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hapi-fhir
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Merge branch 'master' into hapi3_refactor

This commit is contained in:
James Agnew 2017-07-03 20:34:16 -04:00
parent ea1264cd8e 294d080bd3
commit 9281ccafc3
49 changed files with 2235 additions and 1084 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

29
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/NumberParam.java
View File

@ -32,6 +32,7 @@ import ca.uhn.fhir.model.api.IQueryParameterType;
public class NumberParam extends BaseParamWithPrefix<NumberParam> implements IQueryParameterType {
private static final long serialVersionUID = 1L;
private BigDecimal myQuantity;
/**
@ -41,6 +42,16 @@ public class NumberParam extends BaseParamWithPrefix<NumberParam> implements IQu
super();
}
/**
* Constructor
*
* @param theValue
* A value, e.g. "10"
*/
public NumberParam(int theValue) {
setValue(new BigDecimal(theValue));
}
/**
* Constructor
*
@ -79,6 +90,15 @@ public class NumberParam extends BaseParamWithPrefix<NumberParam> implements IQu
}
public BigDecimal getValue() {
return myQuantity;
}
public NumberParam setValue(BigDecimal theValue) {
myQuantity = theValue;
return this;
}
@Override
public String toString() {
ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SIMPLE_STYLE);
@ -87,13 +107,4 @@ public class NumberParam extends BaseParamWithPrefix<NumberParam> implements IQu
return b.build();
}
public BigDecimal getValue() {
return myQuantity;
}
public NumberParam setValue(BigDecimal theValue) {
myQuantity = theValue;
return this;
}
}

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ReferenceParam.java
View File

@ -173,12 +173,14 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
return true;
}
public void setChain(String theChain) {
public ReferenceParam setChain(String theChain) {
myChain = theChain;
return this;
}
public void setValue(String theValue) {
public ReferenceParam setValue(String theValue) {
myId.setValue(theValue);
return this;
}
/**

407
hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsProvider.java
View File

@ -48,6 +48,7 @@ import ca.uhn.fhir.rest.server.AddProfileTagEnum;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
import ca.uhn.fhir.rest.server.IPagingProvider;
import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
import ca.uhn.fhir.rest.server.IServerAddressStrategy;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -62,216 +63,246 @@ import ca.uhn.fhir.util.OperationOutcomeUtil;
*/
public abstract class AbstractJaxRsProvider implements IRestfulServerDefaults {
private final FhirContext CTX;
private static final String ERROR = "error";
private static final String PROCESSING = "processing";
private static final String ERROR = "error";
private static final String PROCESSING = "processing";
/** the uri info */
@Context
private UriInfo theUriInfo;
/** the http headers */
@Context
private HttpHeaders theHeaders;
private final FhirContext CTX;
/** the http headers */
@Context
private HttpHeaders theHeaders;
@Override
public FhirContext getFhirContext() {
return CTX;
}
/** the uri info */
@Context
private UriInfo theUriInfo;
/**
* Default is DSTU2. Use {@link AbstractJaxRsProvider#AbstractJaxRsProvider(FhirContext)} to specify a DSTU3 context.
*/
protected AbstractJaxRsProvider() {
CTX = FhirContext.forDstu2();
}
/**
* Default is DSTU2. Use {@link AbstractJaxRsProvider#AbstractJaxRsProvider(FhirContext)} to specify a DSTU3 context.
*/
protected AbstractJaxRsProvider() {
CTX = FhirContext.forDstu2();
}
/**
*
* @param ctx the {@link FhirContext} to support.
*/
protected AbstractJaxRsProvider(final FhirContext ctx) {
CTX = ctx;
}
/**
*
* @param ctx
* the {@link FhirContext} to support.
*/
protected AbstractJaxRsProvider(final FhirContext ctx) {
CTX = ctx;
}
/**
* This method returns the query parameters
* @return the query parameters
*/
public Map<String, String[]> getParameters() {
final MultivaluedMap<String, String> queryParameters = getUriInfo().getQueryParameters();
final HashMap<String, String[]> params = new HashMap<String, String[]>();
for (final Entry<String, List<String>> paramEntry : queryParameters.entrySet()) {
params.put(paramEntry.getKey(), paramEntry.getValue().toArray(new String[paramEntry.getValue().size()]));
}
return params;
}
private IBaseOperationOutcome createOutcome(final DataFormatException theException) {
final IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getFhirContext());
final String detailsValue = theException.getMessage() + "\n\n" + ExceptionUtils.getStackTrace(theException);
OperationOutcomeUtil.addIssue(getFhirContext(), oo, ERROR, detailsValue, null, PROCESSING);
return oo;
}
/**
* This method returns the default server address strategy. The default strategy return the
* base uri for the request {@link AbstractJaxRsProvider#getBaseForRequest() getBaseForRequest()}
* @return
*/
public IServerAddressStrategy getServerAddressStrategy() {
final HardcodedServerAddressStrategy addressStrategy = new HardcodedServerAddressStrategy();
addressStrategy.setValue(getBaseForRequest());
return addressStrategy;
}
/**
* DEFAULT = AddProfileTagEnum.NEVER
*/
@Override
public AddProfileTagEnum getAddProfileTag() {
return AddProfileTagEnum.NEVER;
}
/**
* This method returns the server base, independent of the request or resource.
* @see javax.ws.rs.core.UriInfo#getBaseUri()
* @return the ascii string for the server base
*/
public String getBaseForServer() {
final String url = getUriInfo().getBaseUri().toASCIIString();
return StringUtils.isNotBlank(url) && url.endsWith("/") ? url.substring(0, url.length() - 1) : url;
}
/**
* This method returns the server base, including the resource path.
* {@link javax.ws.rs.core.UriInfo#getBaseUri() UriInfo#getBaseUri()}
*
* @return the ascii string for the base resource provider path
*/
public String getBaseForRequest() {
return getBaseForServer();
}
/**
* This method returns the server base, including the resource path.
* {@link javax.ws.rs.core.UriInfo#getBaseUri() UriInfo#getBaseUri()}
* @return the ascii string for the base resource provider path
*/
public String getBaseForRequest() {
return getBaseForServer();
}
/**
* This method returns the server base, independent of the request or resource.
*
* @see javax.ws.rs.core.UriInfo#getBaseUri()
* @return the ascii string for the server base
*/
public String getBaseForServer() {
final String url = getUriInfo().getBaseUri().toASCIIString();
return StringUtils.isNotBlank(url) && url.endsWith("/") ? url.substring(0, url.length() - 1) : url;
}
/**
* Default: an empty list of interceptors (Interceptors are not yet supported
* in the JAX-RS server). Please get in touch if you'd like to help!
*
* @see ca.uhn.fhir.rest.server.IRestfulServer#getInterceptors()
*/
@Override
public List<IServerInterceptor> getInterceptors() {
return Collections.emptyList();
}
/**
* DEFAULT = EncodingEnum.JSON
*/
@Override
public EncodingEnum getDefaultResponseEncoding() {
return EncodingEnum.JSON;
}
/**
* Get the uriInfo
* @return the uri info
*/
public UriInfo getUriInfo() {
return this.theUriInfo;
}
/**
* DEFAULT = ETagSupportEnum.DISABLED
*/
@Override
public ETagSupportEnum getETagSupport() {
return ETagSupportEnum.DISABLED;
}
/**
* Set the Uri Info
* @param uriInfo the uri info
*/
public void setUriInfo(final UriInfo uriInfo) {
this.theUriInfo = uriInfo;
}
@Override
public FhirContext getFhirContext() {
return CTX;
}
/**
* Get the headers
* @return the headers
*/
public HttpHeaders getHeaders() {
return this.theHeaders;
}
/**
* Get the headers
*
* @return the headers
*/
public HttpHeaders getHeaders() {
return this.theHeaders;
}
/**
* Set the headers
* @param headers the headers to set
*/
public void setHeaders(final HttpHeaders headers) {
this.theHeaders = headers;
}
/**
* Default: an empty list of interceptors (Interceptors are not yet supported
* in the JAX-RS server). Please get in touch if you'd like to help!
*
* @see ca.uhn.fhir.rest.server.IRestfulServer#getInterceptors()
*/
@Override
public List<IServerInterceptor> getInterceptors() {
return Collections.emptyList();
}
/**
* Return the requestbuilder for the server
* @param requestType the type of the request
* @param restOperation the rest operation type
* @param theResourceName the resource name
* @return the requestbuilder
*/
public Builder getRequest(final RequestTypeEnum requestType, final RestOperationTypeEnum restOperation, final String theResourceName) {
return new JaxRsRequest.Builder(this, requestType, restOperation, theUriInfo.getRequestUri().toString(), theResourceName);
}
/**
* By default, no paging provider is used
*/
@Override
public IPagingProvider getPagingProvider() {
return null;
}
/**
* Return the requestbuilder for the server
* @param requestType the type of the request
* @param restOperation the rest operation type
* @return the requestbuilder
*/
public Builder getRequest(final RequestTypeEnum requestType, final RestOperationTypeEnum restOperation) {
return getRequest(requestType, restOperation, null);
}
/**
* This method returns the query parameters
*
* @return the query parameters
*/
public Map<String, String[]> getParameters() {
final MultivaluedMap<String, String> queryParameters = getUriInfo().getQueryParameters();
final HashMap<String, String[]> params = new HashMap<String, String[]>();
for (final Entry<String, List<String>> paramEntry : queryParameters.entrySet()) {
params.put(paramEntry.getKey(), paramEntry.getValue().toArray(new String[paramEntry.getValue().size()]));
}
return params;
}
/**
* DEFAULT = EncodingEnum.JSON
*/
@Override
public EncodingEnum getDefaultResponseEncoding() {
return EncodingEnum.JSON;
}
/**
* Return the requestbuilder for the server
*
* @param requestType
* the type of the request
* @param restOperation
* the rest operation type
* @return the requestbuilder
*/
public Builder getRequest(final RequestTypeEnum requestType, final RestOperationTypeEnum restOperation) {
return getRequest(requestType, restOperation, null);
}
/**
* DEFAULT = true
*/
@Override
public boolean isDefaultPrettyPrint() {
return true;
}
/**
* Return the requestbuilder for the server
*
* @param requestType
* the type of the request
* @param restOperation
* the rest operation type
* @param theResourceName
* the resource name
* @return the requestbuilder
*/
public Builder getRequest(final RequestTypeEnum requestType, final RestOperationTypeEnum restOperation, final String theResourceName) {
return new JaxRsRequest.Builder(this, requestType, restOperation, theUriInfo.getRequestUri().toString(), theResourceName);
}
/**
* DEFAULT = ETagSupportEnum.DISABLED
*/
@Override
public ETagSupportEnum getETagSupport() {
return ETagSupportEnum.DISABLED;
}
/**
* This method returns the default server address strategy. The default strategy return the
* base uri for the request {@link AbstractJaxRsProvider#getBaseForRequest() getBaseForRequest()}
*
* @return
*/
public IServerAddressStrategy getServerAddressStrategy() {
final HardcodedServerAddressStrategy addressStrategy = new HardcodedServerAddressStrategy();
addressStrategy.setValue(getBaseForRequest());
return addressStrategy;
}
/**
* DEFAULT = AddProfileTagEnum.NEVER
*/
@Override
public AddProfileTagEnum getAddProfileTag() {
return AddProfileTagEnum.NEVER;
}
/**
* Get the uriInfo
*
* @return the uri info
*/
public UriInfo getUriInfo() {
return this.theUriInfo;
}
/**
* DEFAULT = false
*/
@Override
public boolean isUseBrowserFriendlyContentTypes() {
return true;
}
/**
* Convert an exception to a response
*
* @param theRequest
* the incoming request
* @param theException
* the exception to convert
* @return response
* @throws IOException
*/
public Response handleException(final JaxRsRequest theRequest, final Throwable theException)
throws IOException {
if (theException instanceof JaxRsResponseException) {
return new JaxRsExceptionInterceptor().convertExceptionIntoResponse(theRequest, (JaxRsResponseException) theException);
} else if (theException instanceof DataFormatException) {
return new JaxRsExceptionInterceptor().convertExceptionIntoResponse(theRequest, new JaxRsResponseException(
new InvalidRequestException(theException.getMessage(), createOutcome((DataFormatException) theException))));
} else {
return new JaxRsExceptionInterceptor().convertExceptionIntoResponse(theRequest,
new JaxRsExceptionInterceptor().convertException(this, theException));
}
}
/**
* DEFAULT = false
*/
public boolean withStackTrace() {
return false;
}
/**
* DEFAULT = true
*/
@Override
public boolean isDefaultPrettyPrint() {
return true;
}
/**
* Convert an exception to a response
* @param theRequest the incoming request
* @param theException the exception to convert
* @return response
* @throws IOException
*/
public Response handleException(final JaxRsRequest theRequest, final Throwable theException)
throws IOException {
if (theException instanceof JaxRsResponseException) {
return new JaxRsExceptionInterceptor().convertExceptionIntoResponse(theRequest, (JaxRsResponseException) theException);
} else if (theException instanceof DataFormatException) {
return new JaxRsExceptionInterceptor().convertExceptionIntoResponse(theRequest, new JaxRsResponseException(
new InvalidRequestException(theException.getMessage(), createOutcome((DataFormatException) theException))));
} else {
return new JaxRsExceptionInterceptor().convertExceptionIntoResponse(theRequest,
new JaxRsExceptionInterceptor().convertException(this, theException));
}
}
/**
* DEFAULT = false
*/
@Override
public boolean isUseBrowserFriendlyContentTypes() {
return true;
}
private IBaseOperationOutcome createOutcome(final DataFormatException theException) {
final IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getFhirContext());
final String detailsValue = theException.getMessage() + "\n\n" + ExceptionUtils.getStackTrace(theException);
OperationOutcomeUtil.addIssue(getFhirContext(), oo, ERROR, detailsValue, null, PROCESSING);
return oo;
}
/**
* Set the headers
*
* @param headers
* the headers to set
*/
public void setHeaders(final HttpHeaders headers) {
this.theHeaders = headers;
}
/**
* Set the Uri Info
*
* @param uriInfo
* the uri info
*/
public void setUriInfo(final UriInfo uriInfo) {
this.theUriInfo = uriInfo;
}
/**
* DEFAULT = false
*/
public boolean withStackTrace() {
return false;
}
}

161
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -26,52 +26,21 @@ import static org.apache.commons.lang3.StringUtils.trim;
import java.io.UnsupportedEncodingException;
import java.text.Normalizer;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.*;
import java.util.Map.Entry;
import java.util.Set;
import java.util.UUID;
import javax.persistence.EntityManager;
import javax.persistence.NoResultException;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.Tuple;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import javax.persistence.*;
import javax.persistence.criteria.*;
import javax.xml.stream.events.Characters;
import javax.xml.stream.events.XMLEvent;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.*;
import org.apache.http.NameValuePair;
import org.apache.http.client.utils.URLEncodedUtils;
import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IDomainResource;
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.transaction.PlatformTransactionManager;
@ -81,89 +50,31 @@ import com.google.common.collect.Sets;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.BaseHasResource;
import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.entity.BaseTag;
import ca.uhn.fhir.jpa.entity.ForcedId;
import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTag;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.entity.ResourceLink;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.ResourceTag;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchStatusEnum;
import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.entity.TagDefinition;
import ca.uhn.fhir.jpa.entity.TagTypeEnum;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.util.DeleteConflict;
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.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
import ca.uhn.fhir.model.dstu.resource.BaseResource;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.XhtmlDt;
import ca.uhn.fhir.model.primitive.*;
import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.parser.*;
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.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriAndListParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.method.*;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.Constants;
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.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.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.OperationOutcomeUtil;
import ca.uhn.fhir.util.*;
public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
@ -442,6 +353,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
"Resource contains reference to " + nextId.getValue() + " but resource with ID " + nextId.getIdPart() + " is actually of type " + target.getResourceType());
}
if (target.getDeleted() != null) {
String resName = targetResourceDef.getName();
throw new InvalidRequestException("Resource " + resName + "/" + id + " is deleted, specified in path: " + nextPathsUnsplit);
}
if (nextSpDef.getTargets() != null && !nextSpDef.getTargets().contains(typeString)) {
continue;
}
@ -634,6 +550,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
}
}
private Set<TagDefinition> getAllTagDefinitions(ResourceTable theEntity) {
HashSet<TagDefinition> retVal = Sets.newHashSet();
for (ResourceTag next : theEntity.getTags()) {
retVal.add(next.getTag());
}
return retVal;
}
protected DaoConfig getConfig() {
return myConfig;
}
@ -1000,14 +924,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
return changed;
}
private Set<TagDefinition> getAllTagDefinitions(ResourceTable theEntity) {
HashSet<TagDefinition> retVal = Sets.newHashSet();
for (ResourceTag next : theEntity.getTags()) {
retVal.add(next.getTag());
}
return retVal;
}
@SuppressWarnings("unchecked")
private <R extends IBaseResource> R populateResourceMetadataHapi(Class<R> theResourceType, BaseHasResource theEntity, boolean theForHistoryOperation, IResource res) {
R retVal = (R) res;
@ -1806,6 +1722,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
throw new ResourceVersionConflictException(firstMsg, oo);
}
protected void validateMetaCount(int theMetaCount) {
if (myConfig.getResourceMetaCountHardLimit() != null) {
if (theMetaCount > myConfig.getResourceMetaCountHardLimit()) {
throw new UnprocessableEntityException("Resource contains " + theMetaCount + " meta entries (tag/profile/security label), maximum is " + myConfig.getResourceMetaCountHardLimit());
}
}
}
/**
* This method is invoked immediately before storing a new resource, or an update to an existing resource to allow the DAO to ensure that it is valid for persistence. By default, checks for the
* "subsetted" tag and rejects resources which have it. Subclasses should call the superclass implementation to preserve this check.
@ -1817,15 +1741,26 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
*/
protected void validateResourceForStorage(T theResource, ResourceTable theEntityToSave) {
Object tag = null;
int totalMetaCount = 0;
if (theResource instanceof IResource) {
IResource res = (IResource) theResource;
TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(res);
if (tagList != null) {
tag = tagList.getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
totalMetaCount += tagList.size();
}
List<IdDt> profileList = ResourceMetadataKeyEnum.PROFILES.get(res);
if (profileList != null) {
totalMetaCount += profileList.size();
}
} else {
IAnyResource res = (IAnyResource) theResource;
tag = res.getMeta().getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
totalMetaCount += res.getMeta().getTag().size();
totalMetaCount += res.getMeta().getProfile().size();
totalMetaCount += res.getMeta().getSecurity().size();
}
if (tag != null) {
@ -1835,6 +1770,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
String resName = getContext().getResourceDefinition(theResource).getName();
validateChildReferences(theResource, resName);
validateMetaCount(totalMetaCount);
}
protected static boolean isValidPid(IIdType theId) {

49
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -29,6 +29,7 @@ import javax.annotation.PostConstruct;
import javax.persistence.NoResultException;
import javax.persistence.TypedQuery;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.instance.model.api.*;
import org.springframework.beans.factory.annotation.Autowired;
@ -48,6 +49,7 @@ import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.interceptor.IJpaServerInterceptor;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.util.DeleteConflict;
import ca.uhn.fhir.jpa.util.StopWatch;
@ -117,9 +119,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
TagDefinition def = getTagOrNull(TagTypeEnum.TAG, theScheme, theTerm, theLabel);
if (def != null) {
BaseTag newEntity = entity.addTag(def);
myEntityManager.persist(newEntity);
myEntityManager.merge(entity);
if (newEntity.getTagId() == null) {
myEntityManager.persist(newEntity);
myEntityManager.merge(entity);
}
}
ourLog.info("Processed addTag {}/{} on {} in {}ms", new Object[] { theScheme, theTerm, theId, w.getMillisAndRestart() });
@ -430,7 +433,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
private <MT extends IBaseMetaType> void doMetaAdd(MT theMetaAdd, BaseHasResource entity) {
List<TagDefinition> tags = toTagList(theMetaAdd);
//@formatter:off
for (TagDefinition nextDef : tags) {
boolean hasTag = false;
@ -449,12 +451,15 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
TagDefinition def = getTagOrNull(nextDef.getTagType(), nextDef.getSystem(), nextDef.getCode(), nextDef.getDisplay());
if (def != null) {
BaseTag newEntity = entity.addTag(def);
myEntityManager.persist(newEntity);
if (newEntity.getTagId() == null) {
myEntityManager.persist(newEntity);
}
}
}
}
//@formatter:on
validateMetaCount(entity.getTags().size());
myEntityManager.merge(entity);
}
@ -562,6 +567,16 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
theSavedEntity.setVersion(newVersionLong);
}
protected boolean isPagingProviderDatabaseBacked(RequestDetails theRequestDetails) {
if (theRequestDetails == null || theRequestDetails.getServer() == null) {
return false;
}
if (theRequestDetails.getServer().getPagingProvider() instanceof DatabaseBackedPagingProvider) {
return true;
}
return false;
}
@Override
public <MT extends IBaseMetaType> MT metaAddOperation(IIdType theResourceId, MT theMetaAdd, RequestDetails theRequestDetails) {
// Notify interceptors
@ -594,6 +609,7 @@ 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
@ -628,7 +644,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return retVal;
}
@Override
public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, IIdType theId, RequestDetails theRequestDetails) {
// Notify interceptors
@ -860,12 +875,12 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
ourLog.debug("Indexing resource {} - PID {}", theResource.getIdElement().getValue(), theEntity.getId());
updateEntity(theResource, theEntity, null, true, false, theEntity.getUpdatedDate(), true, false);
}
@Override
public void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm) {
removeTag(theId, theTagType, theScheme, theTerm, null);
}
@Override
public void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, RequestDetails theRequestDetails) {
// Notify interceptors
@ -915,19 +930,21 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
notifyInterceptors(RestOperationTypeEnum.SEARCH_TYPE, requestDetails);
if (theRequestDetails.isSubRequest()) {
theParams.setLoadSynchronous(true);
int max = myDaoConfig.getMaximumSearchResultCountInTransaction();
theParams.setLoadSynchronousUpTo(myDaoConfig.getMaximumSearchResultCountInTransaction());
Integer max = myDaoConfig.getMaximumSearchResultCountInTransaction();
if (max != null) {
Validate.inclusiveBetween(1, Integer.MAX_VALUE, max.intValue(), "Maximum search result count in transaction ust be a positive integer");
theParams.setLoadSynchronousUpTo(myDaoConfig.getMaximumSearchResultCountInTransaction());
}
}
if (!isPagingProviderDatabaseBacked(theRequestDetails)) {
theParams.setLoadSynchronous(true);
}
}
return mySearchCoordinatorSvc.registerSearch(this, theParams, getResourceName());
}
@Override
public Set<Long> searchForIds(SearchParameterMap theParams) {

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

@ -57,7 +57,7 @@ public class DaoConfig {
*
* @see #setMaximumSearchResultCountInTransaction(int)
*/
private static final int DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = 500;
private static final Integer DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = null;
/**
* Default value for {@link #setReuseCachedSearchResultsForMillis(Long)}: 60000ms (one minute)
@ -103,13 +103,19 @@ public class DaoConfig {
* update setter javadoc if default changes
*/
private boolean myIndexContainedResources = true;
private List<IServerInterceptor> myInterceptors;
/**
* update setter javadoc if default changes
*/
private int myMaximumExpansionSize = 5000;
private int myMaximumSearchResultCountInTransaction = DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION;
private Integer myMaximumSearchResultCountInTransaction = DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION;
private ResourceEncodingEnum myResourceEncoding = ResourceEncodingEnum.JSONC;
/**
* update setter javadoc if default changes
*/
private Integer myResourceMetaCountHardLimit = 1000;
private Long myReuseCachedSearchResultsForMillis = DEFAULT_REUSE_CACHED_SEARCH_RESULTS_FOR_MILLIS;
private boolean mySchedulingDisabled;
private boolean mySubscriptionEnabled;
@ -121,7 +127,6 @@ public class DaoConfig {
private boolean mySuppressUpdatesWithNoChange = true;
private Set<String> myTreatBaseUrlsAsLocal = new HashSet<String>();
private Set<String> myTreatReferencesAsLogical = new HashSet<String>(DEFAULT_LOGICAL_BASE_URLS);
/**
* Add a value to the {@link #setTreatReferencesAsLogical(Set) logical references list}.
*
@ -135,7 +140,6 @@ public class DaoConfig {
}
myTreatReferencesAsLogical.add(theTreatReferencesAsLogical);
}
/**
* When a code system is added that contains more than this number of codes,
* the code system will be indexed later in an incremental process in order to
@ -229,14 +233,17 @@ public class DaoConfig {
}
/**
* Provides the maximum number of results which may be returned by a search within a FHIR <code>transaction</code>
* operation. For example, if this value is set to <code>100</code> and a FHIR transaction is processed with a sub-request
* for <code>Patient?gender=male</code>, the server will throw an error (and the transaction will fail) if there are more than
* Provides the maximum number of results which may be returned by a search (HTTP GET) which
* is executed as a sub-operation within within a FHIR <code>transaction</code> or
* <code>batch</code> operation. For example, if this value is set to <code>100</code> and
* a FHIR transaction is processed with a sub-request for <code>Patient?gender=male</code>,
* the server will throw an error (and the transaction will fail) if there are more than
* 100 resources on the server which match this query.
*
* @see #DEFAULT_LOGICAL_BASE_URLS The default value for this setting
* <p>
* The default value is <code>null</code>, which means that there is no limit.
* </p>
*/
public int getMaximumSearchResultCountInTransaction() {
public Integer getMaximumSearchResultCountInTransaction() {
return myMaximumSearchResultCountInTransaction;
}
@ -244,6 +251,21 @@ public class DaoConfig {
return myResourceEncoding;
}
/**
* If set, an individual resource will not be allowed to have more than the
* given number of tags, profiles, and security labels (the limit is for the combined
* total for all of these things on an individual resource).
* <p>
* If set to <code>null</code>, no limit will be applied.
* </p>
* <p>
* The default value for this setting is 1000.
* </p>
*/
public Integer getResourceMetaCountHardLimit() {
return myResourceMetaCountHardLimit;
}
/**
* If set to a non {@literal null} value (default is {@link #DEFAULT_REUSE_CACHED_SEARCH_RESULTS_FOR_MILLIS non null})
* if an identical search is requested multiple times within this window, the same results will be returned
@ -376,8 +398,6 @@ public class DaoConfig {
* and other FHIR features may not behave as expected when referential integrity is not
* preserved. Use this feature with caution.
* </p>
*
* @return
*/
public boolean isEnforceReferentialIntegrityOnDelete() {
return myEnforceReferentialIntegrityOnDelete;
@ -682,14 +702,17 @@ public class DaoConfig {
}
/**
* Provides the maximum number of results which may be returned by a search within a FHIR <code>transaction</code>
* operation. For example, if this value is set to <code>100</code> and a FHIR transaction is processed with a sub-request
* for <code>Patient?gender=male</code>, the server will throw an error (and the transaction will fail) if there are more than
* Provides the maximum number of results which may be returned by a search (HTTP GET) which
* is executed as a sub-operation within within a FHIR <code>transaction</code> or
* <code>batch</code> operation. For example, if this value is set to <code>100</code> and
* a FHIR transaction is processed with a sub-request for <code>Patient?gender=male</code>,
* the server will throw an error (and the transaction will fail) if there are more than
* 100 resources on the server which match this query.
*
* @see #DEFAULT_LOGICAL_BASE_URLS The default value for this setting
* <p>
* The default value is <code>null</code>, which means that there is no limit.
* </p>
*/
public void setMaximumSearchResultCountInTransaction(int theMaximumSearchResultCountInTransaction) {
public void setMaximumSearchResultCountInTransaction(Integer theMaximumSearchResultCountInTransaction) {
myMaximumSearchResultCountInTransaction = theMaximumSearchResultCountInTransaction;
}
@ -697,6 +720,21 @@ public class DaoConfig {
myResourceEncoding = theResourceEncoding;
}
/**
* If set, an individual resource will not be allowed to have more than the
* given number of tags, profiles, and security labels (the limit is for the combined
* total for all of these things on an individual resource).
* <p>
* If set to <code>null</code>, no limit will be applied.
* </p>
* <p>
* The default value for this setting is 1000.
* </p>
*/
public void setResourceMetaCountHardLimit(Integer theResourceMetaCountHardLimit) {
myResourceMetaCountHardLimit = theResourceMetaCountHardLimit;
}
/**
* If set to a non {@literal null} value (default is {@link #DEFAULT_REUSE_CACHED_SEARCH_RESULTS_FOR_MILLIS non null})
* if an identical search is requested multiple times within this window, the same results will be returned

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoPatientDstu2.java
View File

@ -46,7 +46,7 @@ public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>im
super();
}
private IBundleProvider doEverythingOperation(IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative) {
private IBundleProvider doEverythingOperation(IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative, RequestDetails theRequestDetails) {
SearchParameterMap paramMap = new SearchParameterMap();
if (theCount != null) {
paramMap.setCount(theCount.getValue());
@ -65,6 +65,10 @@ public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>im
paramMap.add("_id", new StringParam(theId.getIdPart()));
}
if (!isPagingProviderDatabaseBacked(theRequestDetails)) {
paramMap.setLoadSynchronous(true);
}
return mySearchCoordinatorSvc.registerSearch(this, paramMap, getResourceName());
}
@ -74,7 +78,7 @@ public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>im
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), null);
notifyInterceptors(RestOperationTypeEnum.EXTENDED_OPERATION_INSTANCE, requestDetails);
return doEverythingOperation(theId, theCount, theLastUpdated, theSort, theContent, theNarrative);
return doEverythingOperation(theId, theCount, theLastUpdated, theSort, theContent, theNarrative, theRequestDetails);
}
@Override
@ -83,7 +87,7 @@ public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>im
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), null);
notifyInterceptors(RestOperationTypeEnum.EXTENDED_OPERATION_TYPE, requestDetails);
return doEverythingOperation(null, theCount, theLastUpdated, theSort, theContent, theNarrative);
return doEverythingOperation(null, theCount, theLastUpdated, theSort, theContent, theNarrative, theRequestDetails);
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java
View File

@ -106,8 +106,6 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
Bundle resp = new Bundle();
resp.setType(BundleTypeEnum.BATCH_RESPONSE);
OperationOutcome ooResp = new OperationOutcome();
resp.addEntry().setResource(ooResp);
/*
* For batch, we handle each entry as a mini-transaction in its own database transaction so that if one fails, it doesn't prevent others
@ -163,7 +161,6 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
long delay = System.currentTimeMillis() - start;
ourLog.info("Batch completed in {}ms", new Object[] { delay });
ooResp.addIssue().setSeverity(IssueSeverityEnum.INFORMATION).setDiagnostics("Batch completed in " + delay + "ms");
return resp;
}

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

@ -27,86 +27,34 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.math.BigDecimal;
import java.math.MathContext;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.*;
import java.util.Map.Entry;
import java.util.Set;
import javax.persistence.EntityManager;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.AbstractQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.*;
import javax.persistence.criteria.CriteriaBuilder.In;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Expression;
import javax.persistence.criteria.From;
import javax.persistence.criteria.Join;
import javax.persistence.criteria.JoinType;
import javax.persistence.criteria.Order;
import javax.persistence.criteria.Path;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import javax.persistence.criteria.Subquery;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.*;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hibernate.ScrollMode;
import org.hibernate.ScrollableResults;
import org.hibernate.query.Query;
import org.hl7.fhir.instance.model.api.*;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import com.google.common.collect.*;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
import ca.uhn.fhir.jpa.entity.BaseHasResource;
import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.entity.ResourceLink;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.ResourceTag;
import ca.uhn.fhir.jpa.entity.SearchParam;
import ca.uhn.fhir.jpa.entity.SearchParamPresent;
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.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
import ca.uhn.fhir.jpa.util.StopWatch;
import ca.uhn.fhir.model.api.IPrimitiveDatatype;
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.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
import ca.uhn.fhir.model.base.composite.BaseQuantityDt;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.base.composite.*;
import ca.uhn.fhir.model.dstu.resource.BaseResource;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
@ -115,23 +63,9 @@ import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.param.CompositeParam;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.NumberParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.param.UriParamQualifierEnum;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.util.UrlUtil;
/**
@ -139,8 +73,8 @@ import ca.uhn.fhir.util.UrlUtil;
* searchs for resources
*/
public class SearchBuilder implements ISearchBuilder {
private static final List<Long> EMPTY_LONG_LIST = Collections.unmodifiableList(new ArrayList<Long>());
private static Long NO_MORE = Long.valueOf(-1);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchBuilder.class);
private List<Long> myAlsoIncludePids;
@ -161,7 +95,7 @@ public class SearchBuilder implements ISearchBuilder {
private ISearchParamRegistry mySearchParamRegistry;
private String mySearchUuid;
private IHapiTerminologySvc myTerminologySvc;
/**
* Constructor
*/
@ -2037,6 +1971,7 @@ public class SearchBuilder implements ISearchBuilder {
static Predicate[] toArray(List<Predicate> thePredicates) {
return thePredicates.toArray(new Predicate[thePredicates.size()]);
}
public class IncludesIterator implements Iterator<Long>{
private Iterator<Long> myCurrentIterator;
@ -2094,7 +2029,6 @@ public class SearchBuilder implements ISearchBuilder {
}
}
private enum JoinEnum {
DATE, NUMBER, QUANTITY, REFERENCE, STRING, TOKEN, URI
@ -2160,8 +2094,11 @@ public class SearchBuilder implements ISearchBuilder {
Integer maximumResults = myCallingDao.getConfig().getFetchSizeDefaultMaximum();
final TypedQuery<Long> query = createQuery(mySort, maximumResults);
myResultsIterator = query.getResultList().iterator();
Query<Long> hibernateQuery = (Query<Long>) query;
ScrollableResults scroll = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
myResultsIterator = new ScrollableResultsIterator(scroll);
// If the query resulted in extra results being requested
if (myAlsoIncludePids != null) {
myPreResultsIterator = myAlsoIncludePids.iterator();
@ -2245,4 +2182,40 @@ public class SearchBuilder implements ISearchBuilder {
}
}
public class ScrollableResultsIterator implements Iterator<Long> {
private Long myNext;
private ScrollableResults myScroll;
public ScrollableResultsIterator(ScrollableResults theScroll) {
myScroll = theScroll;
}
private void ensureHaveNext() {
if (myNext == null) {
if (myScroll.next()) {
myNext = (Long) myScroll.get(0);
} else {
myNext = NO_MORE;
}
}
}
@Override
public boolean hasNext() {
ensureHaveNext();
return myNext != NO_MORE;
}
@Override
public Long next() {
ensureHaveNext();
Validate.isTrue(myNext != NO_MORE);
Long next = myNext;
myNext = null;
return next;
}
}
}

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

@ -35,8 +35,8 @@ public interface ISearchDao extends JpaRepository<Search, Long> {
@Query("SELECT s FROM Search s WHERE s.myUuid = :uuid")
public Search findByUuid(@Param("uuid") String theUuid);
@Query("SELECT s FROM Search s WHERE s.mySearchLastReturned < :cutoff")
public Collection<Search> findWhereLastReturnedBefore(@Param("cutoff") Date theCutoff);
@Query("SELECT s.myId FROM Search s WHERE s.mySearchLastReturned < :cutoff")
public Collection<Long> findWhereLastReturnedBefore(@Param("cutoff") Date theCutoff);
// @Query("SELECT s FROM Search s WHERE s.myCreated < :cutoff")
// public Collection<Search> findWhereCreatedBefore(@Param("cutoff") Date theCutoff);

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoPatientDstu3.java
View File

@ -50,7 +50,7 @@ public class FhirResourceDaoPatientDstu3 extends FhirResourceDaoDstu3<Patient>im
@Autowired
private ISearchParamRegistry mySerarchParamRegistry;
private IBundleProvider doEverythingOperation(IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative) {
private IBundleProvider doEverythingOperation(IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative, RequestDetails theRequestDetails) {
SearchParameterMap paramMap = new SearchParameterMap();
if (theCount != null) {
paramMap.setCount(theCount.getValue());
@ -69,17 +69,21 @@ public class FhirResourceDaoPatientDstu3 extends FhirResourceDaoDstu3<Patient>im
paramMap.add("_id", new StringParam(theId.getIdPart()));
}
if (!isPagingProviderDatabaseBacked(theRequestDetails)) {
paramMap.setLoadSynchronous(true);
}
return mySearchCoordinatorSvc.registerSearch(this, paramMap, getResourceName());
}
@Override
public IBundleProvider patientInstanceEverything(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative, RequestDetails theRequestDetails) {
return doEverythingOperation(theId, theCount, theLastUpdated, theSort, theContent, theNarrative);
return doEverythingOperation(theId, theCount, theLastUpdated, theSort, theContent, theNarrative, theRequestDetails);
}
@Override
public IBundleProvider patientTypeEverything(HttpServletRequest theServletRequest, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative, RequestDetails theRequestDetails) {
return doEverythingOperation(null, theCount, theLastUpdated, theSort, theContent, theNarrative);
return doEverythingOperation(null, theCount, theLastUpdated, theSort, theContent, theNarrative, theRequestDetails);
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java
View File

@ -114,8 +114,6 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
Bundle resp = new Bundle();
resp.setType(BundleType.BATCHRESPONSE);
OperationOutcome ooResp = new OperationOutcome();
resp.addEntry().setResource(ooResp);
/*
* For batch, we handle each entry as a mini-transaction in its own database transaction so that if one fails, it doesn't prevent others
@ -171,7 +169,6 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
long delay = System.currentTimeMillis() - start;
ourLog.info("Batch completed in {}ms", new Object[] { delay });
ooResp.addIssue().setSeverity(IssueSeverity.INFORMATION).setDiagnostics("Batch completed in " + delay + "ms");
return resp;
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseHasResource.java
View File

@ -23,16 +23,7 @@ package ca.uhn.fhir.jpa.entity;
import java.util.Collection;
import java.util.Date;
import javax.persistence.Column;
import javax.persistence.EnumType;
import javax.persistence.Enumerated;
import javax.persistence.FetchType;
import javax.persistence.JoinColumn;
import javax.persistence.Lob;
import javax.persistence.MappedSuperclass;
import javax.persistence.OneToOne;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import javax.persistence.*;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.model.primitive.IdDt;

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseTag.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,
@ -32,13 +32,17 @@ public class BaseTag implements Serializable {
private static final long serialVersionUID = 1L;
@ManyToOne(cascade= {})
@JoinColumn(name="TAG_ID", nullable=false)
@ManyToOne(cascade = {})
@JoinColumn(name = "TAG_ID", nullable = false)
private TagDefinition myTag;
@Column(name="TAG_ID", insertable=false,updatable=false)
@Column(name = "TAG_ID", insertable = false, updatable = false)
private Long myTagId;
public Long getTagId() {
return myTagId;
}
public TagDefinition getTag() {
return myTag;
}
@ -46,6 +50,5 @@ public class BaseTag implements Serializable {
public void setTag(TagDefinition theTag) {
myTag = theTag;
}
}

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceHistoryTable.java
View File

@ -93,8 +93,13 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
}
@Override
public BaseTag addTag(TagDefinition theDef) {
ResourceHistoryTag historyTag = new ResourceHistoryTag(this, theDef);
public ResourceHistoryTag addTag(TagDefinition theTag) {
for (ResourceHistoryTag next : getTags()) {
if (next.getTag().equals(theTag)) {
return next;
}
}
ResourceHistoryTag historyTag = new ResourceHistoryTag(this, theTag);
getTags().add(historyTag);
return historyTag;
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceHistoryTag.java
View File

@ -22,21 +22,13 @@ package ca.uhn.fhir.jpa.entity;
import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Embeddable;
import javax.persistence.Entity;
import javax.persistence.ForeignKey;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import javax.persistence.*;
@Embeddable
@Entity
@Table(name = "HFJ_HISTORY_TAG")
@Table(name = "HFJ_HISTORY_TAG", uniqueConstraints= {
@UniqueConstraint(name="IDX_RESHISTTAG_TAGID", columnNames= {"RES_VER_PID","TAG_ID"})
})
public class ResourceHistoryTag extends BaseTag implements Serializable {
private static final long serialVersionUID = 1L;

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

@ -250,6 +250,11 @@ public class ResourceTable extends BaseHasResource implements Serializable {
@Override
public ResourceTag addTag(TagDefinition theTag) {
for (ResourceTag next : getTags()) {
if (next.getTag().equals(theTag)) {
return next;
}
}
ResourceTag tag = new ResourceTag(this, theTag);
getTags().add(tag);
return tag;

27
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTag.java
View File

@ -19,23 +19,14 @@ package ca.uhn.fhir.jpa.entity;
* limitations under the License.
* #L%
*/
import javax.persistence.*;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.ForeignKey;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.*;
@Entity
@Table(name = "HFJ_RES_TAG")
@Table(name = "HFJ_RES_TAG", uniqueConstraints= {
@UniqueConstraint(name="IDX_RESTAG_TAGID", columnNames= {"RES_ID","TAG_ID"})
})
public class ResourceTag extends BaseTag {
private static final long serialVersionUID = 1L;
@ -116,4 +107,12 @@ public class ResourceTag extends BaseTag {
return b.toHashCode();
}
@Override
public String toString() {
ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
b.append("resId", getResourceId());
b.append("tag", getTag().getId());
return b.build();
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TagDefinition.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,
@ -45,8 +45,8 @@ import ca.uhn.fhir.model.api.Tag;
//@formatter:on
@Entity
@Table(name = "HFJ_TAG_DEF", uniqueConstraints = {
@UniqueConstraint(name="IDX_TAGDEF_TYPESYSCODE", columnNames = { "TAG_TYPE", "TAG_SYSTEM", "TAG_CODE" })
@Table(name = "HFJ_TAG_DEF", uniqueConstraints = {
@UniqueConstraint(name = "IDX_TAGDEF_TYPESYSCODE", columnNames = { "TAG_TYPE", "TAG_SYSTEM", "TAG_CODE" })
})
//@formatter:off
public class TagDefinition implements Serializable {
@ -78,6 +78,8 @@ public class TagDefinition implements Serializable {
@Enumerated(EnumType.ORDINAL)
private TagTypeEnum myTagType;
private Integer myHashCode;
public TagDefinition() {
}
@ -110,6 +112,7 @@ public class TagDefinition implements Serializable {
public void setCode(String theCode) {
myCode = theCode;
myHashCode = null;
}
public void setDisplay(String theDisplay) {
@ -118,10 +121,12 @@ public class TagDefinition implements Serializable {
public void setSystem(String theSystem) {
mySystem = theSystem;
myHashCode = null;
}
public void setTagType(TagTypeEnum theTagType) {
myTagType = theTagType;
myHashCode = null;
}
public Tag toTag() {
@ -155,15 +160,14 @@ public class TagDefinition implements Serializable {
@Override
public int hashCode() {
HashCodeBuilder b = new HashCodeBuilder();
if (myId != null) {
b.append(myId);
} else {
if (myHashCode == null) {
HashCodeBuilder b = new HashCodeBuilder();
b.append(myTagType);
b.append(mySystem);
b.append(myCode);
myHashCode = b.toHashCode();
}
return b.toHashCode();
return myHashCode;
}
@Override

91
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/BaseRestHookSubscriptionInterceptor.java Normal file
View File

@ -0,0 +1,91 @@
package ca.uhn.fhir.jpa.interceptor;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* 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
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.interceptor.ServerOperationInterceptorAdapter;
public abstract class BaseRestHookSubscriptionInterceptor extends ServerOperationInterceptorAdapter {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseRestHookSubscriptionInterceptor.class);
protected static final Integer MAX_SUBSCRIPTION_RESULTS = 10000;
protected abstract IFhirResourceDao<?> getSubscriptionDao();
protected void checkSubscriptionCriterias(String theCriteria) {
try {
IBundleProvider results = executeSubscriptionCriteria(theCriteria, null);
} catch (Exception e) {
ourLog.warn("Invalid criteria when creating subscription", e);
throw new InvalidRequestException("Invalid criteria: " + e.getMessage());
}
}
private IBundleProvider executeSubscriptionCriteria(String theCriteria, IIdType idType) {
String criteria = theCriteria;
/*
* Run the subscriptions query and look for matches, add the id as part of the criteria
* to avoid getting matches of previous resources rather than the recent resource
*/
if (idType != null) {
criteria += "&_id=" + idType.getResourceType() + "/" + idType.getIdPart();
}
IBundleProvider results = getBundleProvider(criteria, true);
return results;
}
/**
* Search based on a query criteria
*
* @param theCheckOnly Is this just a test that the search works
*/
protected IBundleProvider getBundleProvider(String theCriteria, boolean theCheckOnly) {
RuntimeResourceDefinition responseResourceDef = getSubscriptionDao().validateCriteriaAndReturnResourceDefinition(theCriteria);
SearchParameterMap responseCriteriaUrl = BaseHapiFhirDao.translateMatchUrl(getSubscriptionDao(), getSubscriptionDao().getContext(), theCriteria, responseResourceDef);
RequestDetails req = new ServletSubRequestDetails();
req.setSubRequest(true);
IFhirResourceDao<? extends IBaseResource> responseDao = getSubscriptionDao().getDao(responseResourceDef.getImplementingClass());
if (theCheckOnly) {
responseCriteriaUrl.setLoadSynchronousUpTo(1);
} else {
responseCriteriaUrl.setLoadSynchronousUpTo(MAX_SUBSCRIPTION_RESULTS);
}
IBundleProvider responseResults = responseDao.search(responseCriteriaUrl, req);
return responseResults;
}
}

114
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/RestHookSubscriptionDstu2Interceptor.java
View File

@ -29,12 +29,9 @@ import javax.annotation.PostConstruct;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.apache.http.NameValuePair;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.client.methods.HttpUriRequest;
import org.apache.http.client.utils.URLEncodedUtils;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -45,8 +42,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
@ -62,11 +57,9 @@ import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.interceptor.*;
public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterceptorAdapter {
public class RestHookSubscriptionDstu2Interceptor extends BaseRestHookSubscriptionInterceptor {
private static final Integer MAX_SUBSCRIPTION_RESULTS = 10000;
private static volatile ExecutorService executor;
private final static int MAX_THREADS = 1;
@ -75,13 +68,13 @@ public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterce
@Autowired
private FhirContext myFhirContext;
private boolean myNotifyOnDelete = false;
private final List<Subscription> myRestHookSubscriptions = new ArrayList<Subscription>();
@Autowired
@Qualifier("mySubscriptionDaoDstu2")
private IFhirResourceDao<Subscription> mySubscriptionDao;
private boolean myNotifyOnDelete = false;
private final List<Subscription> myRestHookSubscriptions = new ArrayList<Subscription>();
/**
* Check subscriptions and send notifications or payload
*
@ -101,7 +94,7 @@ public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterce
}
if (resourceType != null && subscription.getCriteria() != null && !criteriaResource.equals(resourceType)) {
ourLog.info("Skipping subscription search for {} because it does not match the criteria {}", resourceType , subscription.getCriteria());
ourLog.info("Skipping subscription search for {} because it does not match the criteria {}", resourceType, subscription.getCriteria());
continue;
}
@ -110,7 +103,7 @@ public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterce
criteria += "&_id=" + idType.getResourceType() + "/" + idType.getIdPart();
criteria = massageCriteria(criteria);
IBundleProvider results = getBundleProvider(criteria);
IBundleProvider results = getBundleProvider(criteria, false);
if (results.size() == 0) {
continue;
@ -195,25 +188,6 @@ public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterce
return request;
}
/**
* Search based on a query criteria
*
* @param criteria
* @return
*/
private IBundleProvider getBundleProvider(String criteria) {
RuntimeResourceDefinition responseResourceDef = mySubscriptionDao.validateCriteriaAndReturnResourceDefinition(criteria);
SearchParameterMap responseCriteriaUrl = BaseHapiFhirDao.translateMatchUrl(mySubscriptionDao, mySubscriptionDao.getContext(), criteria, responseResourceDef);
RequestDetails req = new ServletSubRequestDetails();
req.setSubRequest(true);
IFhirResourceDao<? extends IBaseResource> responseDao = mySubscriptionDao.getDao(responseResourceDef.getImplementingClass());
responseCriteriaUrl.setCount(MAX_SUBSCRIPTION_RESULTS);
IBundleProvider responseResults = responseDao.search(responseCriteriaUrl, req);
return responseResults;
}
/**
* Get subscription from cache
*
@ -259,6 +233,27 @@ public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterce
return entity;
}
@Override
protected IFhirResourceDao<?> getSubscriptionDao() {
return mySubscriptionDao;
}
@Override
public void incomingRequestPreHandled(RestOperationTypeEnum theOperation, ActionRequestDetails theDetails) {
// check the subscription criteria to see if its valid before creating or updating a subscription
if (RestOperationTypeEnum.CREATE.equals(theOperation) || RestOperationTypeEnum.UPDATE.equals(theOperation)) {
String resourceType = theDetails.getResourceType();
ourLog.info("prehandled resource type: " + resourceType);
if (resourceType != null && resourceType.equals(Subscription.class.getSimpleName())) {
Subscription subscription = (Subscription) theDetails.getResource();
if (subscription != null) {
checkSubscriptionCriterias(subscription.getCriteria());
}
}
}
super.incomingRequestPreHandled(theOperation, theDetails);
}
/**
* Read the existing subscriptions from the database
*/
@ -273,7 +268,7 @@ public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterce
map.setCount(MAX_SUBSCRIPTION_RESULTS);
IBundleProvider subscriptionBundleList = mySubscriptionDao.search(map, req);
if (subscriptionBundleList.size() >= MAX_SUBSCRIPTION_RESULTS) {
ourLog.error("Currently over "+MAX_SUBSCRIPTION_RESULTS+" subscriptions. Some subscriptions have not been loaded.");
ourLog.error("Currently over " + MAX_SUBSCRIPTION_RESULTS + " subscriptions. Some subscriptions have not been loaded.");
}
List<IBaseResource> resourceList = subscriptionBundleList.getResources(0, subscriptionBundleList.size());
@ -409,57 +404,4 @@ public class RestHookSubscriptionDstu2Interceptor extends ServerOperationInterce
mySubscriptionDao = theSubscriptionDao;
}
@Override
public void incomingRequestPreHandled(RestOperationTypeEnum theOperation, ActionRequestDetails theDetails) {
//check the subscription criteria to see if its valid before creating or updating a subscription
if (RestOperationTypeEnum.CREATE.equals(theOperation) || RestOperationTypeEnum.UPDATE.equals(theOperation)) {
String resourceType = theDetails.getResourceType();
ourLog.info("prehandled resource type: " + resourceType);
if (resourceType != null && resourceType.equals(Subscription.class.getSimpleName())) {
Subscription subscription = (Subscription) theDetails.getResource();
if (subscription != null) {
checkSubscriptionCriterias(subscription);
}
}
}
super.incomingRequestPreHandled(theOperation, theDetails);
}
private void checkSubscriptionCriterias(Subscription subscription){
try {
IBundleProvider results = executeSubscriptionCriteria(subscription, null);
}catch (Exception e){
throw new InvalidRequestException("Invalid criteria");
}
}
private IBundleProvider executeSubscriptionCriteria(Subscription subscription, IIdType idType){
//run the subscriptions query and look for matches, add the id as part of the criteria to avoid getting matches of previous resources rather than the recent resource
String criteria = subscription.getCriteria();
if(idType != null) {
criteria += "&_id=" + idType.getResourceType() + "/" + idType.getIdPart();
}
IBundleProvider results = getBundleProvider(criteria);
return results;
}
/**
* Get the encoding from the criteria or return JSON encoding if its not found
*
* @param criteria
* @return
*/
private EncodingEnum getEncoding(String criteria) {
//check criteria
String params = criteria.substring(criteria.indexOf('?') + 1);
List<NameValuePair> paramValues = URLEncodedUtils.parse(params, Constants.CHARSET_UTF8, '&');
for (NameValuePair nameValuePair : paramValues) {
if (Constants.PARAM_FORMAT.equals(nameValuePair.getName())) {
return EncodingEnum.forContentType(nameValuePair.getValue());
}
}
return EncodingEnum.JSON;
}
}

123
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/RestHookSubscriptionDstu3Interceptor.java
View File

@ -30,12 +30,9 @@ import javax.annotation.PostConstruct;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.apache.http.NameValuePair;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.client.methods.HttpUriRequest;
import org.apache.http.client.utils.URLEncodedUtils;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.hl7.fhir.dstu3.model.Subscription;
@ -48,8 +45,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
@ -60,32 +55,31 @@ import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.interceptor.*;
public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterceptorAdapter {
public class RestHookSubscriptionDstu3Interceptor extends BaseRestHookSubscriptionInterceptor {
private static final Integer MAX_SUBSCRIPTION_RESULTS = 10000;
private static volatile ExecutorService executor;
private final static int MAX_THREADS = 1;
private final static int MAX_THREADS = 1;
private static final Logger ourLog = LoggerFactory.getLogger(RestHookSubscriptionDstu3Interceptor.class);
@Autowired
private FhirContext myFhirContext;
private final List<Subscription> myRestHookSubscriptions = new ArrayList<Subscription>();
@Autowired
@Qualifier("mySubscriptionDaoDstu3")
private IFhirResourceDao<Subscription> mySubscriptionDao;
private boolean notifyOnDelete = false;
private final List<Subscription> myRestHookSubscriptions = new ArrayList<Subscription>();
/**
* Check subscriptions and send notifications or payload
*
* @param idType
* @param resourceType
* @param theOperation
* @param theOperation
*/
private void checkSubscriptions(IIdType idType, String resourceType, RestOperationTypeEnum theOperation) {
for (Subscription subscription : myRestHookSubscriptions) {
@ -99,7 +93,7 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
}
if (resourceType != null && subscription.getCriteria() != null && !criteriaResource.equals(resourceType)) {
ourLog.info("Skipping subscription search for {} because it does not match the criteria {}", resourceType , subscription.getCriteria());
ourLog.info("Skipping subscription search for {} because it does not match the criteria {}", resourceType, subscription.getCriteria());
continue;
}
@ -108,7 +102,7 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
criteria += "&_id=" + idType.getResourceType() + "/" + idType.getIdPart();
criteria = massageCriteria(criteria);
IBundleProvider results = getBundleProvider(criteria);
IBundleProvider results = getBundleProvider(criteria, false);
if (results.size() == 0) {
continue;
@ -134,13 +128,13 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
while (url.endsWith("/")) {
url = url.substring(0, url.length() - 1);
}
HttpUriRequest request = null;
String resourceName = myFhirContext.getResourceDefinition(theResource).getName();
String resourceName = myFhirContext.getResourceDefinition(theResource).getName();
String payload = theSubscription.getChannel().getPayload();
String resourceId = theResource.getIdElement().getIdPart();
// HTTP put
if (theOperation == RestOperationTypeEnum.UPDATE && EncodingEnum.XML.equals(EncodingEnum.forContentType(payload))) {
ourLog.info("XML payload found");
@ -186,25 +180,6 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
return request;
}
/**
* Search based on a query criteria
*
* @param criteria
* @return
*/
private IBundleProvider getBundleProvider(String criteria) {
RuntimeResourceDefinition responseResourceDef = mySubscriptionDao.validateCriteriaAndReturnResourceDefinition(criteria);
SearchParameterMap responseCriteriaUrl = BaseHapiFhirDao.translateMatchUrl(mySubscriptionDao, mySubscriptionDao.getContext(), criteria, responseResourceDef);
RequestDetails req = new ServletSubRequestDetails();
req.setSubRequest(true);
IFhirResourceDao<? extends IBaseResource> responseDao = mySubscriptionDao.getDao(responseResourceDef.getImplementingClass());
responseCriteriaUrl.setCount(MAX_SUBSCRIPTION_RESULTS);
IBundleProvider responseResults = responseDao.search(responseCriteriaUrl, req);
return responseResults;
}
/**
* Get subscription from cache
*
@ -250,6 +225,27 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
return entity;
}
@Override
protected IFhirResourceDao<?> getSubscriptionDao() {
return mySubscriptionDao;
}
@Override
public void incomingRequestPreHandled(RestOperationTypeEnum theOperation, ActionRequestDetails theDetails) {
// check the subscription criteria to see if its valid before creating or updating a subscription
if (RestOperationTypeEnum.CREATE.equals(theOperation) || RestOperationTypeEnum.UPDATE.equals(theOperation)) {
String resourceType = theDetails.getResourceType();
ourLog.info("prehandled resource type: " + resourceType);
if (resourceType != null && resourceType.equals(Subscription.class.getSimpleName())) {
Subscription subscription = (Subscription) theDetails.getResource();
if (subscription != null) {
checkSubscriptionCriterias(subscription.getCriteria());
}
}
}
super.incomingRequestPreHandled(theOperation, theDetails);
}
/**
* Read the existing subscriptions from the database
*/
@ -264,7 +260,7 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
map.setCount(MAX_SUBSCRIPTION_RESULTS);
IBundleProvider subscriptionBundleList = mySubscriptionDao.search(map, req);
if (subscriptionBundleList.size() >= MAX_SUBSCRIPTION_RESULTS) {
ourLog.error("Currently over "+MAX_SUBSCRIPTION_RESULTS+" subscriptions. Some subscriptions have not been loaded.");
ourLog.error("Currently over " + MAX_SUBSCRIPTION_RESULTS + " subscriptions. Some subscriptions have not been loaded.");
}
List<IBaseResource> resourceList = subscriptionBundleList.getResources(0, subscriptionBundleList.size());
@ -400,57 +396,4 @@ public class RestHookSubscriptionDstu3Interceptor extends ServerOperationInterce
mySubscriptionDao = theSubscriptionDao;
}
@Override
public void incomingRequestPreHandled(RestOperationTypeEnum theOperation, ActionRequestDetails theDetails) {
//check the subscription criteria to see if its valid before creating or updating a subscription
if (RestOperationTypeEnum.CREATE.equals(theOperation) || RestOperationTypeEnum.UPDATE.equals(theOperation)) {
String resourceType = theDetails.getResourceType();
ourLog.info("prehandled resource type: " + resourceType);
if (resourceType != null && resourceType.equals(Subscription.class.getSimpleName())) {
Subscription subscription = (Subscription) theDetails.getResource();
if (subscription != null) {
checkSubscriptionCriterias(subscription);
}
}
}
super.incomingRequestPreHandled(theOperation, theDetails);
}
private void checkSubscriptionCriterias(Subscription subscription){
try {
IBundleProvider results = executeSubscriptionCriteria(subscription, null);
}catch (Exception e){
throw new InvalidRequestException("Invalid criteria");
}
}
private IBundleProvider executeSubscriptionCriteria(Subscription subscription, IIdType idType){
//run the subscriptions query and look for matches, add the id as part of the criteria to avoid getting matches of previous resources rather than the recent resource
String criteria = subscription.getCriteria();
if(idType != null) {
criteria += "&_id=" + idType.getResourceType() + "/" + idType.getIdPart();
}
IBundleProvider results = getBundleProvider(criteria);
return results;
}
/**
* Get the encoding from the criteria or return JSON encoding if its not found
*
* @param criteria
* @return
*/
private EncodingEnum getEncoding(String criteria) {
//check criteria
String params = criteria.substring(criteria.indexOf('?') + 1);
List<NameValuePair> paramValues = URLEncodedUtils.parse(params, Constants.CHARSET_UTF8, '&');
for (NameValuePair nameValuePair : paramValues) {
if (Constants.PARAM_FORMAT.equals(nameValuePair.getName())) {
return EncodingEnum.forContentType(nameValuePair.getValue());
}
}
return EncodingEnum.JSON;
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/JpaConformanceProviderDstu2.java
View File

@ -19,9 +19,7 @@ package ca.uhn.fhir.jpa.provider;
* limitations under the License.
* #L%
*/
import java.util.List;
import java.util.Map;
import java.util.*;
import javax.servlet.http.HttpServletRequest;
@ -51,6 +49,7 @@ public class JpaConformanceProviderDstu2 extends ServerConformanceProvider {
private volatile Conformance myCachedValue;
private DaoConfig myDaoConfig;
private String myImplementationDescription;
private boolean myIncludeResourceCounts;
private RestfulServer myRestfulServer;
private IFhirSystemDao<Bundle, MetaDt> mySystemDao;
@ -61,6 +60,7 @@ public class JpaConformanceProviderDstu2 extends ServerConformanceProvider {
public JpaConformanceProviderDstu2(){
super();
super.setCache(false);
setIncludeResourceCounts(true);
}
/**
@ -72,13 +72,17 @@ public class JpaConformanceProviderDstu2 extends ServerConformanceProvider {
mySystemDao = theSystemDao;
myDaoConfig = theDaoConfig;
super.setCache(false);
setIncludeResourceCounts(true);
}
@Override
public Conformance getServerConformance(HttpServletRequest theRequest) {
Conformance retVal = myCachedValue;
Map<String, Long> counts = mySystemDao.getResourceCounts();
Map<String, Long> counts = Collections.emptyMap();
if (myIncludeResourceCounts) {
counts = mySystemDao.getResourceCounts();
}
FhirContext ctx = myRestfulServer.getFhirContext();
@ -119,6 +123,10 @@ public class JpaConformanceProviderDstu2 extends ServerConformanceProvider {
return retVal;
}
public boolean isIncludeResourceCounts() {
return myIncludeResourceCounts;
}
public void setDaoConfig(DaoConfig myDaoConfig) {
this.myDaoConfig = myDaoConfig;
}
@ -128,6 +136,10 @@ public class JpaConformanceProviderDstu2 extends ServerConformanceProvider {
myImplementationDescription = theImplDesc;
}
public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
myIncludeResourceCounts = theIncludeResourceCounts;
}
@Override
public void setRestfulServer(RestfulServer theRestfulServer) {
this.myRestfulServer = theRestfulServer;

33
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaConformanceProviderDstu3.java
View File

@ -1,7 +1,5 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import java.util.Collection;
/*
* #%L
* HAPI FHIR JPA Server
@ -21,23 +19,18 @@ import java.util.Collection;
* limitations under the License.
* #L%
*/
import java.util.Map;
import java.util.*;
import javax.servlet.http.HttpServletRequest;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.CapabilityStatement.*;
import org.hl7.fhir.dstu3.model.Enumerations.SearchParamType;
import org.springframework.beans.factory.annotation.Autowired;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.ExtensionConstants;
@ -47,9 +40,10 @@ public class JpaConformanceProviderDstu3 extends org.hl7.fhir.dstu3.hapi.rest.se
private volatile CapabilityStatement myCachedValue;
private DaoConfig myDaoConfig;
private String myImplementationDescription;
private boolean myIncludeResourceCounts;
private RestfulServer myRestfulServer;
private IFhirSystemDao<Bundle, Meta> mySystemDao;
/**
* Constructor
*/
@ -57,8 +51,9 @@ public class JpaConformanceProviderDstu3 extends org.hl7.fhir.dstu3.hapi.rest.se
public JpaConformanceProviderDstu3(){
super();
super.setCache(false);
setIncludeResourceCounts(true);
}
/**
* Constructor
*/
@ -68,15 +63,17 @@ public class JpaConformanceProviderDstu3 extends org.hl7.fhir.dstu3.hapi.rest.se
mySystemDao = theSystemDao;
myDaoConfig = theDaoConfig;
super.setCache(false);
setIncludeResourceCounts(true);
}
@Override
public CapabilityStatement getServerConformance(HttpServletRequest theRequest) {
CapabilityStatement retVal = myCachedValue;
Map<String, Long> counts = mySystemDao.getResourceCounts();
FhirContext ctx = myRestfulServer.getFhirContext();
Map<String, Long> counts = Collections.emptyMap();
if (myIncludeResourceCounts) {
counts = mySystemDao.getResourceCounts();
}
retVal = super.getServerConformance(theRequest);
for (CapabilityStatementRestComponent nextRest : retVal.getRest()) {
@ -148,6 +145,10 @@ public class JpaConformanceProviderDstu3 extends org.hl7.fhir.dstu3.hapi.rest.se
return retVal;
}
public boolean isIncludeResourceCounts() {
return myIncludeResourceCounts;
}
/**
* Subclasses may override
*/
@ -164,6 +165,10 @@ public class JpaConformanceProviderDstu3 extends org.hl7.fhir.dstu3.hapi.rest.se
myImplementationDescription = theImplDesc;
}
public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
myIncludeResourceCounts = theIncludeResourceCounts;
}
@Override
public void setRestfulServer(RestfulServer theRestfulServer) {
this.myRestfulServer = theRestfulServer;

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

@ -77,7 +77,6 @@ public class DatabaseBackedPagingProvider extends BasePagingProvider implements
@Override
public synchronized String storeResultList(IBundleProvider theList) {
String uuid = theList.getUuid();
Validate.notNull(uuid);
return uuid;
}

56
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
View File

@ -19,24 +19,9 @@ package ca.uhn.fhir.jpa.search;
* limitations under the License.
* #L%
*/
import java.util.*;
import java.util.concurrent.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.UUID;
import java.util.concurrent.Callable;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
import javax.transaction.Transactional;
import javax.transaction.Transactional.TxType;
@ -47,34 +32,18 @@ import org.apache.commons.lang3.exception.ExceptionUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.data.domain.*;
import org.springframework.scheduling.concurrent.CustomizableThreadFactory;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import org.springframework.transaction.*;
import org.springframework.transaction.support.*;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Lists;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IDao;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.ISearchIncludeDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchInclude;
import ca.uhn.fhir.jpa.entity.SearchResult;
import ca.uhn.fhir.jpa.entity.SearchStatusEnum;
import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.util.StopWatch;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.method.PageMethodBinding;
@ -83,7 +52,7 @@ import ca.uhn.fhir.rest.server.SimpleBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.*;
public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
static final int DEFAULT_SYNC_SIZE = 250;
public static final int DEFAULT_SYNC_SIZE = 250;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchCoordinatorSvcImpl.class);
@ -360,7 +329,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
@VisibleForTesting
void setLoadingThrottleForUnitTests(Integer theLoadingThrottleForUnitTests) {
public void setLoadingThrottleForUnitTests(Integer theLoadingThrottleForUnitTests) {
myLoadingThrottleForUnitTests = theLoadingThrottleForUnitTests;
}
@ -369,7 +338,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
myMaxMillisToWaitForRemoteResults = theMaxMillisToWaitForRemoteResults;
}
void setNeverUseLocalSearchForUnitTests(boolean theNeverUseLocalSearchForUnitTests) {
@VisibleForTesting
public void setNeverUseLocalSearchForUnitTests(boolean theNeverUseLocalSearchForUnitTests) {
myNeverUseLocalSearchForUnitTests = theNeverUseLocalSearchForUnitTests;
}
@ -389,7 +359,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
@VisibleForTesting
void setSyncSizeForUnitTests(int theSyncSize) {
public void setSyncSizeForUnitTests(int theSyncSize) {
mySyncSize = theSyncSize;
}

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

@ -71,13 +71,13 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
@Autowired
private PlatformTransactionManager myTransactionManager;
protected void deleteSearch(final Search next) {
protected void deleteSearch(final Long theSearchPid) {
TransactionTemplate tt = new TransactionTemplate(myTransactionManager);
tt.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
Search searchToDelete = mySearchDao.findOne(next.getId());
ourLog.info("Expiring stale search {} / {}", searchToDelete.getId(), searchToDelete.getUuid());
Search searchToDelete = mySearchDao.findOne(theSearchPid);
ourLog.info("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), searchToDelete.getCreated(), searchToDelete.getSearchLastReturned());
mySearchIncludeDao.deleteForSearch(searchToDelete.getId());
mySearchResultDao.deleteForSearch(searchToDelete.getId());
mySearchDao.delete(searchToDelete);
@ -97,13 +97,10 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
ourLog.debug("Searching for searches which are before {}", cutoff);
Collection<Search> toDelete = mySearchDao.findWhereLastReturnedBefore(cutoff);
Collection<Long> toDelete = mySearchDao.findWhereLastReturnedBefore(cutoff);
if (!toDelete.isEmpty()) {
for (final Search next : toDelete) {
ourLog.info("Deleting search {} - Created[{}] -- Last returned[{}]", next.getUuid(), next.getCreated(), next.getSearchLastReturned());
for (final Long next : toDelete) {
deleteSearch(next);
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java
View File

@ -69,7 +69,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
private Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.jdbc.batch_size", "50");
extraProperties.put("hibernate.format_sql", "true");
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.dialect", "org.hibernate.dialect.DerbyTenSevenDialect");

22
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java
View File

@ -37,6 +37,7 @@ import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
@ -75,7 +76,6 @@ import ca.uhn.fhir.util.TestUtil;
@ContextConfiguration(classes= {TestDstu2Config.class, ca.uhn.fhir.jpa.config.WebsocketDstu2DispatcherConfig.class})
//@formatter:on
public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@Autowired
protected ApplicationContext myAppCtx;
@Autowired
@ -114,18 +114,18 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@Autowired
@Qualifier("myLocationDaoDstu2")
protected IFhirResourceDao<Location> myLocationDao;
@Autowired
@Qualifier("myMediaDaoDstu2")
protected IFhirResourceDao<Media> myMediaDao;
@Autowired
@Qualifier("myMediaDaoDstu2")
protected IFhirResourceDao<Media> myMediaDao;
@Qualifier("myMedicationAdministrationDaoDstu2")
protected IFhirResourceDao<MedicationAdministration> myMedicationAdministrationDao;
@Autowired
@Qualifier("myMedicationDaoDstu2")
protected IFhirResourceDao<Medication> myMedicationDao;
@Autowired
@Qualifier("myMedicationAdministrationDaoDstu2")
protected IFhirResourceDao<MedicationAdministration> myMedicationAdministrationDao;
@Autowired
@Qualifier("myMedicationOrderDaoDstu2")
protected IFhirResourceDao<MedicationOrder> myMedicationOrderDao;
@Autowired
@ -135,6 +135,8 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@Qualifier("myOrganizationDaoDstu2")
protected IFhirResourceDao<Organization> myOrganizationDao;
@Autowired
protected DatabaseBackedPagingProvider myPagingProvider;
@Autowired
@Qualifier("myPatientDaoDstu2")
protected IFhirResourceDaoPatient<Patient> myPatientDao;
@Autowired
@ -150,8 +152,12 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@Qualifier("myResourceProvidersDstu2")
protected Object myResourceProviders;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@Autowired
protected IFulltextSearchSvc mySearchDao;
@Autowired
protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
@Autowired
@Qualifier("myStructureDefinitionDaoDstu2")
protected IFhirResourceDao<StructureDefinition> myStructureDefinitionDao;
@Autowired
@ -171,10 +177,6 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@Autowired
@Qualifier("myValueSetDaoDstu2")
protected IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt> myValueSetDao;
@Autowired
protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@Before
public void beforeCreateInterceptor() {

23
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSystemDaoDstu2Test.java
View File

@ -303,36 +303,31 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
request.addEntry().getRequest().setMethod(HTTPVerbEnum.GET).setUrl("Patient/THIS_ID_DOESNT_EXIST");
Bundle resp = mySystemDao.transaction(mySrd, request);
assertEquals(3, resp.getEntry().size());
assertEquals(2, resp.getEntry().size());
assertEquals(BundleTypeEnum.BATCH_RESPONSE, resp.getTypeElement().getValueAsEnum());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
EntryResponse respEntry;
// Bundle.entry[0] is operation outcome
assertEquals(OperationOutcome.class, resp.getEntry().get(0).getResource().getClass());
assertEquals(IssueSeverityEnum.INFORMATION, ((OperationOutcome) resp.getEntry().get(0).getResource()).getIssue().get(0).getSeverityElement().getValueAsEnum());
assertThat(((OperationOutcome) resp.getEntry().get(0).getResource()).getIssue().get(0).getDiagnostics(), startsWith("Batch completed in "));
// Bundle.entry[1] is create response
assertEquals("201 Created", resp.getEntry().get(1).getResponse().getStatus());
assertThat(resp.getEntry().get(1).getResponse().getLocation(), startsWith("Patient/"));
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
assertThat(resp.getEntry().get(0).getResponse().getLocation(), startsWith("Patient/"));
// Bundle.entry[2] is failed read response
assertEquals(OperationOutcome.class, resp.getEntry().get(2).getResource().getClass());
assertEquals(IssueSeverityEnum.ERROR, ((OperationOutcome) resp.getEntry().get(2).getResource()).getIssue().get(0).getSeverityElement().getValueAsEnum());
assertEquals("Resource Patient/THIS_ID_DOESNT_EXIST is not known", ((OperationOutcome) resp.getEntry().get(2).getResource()).getIssue().get(0).getDiagnostics());
assertEquals("404 Not Found", resp.getEntry().get(2).getResponse().getStatus());
assertEquals(OperationOutcome.class, resp.getEntry().get(1).getResource().getClass());
assertEquals(IssueSeverityEnum.ERROR, ((OperationOutcome) resp.getEntry().get(1).getResource()).getIssue().get(0).getSeverityElement().getValueAsEnum());
assertEquals("Resource Patient/THIS_ID_DOESNT_EXIST is not known", ((OperationOutcome) resp.getEntry().get(1).getResource()).getIssue().get(0).getDiagnostics());
assertEquals("404 Not Found", resp.getEntry().get(1).getResponse().getStatus());
// Check POST
respEntry = resp.getEntry().get(1).getResponse();
respEntry = resp.getEntry().get(0).getResponse();
assertEquals("201 Created", respEntry.getStatus());
IdDt createdId = new IdDt(respEntry.getLocation());
assertEquals("Patient", createdId.getResourceType());
myPatientDao.read(createdId, mySrd); // shouldn't fail
// Check GET
respEntry = resp.getEntry().get(2).getResponse();
respEntry = resp.getEntry().get(1).getResponse();
assertThat(respEntry.getStatus(), startsWith("404"));
}

80
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -27,6 +27,7 @@ import org.hl7.fhir.dstu3.model.Condition;
import org.hl7.fhir.dstu3.model.Device;
import org.hl7.fhir.dstu3.model.DiagnosticReport;
import org.hl7.fhir.dstu3.model.Encounter;
import org.hl7.fhir.dstu3.model.Group;
import org.hl7.fhir.dstu3.model.Immunization;
import org.hl7.fhir.dstu3.model.ImmunizationRecommendation;
import org.hl7.fhir.dstu3.model.Location;
@ -77,13 +78,15 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.ITagDefinitionDao;
import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.*;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
@ -104,19 +107,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
private static JpaValidationSupportChainDstu3 ourJpaValidationSupportChainDstu3;
private static IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> ourValueSetDao;
@Autowired
protected ITagDefinitionDao myTagDefinitionDao;
@Autowired
protected IResourceTagDao myResourceTagDao;
@Autowired
protected ISearchDao mySearchEntityDao;
@Autowired
@Qualifier("mySearchParameterDaoDstu3")
protected IFhirResourceDao<SearchParameter> mySearchParameterDao;
@Autowired
protected ISearchParamRegistry mySearchParamRegsitry;
// @Autowired
// protected HapiWorkerContext myHapiWorkerContext;
// @Autowired
// protected HapiWorkerContext myHapiWorkerContext;
@Autowired
@Qualifier("myAllergyIntoleranceDaoDstu3")
protected IFhirResourceDao<AllergyIntolerance> myAllergyIntoleranceDao;
@ -135,9 +127,6 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Qualifier("myCarePlanDaoDstu3")
protected IFhirResourceDao<CarePlan> myCarePlanDao;
@Autowired
@Qualifier("myProcedureRequestDaoDstu3")
protected IFhirResourceDao<ProcedureRequest> myProcedureRequestDao;
@Autowired
@Qualifier("myCodeSystemDaoDstu3")
protected IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
@Autowired
@ -166,6 +155,9 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Autowired
protected FhirContext myFhirCtx;
@Autowired
@Qualifier("myGroupDaoDstu3")
protected IFhirResourceDao<Group> myGroupDao;
@Autowired
@Qualifier("myImmunizationDaoDstu3")
protected IFhirResourceDao<Immunization> myImmunizationDao;
@Autowired
@ -181,12 +173,12 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Qualifier("myMediaDaoDstu3")
protected IFhirResourceDao<Media> myMediaDao;
@Autowired
@Qualifier("myMedicationDaoDstu3")
protected IFhirResourceDao<Medication> myMedicationDao;
@Autowired
@Qualifier("myMedicationAdministrationDaoDstu3")
protected IFhirResourceDao<MedicationAdministration> myMedicationAdministrationDao;
@Autowired
@Qualifier("myMedicationDaoDstu3")
protected IFhirResourceDao<Medication> myMedicationDao;
@Autowired
@Qualifier("myMedicationRequestDaoDstu3")
protected IFhirResourceDao<MedicationRequest> myMedicationRequestDao;
@Autowired
@ -202,8 +194,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Qualifier("myOrganizationDaoDstu3")
protected IFhirResourceDao<Organization> myOrganizationDao;
@Autowired
@Qualifier("myTaskDaoDstu3")
protected IFhirResourceDao<Task> myTaskDao;
protected DatabaseBackedPagingProvider myPagingProvider;
@Autowired
@Qualifier("myPatientDaoDstu3")
protected IFhirResourceDaoPatient<Patient> myPatientDao;
@ -211,6 +202,9 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Qualifier("myPractitionerDaoDstu3")
protected IFhirResourceDao<Practitioner> myPractitionerDao;
@Autowired
@Qualifier("myProcedureRequestDaoDstu3")
protected IFhirResourceDao<ProcedureRequest> myProcedureRequestDao;
@Autowired
@Qualifier("myQuestionnaireDaoDstu3")
protected IFhirResourceDao<Questionnaire> myQuestionnaireDao;
@Autowired
@ -222,8 +216,21 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Autowired
protected IResourceTableDao myResourceTableDao;
@Autowired
protected IResourceTagDao myResourceTagDao;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@Autowired
protected IFulltextSearchSvc mySearchDao;
@Autowired
protected ISearchDao mySearchEntityDao;
@Autowired
@Qualifier("mySearchParameterDaoDstu3")
protected IFhirResourceDao<SearchParameter> mySearchParameterDao;
@Autowired
protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
@Autowired
protected ISearchParamRegistry mySearchParamRegsitry;
@Autowired
protected IStaleSearchDeletingSvc myStaleSearchDeletingSvc;
@Autowired
@Qualifier("myStructureDefinitionDaoDstu3")
@ -241,8 +248,15 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Qualifier("mySystemProviderDstu3")
protected JpaSystemProviderDstu3 mySystemProvider;
@Autowired
protected ITagDefinitionDao myTagDefinitionDao;
@Autowired
@Qualifier("myTaskDaoDstu3")
protected IFhirResourceDao<Task> myTaskDao;
@Autowired
protected IHapiTerminologySvc myTermSvc;
@Autowired
protected PlatformTransactionManager myTransactionMgr;
@Autowired
protected PlatformTransactionManager myTxManager;
@Autowired
@Qualifier("myJpaValidationSupportChainDstu3")
@ -250,18 +264,6 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Autowired
@Qualifier("myValueSetDaoDstu3")
protected IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
@Autowired
protected PlatformTransactionManager myTransactionMgr;
@Autowired
protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@After()
public void afterGrabCaches() {
ourValueSetDao = myValueSetDao;
ourJpaValidationSupportChainDstu3 = myJpaValidationSupportChainDstu3;
}
@After()
public void afterCleanupDao() {
@ -271,6 +273,12 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
myDaoConfig.setSuppressUpdatesWithNoChange(new DaoConfig().isSuppressUpdatesWithNoChange());
}
@After()
public void afterGrabCaches() {
ourValueSetDao = myValueSetDao;
ourJpaValidationSupportChainDstu3 = myJpaValidationSupportChainDstu3;
}
@Before
public void beforeCreateInterceptor() {
myInterceptor = mock(IServerInterceptor.class);

62
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java
View File

@ -43,6 +43,7 @@ import org.hl7.fhir.dstu3.model.Device;
import org.hl7.fhir.dstu3.model.DiagnosticReport;
import org.hl7.fhir.dstu3.model.Encounter;
import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.dstu3.model.Group;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Immunization;
import org.hl7.fhir.dstu3.model.ImmunizationRecommendation;
@ -153,6 +154,67 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
assertThat(ids, contains(moId.getValue()));
}
@Test
public void testEmptyChain() {
SearchParameterMap map = new SearchParameterMap();
map.add(Encounter.SP_SUBJECT, new ReferenceAndListParam().addAnd(new ReferenceOrListParam().add(new ReferenceParam("subject", "04823543").setChain("identifier"))));
IBundleProvider results = myMedicationAdministrationDao.search(map);
List<String> ids = toUnqualifiedIdValues(results);
assertThat(ids, empty());
}
@Test
public void testChainWithMultipleTypePossibilities() {
Patient sub1 = new Patient();
sub1.setActive(true);
sub1.addIdentifier().setSystem("foo").setValue("bar");
String sub1Id = myPatientDao.create(sub1).getId().toUnqualifiedVersionless().getValue();
Group sub2 = new Group();
sub2.setActive(true);
sub2.addIdentifier().setSystem("foo").setValue("bar");
String sub2Id = myGroupDao.create(sub2).getId().toUnqualifiedVersionless().getValue();
Encounter enc1 = new Encounter();
enc1.getSubject().setReference(sub1Id);
String enc1Id = myEncounterDao.create(enc1).getId().toUnqualifiedVersionless().getValue();
Encounter enc2 = new Encounter();
enc2.getSubject().setReference(sub2Id);
String enc2Id = myEncounterDao.create(enc2).getId().toUnqualifiedVersionless().getValue();
List<String> ids;
SearchParameterMap map;
IBundleProvider results;
map = new SearchParameterMap();
map.add(Encounter.SP_SUBJECT, new ReferenceParam("subject", "foo|bar").setChain("identifier"));
results = myEncounterDao.search(map);
ids = toUnqualifiedVersionlessIdValues(results);
assertThat(ids, hasItems(enc1Id, enc2Id));
map = new SearchParameterMap();
map.add(Encounter.SP_SUBJECT, new ReferenceParam("subject:Patient", "foo|bar").setChain("identifier"));
results = myEncounterDao.search(map);
ids = toUnqualifiedVersionlessIdValues(results);
assertThat(ids, hasItems(enc1Id));
map = new SearchParameterMap();
map.add(Encounter.SP_SUBJECT, new ReferenceParam("subject:Group", "foo|bar").setChain("identifier"));
results = myEncounterDao.search(map);
ids = toUnqualifiedVersionlessIdValues(results);
assertThat(ids, hasItems(enc2Id));
map = new SearchParameterMap();
map.add(Encounter.SP_SUBJECT, new ReferenceParam("subject", "04823543").setChain("identifier"));
results = myEncounterDao.search(map);
ids = toUnqualifiedVersionlessIdValues(results);
assertThat(ids, empty());
}
@Test
public void testEverythingTimings() throws Exception {
String methodName = "testEverythingTimings";

18
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java
View File

@ -155,6 +155,24 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
}
}
@Test
public void testCreateReferenceToDeletedResource() {
Organization org = new Organization();
org.setActive(true);
IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
myOrganizationDao.delete(orgId);
Patient p = new Patient();
p.getManagingOrganization().setReferenceElement(orgId);
try {
myPatientDao.create(p);
fail();
} catch (InvalidRequestException e) {
assertEquals("Resource Organization/" + orgId.getIdPart() + " is deleted, specified in path: Patient.managingOrganization", e.getMessage());
}
}
@Test
public void testCreateDuplicateTagsDoesNotCauseDuplicates() {
Patient p = new Patient();

136
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UpdateTest.java
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@ -33,11 +33,10 @@ import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.*;
import org.mockito.ArgumentCaptor;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.api.MethodOutcome;
@ -123,6 +122,137 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
}
@After
public void afterResetDao() {
myDaoConfig.setResourceMetaCountHardLimit(new DaoConfig().getResourceMetaCountHardLimit());
}
@Test
public void testHardMetaCapIsEnforcedOnCreate() {
myDaoConfig.setResourceMetaCountHardLimit(3);
IIdType id;
{
Patient patient = new Patient();
patient.getMeta().addTag().setSystem("http://foo").setCode("1");
patient.getMeta().addTag().setSystem("http://foo").setCode("2");
patient.getMeta().addTag().setSystem("http://foo").setCode("3");
patient.getMeta().addTag().setSystem("http://foo").setCode("4");
patient.setActive(true);
try {
id = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Resource contains 4 meta entries (tag/profile/security label), maximum is 3", e.getMessage());
}
}
}
@Test
public void testHardMetaCapIsEnforcedOnMetaAdd() {
myDaoConfig.setResourceMetaCountHardLimit(3);
IIdType id;
{
Patient patient = new Patient();
patient.setActive(true);
id = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
{
Meta meta = new Meta();
meta.addTag().setSystem("http://foo").setCode("1");
meta.addTag().setSystem("http://foo").setCode("2");
meta.addTag().setSystem("http://foo").setCode("3");
meta.addTag().setSystem("http://foo").setCode("4");
try {
myPatientDao.metaAddOperation(id, meta, null);
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Resource contains 4 meta entries (tag/profile/security label), maximum is 3", e.getMessage());
}
}
}
@Test
public void testDuplicateTagsOnAddTagsIgnored() {
IIdType id;
{
Patient patient = new Patient();
patient.setActive(true);
id = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Meta meta = new Meta();
meta.addTag().setSystem("http://foo").setCode("bar").setDisplay("Val1");
meta.addTag().setSystem("http://foo").setCode("bar").setDisplay("Val2");
meta.addTag().setSystem("http://foo").setCode("bar").setDisplay("Val3");
myPatientDao.metaAddOperation(id, meta, null);
// Do a read
{
Patient patient = myPatientDao.read(id, mySrd);
List<Coding> tl = patient.getMeta().getTag();
assertEquals(1, tl.size());
assertEquals("http://foo", tl.get(0).getSystem());
assertEquals("bar", tl.get(0).getCode());
}
}
@Test
public void testDuplicateTagsOnUpdateIgnored() {
IIdType id;
{
Patient patient = new Patient();
patient.setActive(true);
id = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
{
Patient patient = new Patient();
patient.setId(id);
patient.setActive(true);
patient.getMeta().addTag().setSystem("http://foo").setCode("bar").setDisplay("Val1");
patient.getMeta().addTag().setSystem("http://foo").setCode("bar").setDisplay("Val2");
patient.getMeta().addTag().setSystem("http://foo").setCode("bar").setDisplay("Val3");
myPatientDao.update(patient, mySrd).getId().toUnqualifiedVersionless();
}
// Do a read on second version
{
Patient patient = myPatientDao.read(id, mySrd);
List<Coding> tl = patient.getMeta().getTag();
assertEquals(1, tl.size());
assertEquals("http://foo", tl.get(0).getSystem());
assertEquals("bar", tl.get(0).getCode());
}
// Do a read on first version
{
Patient patient = myPatientDao.read(id.withVersion("1"), mySrd);
List<Coding> tl = patient.getMeta().getTag();
assertEquals(0, tl.size());
}
Meta meta = new Meta();
meta.addTag().setSystem("http://foo").setCode("bar").setDisplay("Val1");
meta.addTag().setSystem("http://foo").setCode("bar").setDisplay("Val2");
meta.addTag().setSystem("http://foo").setCode("bar").setDisplay("Val3");
myPatientDao.metaAddOperation(id.withVersion("1"), meta, null);
// Do a read on first version
{
Patient patient = myPatientDao.read(id.withVersion("1"), mySrd);
List<Coding> tl = patient.getMeta().getTag();
assertEquals(1, tl.size());
assertEquals("http://foo", tl.get(0).getSystem());
assertEquals("bar", tl.get(0).getCode());
}
}
@Test
public void testMultipleUpdatesWithNoChangesDoesNotResultInAnUpdateForDiscreteUpdates() {

48
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java
View File

@ -23,7 +23,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.nio.charset.StandardCharsets;
import java.util.List;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.Appointment;
@ -68,9 +68,7 @@ import org.springframework.transaction.support.TransactionTemplate;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.primitive.IdDt;
@ -488,36 +486,31 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
request.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl("Patient/THIS_ID_DOESNT_EXIST");
Bundle resp = mySystemDao.transaction(mySrd, request);
assertEquals(3, resp.getEntry().size());
assertEquals(2, resp.getEntry().size());
assertEquals(BundleType.BATCHRESPONSE, resp.getTypeElement().getValue());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
BundleEntryResponseComponent respEntry;
// Bundle.entry[0] is operation outcome
assertEquals(OperationOutcome.class, resp.getEntry().get(0).getResource().getClass());
assertEquals(IssueSeverity.INFORMATION, ((OperationOutcome) resp.getEntry().get(0).getResource()).getIssue().get(0).getSeverityElement().getValue());
assertThat(((OperationOutcome) resp.getEntry().get(0).getResource()).getIssue().get(0).getDiagnostics(), startsWith("Batch completed in "));
// Bundle.entry[0] is create response
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
assertThat(resp.getEntry().get(0).getResponse().getLocation(), startsWith("Patient/"));
// Bundle.entry[1] is create response
assertEquals("201 Created", resp.getEntry().get(1).getResponse().getStatus());
assertThat(resp.getEntry().get(1).getResponse().getLocation(), startsWith("Patient/"));
// Bundle.entry[2] is failed read response
assertEquals(OperationOutcome.class, resp.getEntry().get(2).getResource().getClass());
assertEquals(IssueSeverity.ERROR, ((OperationOutcome) resp.getEntry().get(2).getResource()).getIssue().get(0).getSeverityElement().getValue());
assertEquals("Resource Patient/THIS_ID_DOESNT_EXIST is not known", ((OperationOutcome) resp.getEntry().get(2).getResource()).getIssue().get(0).getDiagnostics());
assertEquals("404 Not Found", resp.getEntry().get(2).getResponse().getStatus());
// Bundle.entry[1] is failed read response
assertEquals(OperationOutcome.class, resp.getEntry().get(1).getResource().getClass());
assertEquals(IssueSeverity.ERROR, ((OperationOutcome) resp.getEntry().get(1).getResource()).getIssue().get(0).getSeverityElement().getValue());
assertEquals("Resource Patient/THIS_ID_DOESNT_EXIST is not known", ((OperationOutcome) resp.getEntry().get(1).getResource()).getIssue().get(0).getDiagnostics());
assertEquals("404 Not Found", resp.getEntry().get(1).getResponse().getStatus());
// Check POST
respEntry = resp.getEntry().get(1).getResponse();
respEntry = resp.getEntry().get(0).getResponse();
assertEquals("201 Created", respEntry.getStatus());
IdType createdId = new IdType(respEntry.getLocation());
assertEquals("Patient", createdId.getResourceType());
myPatientDao.read(createdId, mySrd); // shouldn't fail
// Check GET
respEntry = resp.getEntry().get(2).getResponse();
respEntry = resp.getEntry().get(1).getResponse();
assertThat(respEntry.getStatus(), startsWith("404"));
}
@ -2081,6 +2074,21 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
Set<String> values = new HashSet<String>();
for (ResourceTag next : myResourceTagDao.findAll()) {
if (!values.add(next.toString())) {
ourLog.info("Found duplicate tag on resource of type {}", next.getResource().getResourceType());
ourLog.info("Tag was: {} / {}", next.getTag().getSystem(), next.getTag().getCode());
}
}
}
});
}
@Test

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/BaseResourceProviderDstu2Test.java
View File

@ -12,9 +12,7 @@ import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.*;
import org.springframework.web.context.ContextLoader;
import org.springframework.web.context.WebApplicationContext;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
@ -25,17 +23,16 @@ import ca.uhn.fhir.jpa.config.WebsocketDstu2Config;
import ca.uhn.fhir.jpa.config.WebsocketDstu2DispatcherConfig;
import ca.uhn.fhir.jpa.dao.dstu2.BaseJpaDstu2Test;
import ca.uhn.fhir.jpa.interceptor.RestHookSubscriptionDstu2Interceptor;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.BundleEntry;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.util.TestUtil;
@ -45,10 +42,11 @@ public abstract class BaseResourceProviderDstu2Test extends BaseJpaDstu2Test {
protected static CloseableHttpClient ourHttpClient;
protected static int ourPort;
protected static RestfulServer ourRestServer;
private static Server ourServer;
protected static Server ourServer;
protected static String ourServerBase;
private static GenericWebApplicationContext ourWebApplicationContext;
protected static GenericWebApplicationContext ourWebApplicationContext;
protected static RestHookSubscriptionDstu2Interceptor ourRestHookSubscriptionInterceptor;
protected static DatabaseBackedPagingProvider ourPagingProvider;
public BaseResourceProviderDstu2Test() {
super();
@ -83,7 +81,8 @@ public abstract class BaseResourceProviderDstu2Test extends BaseJpaDstu2Test {
confProvider.setImplementationDescription("THIS IS THE DESC");
ourRestServer.setServerConformanceProvider(confProvider);
ourRestServer.setPagingProvider(new FifoMemoryPagingProvider(10));
ourPagingProvider = myAppCtx.getBean(DatabaseBackedPagingProvider.class);
ourRestServer.setPagingProvider(ourPagingProvider);
Server server = new Server(ourPort);
@ -126,6 +125,8 @@ public abstract class BaseResourceProviderDstu2Test extends BaseJpaDstu2Test {
ourServer = server;
}
ourRestServer.setPagingProvider(ourPagingProvider);
}
protected List<IdDt> toIdListUnqualifiedVersionless(Bundle found) {

116
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java
View File

@ -5,6 +5,7 @@ import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsInRelativeOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.emptyString;
import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.hasItems;
import static org.hamcrest.Matchers.not;
@ -47,11 +48,12 @@ import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.*;
import org.junit.Test;
import org.springframework.test.util.AopTestUtils;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.BundleEntry;
@ -85,10 +87,7 @@ import ca.uhn.fhir.model.valueset.BundleTypeEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
@ -100,10 +99,27 @@ import ca.uhn.fhir.util.UrlUtil;
public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderDstu2Test.class);
private SearchCoordinatorSvcImpl mySearchCoordinatorSvcRaw;
@Override
@After
public void after() throws Exception {
super.after();
myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
mySearchCoordinatorSvcRaw.setLoadingThrottleForUnitTests(null);
mySearchCoordinatorSvcRaw.setSyncSizeForUnitTests(SearchCoordinatorSvcImpl.DEFAULT_SYNC_SIZE);
mySearchCoordinatorSvcRaw.setNeverUseLocalSearchForUnitTests(false);
}
@Before
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
mySearchCoordinatorSvcRaw = AopTestUtils.getTargetObject(mySearchCoordinatorSvc);
}
@AfterClass
@ -118,6 +134,92 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
myDaoConfig.setAllowMultipleDelete(true);
}
@Test
public void testPagingOverEverythingSet() throws InterruptedException {
Patient p = new Patient();
p.setActive(true);
String pid = myPatientDao.create(p).getId().toUnqualifiedVersionless().getValue();
for (int i = 0; i < 20; i++) {
Observation o = new Observation();
o.getSubject().setReference(pid);
o.addIdentifier().setSystem("foo").setValue(Integer.toString(i));
myObservationDao.create(o);
}
mySearchCoordinatorSvcRaw.setLoadingThrottleForUnitTests(50);
mySearchCoordinatorSvcRaw.setSyncSizeForUnitTests(10);
mySearchCoordinatorSvcRaw.setNeverUseLocalSearchForUnitTests(true);
ca.uhn.fhir.model.dstu2.resource.Bundle response = ourClient
.operation()
.onInstance(new IdDt(pid))
.named("everything")
.withSearchParameter(Parameters.class, "_count", new NumberParam(10))
.returnResourceType(ca.uhn.fhir.model.dstu2.resource.Bundle.class)
.useHttpGet()
.execute();
assertEquals(10, response.getEntry().size());
assertEquals(null, response.getTotalElement().getValueAsString());
assertThat(response.getLink("next").getUrl(), not(emptyString()));
// Load page 2
String nextUrl = response.getLink("next").getUrl();
response = ourClient.fetchResourceFromUrl(ca.uhn.fhir.model.dstu2.resource.Bundle.class, nextUrl);
assertEquals(10, response.getEntry().size());
assertThat(response.getLink("next").getUrl(), not(emptyString()));
// Load page 3
Thread.sleep(2000);
nextUrl = response.getLink("next").getUrl();
response = ourClient.fetchResourceFromUrl(ca.uhn.fhir.model.dstu2.resource.Bundle.class, nextUrl);
assertEquals(1, response.getEntry().size());
assertEquals(21, response.getTotal().intValue());
assertEquals(null, response.getLink("next"));
}
@Test
public void testPagingOverEverythingSetWithNoPagingProvider() throws InterruptedException {
ourRestServer.setPagingProvider(null);
Patient p = new Patient();
p.setActive(true);
String pid = myPatientDao.create(p).getId().toUnqualifiedVersionless().getValue();
for (int i = 0; i < 20; i++) {
Observation o = new Observation();
o.getSubject().setReference(pid);
o.addIdentifier().setSystem("foo").setValue(Integer.toString(i));
myObservationDao.create(o);
}
mySearchCoordinatorSvcRaw.setLoadingThrottleForUnitTests(50);
mySearchCoordinatorSvcRaw.setSyncSizeForUnitTests(10);
mySearchCoordinatorSvcRaw.setNeverUseLocalSearchForUnitTests(true);
ca.uhn.fhir.model.dstu2.resource.Bundle response = ourClient
.operation()
.onInstance(new IdDt(pid))
.named("everything")
.withSearchParameter(Parameters.class, "_count", new NumberParam(10))
.returnResourceType(ca.uhn.fhir.model.dstu2.resource.Bundle.class)
.useHttpGet()
.execute();
assertEquals(21, response.getEntry().size());
assertEquals(21, response.getTotalElement().getValue().intValue());
assertEquals(null, response.getLink("next"));
}
private void checkParamMissing(String paramName) throws IOException, ClientProtocolException {
HttpGet get = new HttpGet(ourServerBase + "/Observation?" + paramName + ":missing=false");
CloseableHttpResponse resp = ourHttpClient.execute(get);

304
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderTransactionSearchDstu2Test.java Normal file
View File

@ -0,0 +1,304 @@
package ca.uhn.fhir.jpa.provider;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.nullValue;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import java.util.ArrayList;
import java.util.List;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.junit.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.dstu2.BaseJpaDstu2Test;
import ca.uhn.fhir.jpa.rp.dstu2.*;
import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.valueset.*;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.util.TestUtil;
public class SystemProviderTransactionSearchDstu2Test extends BaseJpaDstu2Test {
private static RestfulServer myRestServer;
private static IGenericClient ourClient;
private static FhirContext ourCtx;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderTransactionSearchDstu2Test.class);
private static Server ourServer;
private static String ourServerBase;
private SimpleRequestHeaderInterceptor mySimpleHeaderInterceptor;
@SuppressWarnings("deprecation")
@After
public void after() {
myRestServer.setUseBrowserFriendlyContentTypes(true);
ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
myDaoConfig.setMaximumSearchResultCountInTransaction(new DaoConfig().getMaximumSearchResultCountInTransaction());
}
@Before
public void before() {
mySimpleHeaderInterceptor = new SimpleRequestHeaderInterceptor();
ourClient.registerInterceptor(mySimpleHeaderInterceptor);
}
@Before
public void beforeStartServer() throws Exception {
if (myRestServer == null) {
PatientResourceProvider patientRp = new PatientResourceProvider();
patientRp.setDao(myPatientDao);
QuestionnaireResourceProviderDstu2 questionnaireRp = new QuestionnaireResourceProviderDstu2();
questionnaireRp.setDao(myQuestionnaireDao);
ObservationResourceProvider observationRp = new ObservationResourceProvider();
observationRp.setDao(myObservationDao);
OrganizationResourceProvider organizationRp = new OrganizationResourceProvider();
organizationRp.setDao(myOrganizationDao);
RestfulServer restServer = new RestfulServer(ourCtx);
restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
restServer.setPlainProviders(mySystemProvider);
int myPort = RandomServerPortProvider.findFreePort();
ourServer = new Server(myPort);
ServletContextHandler proxyHandler = new ServletContextHandler();
proxyHandler.setContextPath("/");
ourServerBase = "http://localhost:" + myPort + "/fhir/context";
ServletHolder servletHolder = new ServletHolder();
servletHolder.setServlet(restServer);
proxyHandler.addServlet(servletHolder, "/fhir/context/*");
ourCtx = FhirContext.forDstu2();
restServer.setFhirContext(ourCtx);
ourServer.setHandler(proxyHandler);
ourServer.start();
ourCtx.getRestfulClientFactory().setSocketTimeout(600 * 1000);
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
myRestServer = restServer;
}
myRestServer.setDefaultResponseEncoding(EncodingEnum.XML);
myRestServer.setPagingProvider(myPagingProvider);
}
private List<String> create20Patients() {
List<String> ids = new ArrayList<String>();
for (int i = 0; i < 20; i++) {
Patient patient = new Patient();
patient.setGender(AdministrativeGenderEnum.MALE);
patient.addIdentifier().setSystem("urn:foo").setValue("A");
patient.addName().addFamily("abcdefghijklmnopqrstuvwxyz".substring(i, i+1));
String id = myPatientDao.create(patient).getId().toUnqualifiedVersionless().getValue();
ids.add(id);
}
return ids;
}
@Test
public void testBatchWithGetHardLimitLargeSynchronous() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleTypeEnum.BATCH);
input
.addEntry()
.getRequest()
.setMethod(HTTPVerbEnum.GET)
.setUrl("Patient?_count=5");
myDaoConfig.setMaximumSearchResultCountInTransaction(100);
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(1, output.getEntry().size());
Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
assertEquals(5, respBundle.getEntry().size());
assertEquals(null, respBundle.getLink("next"));
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
}
@Test
public void testBatchWithGetNormalSearch() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleTypeEnum.BATCH);
input
.addEntry()
.getRequest()
.setMethod(HTTPVerbEnum.GET)
.setUrl("Patient?_count=5&_sort=name");
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(1, output.getEntry().size());
Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
assertEquals(5, respBundle.getEntry().size());
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
String nextPageLink = respBundle.getLink("next").getUrl();
output = ourClient.loadPage().byUrl(nextPageLink).andReturnBundle(Bundle.class).execute();
respBundle = output;
assertEquals(5, respBundle.getEntry().size());
actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(5, 10).toArray(new String[0])));
}
/**
* 30 searches in one batch! Whoa!
*/
@Test
public void testBatchWithManyGets() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleTypeEnum.BATCH);
for (int i = 0; i < 30; i++) {
input
.addEntry()
.getRequest()
.setMethod(HTTPVerbEnum.GET)
.setUrl("Patient?_count=5&identifier=urn:foo|A,AAAAA" + i);
}
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(30, output.getEntry().size());
for (int i = 0; i < 30; i++) {
Bundle respBundle = (Bundle) output.getEntry().get(i).getResource();
assertEquals(5, respBundle.getEntry().size());
assertThat(respBundle.getLink("next").getUrl(), not(nullValue()));
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
}
}
@Test
public void testTransactionWithGetHardLimitLargeSynchronous() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleTypeEnum.TRANSACTION);
input
.addEntry()
.getRequest()
.setMethod(HTTPVerbEnum.GET)
.setUrl("Patient?_count=5");
myDaoConfig.setMaximumSearchResultCountInTransaction(100);
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(1, output.getEntry().size());
Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
assertEquals(5, respBundle.getEntry().size());
assertEquals(null, respBundle.getLink("next"));
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
}
@Test
public void testTransactionWithGetNormalSearch() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleTypeEnum.TRANSACTION);
input
.addEntry()
.getRequest()
.setMethod(HTTPVerbEnum.GET)
.setUrl("Patient?_count=5&_sort=name");
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(1, output.getEntry().size());
Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
assertEquals(5, respBundle.getEntry().size());
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
String nextPageLink = respBundle.getLink("next").getUrl();
output = ourClient.loadPage().byUrl(nextPageLink).andReturnBundle(Bundle.class).execute();
respBundle = output;
assertEquals(5, respBundle.getEntry().size());
actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(5, 10).toArray(new String[0])));
}
/**
* 30 searches in one Transaction! Whoa!
*/
@Test
public void testTransactionWithManyGets() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleTypeEnum.TRANSACTION);
for (int i = 0; i < 30; i++) {
input
.addEntry()
.getRequest()
.setMethod(HTTPVerbEnum.GET)
.setUrl("Patient?_count=5&identifier=urn:foo|A,AAAAA" + i);
}
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(30, output.getEntry().size());
for (int i = 0; i < 30; i++) {
Bundle respBundle = (Bundle) output.getEntry().get(i).getResource();
assertEquals(5, respBundle.getEntry().size());
assertThat(respBundle.getLink("next").getUrl(), not(nullValue()));
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
}
}
private List<String> toIds(Bundle theRespBundle) {
ArrayList<String> retVal = new ArrayList<String>();
for (Entry next : theRespBundle.getEntry()) {
retVal.add(next.getResource().getIdElement().toUnqualifiedVersionless().getValue());
}
return retVal;
}
@AfterClass
public static void afterClassClearContext() throws Exception {
ourServer.stop();
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/BaseResourceProviderDstu3Test.java
View File

@ -56,6 +56,7 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
protected static String ourServerBase;
private static GenericWebApplicationContext ourWebApplicationContext;
private TerminologyUploaderProviderDstu3 myTerminologyUploaderProvider;
protected static DatabaseBackedPagingProvider ourPagingProvider;
protected static RestHookSubscriptionDstu3Interceptor ourRestHookSubscriptionInterceptor;
protected static ISearchDao mySearchEntityDao;
protected static ISearchCoordinatorSvc mySearchCoordinatorSvc;
@ -95,7 +96,7 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
confProvider.setImplementationDescription("THIS IS THE DESC");
ourRestServer.setServerConformanceProvider(confProvider);
ourRestServer.setPagingProvider(myAppCtx.getBean(DatabaseBackedPagingProvider.class));
ourPagingProvider = myAppCtx.getBean(DatabaseBackedPagingProvider.class);
Server server = new Server(ourPort);
@ -162,6 +163,8 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
ourServer = server;
}
ourRestServer.setPagingProvider(ourPagingProvider);
}
protected boolean shouldLogClient() {

469
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
View File

@ -6,11 +6,11 @@ import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsInRelativeOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.emptyString;
import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.hasItems;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.lessThan;
import static org.hamcrest.Matchers.lessThanOrEqualTo;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.startsWith;
@ -47,9 +47,9 @@ import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
import org.hl7.fhir.instance.model.Encounter.EncounterState;
import org.hl7.fhir.instance.model.api.*;
import org.junit.*;
import org.springframework.test.util.AopTestUtils;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
@ -57,6 +57,7 @@ import com.google.common.collect.Lists;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.UriDt;
@ -76,11 +77,7 @@ import ca.uhn.fhir.util.UrlUtil;
public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderDstu3Test.class);
@Before
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
private SearchCoordinatorSvcImpl mySearchCoordinatorSvcRaw;
@Override
@After
@ -90,6 +87,11 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
mySearchCoordinatorSvcRaw.setLoadingThrottleForUnitTests(null);
mySearchCoordinatorSvcRaw.setSyncSizeForUnitTests(SearchCoordinatorSvcImpl.DEFAULT_SYNC_SIZE);
mySearchCoordinatorSvcRaw.setNeverUseLocalSearchForUnitTests(false);
}
@Override
@ -100,95 +102,10 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
myDaoConfig.setAllowMultipleDelete(true);
}
@Test
public void testSearchWithEmptyParameter() throws Exception {
Observation obs= new Observation();
obs.setStatus(ObservationStatus.FINAL);
obs.getCode().addCoding().setSystem("foo").setCode("bar");
ourClient.create().resource(obs).execute();
testSearchWithEmptyParameter("/Observation?value-quantity=");
testSearchWithEmptyParameter("/Observation?code=bar&value-quantity=");
testSearchWithEmptyParameter("/Observation?value-date=");
testSearchWithEmptyParameter("/Observation?code=bar&value-date=");
testSearchWithEmptyParameter("/Observation?value-concept=");
testSearchWithEmptyParameter("/Observation?code=bar&value-concept=");
}
private void testSearchWithEmptyParameter(String url) throws IOException, ClientProtocolException {
HttpGet get = new HttpGet(ourServerBase + url);
CloseableHttpResponse resp = ourHttpClient.execute(get);
try {
assertEquals(200, resp.getStatusLine().getStatusCode());
String respString = IOUtils.toString(resp.getEntity().getContent(), Constants.CHARSET_UTF8);
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, respString);
assertEquals(1, bundle.getEntry().size());
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
}
}
@Test
public void testSearchWithMissingDate2() throws Exception {
MedicationRequest mr1 = new MedicationRequest();
mr1.getCategory().addCoding().setSystem("urn:medicationroute").setCode("oral");
mr1.addDosageInstruction().getTiming().addEventElement().setValueAsString("2017-01-01");
IIdType id1 = myMedicationRequestDao.create(mr1).getId().toUnqualifiedVersionless();
MedicationRequest mr2 = new MedicationRequest();
mr2.getCategory().addCoding().setSystem("urn:medicationroute").setCode("oral");
IIdType id2 = myMedicationRequestDao.create(mr2).getId().toUnqualifiedVersionless();
HttpGet get = new HttpGet(ourServerBase + "/MedicationRequest?date:missing=false");
CloseableHttpResponse resp = ourHttpClient.execute(get);
try {
assertEquals(200, resp.getStatusLine().getStatusCode());
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, IOUtils.toString(resp.getEntity().getContent(), Constants.CHARSET_UTF8));
List<String> ids = toUnqualifiedVersionlessIdValues(bundle);
assertThat(ids, contains(id1.getValue()));
} finally {
IOUtils.closeQuietly(resp);
}
}
@Test
public void testEverythingWithOnlyPatient() {
Patient p = new Patient();
p.setActive(true);
IIdType id = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
myFhirCtx.getRestfulClientFactory().setSocketTimeout(300 * 1000);
Bundle response = ourClient
.operation()
.onInstance(id)
.named("everything")
.withNoParameters(Parameters.class)
.returnResourceType(Bundle.class)
.execute();
assertEquals(1, response.getEntry().size());
}
@Test
public void testSaveAndRetrieveResourceWithExtension() {
Patient nextPatient = new Patient();
nextPatient.setId("Patient/B");
nextPatient
.addExtension()
.setUrl("http://foo")
.setValue(new Reference("Practitioner/A"));
ourClient.update().resource(nextPatient).execute();
Patient p = ourClient.read().resource(Patient.class).withId("B").execute();
String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(encoded);
assertThat(encoded, containsString("http://foo"));
@Before
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
mySearchCoordinatorSvcRaw = AopTestUtils.getTargetObject(mySearchCoordinatorSvc);
}
private void checkParamMissing(String paramName) throws IOException, ClientProtocolException {
@ -197,7 +114,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
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()) {
@ -354,8 +272,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
/**
* See #438
*/
@ -429,7 +345,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
Validate.notNull(input);
ourClient.create().resource(input).execute().getResource();
}
@Test
public void testCreateConditional() {
@ -552,6 +467,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
@Test
public void testCreateResourceConditionalComplex() throws IOException {
Patient pt = new Patient();
@ -614,6 +531,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
response.close();
}
}
@Test
public void testCreateResourceWithNumericId() throws IOException {
@ -1300,31 +1218,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
// private void delete(String theResourceType, String theParamName, String theParamValue) {
// Bundle resources;
// do {
// IQuery<Bundle> forResource = ourClient.search().forResource(theResourceType);
// if (theParamName != null) {
// forResource = forResource.where(new StringClientParam(theParamName).matches().value(theParamValue));
// }
// resources = forResource.execute();
// for (IResource next : resources.toListOfResources()) {
// ourLog.info("Deleting resource: {}", next.getId());
// ourClient.delete().resource(next).execute();
// }
// } while (resources.size() > 0);
// }
//
// private void deleteToken(String theResourceType, String theParamName, String theParamSystem, String theParamValue)
// {
// Bundle resources = ourClient.search().forResource(theResourceType).where(new
// TokenClientParam(theParamName).exactly().systemAndCode(theParamSystem, theParamValue)).execute();
// for (IResource next : resources.toListOfResources()) {
// ourLog.info("Deleting resource: {}", next.getId());
// ourClient.delete().resource(next).execute();
// }
// }
@Test
public void testEverythingPatientOperation() throws Exception {
String methodName = "testEverythingOperation";
@ -1370,53 +1263,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
ourLog.info(ids.toString());
}
@Test
public void testSearchByLastUpdated() throws Exception {
String methodName = "testSearchByLastUpdated";
Patient p = new Patient();
p.addName().setFamily(methodName+"1");
IIdType pid1 = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
Thread.sleep(10);
long time1 = System.currentTimeMillis();
Thread.sleep(10);
Patient p2 = new Patient();
p2.addName().setFamily(methodName+"2");
IIdType pid2 = ourClient.create().resource(p2).execute().getId().toUnqualifiedVersionless();
HttpGet get = new HttpGet(ourServerBase + "/Patient?_lastUpdated=lt" + new InstantType(new Date(time1)).getValueAsString());
CloseableHttpResponse response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IIdType> ids = toUnqualifiedVersionlessIds(myFhirCtx.newXmlParser().parseResource(Bundle.class, output));
ourLog.info(ids.toString());
assertThat(ids, containsInAnyOrder(pid1));
} finally {
response.close();
}
get = new HttpGet(ourServerBase + "/Patient?_lastUpdated=gt" + new InstantType(new Date(time1)).getValueAsString());
response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IIdType> ids = toUnqualifiedVersionlessIds(myFhirCtx.newXmlParser().parseResource(Bundle.class, output));
ourLog.info(ids.toString());
assertThat(ids, containsInAnyOrder(pid2));
} finally {
response.close();
}
}
@Test
public void testEverythingPatientType() throws Exception {
String methodName = "testEverythingPatientType";
@ -1679,6 +1525,50 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
assertEquals(77, ids.size());
}
@Test
public void testEverythingWithOnlyPatient() {
Patient p = new Patient();
p.setActive(true);
IIdType id = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
myFhirCtx.getRestfulClientFactory().setSocketTimeout(300 * 1000);
Bundle response = ourClient
.operation()
.onInstance(id)
.named("everything")
.withNoParameters(Parameters.class)
.returnResourceType(Bundle.class)
.execute();
assertEquals(1, response.getEntry().size());
}
// private void delete(String theResourceType, String theParamName, String theParamValue) {
// Bundle resources;
// do {
// IQuery<Bundle> forResource = ourClient.search().forResource(theResourceType);
// if (theParamName != null) {
// forResource = forResource.where(new StringClientParam(theParamName).matches().value(theParamValue));
// }
// resources = forResource.execute();
// for (IResource next : resources.toListOfResources()) {
// ourLog.info("Deleting resource: {}", next.getId());
// ourClient.delete().resource(next).execute();
// }
// } while (resources.size() > 0);
// }
//
// private void deleteToken(String theResourceType, String theParamName, String theParamSystem, String theParamValue)
// {
// Bundle resources = ourClient.search().forResource(theResourceType).where(new
// TokenClientParam(theParamName).exactly().systemAndCode(theParamSystem, theParamValue)).execute();
// for (IResource next : resources.toListOfResources()) {
// ourLog.info("Deleting resource: {}", next.getId());
// ourClient.delete().resource(next).execute();
// }
// }
@SuppressWarnings("unused")
@Test
public void testFullTextSearch() throws RuntimeException, Exception {
@ -1727,7 +1617,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
response.close();
}
}
@Test
public void testHasParameter() throws Exception {
IIdType pid0;
@ -2074,6 +1965,91 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
@Test
public void testPagingOverEverythingSet() throws InterruptedException {
Patient p = new Patient();
p.setActive(true);
String pid = myPatientDao.create(p).getId().toUnqualifiedVersionless().getValue();
for (int i = 0; i < 20; i++) {
Observation o = new Observation();
o.getSubject().setReference(pid);
o.addIdentifier().setSystem("foo").setValue(Integer.toString(i));
myObservationDao.create(o);
}
mySearchCoordinatorSvcRaw.setLoadingThrottleForUnitTests(50);
mySearchCoordinatorSvcRaw.setSyncSizeForUnitTests(10);
mySearchCoordinatorSvcRaw.setNeverUseLocalSearchForUnitTests(true);
Bundle response = ourClient
.operation()
.onInstance(new IdType(pid))
.named("everything")
.withSearchParameter(Parameters.class, "_count", new NumberParam(10))
.returnResourceType(Bundle.class)
.useHttpGet()
.execute();
assertEquals(10, response.getEntry().size());
assertEquals(null, response.getTotalElement().getValueAsString());
assertThat(response.getLink("next").getUrl(), not(emptyString()));
// Load page 2
String nextUrl = response.getLink("next").getUrl();
response = ourClient.fetchResourceFromUrl(Bundle.class, nextUrl);
assertEquals(10, response.getEntry().size());
assertEquals(null, response.getTotalElement().getValueAsString());
assertThat(response.getLink("next").getUrl(), not(emptyString()));
// Load page 3
Thread.sleep(2000);
nextUrl = response.getLink("next").getUrl();
response = ourClient.fetchResourceFromUrl(Bundle.class, nextUrl);
assertEquals(1, response.getEntry().size());
assertEquals(21, response.getTotal());
assertEquals(null, response.getLink("next"));
}
@Test
public void testPagingOverEverythingSetWithNoPagingProvider() throws InterruptedException {
ourRestServer.setPagingProvider(null);
Patient p = new Patient();
p.setActive(true);
String pid = myPatientDao.create(p).getId().toUnqualifiedVersionless().getValue();
for (int i = 0; i < 20; i++) {
Observation o = new Observation();
o.getSubject().setReference(pid);
o.addIdentifier().setSystem("foo").setValue(Integer.toString(i));
myObservationDao.create(o);
}
mySearchCoordinatorSvcRaw.setLoadingThrottleForUnitTests(50);
mySearchCoordinatorSvcRaw.setSyncSizeForUnitTests(10);
mySearchCoordinatorSvcRaw.setNeverUseLocalSearchForUnitTests(true);
Bundle response = ourClient
.operation()
.onInstance(new IdType(pid))
.named("everything")
.withSearchParameter(Parameters.class, "_count", new NumberParam(10))
.returnResourceType(Bundle.class)
.useHttpGet()
.execute();
assertEquals(21, response.getEntry().size());
assertEquals(21, response.getTotalElement().getValue().intValue());
assertEquals(null, response.getLink("next"));
}
@Test
public void testPatchUsingJsonPatch() throws Exception {
String methodName = "testPatchUsingJsonPatch";
@ -2297,6 +2273,25 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">HELLO WORLD</div>", actual.getText().getDiv().getValueAsString());
}
@Test
public void testSaveAndRetrieveResourceWithExtension() {
Patient nextPatient = new Patient();
nextPatient.setId("Patient/B");
nextPatient
.addExtension()
.setUrl("http://foo")
.setValue(new Reference("Practitioner/A"));
ourClient.update().resource(nextPatient).execute();
Patient p = ourClient.read().resource(Patient.class).withId("B").execute();
String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(encoded);
assertThat(encoded, containsString("http://foo"));
}
@Test
public void testSaveAndRetrieveWithContained() {
Patient p1 = new Patient();
@ -2517,6 +2512,52 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
@Test
public void testSearchByLastUpdated() throws Exception {
String methodName = "testSearchByLastUpdated";
Patient p = new Patient();
p.addName().setFamily(methodName+"1");
IIdType pid1 = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
Thread.sleep(10);
long time1 = System.currentTimeMillis();
Thread.sleep(10);
Patient p2 = new Patient();
p2.addName().setFamily(methodName+"2");
IIdType pid2 = ourClient.create().resource(p2).execute().getId().toUnqualifiedVersionless();
HttpGet get = new HttpGet(ourServerBase + "/Patient?_lastUpdated=lt" + new InstantType(new Date(time1)).getValueAsString());
CloseableHttpResponse response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IIdType> ids = toUnqualifiedVersionlessIds(myFhirCtx.newXmlParser().parseResource(Bundle.class, output));
ourLog.info(ids.toString());
assertThat(ids, containsInAnyOrder(pid1));
} finally {
response.close();
}
get = new HttpGet(ourServerBase + "/Patient?_lastUpdated=gt" + new InstantType(new Date(time1)).getValueAsString());
response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IIdType> ids = toUnqualifiedVersionlessIds(myFhirCtx.newXmlParser().parseResource(Bundle.class, output));
ourLog.info(ids.toString());
assertThat(ids, containsInAnyOrder(pid2));
} finally {
response.close();
}
}
@Test
public void testSearchByReferenceIds() {
Organization o1 = new Organization();
@ -2587,6 +2628,28 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
@Test
public void testSearchInvalidParam() throws Exception {
Patient patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue("0");
patient.addName().setFamily("testSearchWithMixedParams").addGiven("Joe");
myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
// should be subject._id
HttpGet httpPost = new HttpGet(ourServerBase + "/Observation?subject.id=FOO");
CloseableHttpResponse resp = ourHttpClient.execute(httpPost);
try {
String respString = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(respString);
assertThat(respString, containsString("Invalid parameter chain: subject.id"));
assertEquals(400, resp.getStatusLine().getStatusCode());
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
}
ourLog.info("Outgoing post: {}", httpPost);
}
@Test
public void testSearchLastUpdatedParamRp() throws InterruptedException {
String methodName = "testSearchLastUpdatedParamRp";
@ -3047,6 +3110,34 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
assertEquals(2, response.getEntry().size());
}
@Test
public void testSearchWithEmptyParameter() throws Exception {
Observation obs= new Observation();
obs.setStatus(ObservationStatus.FINAL);
obs.getCode().addCoding().setSystem("foo").setCode("bar");
ourClient.create().resource(obs).execute();
testSearchWithEmptyParameter("/Observation?value-quantity=");
testSearchWithEmptyParameter("/Observation?code=bar&value-quantity=");
testSearchWithEmptyParameter("/Observation?value-date=");
testSearchWithEmptyParameter("/Observation?code=bar&value-date=");
testSearchWithEmptyParameter("/Observation?value-concept=");
testSearchWithEmptyParameter("/Observation?code=bar&value-concept=");
}
private void testSearchWithEmptyParameter(String url) throws IOException, ClientProtocolException {
HttpGet get = new HttpGet(ourServerBase + url);
CloseableHttpResponse resp = ourHttpClient.execute(get);
try {
assertEquals(200, resp.getStatusLine().getStatusCode());
String respString = IOUtils.toString(resp.getEntity().getContent(), Constants.CHARSET_UTF8);
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, respString);
assertEquals(1, bundle.getEntry().size());
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
}
}
@Test
public void testSearchWithInclude() throws Exception {
Organization org = new Organization();
@ -3211,25 +3302,29 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
@Test
public void testSearchInvalidParam() throws Exception {
Patient patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue("0");
patient.addName().setFamily("testSearchWithMixedParams").addGiven("Joe");
myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
public void testSearchWithMissingDate2() throws Exception {
MedicationRequest mr1 = new MedicationRequest();
mr1.getCategory().addCoding().setSystem("urn:medicationroute").setCode("oral");
mr1.addDosageInstruction().getTiming().addEventElement().setValueAsString("2017-01-01");
IIdType id1 = myMedicationRequestDao.create(mr1).getId().toUnqualifiedVersionless();
// should be subject._id
HttpGet httpPost = new HttpGet(ourServerBase + "/Observation?subject.id=FOO");
MedicationRequest mr2 = new MedicationRequest();
mr2.getCategory().addCoding().setSystem("urn:medicationroute").setCode("oral");
IIdType id2 = myMedicationRequestDao.create(mr2).getId().toUnqualifiedVersionless();
CloseableHttpResponse resp = ourHttpClient.execute(httpPost);
HttpGet get = new HttpGet(ourServerBase + "/MedicationRequest?date:missing=false");
CloseableHttpResponse resp = ourHttpClient.execute(get);
try {
String respString = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(respString);
assertThat(respString, containsString("Invalid parameter chain: subject.id"));
assertEquals(400, resp.getStatusLine().getStatusCode());
assertEquals(200, resp.getStatusLine().getStatusCode());
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, IOUtils.toString(resp.getEntity().getContent(), Constants.CHARSET_UTF8));
List<String> ids = toUnqualifiedVersionlessIdValues(bundle);
assertThat(ids, contains(id1.getValue()));
assertThat(ids, not(contains(id2.getValue())));
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
IOUtils.closeQuietly(resp);
}
ourLog.info("Outgoing post: {}", httpPost);
}
/**

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderDstu3Test.java
View File

@ -58,6 +58,7 @@ import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
import ca.uhn.fhir.jpa.rp.dstu3.ObservationResourceProvider;
import ca.uhn.fhir.jpa.rp.dstu3.OrganizationResourceProvider;
import ca.uhn.fhir.jpa.rp.dstu3.PatientResourceProvider;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
@ -202,7 +203,6 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
organizationRp.setDao(myOrganizationDao);
RestfulServer restServer = new RestfulServer(ourCtx);
restServer.setPagingProvider(new FifoMemoryPagingProvider(10).setDefaultPageSize(10));
restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
restServer.setPlainProviders(mySystemProvider);
@ -237,6 +237,7 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
}
myRestServer.setDefaultResponseEncoding(EncodingEnum.XML);
myRestServer.setPagingProvider(myPagingProvider);
}
@Before

358
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderTransactionSearchDstu3Test.java Normal file
View File

@ -0,0 +1,358 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.nullValue;
import static org.hamcrest.Matchers.startsWith;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.TimeUnit;
import org.apache.commons.io.IOUtils;
import org.apache.http.Header;
import org.apache.http.client.ClientProtocolException;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.*;
import org.hl7.fhir.dstu3.model.DecimalType;
import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.OperationDefinition;
import org.hl7.fhir.dstu3.model.OperationOutcome;
import org.hl7.fhir.dstu3.model.Organization;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.DaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
import ca.uhn.fhir.jpa.rp.dstu3.ObservationResourceProvider;
import ca.uhn.fhir.jpa.rp.dstu3.OrganizationResourceProvider;
import ca.uhn.fhir.jpa.rp.dstu3.PatientResourceProvider;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.validation.ResultSeverityEnum;
public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
private static RestfulServer myRestServer;
private static IGenericClient ourClient;
private static FhirContext ourCtx;
private static CloseableHttpClient ourHttpClient;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderTransactionSearchDstu3Test.class);
private static Server ourServer;
private static String ourServerBase;
private SimpleRequestHeaderInterceptor mySimpleHeaderInterceptor;
@SuppressWarnings("deprecation")
@After
public void after() {
myRestServer.setUseBrowserFriendlyContentTypes(true);
ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
myDaoConfig.setMaximumSearchResultCountInTransaction(new DaoConfig().getMaximumSearchResultCountInTransaction());
}
@Before
public void before() {
mySimpleHeaderInterceptor = new SimpleRequestHeaderInterceptor();
ourClient.registerInterceptor(mySimpleHeaderInterceptor);
}
@Before
public void beforeStartServer() throws Exception {
if (myRestServer == null) {
PatientResourceProvider patientRp = new PatientResourceProvider();
patientRp.setDao(myPatientDao);
QuestionnaireResourceProviderDstu3 questionnaireRp = new QuestionnaireResourceProviderDstu3();
questionnaireRp.setDao(myQuestionnaireDao);
ObservationResourceProvider observationRp = new ObservationResourceProvider();
observationRp.setDao(myObservationDao);
OrganizationResourceProvider organizationRp = new OrganizationResourceProvider();
organizationRp.setDao(myOrganizationDao);
RestfulServer restServer = new RestfulServer(ourCtx);
restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
restServer.setPlainProviders(mySystemProvider);
int myPort = RandomServerPortProvider.findFreePort();
ourServer = new Server(myPort);
ServletContextHandler proxyHandler = new ServletContextHandler();
proxyHandler.setContextPath("/");
ourServerBase = "http://localhost:" + myPort + "/fhir/context";
ServletHolder servletHolder = new ServletHolder();
servletHolder.setServlet(restServer);
proxyHandler.addServlet(servletHolder, "/fhir/context/*");
ourCtx = FhirContext.forDstu3();
restServer.setFhirContext(ourCtx);
ourServer.setHandler(proxyHandler);
ourServer.start();
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
ourHttpClient = builder.build();
ourCtx.getRestfulClientFactory().setSocketTimeout(600 * 1000);
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourClient.setLogRequestAndResponse(true);
myRestServer = restServer;
}
myRestServer.setDefaultResponseEncoding(EncodingEnum.XML);
myRestServer.setPagingProvider(myPagingProvider);
}
private List<String> create20Patients() {
List<String> ids = new ArrayList<String>();
for (int i = 0; i < 20; i++) {
Patient patient = new Patient();
patient.setGender(AdministrativeGender.MALE);
patient.addIdentifier().setSystem("urn:foo").setValue("A");
patient.addName().setFamily("abcdefghijklmnopqrstuvwxyz".substring(i, i+1));
String id = myPatientDao.create(patient).getId().toUnqualifiedVersionless().getValue();
ids.add(id);
}
return ids;
}
@Test
public void testBatchWithGetHardLimitLargeSynchronous() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleType.BATCH);
input
.addEntry()
.getRequest()
.setMethod(HTTPVerb.GET)
.setUrl("Patient?_count=5");
myDaoConfig.setMaximumSearchResultCountInTransaction(100);
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(1, output.getEntry().size());
Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
assertEquals(5, respBundle.getEntry().size());
assertEquals(null, respBundle.getLink("next"));
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
}
@Test
public void testBatchWithGetNormalSearch() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleType.BATCH);
input
.addEntry()
.getRequest()
.setMethod(HTTPVerb.GET)
.setUrl("Patient?_count=5&_sort=name");
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(1, output.getEntry().size());
Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
assertEquals(5, respBundle.getEntry().size());
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
String nextPageLink = respBundle.getLink("next").getUrl();
output = ourClient.loadPage().byUrl(nextPageLink).andReturnBundle(Bundle.class).execute();
respBundle = output;
assertEquals(5, respBundle.getEntry().size());
actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(5, 10).toArray(new String[0])));
}
/**
* 30 searches in one batch! Whoa!
*/
@Test
public void testBatchWithManyGets() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleType.BATCH);
for (int i = 0; i < 30; i++) {
input
.addEntry()
.getRequest()
.setMethod(HTTPVerb.GET)
.setUrl("Patient?_count=5&identifier=urn:foo|A,AAAAA" + i);
}
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(30, output.getEntry().size());
for (int i = 0; i < 30; i++) {
Bundle respBundle = (Bundle) output.getEntry().get(i).getResource();
assertEquals(5, respBundle.getEntry().size());
assertThat(respBundle.getLink("next").getUrl(), not(nullValue()));
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
}
}
@Test
public void testTransactionWithGetHardLimitLargeSynchronous() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleType.TRANSACTION);
input
.addEntry()
.getRequest()
.setMethod(HTTPVerb.GET)
.setUrl("Patient?_count=5");
myDaoConfig.setMaximumSearchResultCountInTransaction(100);
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(1, output.getEntry().size());
Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
assertEquals(5, respBundle.getEntry().size());
assertEquals(null, respBundle.getLink("next"));
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
}
@Test
public void testTransactionWithGetNormalSearch() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleType.TRANSACTION);
input
.addEntry()
.getRequest()
.setMethod(HTTPVerb.GET)
.setUrl("Patient?_count=5&_sort=name");
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(1, output.getEntry().size());
Bundle respBundle = (Bundle) output.getEntry().get(0).getResource();
assertEquals(5, respBundle.getEntry().size());
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
String nextPageLink = respBundle.getLink("next").getUrl();
output = ourClient.loadPage().byUrl(nextPageLink).andReturnBundle(Bundle.class).execute();
respBundle = output;
assertEquals(5, respBundle.getEntry().size());
actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(5, 10).toArray(new String[0])));
}
/**
* 30 searches in one Transaction! Whoa!
*/
@Test
public void testTransactionWithManyGets() throws Exception {
List<String> ids = create20Patients();
Bundle input = new Bundle();
input.setType(BundleType.TRANSACTION);
for (int i = 0; i < 30; i++) {
input
.addEntry()
.getRequest()
.setMethod(HTTPVerb.GET)
.setUrl("Patient?_count=5&identifier=urn:foo|A,AAAAA" + i);
}
Bundle output = ourClient.transaction().withBundle(input).execute();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(30, output.getEntry().size());
for (int i = 0; i < 30; i++) {
Bundle respBundle = (Bundle) output.getEntry().get(i).getResource();
assertEquals(5, respBundle.getEntry().size());
assertThat(respBundle.getLink("next").getUrl(), not(nullValue()));
List<String> actualIds = toIds(respBundle);
assertThat(actualIds, contains(ids.subList(0, 5).toArray(new String[0])));
}
}
private List<String> toIds(Bundle theRespBundle) {
ArrayList<String> retVal = new ArrayList<String>();
for (BundleEntryComponent next : theRespBundle.getEntry()) {
retVal.add(next.getResource().getIdElement().toUnqualifiedVersionless().getValue());
}
return retVal;
}
@AfterClass
public static void afterClassClearContext() throws Exception {
ourServer.stop();
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/PagingMultinodeProviderDstu3Test.java
View File

@ -42,8 +42,6 @@ public class PagingMultinodeProviderDstu3Test extends BaseResourceProviderDstu3T
myDaoConfig.setAllowMultipleDelete(true);
mySearchCoordinatorSvcRaw = AopTestUtils.getTargetObject(mySearchCoordinatorSvc);
// mySearchCoordinatorSvcRaw = (SearchCoordinatorSvcImpl)mySearchCoordinatorSvc;
}
@Test

35
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/RestHookTestDstu2Test.java
View File

@ -1,7 +1,7 @@
package ca.uhn.fhir.jpa.subscription;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.*;
import java.util.List;
@ -36,6 +36,7 @@ import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.PortUtil;
/**
@ -58,13 +59,12 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
ourClient.delete().resourceConditionalByUrl("Subscription?status=active").execute();
ourLog.info("Done deleting all subscriptions");
myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
ourRestServer.unregisterInterceptor(ourRestHookSubscriptionInterceptor);
}
@Before
public void beforeRegisterRestHookListener() {
// ourRestHookSubscriptionInterceptor.set
ourRestServer.registerInterceptor(ourRestHookSubscriptionInterceptor);
}
@ -127,22 +127,21 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
Thread.sleep(500);
assertEquals(1, ourCreatedObservations.size());
assertEquals(0, ourUpdatedObservations.size());
Subscription subscriptionTemp = ourClient.read(Subscription.class, subscription2.getId());
Assert.assertNotNull(subscriptionTemp);
subscriptionTemp.setCriteria(criteria1);
ourClient.update().resource(subscriptionTemp).withId(subscriptionTemp.getIdElement()).execute();
Observation observation2 = sendObservation(code, "SNOMED-CT");
// Should see two subscription notifications
Thread.sleep(500);
assertEquals(3, ourCreatedObservations.size());
assertEquals(0, ourUpdatedObservations.size());
ourClient.delete().resourceById(new IdDt("Subscription/"+ subscription2.getId())).execute();
ourClient.delete().resourceById(new IdDt("Subscription/" + subscription2.getId())).execute();
Observation observationTemp3 = sendObservation(code, "SNOMED-CT");
@ -183,6 +182,20 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
Assert.assertFalse(observation2.getId().isEmpty());
}
@Test
public void testRestHookSubscriptionInvalidCriteria() throws Exception {
String payload = "application/xml";
String criteria1 = "Observation?codeeeee=SNOMED-CT";
try {
createSubscription(criteria1, payload, ourListenerServerBase);
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid criteria: Failed to parse match URL[Observation?codeeeee=SNOMED-CT] - Resource type Observation does not have a parameter with name: codeeeee", e.getMessage());
}
}
@Test
public void testRestHookSubscriptionXml() throws Exception {
String payload = "application/xml";
@ -200,22 +213,21 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
Thread.sleep(500);
assertEquals(1, ourCreatedObservations.size());
assertEquals(0, ourUpdatedObservations.size());
Subscription subscriptionTemp = ourClient.read(Subscription.class, subscription2.getId());
Assert.assertNotNull(subscriptionTemp);
subscriptionTemp.setCriteria(criteria1);
ourClient.update().resource(subscriptionTemp).withId(subscriptionTemp.getIdElement()).execute();
Observation observation2 = sendObservation(code, "SNOMED-CT");
// Should see two subscription notifications
Thread.sleep(500);
assertEquals(3, ourCreatedObservations.size());
assertEquals(0, ourUpdatedObservations.size());
ourClient.delete().resourceById(new IdDt("Subscription/"+ subscription2.getId())).execute();
ourClient.delete().resourceById(new IdDt("Subscription/" + subscription2.getId())).execute();
Observation observationTemp3 = sendObservation(code, "SNOMED-CT");
@ -256,7 +268,6 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
Assert.assertFalse(observation2.getId().isEmpty());
}
@BeforeClass
public static void startListenerServer() throws Exception {
ourListenerPort = PortUtil.findFreePort();

16
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/RestHookTestDstu3Test.java
View File

@ -27,6 +27,7 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
/**
* Test the rest-hook subscriptions
@ -65,6 +66,21 @@ public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
ourUpdatedObservations.clear();
ourContentTypes.clear();
}
@Test
public void testRestHookSubscriptionInvalidCriteria() throws Exception {
String payload = "application/xml";
String criteria1 = "Observation?codeeeee=SNOMED-CT";
try {
createSubscription(criteria1, payload, ourListenerServerBase);
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid criteria: Failed to parse match URL[Observation?codeeeee=SNOMED-CT] - Resource type Observation does not have a parameter with name: codeeeee", e.getMessage());
}
}
private Subscription createSubscription(String theCriteria, String thePayload, String theEndpoint) {
Subscription subscription = new Subscription();

67
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/IRestfulServerDefaults.java
View File

@ -28,37 +28,6 @@ import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
public interface IRestfulServerDefaults {
/**
* Returns the list of interceptors registered against this server
*/
List<IServerInterceptor> getInterceptors();
/**
* Gets the {@link FhirContext} associated with this server. For efficient processing, resource providers and plain
* providers should generally use this context if one is needed, as opposed to
* creating their own.
*/
FhirContext getFhirContext();
/**
* Should the server "pretty print" responses by default (requesting clients can always override this default by
* supplying an <code>Accept</code> header in the request, or a <code>_pretty</code>
* parameter in the request URL.
* <p>
* The default is <code>false</code>
* </p>
*
* @return Returns the default pretty print setting
*/
boolean isDefaultPrettyPrint();
/**
* @return Returns the server support for ETags (will not be <code>null</code>). Default is
* {@link RestfulServer#DEFAULT_ETAG_SUPPORT}
*/
ETagSupportEnum getETagSupport();
/**
* @return Returns the setting for automatically adding profile tags
* @deprecated As of HAPI FHIR 1.5, this property has been moved to
@ -74,6 +43,41 @@ public interface IRestfulServerDefaults {
*/
EncodingEnum getDefaultResponseEncoding();
/**
* @return Returns the server support for ETags (will not be <code>null</code>). Default is
* {@link RestfulServer#DEFAULT_ETAG_SUPPORT}
*/
ETagSupportEnum getETagSupport();
/**
* Gets the {@link FhirContext} associated with this server. For efficient processing, resource providers and plain
* providers should generally use this context if one is needed, as opposed to
* creating their own.
*/
FhirContext getFhirContext();
/**
* Returns the list of interceptors registered against this server
*/
List<IServerInterceptor> getInterceptors();
/**
* Returns the paging provider for this server
*/
IPagingProvider getPagingProvider();
/**
* Should the server "pretty print" responses by default (requesting clients can always override this default by
* supplying an <code>Accept</code> header in the request, or a <code>_pretty</code>
* parameter in the request URL.
* <p>
* The default is <code>false</code>
* </p>
*
* @return Returns the default pretty print setting
*/
boolean isDefaultPrettyPrint();
/**
* @return If <code>true</code> the server will use browser friendly content-types (instead of standard FHIR ones)
* when it detects that the request is coming from a browser
@ -81,4 +85,5 @@ public interface IRestfulServerDefaults {
*/
boolean isUseBrowserFriendlyContentTypes();
}

16
hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2/Dstu2BundleFactory.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.rest.server.provider.dstu2;
import static org.apache.commons.lang3.StringUtils.isBlank;
/*
* #%L
* HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
@ -10,7 +11,7 @@ package ca.uhn.fhir.rest.server.provider.dstu2;
* 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,
@ -62,6 +63,7 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.ResourceReferenceInfo;
public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Dstu2BundleFactory.class);
private Bundle myBundle;
private FhirContext myContext;
@ -223,7 +225,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
entry.getRequest().getMethodElement().setValueAsString(httpVerb.getCode());
}
populateBundleEntryFullUrl(next, entry);
BundleEntrySearchModeEnum searchMode = ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(next);
if (searchMode != null) {
entry.getSearch().getModeElement().setValue(searchMode.getCode());
@ -257,7 +259,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
public void addRootPropertiesToBundle(String theAuthor, String theServerBase, String theCompleteUrl, Integer theTotalResults, BundleTypeEnum theBundleType, IPrimitiveType<Date> theLastUpdated) {
myBase = theServerBase;
if (myBundle.getId().isEmpty()) {
myBundle.setId(UUID.randomUUID().toString());
}
@ -302,7 +304,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
public void initializeBundleFromBundleProvider(IRestfulServer<?> theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl,
boolean thePrettyPrint, int theOffset, Integer theLimit, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes) {
myBase = theServerBase;
int numToReturn;
String searchId = null;
List<IBaseResource> resourceList;
@ -327,7 +329,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
if (numTotalResults != null) {
numToReturn = Math.min(numToReturn, numTotalResults - theOffset);
}
if (numToReturn > 0) {
resourceList = theResult.getResources(theOffset, numToReturn + theOffset);
} else {
@ -340,7 +342,9 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
} else {
if (numTotalResults == null || numTotalResults > numToReturn) {
searchId = pagingProvider.storeResultList(theResult);
Validate.notNull(searchId, "Paging provider returned null searchId");
if (isBlank(searchId)) {
ourLog.info("Found {} results but paging provider did not provide an ID to use for paging", numTotalResults);
}
}
}
}

7
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/rest/server/Dstu3BundleFactory.java
View File

@ -1,5 +1,6 @@
package org.hl7.fhir.dstu3.hapi.rest.server;
import static org.apache.commons.lang3.StringUtils.isBlank;
/*
* #%L
* HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
@ -44,7 +45,7 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.ResourceReferenceInfo;
public class Dstu3BundleFactory implements IVersionSpecificBundleFactory {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Dstu3BundleFactory.class);
private Bundle myBundle;
private FhirContext myContext;
private String myBase;
@ -336,7 +337,9 @@ public class Dstu3BundleFactory implements IVersionSpecificBundleFactory {
} else {
if (numTotalResults == null || numTotalResults > numToReturn) {
searchId = pagingProvider.storeResultList(theResult);
Validate.notNull(searchId, "Paging provider returned null searchId");
if (isBlank(searchId)) {
ourLog.info("Found {} results but paging provider did not provide an ID to use for paging", numTotalResults);
}
}
}
}

60
src/changes/changes.xml
View File

@ -59,7 +59,7 @@
Add configuration to JPA server DaoConfig that allows a maximum
number of search results to be specified. Queries will never return
more than this number, which can be good for avoiding accidental
performance problems in situations where lare queries should not be
performance problems in situations where large queries should not be
needed
</action>
<action type="fix" issue="674">
@ -76,6 +76,64 @@
actually notify listeners of the first 10 subscriptions. Thanks to Jeff Chung
for the pull request!
</action>
<action type="add">
JPA search now uses hibernate ScrollableResults instead of plain JPA List. This
should improve performance over large search results.
</action>
<action type="add">
JPA servers with no paging provider configured, or with a paging provider other than
DatabaseBackedPagingProvider will load all results in a single pass and keep them
in memory. Using this setup is not a good idea unless you know for sure that you
will never have very large queries since it means that all results will be loaded into
memory, but there are valid reasons to need this and it will perform better than
paging to the database in that case. This fix also resolves a NullPointerException
when performing an $everything search. Thanks to Kamal Othman for reporting!
</action>
<action type="fix">
Correct an issue in JPA server on Postgres where searches with a long search URL
were not able to be automatically purged from the database after they were scheduled
for deletion. Thanks to Ravi Kuchi for reporting!
</action>
<action type="add">
Add an optional and configurable hard limit on the total number of meta items
(tags, profiles, and security labels) on an individual resource. The default
is 1000.
</action>
<action type="add">
When executing a search (HTTP GET) as a nested operation in in a transaction or
batch operation, the search now returns a normal page of results with a link to
the next page, like any other search would. Previously the search would return
a small number of results with no paging performed, so this change brings transaction
and batch processing in line with other types of search.
</action>
<action type="add">
JPA server no longer returns an OperationOutcome resource as the first resource
in the Bundle for a response to a batch operation. This behaviour was previously
present, but was not specified in the FHIR specification so it caused confusion and
was inconsistent with behaviour in other servers.
</action>
<action type="fix">
Fix a regression in HAPI FHIR 2.5 JPA server where executing a search in a
transaction or batch operation caused an exception. Thanks to Ravi Kuchi for
reporting!
</action>
<action type="fix">
Correct an issue when processing transactions in JPA server where updates and
creates to resources with tags caused the tags to be created twice in the
database. These duplicates were utomatically filtered upon read so this issue
was not user-visible, but it coule occasionally lead to performance issues
if a resource containing multiple tags was updated many times via
transactions.
</action>
<action type="fix">
JPA server should not allow creation of resources that have a reference to
a resource ID that previously existed but is now deleted. Thanks to Artem
Sopin for reporting!
</action>
<action type="add">
JpaConformanceProvider now has a configuration setting to enable and
disable adding resource counts to the server metadata.
</action>
</release>
<release version="2.5" date="2017-06-08">
<action type="fix">