorResourceFetcher(resourceFetcher);
myVal.validateWithResult(input);
verify(resourceFetcher, times(3)).resolveURL(any(), anyString(), anyString());
verify(resourceFetcher, times(3)).resolveURL(any(), anyString(), anyString(), anyString());
verify(resourceFetcher, times(4)).validationPolicy(any(), anyString(), anyString());
verify(resourceFetcher, times(4)).fetch(any(), anyString());
}

2
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/QuestionnaireResponseValidatorDstu3Test.java
View File

@ -254,7 +254,7 @@ public class QuestionnaireResponseValidatorDstu3Test {
errors = myVal.validateWithResult(qa);
errors = stripBindingHasNoSourceMessage(errors);
ourLog.info(errors.toString());
assertThat(errors.toString(), containsString("Unknown code: http://codesystems.com/system / code1 - QuestionnaireResponse.item[0].answer[0].value.ofType(Coding)"));
assertThat(errors.toString(), containsString("Unknown code: http://codesystems.com/system / code1 for 'http://codesystems.com/system#code1'"));
assertThat(errors.toString(), containsString("QuestionnaireResponse.item[0].answer[0]"));
// Unhandled system

4
hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
View File

@ -1152,7 +1152,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertEquals(1, errors.size());
assertEquals("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked", errors.get(0).getMessage());
assertEquals("Profile reference 'http://foo/structuredefinition/myprofile' has not been checked because it is unknown", errors.get(0).getMessage());
assertEquals(ResultSeverityEnum.ERROR, errors.get(0).getSeverity());
}
@ -1402,7 +1402,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
myInstanceVal.setValidatorResourceFetcher(resourceFetcher);
myVal.validateWithResult(encoded);
verify(resourceFetcher, times(15)).resolveURL(any(), anyString(), anyString());
verify(resourceFetcher, times(15)).resolveURL(any(), anyString(), anyString(), anyString());
verify(resourceFetcher, times(12)).validationPolicy(any(), anyString(), anyString());
verify(resourceFetcher, times(12)).fetch(any(), anyString());
}

6
hapi-fhir-validation/src/test/java/org/hl7/fhir/r5/validation/FhirInstanceValidatorR5Test.java
View File

@ -432,8 +432,8 @@ public class FhirInstanceValidatorR5Test {
myInstanceVal.setValidatorResourceFetcher(resourceFetcher);
myVal.validateWithResult(input);
verify(resourceFetcher, times(13)).resolveURL(any(), anyString(), anyString());
verify(resourceFetcher, times(3)).validationPolicy(any(), anyString(), anyString());
verify(resourceFetcher, times(13)).resolveURL(any(), anyString(), anyString(), anyString());
verify(resourceFetcher, times(4)).validationPolicy(any(), anyString(), anyString());
verify(resourceFetcher, times(3)).fetch(any(), anyString());
}
@ -794,7 +794,7 @@ public class FhirInstanceValidatorR5Test {
myInstanceVal.setValidationSupport(myValidationSupport);
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertThat(errors.toString(), containsString("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked"));
assertThat(errors.toString(), containsString("Profile reference 'http://foo/structuredefinition/myprofile' has not been checked because it is unknown"));
}
@Test

4
pom.xml
View File

@ -712,7 +712,7 @@
<properties>
<fhir_core_version>5.2.0</fhir_core_version>
<fhir_core_version>5.2.16</fhir_core_version>
<ucum_version>1.0.3</ucum_version>
<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>
@ -1462,7 +1462,7 @@
<dependency>
<groupId>org.elasticsearch.client</groupId>
<artifactId>elasticsearch-rest-high-level-client</artifactId>
<version>7.10.0</version>
<version>7.10.2</version>
</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>