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Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
James Agnew 2017-02-07 12:24:35 -05:00
parent ad781334d8 21ea5a070f
commit d28122ff3e
25 changed files with 813 additions and 458 deletions
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6
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/GenericClient.java
View File

@ -1889,7 +1889,11 @@ public class GenericClient extends BaseClient implements IGenericClient {
}
for (Include next : myRevInclude) {
addParam(params, Constants.PARAM_REVINCLUDE, next.getValue());
if (next.isRecurse()) {
addParam(params, Constants.PARAM_REVINCLUDE_RECURSE, next.getValue());
} else {
addParam(params, Constants.PARAM_REVINCLUDE, next.getValue());
}
}
if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU2)) {

13
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/Constants.java
View File

@ -40,11 +40,13 @@ public class Constants {
public static final String CT_HTML = "text/html";
public static final String CT_HTML_WITH_UTF8 = "text/html" + CHARSET_UTF8_CTSUFFIX;
public static final String CT_JSON = "application/json";
public static final String CT_JSON_PATCH = "application/json-patch+json";
public static final String CT_OCTET_STREAM = "application/octet-stream";
public static final String CT_TEXT = "text/plain";
public static final String CT_TEXT_WITH_UTF8 = CT_TEXT + CHARSET_UTF8_CTSUFFIX;
public static final String CT_X_FORM_URLENCODED = "application/x-www-form-urlencoded";
public static final String CT_XML = "application/xml";
public static final String CT_XML_PATCH = "application/xml-patch+xml";
public static final String ENCODING_GZIP = "gzip";
public static final String EXTOP_VALIDATE = "$validate";
public static final String EXTOP_VALIDATE_MODE = "mode";
@ -61,10 +63,10 @@ public class Constants {
public static final String FORMATS_HTML_XML = "html/xml";
public static final String HEADER_ACCEPT = "Accept";
public static final String HEADER_ACCEPT_ENCODING = "Accept-Encoding";
public static final String HEADER_ACCEPT_VALUE_JSON_NON_LEGACY = CT_FHIR_JSON_NEW + ";q=1.0, " + CT_FHIR_JSON + ";q=0.9";
public static final String HEADER_ACCEPT_VALUE_XML_NON_LEGACY = CT_FHIR_XML_NEW + ";q=1.0, " + CT_FHIR_XML + ";q=0.9";
public static final String HEADER_ACCEPT_VALUE_XML_OR_JSON_LEGACY = CT_FHIR_XML + ";q=1.0, " + CT_FHIR_JSON + ";q=1.0";
public static final String HEADER_ACCEPT_VALUE_XML_OR_JSON_NON_LEGACY = CT_FHIR_XML_NEW + ";q=1.0, " + CT_FHIR_JSON_NEW + ";q=1.0, " + HEADER_ACCEPT_VALUE_XML_OR_JSON_LEGACY.replace("1.0", "0.9");
public static final String HEADER_ACCEPT_VALUE_XML_NON_LEGACY = CT_FHIR_XML_NEW + ";q=1.0, " + CT_FHIR_XML + ";q=0.9";
public static final String HEADER_ACCEPT_VALUE_JSON_NON_LEGACY = CT_FHIR_JSON_NEW + ";q=1.0, " + CT_FHIR_JSON + ";q=0.9";
public static final String HEADER_ALLOW = "Allow";
public static final String HEADER_AUTHORIZATION = "Authorization";
public static final String HEADER_AUTHORIZATION_VALPREFIX_BASIC = "Basic ";
@ -127,10 +129,12 @@ public class Constants {
public static final String PARAM_PAGINGACTION = "_getpages";
public static final String PARAM_PAGINGOFFSET = "_getpagesoffset";
public static final String PARAM_PRETTY = "_pretty";
public static final String PARAM_PRETTY_VALUE_FALSE = "false";
public static final String PARAM_PRETTY_VALUE_TRUE = "true";
public static final String PARAM_PROFILE = "_profile";
public static final String PARAM_QUERY = "_query";
public static final String PARAM_REVINCLUDE = "_revinclude";
public static final String PARAM_REVINCLUDE_RECURSE = PARAM_REVINCLUDE+PARAM_INCLUDE_QUALIFIER_RECURSE;
public static final String PARAM_SEARCH = "_search";
public static final String PARAM_SECURITY = "_security";
public static final String PARAM_SINCE = "_since";
@ -156,11 +160,11 @@ public class Constants {
public static final int STATUS_HTTP_401_CLIENT_UNAUTHORIZED = 401;
public static final int STATUS_HTTP_403_FORBIDDEN = 403;
public static final int STATUS_HTTP_404_NOT_FOUND = 404;
public static final int STATUS_HTTP_405_METHOD_NOT_ALLOWED = 405;
public static final int STATUS_HTTP_409_CONFLICT = 409;
public static final int STATUS_HTTP_410_GONE = 410;
public static final int STATUS_HTTP_412_PRECONDITION_FAILED = 412;
public static final int STATUS_HTTP_422_UNPROCESSABLE_ENTITY = 422;
public static final int STATUS_HTTP_500_INTERNAL_ERROR = 500;
public static final int STATUS_HTTP_501_NOT_IMPLEMENTED = 501;
@ -168,9 +172,6 @@ public class Constants {
public static final String TAG_SUBSETTED_SYSTEM = "http://hl7.org/fhir/v3/ObservationValue";
public static final String URL_TOKEN_HISTORY = "_history";
public static final String URL_TOKEN_METADATA = "metadata";
public static final String CT_JSON_PATCH = "application/json-patch+json";
public static final String CT_XML_PATCH = "application/xml-patch+xml";
public static final String PARAM_PRETTY_VALUE_FALSE = "false";
static {
CHARSET_UTF8 = Charset.forName(CHARSET_NAME_UTF8);

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ParametersUtil.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.util;
import java.util.Collection;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseParameters;
@ -84,6 +85,7 @@ public class ParametersUtil {
}
public static IBaseParameters newInstance(FhirContext theContext) {
Validate.notNull(theContext, "theContext must not be null");
return (IBaseParameters) theContext.getResourceDefinition("Parameters").newInstance();
}
}

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java
View File

@ -101,6 +101,7 @@ public class BaseDstu2Config extends BaseConfig {
public ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2 systemProviderDstu2() {
ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2 retVal = new ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2();
retVal.setDao(systemDaoDstu2());
retVal.setContext(fhirContextDstu2());
return retVal;
}

143
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -22,29 +22,15 @@ package ca.uhn.fhir.jpa.dao;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.*;
import java.util.Map.Entry;
import java.util.Set;
import java.util.TreeSet;
import javax.annotation.PostConstruct;
import javax.persistence.NoResultException;
import javax.persistence.TypedQuery;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseMetaType;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
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.hl7.fhir.instance.model.api.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Required;
import org.springframework.transaction.PlatformTransactionManager;
@ -59,42 +45,21 @@ import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.BaseHasResource;
import ca.uhn.fhir.jpa.entity.BaseTag;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.entity.ResourceLink;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TagDefinition;
import ca.uhn.fhir.jpa.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.interceptor.IJpaServerInterceptor;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.util.DeleteConflict;
import ca.uhn.fhir.jpa.util.StopWatch;
import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils;
import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.method.MethodUtil;
import ca.uhn.fhir.rest.method.QualifiedParamList;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.method.SearchMethodBinding;
import ca.uhn.fhir.rest.method.*;
import ca.uhn.fhir.rest.method.SearchMethodBinding.QualifierDetails;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.FhirTerser;
@ -110,14 +75,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Autowired
private DaoConfig myDaoConfig;
@Autowired
protected IResourceTableDao myResourceTableDao;
@Autowired
protected PlatformTransactionManager myPlatformTransactionManager;
@Autowired
private IResourceHistoryTableDao myResourceHistoryTableDao;
@Autowired()
protected IResourceIndexedSearchParamUriDao myResourceIndexedSearchParamUriDao;
private String myResourceName;
@Autowired
protected IResourceTableDao myResourceTableDao;
private Class<T> myResourceType;
@Autowired(required = false)
protected IFulltextSearchSvc mySearchDao;
@ -226,7 +191,9 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
T resourceToDelete = toResource(myResourceType, entity, false);
validateOkToDelete(deleteConflicts, entity);
preDelete(resourceToDelete);
// Notify interceptors
if (theRequestDetails != null) {
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getContext(), theId.getResourceType(), theId);
@ -259,10 +226,18 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", 1, w.getMillis());
String severity = "information";
String code = "informational";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
ourLog.info("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
return toMethodOutcome(savedEntity, null);
DaoMethodOutcome retVal = toMethodOutcome(savedEntity, null);
retVal.setOperationOutcome(oo);
return retVal;
}
@Override
public List<ResourceTable> deleteByUrl(String theUrl, List<DeleteConflict> deleteConflicts, RequestDetails theRequestDetails) {
Set<Long> resource = processMatchUrl(theUrl, myResourceType);
@ -301,7 +276,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return retVal;
}
@Override
public DaoMethodOutcome deleteByUrl(String theUrl, RequestDetails theRequestDetails) {
StopWatch w = new StopWatch();
@ -320,7 +295,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
} else {
oo = OperationOutcomeUtil.newInstance(getContext());
String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", theUrl, deletedResources.size(), w.getMillis());
String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", deletedResources.size(), w.getMillis());
String severity = "information";
String code = "informational";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
@ -553,6 +528,38 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return retVal;
}
@Override
public <MT extends IBaseMetaType> MT metaDeleteOperation(IIdType theResourceId, MT theMetaDel, RequestDetails theRequestDetails) {
// Notify interceptors
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theResourceId);
notifyInterceptors(RestOperationTypeEnum.META_DELETE, requestDetails);
StopWatch w = new StopWatch();
BaseHasResource entity = readEntity(theResourceId);
if (entity == null) {
throw new ResourceNotFoundException(theResourceId);
}
ResourceTable latestVersion = readEntityLatestVersion(theResourceId);
if (latestVersion.getVersion() != entity.getVersion()) {
doMetaDelete(theMetaDel, entity);
} else {
doMetaDelete(theMetaDel, latestVersion);
// Also update history entry
ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersion(entity.getId(), entity.getVersion());
doMetaDelete(theMetaDel, history);
}
myEntityManager.flush();
ourLog.info("Processed metaDeleteOperation on {} in {}ms", new Object[] { theResourceId.getValue(), w.getMillisAndRestart() });
@SuppressWarnings("unchecked")
MT retVal = (MT) metaGetOperation(theMetaDel.getClass(), theResourceId, theRequestDetails);
return retVal;
}
// @Override
// public IBundleProvider everything(IIdType theId) {
// Search search = new Search();
@ -635,38 +642,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
// };
// }
@Override
public <MT extends IBaseMetaType> MT metaDeleteOperation(IIdType theResourceId, MT theMetaDel, RequestDetails theRequestDetails) {
// Notify interceptors
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theResourceId);
notifyInterceptors(RestOperationTypeEnum.META_DELETE, requestDetails);
StopWatch w = new StopWatch();
BaseHasResource entity = readEntity(theResourceId);
if (entity == null) {
throw new ResourceNotFoundException(theResourceId);
}
ResourceTable latestVersion = readEntityLatestVersion(theResourceId);
if (latestVersion.getVersion() != entity.getVersion()) {
doMetaDelete(theMetaDel, entity);
} else {
doMetaDelete(theMetaDel, latestVersion);
// Also update history entry
ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersion(entity.getId(), entity.getVersion());
doMetaDelete(theMetaDel, history);
}
myEntityManager.flush();
ourLog.info("Processed metaDeleteOperation on {} in {}ms", new Object[] { theResourceId.getValue(), w.getMillisAndRestart() });
@SuppressWarnings("unchecked")
MT retVal = (MT) metaGetOperation(theMetaDel.getClass(), theResourceId, theRequestDetails);
return retVal;
}
@Override
public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, IIdType theId, RequestDetails theRequestDetails) {
// Notify interceptors
@ -743,6 +718,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
/**
* Subclasses may override to provide behaviour. Invoked within a delete
* transaction with the resource that is about to be deleted.
*/
protected void preDelete(T theResourceToDelete) {
// nothing by default
}
/**
* May be overridden by subclasses to validate resources prior to storage
*

22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
View File

@ -27,6 +27,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.locks.ReentrantLock;
import javax.persistence.Query;
import javax.persistence.Tuple;
@ -64,15 +65,17 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirSystemDao.class);
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
private IForcedIdDao myForcedIdDao;
private ReentrantLock myReindexLock = new ReentrantLock(false);
@Autowired
private ITermConceptDao myTermConceptDao;
@Autowired
private PlatformTransactionManager myTxManager;
@Transactional(propagation = Propagation.REQUIRED)
@Override
public void deleteAllTagsOnServer(RequestDetails theRequestDetails) {
@ -205,8 +208,14 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
@Transactional()
@Override
public int markAllResourcesForReindexing() {
ourLog.info("Marking all resources as needing reindexing");
int retVal = myEntityManager.createQuery("UPDATE " + ResourceTable.class.getSimpleName() + " t SET t.myIndexStatus = null").executeUpdate();
ourLog.info("Marking all concepts as needing reindexing");
retVal += myTermConceptDao.markAllForReindexing();
ourLog.info("Done marking reindexing");
return retVal;
}
@ -266,16 +275,21 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
}
});
}
@Override
@Transactional(propagation = Propagation.NOT_SUPPORTED)
public int performReindexingPass(final Integer theCount) {
if (!myReindexLock.tryLock()) {
return 0;
}
try {
return doPerformReindexingPass(theCount);
} catch (ReindexFailureException e) {
ourLog.warn("Reindexing failed for resource {}", e.getResourceId());
markResourceAsIndexingFailed(e.getResourceId());
return -1;
} finally {
myReindexLock.unlock();
}
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptParentChildLinkDao.java
View File

@ -1,5 +1,7 @@
package ca.uhn.fhir.jpa.dao.data;
import java.util.Collection;
/*
* #%L
* HAPI FHIR JPA Server
@ -32,5 +34,8 @@ public interface ITermConceptParentChildLinkDao extends JpaRepository<TermConcep
@Query("DELETE FROM TermConceptParentChildLink t WHERE t.myCodeSystem.myId = :cs_pid")
@Modifying
void deleteByCodeSystemVersion(@Param("cs_pid") Long thePid);
@Query("SELECT t FROM TermConceptParentChildLink t WHERE t.myChildPid = :child_pid")
Collection<TermConceptParentChildLink> findAllWithChild(@Param("child_pid") Long theConceptPid);
}

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -41,6 +41,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
@ -187,6 +188,9 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
return retVal;
}
@Autowired
private ITermCodeSystemVersionDao myCsvDao;
@Override
protected ResourceTable updateEntity(IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime) {
@ -198,12 +202,22 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
String codeSystemUrl = cs.getUrl();
if (cs.getContent() == CodeSystemContentMode.COMPLETE || cs.getContent() == null) {
ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", retVal.getIdDt().getValue(), cs.getContentElement().getValueAsString());
TermCodeSystemVersion persCs = new TermCodeSystemVersion();
persCs.setResource(retVal);
persCs.setResourceVersionId(retVal.getVersion());
persCs.getConcepts().addAll(toPersistedConcepts(cs.getConcept(), persCs));
Long codeSystemResourcePid = retVal.getId();
TermCodeSystemVersion persCs = myCsvDao.findByCodeSystemResourceAndVersion(codeSystemResourcePid, retVal.getVersion());
if (persCs != null) {
ourLog.info("Code system version already exists in database");
} else {
persCs = new TermCodeSystemVersion();
persCs.setResource(retVal);
persCs.setResourceVersionId(retVal.getVersion());
persCs.getConcepts().addAll(toPersistedConcepts(cs.getConcept(), persCs));
ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, persCs);
}
myTerminologySvc.storeNewCodeSystemVersion(retVal.getId(), codeSystemUrl, persCs);
}
}

53
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSearchParameterDstu3.java
View File

@ -2,6 +2,8 @@ package ca.uhn.fhir.jpa.dao.dstu3;
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.util.List;
/*
* #%L
* HAPI FHIR JPA Server
@ -33,6 +35,7 @@ import ca.uhn.fhir.jpa.dao.BaseSearchParamExtractor;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSearchParameter;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.util.DeleteConflict;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@ -45,13 +48,16 @@ public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<Se
private IFhirSystemDao<Bundle, Meta> mySystemDao;
private void markAffectedResources(SearchParameter theResource) {
String xpath = theResource.getXpath();
String resourceType = xpath.substring(0, xpath.indexOf('.'));
ourLog.info("Marking all resources of type {} for reindexing due to updated search parameter with path: {}", xpath);
int updatedCount = myResourceTableDao.markResourcesOfTypeAsRequiringReindexing(resourceType);
ourLog.info("Marked {} resources for reindexing", updatedCount);
if (theResource != null) {
String expression = theResource.getExpression();
String resourceType = expression.substring(0, expression.indexOf('.'));
ourLog.info("Marking all resources of type {} for reindexing due to updated search parameter with path: {}", expression);
int updatedCount = myResourceTableDao.markResourcesOfTypeAsRequiringReindexing(resourceType);
ourLog.info("Marked {} resources for reindexing", updatedCount);
}
}
/**
* This method is called once per minute to perform any required re-indexing. During most passes this will
* just check and find that there are no resources requiring re-indexing. In that case the method just returns
@ -77,13 +83,22 @@ public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<Se
}
@Override
protected void preDelete(SearchParameter theResourceToDelete) {
super.preDelete(theResourceToDelete);
markAffectedResources(theResourceToDelete);
}
@Override
protected void postPersist(ResourceTable theEntity, SearchParameter theResource) {
super.postPersist(theEntity, theResource);
markAffectedResources(theResource);
}
@Override
protected void postUpdate(ResourceTable theEntity, SearchParameter theResource) {
super.postUpdate(theEntity, theResource);
markAffectedResources(theResource);
}
@ -92,37 +107,37 @@ public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<Se
super.validateResourceForStorage(theResource, theEntityToSave);
if (theResource.getStatus() == null) {
throw new UnprocessableEntityException("Resource.status is missing or invalid: " + theResource.getStatusElement().getValueAsString());
throw new UnprocessableEntityException("SearchParameter.status is missing or invalid: " + theResource.getStatusElement().getValueAsString());
}
String xpath = theResource.getXpath();
if (isBlank(xpath)) {
throw new UnprocessableEntityException("Resource.xpath is missing");
String expression = theResource.getExpression();
if (isBlank(expression)) {
throw new UnprocessableEntityException("SearchParameter.expression is missing");
}
String[] xpathSplit = BaseSearchParamExtractor.SPLIT.split(xpath);
String[] expressionSplit = BaseSearchParamExtractor.SPLIT.split(expression);
String allResourceName = null;
for (String nextPath : xpathSplit) {
for (String nextPath : expressionSplit) {
int dotIdx = nextPath.indexOf('.');
if (dotIdx == -1) {
throw new UnprocessableEntityException("Invalid path value \"" + nextPath + "\". Must start with a resource name");
throw new UnprocessableEntityException("Invalid SearchParameter.expression value \"" + nextPath + "\". Must start with a resource name");
}
String resourceName = nextPath.substring(0, dotIdx);
try {
getContext().getResourceDefinition(resourceName);
} catch (DataFormatException e) {
throw new UnprocessableEntityException("Invalid path value \"" + nextPath + "\": " + e.getMessage());
throw new UnprocessableEntityException("Invalid SearchParameter.expression value \"" + nextPath + "\": " + e.getMessage());
}
if (allResourceName == null) {
allResourceName = resourceName;
} else {
if (!allResourceName.equals(resourceName)) {
throw new UnprocessableEntityException("Invalid path value \"" + nextPath + "\". All paths in a single SearchParameter must match the same resource type");
throw new UnprocessableEntityException("Invalid SearchParameter.expression value \"" + nextPath + "\". All paths in a single SearchParameter must match the same resource type");
}
}
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/SearchParamRegistryDstu3.java
View File

@ -155,7 +155,7 @@ public class SearchParamRegistryDstu3 extends BaseSearchParamRegistry {
private RuntimeSearchParam toRuntimeSp(SearchParameter theNextSp) {
String name = theNextSp.getCode();
String description = theNextSp.getDescription();
String path = theNextSp.getXpath();
String path = theNextSp.getExpression();
RestSearchParameterTypeEnum paramType = null;
RuntimeSearchParamStatusEnum status = null;
switch (theNextSp.getType()) {

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
View File

@ -233,12 +233,14 @@ public class TermConcept implements Serializable {
@PreUpdate
@PrePersist
public void prePersist() {
Set<Long> parentPids = new HashSet<Long>();
TermConcept entity = this;
parentPids(entity, parentPids);
entity.setParentPids(parentPids);
ourLog.trace("Code {}/{} has parents {}", entity.getId(), entity.getCode(), entity.getParentPidsAsString());
if (myParentPids == null) {
Set<Long> parentPids = new HashSet<Long>();
TermConcept entity = this;
parentPids(entity, parentPids);
entity.setParentPids(parentPids);
ourLog.trace("Code {}/{} has parents {}", entity.getId(), entity.getCode(), entity.getParentPidsAsString());
}
}
public void setCode(String theCode) {
@ -280,6 +282,10 @@ public class TermConcept implements Serializable {
myParentPids = b.toString();
}
public void setParentPids(String theParentPids) {
myParentPids = theParentPids;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE).append("code", myCode).append("display", myDisplay).build();

130
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
View File

@ -10,7 +10,7 @@ package ca.uhn.fhir.jpa.entity;
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@ -36,77 +36,38 @@ import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
@Entity
@Table(name="TRM_CONCEPT_PC_LINK")
@Table(name = "TRM_CONCEPT_PC_LINK")
public class TermConceptParentChildLink implements Serializable {
private static final long serialVersionUID = 1L;
@ManyToOne()
@JoinColumn(name="CHILD_PID", nullable=false, referencedColumnName="PID", foreignKey=@ForeignKey(name="FK_TERM_CONCEPTPC_CHILD"))
@JoinColumn(name = "CHILD_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CHILD"))
private TermConcept myChild;
@Column(name = "CHILD_PID", insertable = false, updatable = false)
private Long myChildPid;
@ManyToOne()
@JoinColumn(name="CODESYSTEM_PID", nullable=false, foreignKey=@ForeignKey(name="FK_TERM_CONCEPTPC_CS"))
@JoinColumn(name = "CODESYSTEM_PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CS"))
private TermCodeSystemVersion myCodeSystem;
@ManyToOne(cascade= {})
@JoinColumn(name="PARENT_PID", nullable=false, referencedColumnName="PID", foreignKey=@ForeignKey(name="FK_TERM_CONCEPTPC_PARENT"))
@ManyToOne(cascade = {})
@JoinColumn(name = "PARENT_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_PARENT"))
private TermConcept myParent;
@Column(name = "PARENT_PID", insertable = false, updatable = false)
private Long myParentPid;
@Id()
@SequenceGenerator(name="SEQ_CONCEPT_PC_PID", sequenceName="SEQ_CONCEPT_PC_PID")
@GeneratedValue(strategy=GenerationType.AUTO, generator="SEQ_CONCEPT_PC_PID")
@Column(name="PID")
@SequenceGenerator(name = "SEQ_CONCEPT_PC_PID", sequenceName = "SEQ_CONCEPT_PC_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PC_PID")
@Column(name = "PID")
private Long myPid;
@Enumerated(EnumType.ORDINAL)
@Column(name="REL_TYPE", length=5, nullable=true)
@Column(name = "REL_TYPE", length = 5, nullable = true)
private RelationshipTypeEnum myRelationshipType;
public TermConcept getChild() {
return myChild;
}
public RelationshipTypeEnum getRelationshipType() {
return myRelationshipType;
}
public TermCodeSystemVersion getCodeSystem() {
return myCodeSystem;
}
public TermConcept getParent() {
return myParent;
}
public void setChild(TermConcept theChild) {
myChild = theChild;
}
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
myCodeSystem = theCodeSystem;
}
public void setParent(TermConcept theParent) {
myParent = theParent;
}
public void setRelationshipType(RelationshipTypeEnum theRelationshipType) {
myRelationshipType = theRelationshipType;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((myChild == null) ? 0 : myChild.hashCode());
result = prime * result + ((myCodeSystem == null) ? 0 : myCodeSystem.hashCode());
result = prime * result + ((myParent == null) ? 0 : myParent.hashCode());
result = prime * result + ((myRelationshipType == null) ? 0 : myRelationshipType.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
@ -136,15 +97,64 @@ public class TermConceptParentChildLink implements Serializable {
return true;
}
public enum RelationshipTypeEnum{
// ********************************************
// IF YOU ADD HERE MAKE SURE ORDER IS PRESERVED
ISA
public TermConcept getChild() {
return myChild;
}
public Long getChildPid() {
return myChildPid;
}
public TermCodeSystemVersion getCodeSystem() {
return myCodeSystem;
}
public Long getId() {
return myPid;
}
public TermConcept getParent() {
return myParent;
}
public Long getParentPid() {
return myParentPid;
}
public RelationshipTypeEnum getRelationshipType() {
return myRelationshipType;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((myChild == null) ? 0 : myChild.hashCode());
result = prime * result + ((myCodeSystem == null) ? 0 : myCodeSystem.hashCode());
result = prime * result + ((myParent == null) ? 0 : myParent.hashCode());
result = prime * result + ((myRelationshipType == null) ? 0 : myRelationshipType.hashCode());
return result;
}
public void setChild(TermConcept theChild) {
myChild = theChild;
}
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
myCodeSystem = theCodeSystem;
}
public void setParent(TermConcept theParent) {
myParent = theParent;
}
public void setRelationshipType(RelationshipTypeEnum theRelationshipType) {
myRelationshipType = theRelationshipType;
}
public enum RelationshipTypeEnum {
// ********************************************
// IF YOU ADD HERE MAKE SURE ORDER IS PRESERVED
ISA
}
}

228
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvc.java
View File

@ -23,9 +23,11 @@ package ca.uhn.fhir.jpa.term;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.TimeUnit;
@ -33,6 +35,7 @@ import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
@ -45,7 +48,10 @@ import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Stopwatch;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Multimaps;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
@ -66,6 +72,7 @@ import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.ValidateUtil;
public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
private static boolean ourForceSaveDeferredAlwaysForUnitTest;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiTerminologySvc.class);
private static final Object PLACEHOLDER_OBJECT = new Object();
@ -94,8 +101,11 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
private boolean myProcessDeferred = true;
private long myNextReindexPass;
private boolean myProcessDeferred = true;
@Autowired
private PlatformTransactionManager myTransactionMgr;
private boolean addToSet(Set<TermConcept> theSetToPopulate, TermConcept theConcept) {
boolean retVal = theSetToPopulate.add(theConcept);
@ -108,6 +118,25 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
return retVal;
}
private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
ourLog.trace("Checking {} parents", theParents.size());
int retVal = 0;
for (TermConceptParentChildLink nextLink : theParents) {
if (nextLink.getRelationshipType() == RelationshipTypeEnum.ISA) {
TermConcept nextParent = nextLink.getParent();
retVal += ensureParentsSaved(nextParent.getParents());
if (nextParent.getId() == null) {
myConceptDao.saveAndFlush(nextParent);
retVal++;
ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
}
}
}
return retVal;
}
private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
TermConcept nextChild = nextChildLink.getChild();
@ -175,6 +204,15 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
return retVal;
}
/**
* Subclasses may override
* @param theSystem The code system
* @param theCode The code
*/
protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
return Collections.emptyList();
}
@Transactional(propagation = Propagation.REQUIRED)
@Override
public Set<TermConcept> findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
@ -206,7 +244,6 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
ArrayList<VersionIndependentConcept> retVal = toVersionIndependentConcepts(theSystem, codes);
return retVal;
}
/**
* Subclasses may override
* @param theSystem The code system
@ -215,16 +252,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
protected List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
return Collections.emptyList();
}
/**
* Subclasses may override
* @param theSystem The code system
* @param theCode The code
*/
protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
return Collections.emptyList();
}
private TermCodeSystemVersion findCurrentCodeSystemVersionForSystem(String theCodeSystem) {
TermCodeSystem cs = getCodeSystem(theCodeSystem);
if (cs == null || cs.getCurrentVersion() == null) {
@ -233,11 +261,12 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
TermCodeSystemVersion csv = cs.getCurrentVersion();
return csv;
}
private TermCodeSystem getCodeSystem(String theSystem) {
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
return cs;
}
private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack, int theTotalConcepts) {
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
return;
@ -271,15 +300,99 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
}
private void saveConceptLink(TermConceptParentChildLink next) {
if (next.getId() == null) {
myConceptParentChildLinkDao.save(next);
private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
if (theNext.getCodeSystem() != null) {
return;
}
theNext.setCodeSystem(theCodeSystemVersion);
for (TermConceptParentChildLink next : theNext.getChildren()) {
populateVersion(next.getChild(), theCodeSystemVersion);
}
}
private ArrayListMultimap<Long, Long> myChildToParentPidCache;
private void processReindexing() {
if (System.currentTimeMillis() < myNextReindexPass && !ourForceSaveDeferredAlwaysForUnitTest) {
return;
}
TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
tt.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
int maxResult = 1000;
Page<TermConcept> concepts = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
if (concepts.hasContent() == false) {
myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
myChildToParentPidCache = null;
return;
}
if (myChildToParentPidCache == null) {
myChildToParentPidCache = ArrayListMultimap.create();
}
ourLog.info("Indexing {} / {} concepts", concepts.getContent().size(), concepts.getTotalElements());
int count = 0;
StopWatch stopwatch = new StopWatch();
for (TermConcept nextConcept : concepts) {
StringBuilder parentsBuilder = new StringBuilder();
createParentsString(parentsBuilder, nextConcept.getId());
nextConcept.setParentPids(parentsBuilder.toString());
saveConcept(nextConcept);
count++;
}
ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, concepts.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
}
private void createParentsString(StringBuilder theParentsBuilder, Long theConceptPid) {
Validate.notNull(theConceptPid, "theConceptPid must not be null");
List<Long> parents = myChildToParentPidCache.get(theConceptPid);
if (parents.contains(-1L)) {
return;
} else if (parents.isEmpty()) {
Collection<TermConceptParentChildLink> parentLinks = myConceptParentChildLinkDao.findAllWithChild(theConceptPid);
if (parentLinks.isEmpty()) {
myChildToParentPidCache.put(theConceptPid, -1L);
return;
} else {
for (TermConceptParentChildLink next : parentLinks) {
myChildToParentPidCache.put(theConceptPid, next.getParentPid());
}
}
}
for (Long nextParent : parents) {
if (theParentsBuilder.length() > 0) {
theParentsBuilder.append(' ');
}
theParentsBuilder.append(nextParent);
createParentsString(theParentsBuilder, nextParent);
}
}
});
}
private int saveConcept(TermConcept theConcept) {
int retVal = 0;
retVal += ensureParentsSaved(theConcept.getParents());
/*
* If the concept has an ID, we're reindexing, so there's no need to
* save parent concepts first (it's way too slow to do that)
*/
if (theConcept.getId() == null) {
retVal += ensureParentsSaved(theConcept.getParents());
}
if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
retVal++;
theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
@ -289,33 +402,10 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
ourLog.trace("Saved {} and got PID {}", theConcept.getCode(), theConcept.getId());
return retVal;
}
private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
ourLog.trace("Checking {} parents", theParents.size());
int retVal = 0;
for (TermConceptParentChildLink nextLink : theParents) {
if (nextLink.getRelationshipType() == RelationshipTypeEnum.ISA) {
TermConcept nextParent = nextLink.getParent();
retVal += ensureParentsSaved(nextParent.getParents());
if (nextParent.getId() == null) {
myConceptDao.saveAndFlush(nextParent);
retVal++;
ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
}
}
}
return retVal;
}
private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
if (theNext.getCodeSystem() != null) {
return;
}
theNext.setCodeSystem(theCodeSystemVersion);
for (TermConceptParentChildLink next : theNext.getChildren()) {
populateVersion(next.getChild(), theCodeSystemVersion);
private void saveConceptLink(TermConceptParentChildLink next) {
if (next.getId() == null) {
myConceptParentChildLinkDao.save(next);
}
}
@ -368,43 +458,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
ourLog.info("All deferred concepts and relationships have now been synchronized to the database");
}
}
@Autowired
private PlatformTransactionManager myTransactionMgr;
private void processReindexing() {
if (System.currentTimeMillis() < myNextReindexPass) {
return;
}
TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
tt.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
int maxResult = 1000;
Page<TermConcept> resources = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
if (resources.hasContent() == false) {
myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
return;
}
ourLog.info("Indexing {} / {} concepts", resources.getContent().size(), resources.getTotalElements());
int count = 0;
StopWatch stopwatch = new StopWatch();
for (TermConcept resourceTable : resources) {
saveConcept(resourceTable);
count++;
}
ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, resources.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
}
});
}
@Override
public void setProcessDeferred(boolean theProcessDeferred) {
myProcessDeferred = theProcessDeferred;
@ -470,7 +524,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
totalCodeCount += validateConceptForStorage(next, theCodeSystemVersion, conceptsStack, allConcepts);
}
ourLog.info("Saving version");
ourLog.info("Saving version containing {} concepts", totalCodeCount);
TermCodeSystemVersion codeSystemVersion = myCodeSystemVersionDao.saveAndFlush(theCodeSystemVersion);
@ -503,13 +557,13 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
ourLog.info("Note that some concept saving was deferred - still have {} concepts and {} relationships", myConceptsToSaveLater.size(), myConceptLinksToSaveLater.size());
}
}
@Override
public boolean supportsSystem(String theSystem) {
TermCodeSystem cs = getCodeSystem(theSystem);
return cs != null;
}
private ArrayList<VersionIndependentConcept> toVersionIndependentConcepts(String theSystem, Set<TermConcept> codes) {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>(codes.size());
for (TermConcept next : codes) {
@ -547,4 +601,12 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
return retVal;
}
/**
* This method is present only for unit tests, do not call from client code
*/
@VisibleForTesting
public static void setForceSaveDeferredAlwaysForUnitTest(boolean theForceSaveDeferredAlwaysForUnitTest) {
ourForceSaveDeferredAlwaysForUnitTest = theForceSaveDeferredAlwaysForUnitTest;
}
}

65
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.term;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
@ -12,7 +13,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
@ -64,6 +65,7 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
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.util.StopWatch;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -79,7 +81,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
@Autowired
private IValidationSupport myValidationSupport;
private void addCodeIfNotAlreadyAdded(String system, ValueSetExpansionComponent retVal, Set<String> addedCodes, TermConcept nextConcept) {
if (addedCodes.add(nextConcept.getCode())) {
ValueSetExpansionContainsComponent contains = retVal.addContains();
@ -126,12 +128,12 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
for (ConceptDefinitionComponent nextChild : theNext.getConcept()) {
foundCodeInChild |= addTreeIfItContainsCode(theSystemString, nextChild, theCode, theListToPopulate);
}
if (theCode.equals(theNext.getCode()) || foundCodeInChild) {
theListToPopulate.add(new VersionIndependentConcept(theSystemString, theNext.getCode()));
return true;
}
return false;
}
@ -159,17 +161,15 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
}
private void addDisplayFilterInexact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
//@formatter:off
Query textQuery = qb
.phrase()
.withSlop(2)
.onField("myDisplay").boostedTo(4.0f)
.andField("myDisplayEdgeNGram").boostedTo(2.0f)
//.andField("myDisplayNGram").boostedTo(1.0f)
//.andField("myDisplayPhonetic").boostedTo(0.5f)
// .andField("myDisplayNGram").boostedTo(1.0f)
// .andField("myDisplayPhonetic").boostedTo(0.5f)
.sentence(nextFilter.getValue().toLowerCase()).createQuery();
bool.must(textQuery);
//@formatter:on
}
@Override
@ -216,26 +216,33 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
bool.must(qb.keyword().onField("myCodeSystemVersionPid").matching(csv.getPid()).createQuery());
for (ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
if (isNotBlank(nextFilter.getValue())) {
if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == FilterOperator.EQUAL) {
addDisplayFilterExact(qb, bool, nextFilter);
} else if (nextFilter.getProperty().equals("display") && nextFilter.getOp() == FilterOperator.EQUAL) {
if (nextFilter.getValue().trim().contains(" ")) {
addDisplayFilterExact(qb, bool, nextFilter);
} else {
addDisplayFilterInexact(qb, bool, nextFilter);
}
} else if ((nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) && nextFilter.getOp() == FilterOperator.ISA) {
TermConcept code = super.findCode(system, nextFilter.getValue());
if (code == null) {
throw new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue());
}
if (isBlank(nextFilter.getValue()) && nextFilter.getOp() == null && isBlank(nextFilter.getProperty())) {
continue;
}
ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
bool.must(qb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
if (isBlank(nextFilter.getValue()) || nextFilter.getOp() == null || isBlank(nextFilter.getProperty())) {
throw new InvalidRequestException("Invalid filter, must have fields populated: property op value");
}
if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == FilterOperator.EQUAL) {
addDisplayFilterExact(qb, bool, nextFilter);
} else if ("display".equals(nextFilter.getProperty()) && nextFilter.getOp() == FilterOperator.EQUAL) {
if (nextFilter.getValue().trim().contains(" ")) {
addDisplayFilterExact(qb, bool, nextFilter);
} else {
throw new InvalidRequestException("Unknown filter property[" + nextFilter + "] + op[" + nextFilter.getOpElement().getValueAsString() + "]");
addDisplayFilterInexact(qb, bool, nextFilter);
}
} else if ((nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) && nextFilter.getOp() == FilterOperator.ISA) {
TermConcept code = super.findCode(system, nextFilter.getValue());
if (code == null) {
throw new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue());
}
ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
bool.must(qb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
} else {
throw new InvalidRequestException("Unknown filter property[" + nextFilter + "] + op[" + nextFilter.getOpElement().getValueAsString() + "]");
}
}
@ -243,12 +250,17 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
jpaQuery.setMaxResults(1000);
StopWatch sw = new StopWatch();
@SuppressWarnings("unchecked")
List<TermConcept> result = jpaQuery.getResultList();
ourLog.info("Expansion completed in {}ms", sw.getMillis());
for (TermConcept nextConcept : result) {
addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
}
retVal.setTotal(jpaQuery.getResultSize());
}
@ -259,7 +271,6 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
}
}
return retVal;
}

44
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java Normal file
View File

@ -0,0 +1,44 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.junit.Assert.assertNotEquals;
import java.nio.charset.StandardCharsets;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc;
import ca.uhn.fhir.util.TestUtil;
public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3CodeSystemTest.class);
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(false);
}
@Test
public void testIndexContained() throws Exception {
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(true);
String input = IOUtils.toString(getClass().getResource("/dstu3_codesystem_complete.json"), StandardCharsets.UTF_8);
CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input);
myCodeSystemDao.create(cs, mySrd);
mySystemDao.markAllResourcesForReindexing();
int outcome = mySystemDao.performReindexingPass(100);
assertNotEquals(-1, outcome); // -1 means there was a failure
myTermSvc.saveDeferred();
}
}

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ContainedTest.java
View File

@ -1,8 +1,5 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.assertThat;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Reference;
@ -11,9 +8,6 @@ import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
public class FhirResourceDaoDstu3ContainedTest extends BaseJpaDstu3Test {

37
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java
View File

@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
@ -18,6 +19,7 @@ import org.junit.Test;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
@ -30,14 +32,14 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
fooSp.setCode("foo");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("FOO SP");
fooSp.setXpath("PatientFoo.gender");
fooSp.setExpression("PatientFoo.gender");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
try {
mySearchParameterDao.create(fooSp, mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Invalid path value \"PatientFoo.gender\": Unknown resource name \"PatientFoo\" (this name is not known in FHIR version \"DSTU3\")", e.getMessage());
assertEquals("Invalid SearchParameter.expression value \"PatientFoo.gender\": Unknown resource name \"PatientFoo\" (this name is not known in FHIR version \"DSTU3\")", e.getMessage());
}
}
@ -47,14 +49,14 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
fooSp.setCode("foo");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("FOO SP");
fooSp.setXpath("Patient.gender or Observation.code");
fooSp.setExpression("Patient.gender or Observation.code");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
try {
mySearchParameterDao.create(fooSp, mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Invalid path value \"Observation.code\". All paths in a single SearchParameter must match the same resource type", e.getMessage());
assertEquals("Invalid SearchParameter.expression value \"Observation.code\". All paths in a single SearchParameter must match the same resource type", e.getMessage());
}
}
@ -70,7 +72,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
mySearchParameterDao.create(fooSp, mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Resource.xpath is missing", e.getMessage());
assertEquals("SearchParameter.expression is missing", e.getMessage());
}
}
@ -80,14 +82,14 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
fooSp.setCode("foo");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("FOO SP");
fooSp.setXpath("gender");
fooSp.setExpression("gender");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
try {
mySearchParameterDao.create(fooSp, mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Invalid path value \"gender\". Must start with a resource name", e.getMessage());
assertEquals("Invalid SearchParameter.expression value \"gender\". Must start with a resource name", e.getMessage());
}
}
@ -98,14 +100,14 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
fooSp.setCode("foo");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("FOO SP");
fooSp.setXpath("Patient.gender");
fooSp.setExpression("Patient.gender");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(null);
try {
mySearchParameterDao.create(fooSp, mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Resource.status is missing or invalid: null", e.getMessage());
assertEquals("SearchParameter.status is missing or invalid: null", e.getMessage());
}
}
@ -117,10 +119,10 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
fooSp.setCode("foo");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("FOO SP");
fooSp.setXpath("Patient.gender");
fooSp.setExpression("Patient.gender");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
mySearchParameterDao.create(fooSp, mySrd);
IIdType spId = mySearchParameterDao.create(fooSp, mySrd).getId().toUnqualifiedVersionless();
mySearchParamRegsitry.forceRefresh();
@ -150,6 +152,17 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
foundResources = toUnqualifiedVersionlessIdValues(results);
assertThat(foundResources, contains(patId.getValue()));
// Delete the param
mySearchParameterDao.delete(spId, mySrd);
mySearchParamRegsitry.forceRefresh();
mySystemDao.performReindexingPass(100);
// Try with custom gender SP
map = new SearchParameterMap();
map.add("foo", new TokenParam(null, "male"));
IBundleProvider res = myPatientDao.search(map);
assertEquals(0, res.size());
}
@Test
@ -159,7 +172,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
fooSp.setCode("foo");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("FOO SP");
fooSp.setXpath("Patient.gender");
fooSp.setExpression("Patient.gender");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.DRAFT);
mySearchParameterDao.create(fooSp, mySrd);

71
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -26,7 +26,9 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
@ -34,6 +36,8 @@ import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
@ -52,6 +56,8 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
@After
public void after() {
myDaoConfig.setDeferIndexingForCodesystemsOfSize(new DaoConfig().getDeferIndexingForCodesystemsOfSize());
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(false);
}
@Before
@ -318,6 +324,71 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
}
}
@Test
public void testExpandWithIsAInExternalValueSet() {
createExternalCsAndLocalVs();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter().setOp(FilterOperator.ISA).setValue("childAA").setProperty("concept");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
}
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
@Test
public void testExpandWithIsAInExternalValueSetReindex() {
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(true);
createExternalCsAndLocalVs();
mySystemDao.markAllResourcesForReindexing();
mySystemDao.performReindexingPass(100);
mySystemDao.performReindexingPass(100);
myHapiTerminologySvc.saveDeferred();
myHapiTerminologySvc.saveDeferred();
myHapiTerminologySvc.saveDeferred();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter().setOp(FilterOperator.ISA).setValue("childAA").setProperty("concept");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
}
@Test
public void testExpandInvalid() {
createExternalCsAndLocalVs();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter();
include.addFilter().setOp(FilterOperator.ISA).setValue("childAA");
try {
myValueSetDao.expand(vs, null);
fail();
} catch (InvalidRequestException e) {
assertEquals("Invalid filter, must have fields populated: property op value", e.getMessage());
}
}
@Test
public void testExpandWithSystemAndCodesInExternalValueSet() {
createExternalCsAndLocalVs();

40
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderDstu2Test.java
View File

@ -10,6 +10,7 @@ import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.concurrent.TimeUnit;
import org.apache.commons.io.IOUtils;
@ -139,7 +140,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
get.addHeader("Accept", "application/xml, text/html");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String response = IOUtils.toString(http.getEntity().getContent());
String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(response);
assertThat(response, (containsString("_format=json")));
assertEquals(200, http.getStatusLine().getStatusCode());
@ -167,7 +168,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
get.addHeader("Accept", "application/xml+fhir");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String response = IOUtils.toString(http.getEntity().getContent());
String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(response);
assertThat(response, not(containsString("_format")));
assertEquals(200, http.getStatusLine().getStatusCode());
@ -216,7 +217,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
assertEquals(200, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
Parameters parameters = ourCtx.newXmlParser().parseResource(Parameters.class, output);
@ -246,7 +247,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'context' must be provided"));
} finally {
@ -257,7 +258,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'searchParam' must be provided"));
} finally {
@ -268,7 +269,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'text' must be provided"));
} finally {
@ -286,7 +287,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
@Test
public void testTransactionFromBundle() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
}
@ -295,7 +296,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
public void testTransactionFromBundle2() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
@ -311,7 +312,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
*/
bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
bundle = IOUtils.toString(bundleRes);
bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
@ -335,7 +336,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
public void testTransactionFromBundle3() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/grahame-transaction.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
}
@ -343,7 +344,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
@Test
public void testTransactionFromBundle4() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
Bundle bundleResp = ourCtx.newXmlParser().parseResource(Bundle.class, response);
@ -358,7 +359,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
@Test
public void testTransactionFromBundle5() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle2.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
try {
ourClient.transaction().withBundle(bundle).prettyPrint().execute();
fail();
@ -372,7 +373,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
@Test
public void testTransactionFromBundle6() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle3.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
ourClient.transaction().withBundle(bundle).prettyPrint().execute();
// try {
// fail();
@ -427,5 +428,18 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
assertEquals(0, respSub.getEntry().size());
}
@Test
public void testMarkResourcesForReindexing() throws Exception {
HttpGet get = new HttpGet(ourServerBase + "/$mark-all-resources-for-reindexing");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertEquals(200, http.getStatusLine().getStatusCode());
} finally {
IOUtils.closeQuietly(http);;
}
}
}

19
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderCustomSearchParamDstu3Test.java
View File

@ -58,7 +58,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
public void saveCreateSearchParamInvalidWithMissingStatus() throws IOException {
SearchParameter sp = new SearchParameter();
sp.setCode("foo");
sp.setXpath("Patient.gender");
sp.setExpression("Patient.gender");
sp.setXpathUsage(XPathUsageType.NORMAL);
sp.setTitle("Foo Param");
@ -66,7 +66,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
ourClient.create().resource(sp).execute();
fail();
} catch (UnprocessableEntityException e) {
assertEquals("HTTP 422 Unprocessable Entity: Resource.status is missing or invalid: null", e.getMessage());
assertEquals("HTTP 422 Unprocessable Entity: SearchParameter.status is missing or invalid: null", e.getMessage());
}
}
@ -100,7 +100,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
fooSp.setCode("foo");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("FOO SP");
fooSp.setXpath("Patient.gender");
fooSp.setExpression("Patient.gender");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
mySearchParameterDao.create(fooSp, mySrd);
@ -110,7 +110,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
fooSp.setCode("gender");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("Gender");
fooSp.setXpath("Patient.gender");
fooSp.setExpression("Patient.gender");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.RETIRED);
mySearchParameterDao.create(fooSp, mySrd);
@ -152,7 +152,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
fooSp.setCode("foo");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("FOO SP");
fooSp.setXpath("Patient.gender");
fooSp.setExpression("Patient.gender");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
mySearchParameterDao.create(fooSp, mySrd);
@ -162,7 +162,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
fooSp.setCode("gender");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("Gender");
fooSp.setXpath("Patient.gender");
fooSp.setExpression("Patient.gender");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.RETIRED);
mySearchParameterDao.create(fooSp, mySrd);
@ -206,7 +206,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
fooSp.setCode("foo");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("FOO SP");
fooSp.setXpath("Patient.gender");
fooSp.setExpression("Patient.gender");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
mySearchParameterDao.create(fooSp, mySrd);
@ -232,6 +232,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
.where(new TokenClientParam("foo").exactly().code("male"))
.returnBundle(Bundle.class)
.execute();
foundResources = toUnqualifiedVersionlessIdValues(result);
assertThat(foundResources, contains(patId.getValue()));
@ -256,7 +257,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
fooSp.setCode("foo");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
fooSp.setTitle("FOO SP");
fooSp.setXpath("Patient.gender");
fooSp.setExpression("Patient.gender");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
mySearchParameterDao.create(fooSp, mySrd);
@ -276,7 +277,7 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
fooSp.setCode("foo");
fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.REFERENCE);
fooSp.setTitle("FOO SP");
fooSp.setXpath("Observation.subject");
fooSp.setExpression("Observation.subject");
fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
mySearchParameterDao.create(fooSp, mySrd);

118
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
View File

@ -149,7 +149,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
@After
public void after() throws Exception {
super.after();
myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
}
@ -160,15 +160,14 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
myDaoConfig.setAllowMultipleDelete(true);
}
private void checkParamMissing(String paramName) throws IOException, ClientProtocolException {
HttpGet get = new HttpGet(ourServerBase + "/Observation?" + paramName + ":missing=false");
CloseableHttpResponse resp = ourHttpClient.execute(get);
IOUtils.closeQuietly(resp.getEntity().getContent());
assertEquals(200, resp.getStatusLine().getStatusCode());
}
private ArrayList<IBaseResource> genResourcesOfType(Bundle theRes, Class<? extends IBaseResource> theClass) {
ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
for (BundleEntryComponent next : theRes.getEntry()) {
@ -197,7 +196,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
List<Extension> exts = basic.getExtensionsByUrl("http://localhost:1080/hapi-fhir-jpaserver-example/baseDstu2/StructureDefinition/DateID");
assertEquals(1, exts.size());
}
private List<String> searchAndReturnUnqualifiedIdValues(String uri) throws IOException, ClientProtocolException {
List<String> ids;
HttpGet get = new HttpGet(uri);
@ -339,9 +338,9 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
Binary binary = new Binary();
binary.setContent(arr);
binary.setContentType("dansk");
IIdType resource = ourClient.create().resource(binary).execute().getId();
Binary fromDB = ourClient.read().resource(Binary.class).withId(resource.toVersionless()).execute();
assertEquals("1", fromDB.getIdElement().getVersionIdPart());
@ -355,7 +354,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
} finally {
IOUtils.closeQuietly(resp);
}
fromDB = ourClient.read().resource(Binary.class).withId(resource.toVersionless()).execute();
assertEquals("2", fromDB.getIdElement().getVersionIdPart());
@ -370,12 +369,12 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
} finally {
IOUtils.closeQuietly(resp);
}
fromDB = ourClient.read().resource(Binary.class).withId(resource.toVersionless()).execute();
assertEquals("3", fromDB.getIdElement().getVersionIdPart());
// Now an update with the wrong ID in the body
arr[0] = 4;
binary.setId("");
encoded = myFhirCtx.newJsonParser().encodeResourceToString(binary);
@ -387,7 +386,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
} finally {
IOUtils.closeQuietly(resp);
}
fromDB = ourClient.read().resource(Binary.class).withId(resource.toVersionless()).execute();
assertEquals("3", fromDB.getIdElement().getVersionIdPart());
@ -674,7 +673,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
String encoded = myFhirCtx.newXmlParser().encodeResourceToString(response);
ourLog.info(encoded);
assertThat(encoded, containsString(
"<issue><severity value=\"information\"/><code value=\"informational\"/><diagnostics value=\"Successfully deleted Patient?identifier=testDeleteConditionalMultiple resource(s) in 2ms\"/></issue>"));
"<issue><severity value=\"information\"/><code value=\"informational\"/><diagnostics value=\"Successfully deleted 2 resource(s) in "));
try {
ourClient.read().resource("Patient").withId(id1).execute();
fail();
@ -726,7 +725,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
* Test for #345
*/
@Test
public void testDeleteNormal() throws IOException {
public void testDeleteNormal() {
Patient p = new Patient();
p.addName().setFamily("FAM");
IIdType id = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
@ -743,6 +742,17 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
}
@Test
public void testDeleteReturnsOperationOutcome() {
Patient p = new Patient();
p.addName().setFamily("FAM");
IIdType id = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
IBaseOperationOutcome resp = ourClient.delete().resourceById(id).execute();
OperationOutcome oo = (OperationOutcome) resp;
assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Successfully deleted 1 resource(s) in "));
}
@Test
public void testDeleteResourceConditional1() throws IOException {
String methodName = "testDeleteResourceConditional1";
@ -768,6 +778,10 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
response = ourHttpClient.execute(delete);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, resp);
assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Successfully deleted 1 resource(s) in "));
} finally {
response.close();
}
@ -777,6 +791,24 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
try {
ourLog.info(response.toString());
assertEquals(Constants.STATUS_HTTP_410_GONE, response.getStatusLine().getStatusCode());
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, resp);
assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Resource was deleted at"));
} finally {
response.close();
}
// Delete should now have no matches
delete = new HttpDelete(ourServerBase + "/Patient?name=" + methodName);
response = ourHttpClient.execute(delete);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, resp);
assertThat(oo.getIssueFirstRep().getDiagnostics(), startsWith("Unable to find resource matching URL \"Patient?name=testDeleteResourceConditional1\". Deletion failed."));
} finally {
response.close();
}
@ -1781,7 +1813,10 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
ourLog.info("Response: {}", respString);
assertEquals(400, response.getStatusLine().getStatusCode());
OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, respString);
assertEquals("Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"AAA\" does not match URL ID of \"" + id.getIdPart() + "\"", oo.getIssue().get(0).getDiagnostics());
assertEquals(
"Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"AAA\" does not match URL ID of \""
+ id.getIdPart() + "\"",
oo.getIssue().get(0).getDiagnostics());
} finally {
response.close();
}
@ -1809,12 +1844,11 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
@Test
public void testIncludeWithExternalReferences() {
myDaoConfig.setAllowExternalReferences(true);
Patient p = new Patient();
p.getManagingOrganization().setReference("http://example.com/Organization/123");
ourClient.create().resource(p).execute();
Bundle b = ourClient.search().forResource("Patient").include(Patient.INCLUDE_ORGANIZATION).returnBundle(Bundle.class).execute();
assertEquals(1, b.getEntry().size());
}
@ -1834,7 +1868,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
}
@Test
public void testMetadataSuperParamsAreIncluded() throws IOException {
StructureDefinition p = new StructureDefinition();
@ -1843,12 +1876,12 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
IIdType id = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
Bundle resp = ourClient
.search()
.forResource(StructureDefinition.class)
.where(StructureDefinition.URL.matches().value("http://example.com/foo"))
.returnBundle(Bundle.class)
.execute();
.search()
.forResource(StructureDefinition.class)
.where(StructureDefinition.URL.matches().value("http://example.com/foo"))
.returnBundle(Bundle.class)
.execute();
assertEquals(1, resp.getTotal());
}
@ -2101,9 +2134,10 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
String input = IOUtils.toString(getClass().getResourceAsStream("/two_questionnaires.json"), StandardCharsets.UTF_8);
String respString = ourClient.transaction().withBundle(input).prettyPrint().execute();
ourLog.info(respString);
ourHttpClient.execute(new HttpGet("http://localhost:" + ourPort + "/QuestionnaireResponse?patient=QR3295&questionnaire=profile&_sort:desc=authored&_count=5&_include=QuestionnaireResponse:questionnaire&_include=QuestionnaireResponse:subject"));
// Bundle bundle =
ourHttpClient.execute(new HttpGet("http://localhost:" + ourPort
+ "/QuestionnaireResponse?patient=QR3295&questionnaire=profile&_sort:desc=authored&_count=5&_include=QuestionnaireResponse:questionnaire&_include=QuestionnaireResponse:subject"));
// Bundle bundle =
}
@Test
@ -2284,14 +2318,14 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
Bundle found = ourClient
.search()
.forResource(Patient.class)
.where(BaseResource.RES_ID.exactly().systemAndValues(null, id1.getIdPart(), id2.getIdPart()))
.returnBundle(Bundle.class)
.execute();
.search()
.forResource(Patient.class)
.where(BaseResource.RES_ID.exactly().systemAndValues(null, id1.getIdPart(), id2.getIdPart()))
.returnBundle(Bundle.class)
.execute();
assertThat(toUnqualifiedVersionlessIds(found), empty());
found = ourClient
.search()
.forResource(Patient.class)
@ -2319,14 +2353,14 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
.execute();
assertThat(toUnqualifiedVersionlessIds(found), containsInAnyOrder(id1));
found = ourClient
.search()
.forResource(Patient.class)
.where(BaseResource.RES_ID.exactly().codes(Arrays.asList(id1.getIdPart(), id2.getIdPart(), "FOOOOO")))
.and(BaseResource.RES_ID.exactly().code(id1.getIdPart()))
.returnBundle(Bundle.class)
.execute();
.search()
.forResource(Patient.class)
.where(BaseResource.RES_ID.exactly().codes(Arrays.asList(id1.getIdPart(), id2.getIdPart(), "FOOOOO")))
.and(BaseResource.RES_ID.exactly().code(id1.getIdPart()))
.returnBundle(Bundle.class)
.execute();
assertThat(toUnqualifiedVersionlessIds(found), containsInAnyOrder(id1));
@ -3445,7 +3479,9 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
ourLog.info(responseString);
assertEquals(400, response.getStatusLine().getStatusCode());
OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, responseString);
assertEquals("Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"333\" does not match URL ID of \"A2\"", oo.getIssue().get(0).getDiagnostics());
assertEquals(
"Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"333\" does not match URL ID of \"A2\"",
oo.getIssue().get(0).getDiagnostics());
} finally {
response.close();
}

34
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderDstu3Test.java
View File

@ -129,7 +129,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent());
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
assertThat(encoded, containsString("transaction-response"));
@ -162,7 +162,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent());
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
assertThat(encoded, containsString("transaction-response"));
@ -271,14 +271,14 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
try {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/questionnaire-sdc-profile-example-ussg-fht.xml");
String bundleStr = IOUtils.toString(bundleRes);
String bundleStr = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
HttpPost req = new HttpPost(ourServerBase);
req.setEntity(new StringEntity(bundleStr, ContentType.parse(Constants.CT_FHIR_XML + "; charset=utf-8")));
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent());
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
//@formatter:off
@ -314,7 +314,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String response = IOUtils.toString(http.getEntity().getContent());
String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(response);
assertThat(response, containsString("_format=json"));
assertEquals(200, http.getStatusLine().getStatusCode());
@ -342,7 +342,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
get.addHeader("Accept", "application/xml+fhir");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String response = IOUtils.toString(http.getEntity().getContent());
String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(response);
assertThat(response, not(containsString("_format")));
assertEquals(200, http.getStatusLine().getStatusCode());
@ -373,7 +373,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
HttpGet get = new HttpGet(ourServerBase + "/$mark-all-resources-for-reindexing");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertEquals(200, http.getStatusLine().getStatusCode());
} finally {
@ -404,7 +404,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
assertEquals(200, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
Parameters parameters = ourCtx.newXmlParser().parseResource(Parameters.class, output);
@ -434,7 +434,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'context' must be provided"));
} finally {
@ -445,7 +445,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'searchParam' must be provided"));
} finally {
@ -456,7 +456,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
http = ourHttpClient.execute(get);
try {
assertEquals(400, http.getStatusLine().getStatusCode());
String output = IOUtils.toString(http.getEntity().getContent());
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(output);
assertThat(output, containsString("Parameter 'text' must be provided"));
} finally {
@ -500,7 +500,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
public void testTransactionFromBundle2() throws Exception {
InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
@ -516,7 +516,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
*/
bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
bundle = IOUtils.toString(bundleRes);
bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
@ -540,7 +540,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
public void testTransactionFromBundle3() throws Exception {
InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/grahame-transaction.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
}
@ -548,7 +548,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
@Test
public void testTransactionFromBundle4() throws Exception {
InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/simone_bundle.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
Bundle bundleResp = ourCtx.newXmlParser().parseResource(Bundle.class, response);
@ -563,7 +563,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
@Test
public void testTransactionFromBundle5() throws Exception {
InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/simone_bundle2.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
try {
ourClient.transaction().withBundle(bundle).prettyPrint().execute();
fail();
@ -577,7 +577,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
@Test
public void testTransactionFromBundle6() throws Exception {
InputStream bundleRes = SystemProviderDstu3Test.class.getResourceAsStream("/simone_bundle3.xml");
String bundle = IOUtils.toString(bundleRes);
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
ourClient.transaction().withBundle(bundle).prettyPrint().execute();
// try {
// fail();

27
hapi-fhir-jpaserver-base/src/test/resources/dstu3_codesystem_complete.json Normal file
View File

@ -0,0 +1,27 @@
{
"resourceType": "CodeSystem",
"id": "22472",
"meta": {
"versionId": "3",
"lastUpdated": "2017-01-27T10:53:39.457-05:00"
},
"url": "xvalue://dedalus.eu/mci/CodeSystem/AddressUse",
"name": "AddressUse",
"status": "active",
"publisher": "x1v1-mci",
"date": "2016-04-07",
"description": "AddressUse",
"caseSensitive": true,
"compositional": false,
"versionNeeded": false,
"content": "complete",
"concept": {
"code": "work",
"display": "Work",
"definition": "An office address. First choice for business related contacts during business hours.",
"designation": {
"language": "IT",
"value": "Lavoro"
}
}
}

155
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/client/GenericClientDstu3Test.java
View File

@ -98,7 +98,7 @@ public class GenericClientDstu3Test {
byte[] body = IOUtils.toByteArray(((HttpEntityEnclosingRequestBase) capt.getAllValues().get(0)).getEntity().getContent());
return body;
}
private String extractBodyAsString(ArgumentCaptor<HttpUriRequest> capt) throws IOException {
String body = IOUtils.toString(((HttpEntityEnclosingRequestBase) capt.getAllValues().get(0)).getEntity().getContent(), "UTF-8");
return body;
@ -120,6 +120,26 @@ public class GenericClientDstu3Test {
return capt;
}
@Test
public void testRevIncludeRecursive() throws ClientProtocolException, IOException {
ArgumentCaptor<HttpUriRequest> capt = prepareClientForSearchResponse();
IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
int idx = 0;
client.search()
.forResource(EpisodeOfCare.class)
.where(EpisodeOfCare.PATIENT.hasId("123"))
.revInclude(Encounter.INCLUDE_EPISODEOFCARE)
.revInclude(Observation.INCLUDE_ENCOUNTER.asRecursive())
.returnBundle(Bundle.class)
.execute();
assertEquals("http://example.com/fhir/EpisodeOfCare?patient=123&_revinclude=Encounter%3Aepisodeofcare&_revinclude%3Arecurse=Observation%3Aencounter", capt.getAllValues().get(idx).getURI().toString());
idx++;
}
@Test
public void testPatchJsonByIdString() throws Exception {
OperationOutcome conf = new OperationOutcome();
@ -143,20 +163,21 @@ public class GenericClientDstu3Test {
String patch = "[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]";
MethodOutcome outcome = client
.patch()
.withBody(patch)
.withId("Patient/123")
.execute();
.patch()
.withBody(patch)
.withId("Patient/123")
.execute();
assertEquals("http://example.com/fhir/Patient/123", UrlUtil.unescape(capt.getAllValues().get(idx).getURI().toString()));
assertEquals("PATCH", capt.getAllValues().get(0).getRequestLine().getMethod());
assertEquals(patch, extractBodyAsString(capt));
assertEquals(Constants.CT_JSON_PATCH, capt.getAllValues().get(idx).getFirstHeader("Content-Type").getValue().replaceAll(";.*", ""));
idx++;
OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
assertThat(oo.getText().getDivAsString(), containsString("OK!"));
}
@Test
public void testPatchJsonByIdType() throws Exception {
OperationOutcome conf = new OperationOutcome();
@ -180,20 +201,21 @@ public class GenericClientDstu3Test {
String patch = "[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]";
MethodOutcome outcome = client
.patch()
.withBody(patch)
.withId(new IdType("http://localhost/fhir/Patient/123/_history/234"))
.execute();
.patch()
.withBody(patch)
.withId(new IdType("http://localhost/fhir/Patient/123/_history/234"))
.execute();
assertEquals("http://example.com/fhir/Patient/123", UrlUtil.unescape(capt.getAllValues().get(idx).getURI().toString()));
assertEquals("PATCH", capt.getAllValues().get(0).getRequestLine().getMethod());
assertEquals(patch, extractBodyAsString(capt));
assertEquals(Constants.CT_JSON_PATCH, capt.getAllValues().get(idx).getFirstHeader("Content-Type").getValue().replaceAll(";.*", ""));
idx++;
OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
assertThat(oo.getText().getDivAsString(), containsString("OK!"));
}
@Test
public void testPatchJsonByConditionalString() throws Exception {
OperationOutcome conf = new OperationOutcome();
@ -217,20 +239,21 @@ public class GenericClientDstu3Test {
String patch = "[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]";
MethodOutcome outcome = client
.patch()
.withBody(patch)
.conditionalByUrl("Patient?foo=bar")
.execute();
.patch()
.withBody(patch)
.conditionalByUrl("Patient?foo=bar")
.execute();
assertEquals("http://example.com/fhir/Patient?foo=bar", UrlUtil.unescape(capt.getAllValues().get(idx).getURI().toString()));
assertEquals("PATCH", capt.getAllValues().get(0).getRequestLine().getMethod());
assertEquals(patch, extractBodyAsString(capt));
assertEquals(Constants.CT_JSON_PATCH, capt.getAllValues().get(idx).getFirstHeader("Content-Type").getValue().replaceAll(";.*", ""));
idx++;
OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
assertThat(oo.getText().getDivAsString(), containsString("OK!"));
}
@Test
public void testPatchJsonByConditionalParam() throws Exception {
OperationOutcome conf = new OperationOutcome();
@ -254,21 +277,22 @@ public class GenericClientDstu3Test {
String patch = "[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]";
MethodOutcome outcome = client
.patch()
.withBody(patch)
.conditional("Patient").where(Patient.NAME.matches().value("TEST"))
.and(Patient.FAMILY.matches().value("TEST2"))
.execute();
.patch()
.withBody(patch)
.conditional("Patient").where(Patient.NAME.matches().value("TEST"))
.and(Patient.FAMILY.matches().value("TEST2"))
.execute();
assertEquals("http://example.com/fhir/Patient?name=TEST&family=TEST2", UrlUtil.unescape(capt.getAllValues().get(idx).getURI().toString()));
assertEquals("PATCH", capt.getAllValues().get(0).getRequestLine().getMethod());
assertEquals(patch, extractBodyAsString(capt));
assertEquals(Constants.CT_JSON_PATCH, capt.getAllValues().get(idx).getFirstHeader("Content-Type").getValue().replaceAll(";.*", ""));
idx++;
OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
assertThat(oo.getText().getDivAsString(), containsString("OK!"));
}
@Test
public void testPatchJsonByConditionalParamResourceType() throws Exception {
OperationOutcome conf = new OperationOutcome();
@ -292,21 +316,22 @@ public class GenericClientDstu3Test {
String patch = "[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]";
MethodOutcome outcome = client
.patch()
.withBody(patch)
.conditional(Patient.class).where(Patient.NAME.matches().value("TEST"))
.and(Patient.FAMILY.matches().value("TEST2"))
.execute();
.patch()
.withBody(patch)
.conditional(Patient.class).where(Patient.NAME.matches().value("TEST"))
.and(Patient.FAMILY.matches().value("TEST2"))
.execute();
assertEquals("http://example.com/fhir/Patient?name=TEST&family=TEST2", UrlUtil.unescape(capt.getAllValues().get(idx).getURI().toString()));
assertEquals("PATCH", capt.getAllValues().get(0).getRequestLine().getMethod());
assertEquals(patch, extractBodyAsString(capt));
assertEquals(Constants.CT_JSON_PATCH, capt.getAllValues().get(idx).getFirstHeader("Content-Type").getValue().replaceAll(";.*", ""));
idx++;
OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
assertThat(oo.getText().getDivAsString(), containsString("OK!"));
}
@Test
public void testPatchXmlByIdString() throws Exception {
OperationOutcome conf = new OperationOutcome();
@ -330,31 +355,31 @@ public class GenericClientDstu3Test {
String patch = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><diff xmlns:fhir=\"http://hl7.org/fhir\"><replace sel=\"fhir:Patient/fhir:active/@value\">false</replace></diff>";
MethodOutcome outcome = client
.patch()
.withBody(patch)
.withId("Patient/123")
.execute();
.patch()
.withBody(patch)
.withId("Patient/123")
.execute();
assertEquals("http://example.com/fhir/Patient/123", UrlUtil.unescape(capt.getAllValues().get(idx).getURI().toString()));
assertEquals("PATCH", capt.getAllValues().get(0).getRequestLine().getMethod());
assertEquals(patch, extractBodyAsString(capt));
assertEquals(Constants.CT_XML_PATCH, capt.getAllValues().get(idx).getFirstHeader("Content-Type").getValue().replaceAll(";.*", ""));
idx++;
OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
assertThat(oo.getText().getDivAsString(), containsString("OK!"));
}
@Test
public void testPatchInvalid() throws Exception {
IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
try {
client
.patch()
.withBody("AA")
.withId("Patient/123")
.execute();
.patch()
.withBody("AA")
.withId("Patient/123")
.execute();
} catch (IllegalArgumentException e) {
assertEquals("Unable to determine encoding of patch", e.getMessage());
}
@ -388,7 +413,7 @@ public class GenericClientDstu3Test {
assertEquals("http://example.com/fhir/Device?_format=json", UrlUtil.unescape(capt.getAllValues().get(idx).getURI().toString()));
assertEquals("application/fhir+json;q=1.0, application/json+fhir;q=0.9", capt.getAllValues().get(idx).getFirstHeader(Constants.HEADER_ACCEPT).getValue());
idx++;
//@formatter:off
client.setEncoding(EncodingEnum.XML);
client.search()
@ -399,7 +424,7 @@ public class GenericClientDstu3Test {
assertEquals("http://example.com/fhir/Device?_format=xml", UrlUtil.unescape(capt.getAllValues().get(idx).getURI().toString()));
assertEquals("application/fhir+xml;q=1.0, application/xml+fhir;q=0.9", capt.getAllValues().get(idx).getFirstHeader(Constants.HEADER_ACCEPT).getValue());
idx++;
}
@Test
@ -480,9 +505,7 @@ public class GenericClientDstu3Test {
assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourCtx.newXmlParser().parseResource(Binary.class, extractBodyAsString(capt)).getContent());
}
@SuppressWarnings("unchecked")
@Test
public void testClientFailures() throws Exception {
@ -592,7 +615,7 @@ public class GenericClientDstu3Test {
assertEquals(myAnswerCount, capt.getAllValues().size());
assertEquals("http://example.com/fhir/Patient", capt.getAllValues().get(0).getURI().toASCIIString());
assertEquals(Constants.CT_FHIR_XML_NEW, capt.getAllValues().get(0).getFirstHeader("content-type").getValue().replaceAll(";.*", ""));
assertEquals("http://foo.com/base/Patient/222/_history/3", capt.getAllValues().get(1).getURI().toASCIIString());
}
@ -1027,7 +1050,7 @@ public class GenericClientDstu3Test {
assertEquals("http://example.com/fhir/Patient", capt.getAllValues().get(idx).getURI().toString());
idx++;
//@formatter:off
client
.search()
@ -1053,22 +1076,22 @@ public class GenericClientDstu3Test {
idx++;
}
@Test
public void testPutDoesntForceAllIdsJson() throws Exception {
IParser p = ourCtx.newJsonParser();
Patient patient = new Patient();
patient.setId("PATIENT1");
patient.addName().setFamily("PATIENT1");
Bundle bundle = new Bundle();
bundle.setId("BUNDLE1");
bundle.addEntry().setResource(patient);
final String encoded = p.encodeResourceToString(bundle);
assertEquals("{\"resourceType\":\"Bundle\",\"id\":\"BUNDLE1\",\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"PATIENT1\",\"name\":[{\"family\":\"PATIENT1\"}]}}]}", encoded);
ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
@ -1251,7 +1274,7 @@ public class GenericClientDstu3Test {
.returnBundle(Bundle.class)
.execute();
//@formatter:on
assertEquals("http://example.com/fhir/Patient?birthdate=gt"+dateString, capt.getAllValues().get(idx).getURI().toString());
assertEquals("http://example.com/fhir/Patient?birthdate=gt" + dateString, capt.getAllValues().get(idx).getURI().toString());
idx++;
//@formatter:off
@ -1261,7 +1284,7 @@ public class GenericClientDstu3Test {
.returnBundle(Bundle.class)
.execute();
//@formatter:on
assertEquals("http://example.com/fhir/Patient?birthdate=gt"+dateString, capt.getAllValues().get(idx).getURI().toString());
assertEquals("http://example.com/fhir/Patient?birthdate=gt" + dateString, capt.getAllValues().get(idx).getURI().toString());
idx++;
//@formatter:off
@ -1271,7 +1294,7 @@ public class GenericClientDstu3Test {
.returnBundle(Bundle.class)
.execute();
//@formatter:on
assertEquals("http://example.com/fhir/Patient?birthdate=ge"+dateString, capt.getAllValues().get(idx).getURI().toString());
assertEquals("http://example.com/fhir/Patient?birthdate=ge" + dateString, capt.getAllValues().get(idx).getURI().toString());
idx++;
//@formatter:off
@ -1281,7 +1304,7 @@ public class GenericClientDstu3Test {
.returnBundle(Bundle.class)
.execute();
//@formatter:on
assertEquals("http://example.com/fhir/Patient?birthdate=lt"+dateString, capt.getAllValues().get(idx).getURI().toString());
assertEquals("http://example.com/fhir/Patient?birthdate=lt" + dateString, capt.getAllValues().get(idx).getURI().toString());
idx++;
//@formatter:off
@ -1291,7 +1314,7 @@ public class GenericClientDstu3Test {
.returnBundle(Bundle.class)
.execute();
//@formatter:on
assertEquals("http://example.com/fhir/Patient?birthdate=le"+dateString, capt.getAllValues().get(idx).getURI().toString());
assertEquals("http://example.com/fhir/Patient?birthdate=le" + dateString, capt.getAllValues().get(idx).getURI().toString());
idx++;
//@formatter:off
@ -1301,7 +1324,7 @@ public class GenericClientDstu3Test {
.returnBundle(Bundle.class)
.execute();
//@formatter:on
assertEquals("http://example.com/fhir/Patient?birthdate="+dateString, capt.getAllValues().get(idx).getURI().toString());
assertEquals("http://example.com/fhir/Patient?birthdate=" + dateString, capt.getAllValues().get(idx).getURI().toString());
idx++;
//@formatter:off
@ -1639,7 +1662,7 @@ public class GenericClientDstu3Test {
int idx = 0;
Collection<String> values = Arrays.asList("VAL1", "VAL2", "VAL3A,B");
//@formatter:off
client.search()
.forResource("Patient")
@ -1743,7 +1766,6 @@ public class GenericClientDstu3Test {
assertEquals("Unable to determing encoding of request (body does not appear to be valid XML or JSON)", e.getMessage());
}
}
@Test
@ -2012,7 +2034,7 @@ public class GenericClientDstu3Test {
MyPatientWithExtensions patient = new MyPatientWithExtensions();
patient.setId("123");
patient.getText().setDivAsString("OK!");
final String respString = p.encodeResourceToString(patient);
ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
@ -2028,7 +2050,7 @@ public class GenericClientDstu3Test {
IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
MyPatientWithExtensions read = client.read().resource(MyPatientWithExtensions.class).withId(new IdType("1")).execute();
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">OK!</div>", read.getText().getDivAsString());
// Ensure that we haven't overridden the default type for the name
assertFalse(MyPatientWithExtensions.class.isAssignableFrom(Patient.class));
assertFalse(Patient.class.isAssignableFrom(MyPatientWithExtensions.class));
@ -2037,7 +2059,7 @@ public class GenericClientDstu3Test {
IParser parser = ourCtx.newXmlParser();
String encoded = parser.encodeResourceToString(pt);
pt = (Patient) parser.parseResource(encoded);
}
@Test
@ -2045,13 +2067,12 @@ public class GenericClientDstu3Test {
IParser p = ourCtx.newXmlParser();
Bundle b = new Bundle();
MyPatientWithExtensions patient = new MyPatientWithExtensions();
patient.setId("123");
patient.getText().setDivAsString("OK!");
b.addEntry().setResource(patient);
final String respString = p.encodeResourceToString(b);
ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
@ -2066,7 +2087,7 @@ public class GenericClientDstu3Test {
IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
Bundle bundle = client.search().forResource(MyPatientWithExtensions.class).returnBundle(Bundle.class).execute();
assertEquals(1, bundle.getEntry().size());
assertEquals(MyPatientWithExtensions.class, bundle.getEntry().get(0).getResource().getClass());
}
@ -2082,8 +2103,6 @@ public class GenericClientDstu3Test {
assertEquals(expectedUserAgent(), capt.getAllValues().get(0).getHeaders("User-Agent")[0].getValue());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
@ -2093,5 +2112,5 @@ public class GenericClientDstu3Test {
public static void beforeClass() {
ourCtx = FhirContext.forDstu3();
}
}

8
src/changes/changes.xml
View File

@ -130,6 +130,14 @@
with the passed in body. Thanks to Artem Sopin for reporting and providing a test
case for this!
</action>
<action type="fix">
Client revincludes did not include the :recurse modifier. Thanks to
Jenny Meinsma for pointing this out on Zulip!
</action>
<action type="add">
JPA server did not return an OperationOutcome in the response for
a normal delete operation.
</action>
</release>
<release version="2.2" date="2016-12-20">
<action type="add">