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Merge remote-tracking branch 'remotes/origin/master' into ja_20190822_1440_infinispan_query_cache 

# Conflicts:
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	src/changes/changes.xml
This commit is contained in:
Ken Stevens 2019-09-04 13:31:00 -04:00
parent d2ae3c24a1 8c6fd9f2d9
commit fa62ab9c9e
42 changed files with 5028 additions and 370 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/MetaUtil.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.util;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2019 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 ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.FhirContext;

12
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/UrlUtil.java
View File

@ -304,13 +304,23 @@ public class UrlUtil {
retVal.setVersionId(id.getVersionIdPart());
return retVal;
}
int parsingStart = 0;
if (url.length() > 2) {
if (url.charAt(0) == '/') {
if (Character.isLetter(url.charAt(1))) {
parsingStart = 1;
}
}
}
if (url.matches("/[a-zA-Z]+\\?.*")) {
url = url.substring(1);
}
int nextStart = 0;
boolean nextIsHistory = false;
for (int idx = 0; idx < url.length(); idx++) {
for (int idx = parsingStart; idx < url.length(); idx++) {
char nextChar = url.charAt(idx);
boolean atEnd = (idx + 1) == url.length();
if (nextChar == '?' || nextChar == '/' || atEnd) {

6
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -127,11 +127,5 @@ ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemU
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.valueSetNotReadyForExpand=ValueSet is not ready for operation $expand; current status: {0} | {1}
ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}
ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum.notExpanded=The ValueSet is waiting to be picked up and pre-expanded by a scheduled task.
ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum.expansionInProgress=The ValueSet has been picked up by a scheduled task and pre-expansion is in progress.
ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum.expanded=The ValueSet has been picked up by a scheduled task and pre-expansion is complete.
ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum.failedToExpand=The ValueSet has been picked up by a scheduled task and pre-expansion has failed.

2
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/UrlUtilTest.java
View File

@ -56,6 +56,8 @@ public class UrlUtilTest {
assertEquals("a=b", UrlUtil.parseUrl("http://hl7.org/fhir/ConceptMap/ussgfht-loincde?a=b").getParams());
assertEquals("a=b", UrlUtil.parseUrl("ConceptMap/ussgfht-loincde?a=b").getParams());
assertEquals("a=b", UrlUtil.parseUrl("/ConceptMap?a=b").getParams());
assertEquals("a=b", UrlUtil.parseUrl("/ConceptMap/ussgfht-loincde?a=b").getParams());
}

57
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ToggleSearchParametersCommand.java Normal file
View File

@ -0,0 +1,57 @@
package ca.uhn.fhir.cli;
/*-
* #%L
* HAPI FHIR - Command Line Client - API
* %%
* Copyright (C) 2014 - 2019 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 ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import java.util.concurrent.ExecutionException;
public class ToggleSearchParametersCommand extends BaseCommand {
@Override
public String getCommandDescription() {
return null;
}
@Override
public String getCommandName() {
return null;
}
@Override
public Options getOptions() {
Options options = new Options();
addFhirVersionOption(options);
addBaseUrlOption(options);
addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
addBasicAuthOption(options);
return options;
}
@Override
public void run(CommandLine theCommandLine) throws ParseException, ExecutionException {
}
}

66
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -16,6 +16,7 @@ import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
@ -27,7 +28,6 @@ import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.util.AddRemoveCount;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
@ -37,7 +37,6 @@ import ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
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.valueset.BundleEntryTransactionMethodEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
@ -149,8 +148,13 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
@Autowired
protected ISearchParamRegistry mySearchParamRegistry;
@Autowired
protected DeleteConflictService myDeleteConflictService;
@Autowired
protected IInterceptorBroadcaster myInterceptorBroadcaster;
@Autowired
ExpungeService myExpungeService;
@Autowired
private DaoConfig myConfig;
@Autowired
private PlatformTransactionManager myPlatformTransactionManager;
@Autowired
@ -167,20 +171,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
private DaoSearchParamSynchronizer myDaoSearchParamSynchronizer;
@Autowired
private SearchBuilderFactory mySearchBuilderFactory;
@Autowired
ExpungeService myExpungeService;
@Autowired
protected DeleteConflictService myDeleteConflictService;
private FhirContext myContext;
private ApplicationContext myApplicationContext;
@Autowired
protected IInterceptorBroadcaster myInterceptorBroadcaster;
@Autowired
public void setContext(FhirContext theContext) {
myContext = theContext;
}
@Override
public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
@ -348,6 +340,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
return myContext;
}
@Autowired
public void setContext(FhirContext theContext) {
myContext = theContext;
}
public FhirContext getContext(FhirVersionEnum theVersion) {
Validate.notNull(theVersion, "theVersion must not be null");
synchronized (ourRetrievalContexts) {
@ -879,7 +876,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
ResourceTable resource = (ResourceTable) theEntity;
version = theEntity.getVersion();
ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theEntity.getId(), version);
((ResourceTable)theEntity).setCurrentVersionEntity(history);
((ResourceTable) theEntity).setCurrentVersionEntity(history);
while (history == null) {
if (version > 1L) {
@ -1457,6 +1454,26 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
return mySearchParamRegistry;
}
@SuppressWarnings("unchecked")
public static String parseContentTextIntoWords(FhirContext theContext, IBaseResource theResource) {
Class<IPrimitiveType<String>> stringType = (Class<IPrimitiveType<String>>) theContext.getElementDefinition("string").getImplementingClass();
StringBuilder retVal = new StringBuilder();
List<IPrimitiveType<String>> childElements = theContext.newTerser().getAllPopulatedChildElementsOfType(theResource, stringType);
for (@SuppressWarnings("rawtypes")
IPrimitiveType<String> nextType : childElements) {
if (stringType.equals(nextType.getClass())) {
String nextValue = nextType.getValueAsString();
if (isNotBlank(nextValue)) {
retVal.append(nextValue.replace("\n", " ").replace("\r", " "));
retVal.append("\n");
}
}
}
return retVal.toString();
}
public static void clearRequestAsProcessingSubRequest(ServletRequestDetails theRequestDetails) {
if (theRequestDetails != null) {
theRequestDetails.getUserData().remove(PROCESSING_SUB_REQUEST);
@ -1469,23 +1486,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
}
public static String parseContentTextIntoWords(FhirContext theContext, IBaseResource theResource) {
StringBuilder retVal = new StringBuilder();
@SuppressWarnings("rawtypes")
List<IPrimitiveType> childElements = theContext.newTerser().getAllPopulatedChildElementsOfType(theResource, IPrimitiveType.class);
for (@SuppressWarnings("rawtypes")
IPrimitiveType nextType : childElements) {
if (nextType instanceof StringDt || nextType.getClass().getSimpleName().equals("StringType")) {
String nextValue = nextType.getValueAsString();
if (isNotBlank(nextValue)) {
retVal.append(nextValue.replace("\n", " ").replace("\r", " "));
retVal.append("\n");
}
}
}
return retVal.toString();
}
public static void populateFullTextFields(final FhirContext theContext, final IBaseResource theResource, ResourceTable theEntity) {
if (theEntity.getDeleted() != null) {
theEntity.setNarrativeTextParsedIntoWords(null);

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
View File

@ -151,7 +151,7 @@ public class DaoConfig {
*/
private boolean myPreExpandValueSetsExperimental = false;
private boolean myFilterParameterEnabled = false;
private StoreMetaSourceInformation myStoreMetaSourceInformation = StoreMetaSourceInformation.SOURCE_URI_AND_REQUEST_ID;
private StoreMetaSourceInformationEnum myStoreMetaSourceInformation = StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code 0}!
*/
@ -1676,10 +1676,10 @@ public class DaoConfig {
* each resource. This adds extra table and index space so it should be disabled if it is not being
* used.
* <p>
* Default is {@link StoreMetaSourceInformation#SOURCE_URI_AND_REQUEST_ID}
* Default is {@link StoreMetaSourceInformationEnum#SOURCE_URI_AND_REQUEST_ID}
* </p>
*/
public StoreMetaSourceInformation getStoreMetaSourceInformation() {
public StoreMetaSourceInformationEnum getStoreMetaSourceInformation() {
return myStoreMetaSourceInformation;
}
@ -1688,15 +1688,15 @@ public class DaoConfig {
* each resource. This adds extra table and index space so it should be disabled if it is not being
* used.
* <p>
* Default is {@link StoreMetaSourceInformation#SOURCE_URI_AND_REQUEST_ID}
* Default is {@link StoreMetaSourceInformationEnum#SOURCE_URI_AND_REQUEST_ID}
* </p>
*/
public void setStoreMetaSourceInformation(StoreMetaSourceInformation theStoreMetaSourceInformation) {
public void setStoreMetaSourceInformation(StoreMetaSourceInformationEnum theStoreMetaSourceInformation) {
Validate.notNull(theStoreMetaSourceInformation, "theStoreMetaSourceInformation must not be null");
myStoreMetaSourceInformation = theStoreMetaSourceInformation;
}
public enum StoreMetaSourceInformation {
public enum StoreMetaSourceInformationEnum {
NONE(false, false),
SOURCE_URI(true, false),
REQUEST_ID(false, true),
@ -1705,7 +1705,7 @@ public class DaoConfig {
private final boolean myStoreSourceUri;
private final boolean myStoreRequestId;
StoreMetaSourceInformation(boolean theStoreSourceUri, boolean theStoreRequestId) {
StoreMetaSourceInformationEnum(boolean theStoreSourceUri, boolean theStoreRequestId) {
myStoreSourceUri = theStoreSourceUri;
myStoreRequestId = theStoreRequestId;
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoRegistry.java
View File

@ -49,9 +49,9 @@ public class DaoRegistry implements ApplicationContextAware, IDaoRegistry {
super();
}
private volatile Map<String, IFhirResourceDao<?>> myResourceNameToResourceDao;
private volatile IFhirSystemDao<?, ?> mySystemDao;
private Set<String> mySupportedResourceTypes;
public void setSupportedResourceTypes(Collection<String> theSupportedResourceTypes) {
@ -156,7 +156,9 @@ public class DaoRegistry implements ApplicationContextAware, IDaoRegistry {
myResourceNameToResourceDao = new HashMap<>();
for (IFhirResourceDao nextResourceDao : theResourceDaos) {
RuntimeResourceDefinition nextResourceDef = myContext.getResourceDefinition(nextResourceDao.getResourceType());
Class resourceType = nextResourceDao.getResourceType();
assert resourceType != null;
RuntimeResourceDefinition nextResourceDef = myContext.getResourceDefinition(resourceType);
if (mySupportedResourceTypes == null || mySupportedResourceTypes.contains(nextResourceDef.getName())) {
myResourceNameToResourceDao.put(nextResourceDef.getName(), nextResourceDao);
}

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

@ -30,6 +30,11 @@ import java.util.Collection;
* #L%
*/
/**
* Note that this interface is not considered a stable interface. While it is possible to build applications
* that use it directly, please be aware that we may modify methods, add methods, or even remove methods from
* time to time, even within minor point releases.
*/
public interface IDao {
MetadataKeyResourcePid RESOURCE_PID = new MetadataKeyResourcePid("RESOURCE_PID");

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

@ -44,8 +44,16 @@ import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import javax.servlet.http.HttpServletResponse;
import java.util.*;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.Set;
/**
* Note that this interface is not considered a stable interface. While it is possible to build applications
* that use it directly, please be aware that we may modify methods, add methods, or even remove methods from
* time to time, even within minor point releases.
*/
public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
void addTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel, RequestDetails theRequest);

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

@ -32,6 +32,10 @@ import java.util.Date;
import java.util.Map;
/**
* Note that this interface is not considered a stable interface. While it is possible to build applications
* that use it directly, please be aware that we may modify methods, add methods, or even remove methods from
* time to time, even within minor point releases.
*
* @param <T> The bundle type
* @param <MT> The Meta datatype type
*/

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

@ -825,7 +825,7 @@ public class SearchBuilder implements ISearchBuilder {
private Predicate addPredicateSource(List<? extends IQueryParameterType> theList, SearchFilterParser.CompareOperation theOperation, RequestDetails theRequest) {
if (myDaoConfig.getStoreMetaSourceInformation() == DaoConfig.StoreMetaSourceInformation.NONE) {
if (myDaoConfig.getStoreMetaSourceInformation() == DaoConfig.StoreMetaSourceInformationEnum.NONE) {
String msg = myContext.getLocalizer().getMessage(SearchBuilder.class, "sourceParamDisabled");
throw new InvalidRequestException(msg);
}
@ -2700,8 +2700,7 @@ public class SearchBuilder implements ISearchBuilder {
private Predicate processFilterParameter(SearchFilterParser.FilterParameter theFilter,
String theResourceName, RequestDetails theRequest) {
RuntimeSearchParam searchParam = mySearchParamRegistry.getActiveSearchParam(theResourceName,
theFilter.getParamPath().getName());
RuntimeSearchParam searchParam = mySearchParamRegistry.getActiveSearchParam(theResourceName, theFilter.getParamPath().getName());
if (searchParam.getName().equals(IAnyResource.SP_RES_ID)) {
if (searchParam.getParamType() == RestSearchParameterTypeEnum.TOKEN) {

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDao.java
View File

@ -40,15 +40,15 @@ public interface ITermValueSetConceptDao extends JpaRepository<TermValueSetConce
@Modifying
void deleteByTermValueSetId(@Param("pid") Long theValueSetId);
@Query("SELECT vsc from TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
Slice<TermValueSetConcept> findByTermValueSetId(Pageable thePage, @Param("pid") Long theValueSetId);
@Query("SELECT vsc from TermValueSetConcept vsc LEFT OUTER JOIN FETCH vsc.myDesignations WHERE vsc.myValueSet.myId = :pid")
Slice<TermValueSetConcept> findByTermValueSetIdAndPreFetchDesignations(Pageable thePage, @Param("pid") Long theValueSetId);
@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
Optional<TermValueSetConcept> findByTermValueSetIdSystemAndCode(@Param("pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.myCode = :codeval")
List<TermValueSetConcept> findOneByValueSetIdAndCode(@Param("resource_pid") Long theValueSetId, @Param("codeval") String theCode);
List<TermValueSetConcept> findByValueSetResourcePidAndCode(@Param("resource_pid") Long theValueSetId, @Param("codeval") String theCode);
@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
List<TermValueSetConcept> findOneByValueSetIdSystemAndCode(@Param("resource_pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
Optional<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(@Param("resource_pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -331,7 +331,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (myDaoConfig.isPreExpandValueSetsExperimental() && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
View File

@ -327,7 +327,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (myDaoConfig.isPreExpandValueSetsExperimental() && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -333,7 +333,7 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (myDaoConfig.isPreExpandValueSetsExperimental() && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);

55
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java
View File

@ -26,6 +26,7 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.annotations.ColumnDefault;
import javax.annotation.Nonnull;
import javax.persistence.*;
@ -69,6 +70,14 @@ public class TermValueSet implements Serializable {
@OneToMany(mappedBy = "myValueSet")
private List<TermValueSetConcept> myConcepts;
@Column(name = "TOTAL_CONCEPTS", nullable = false)
@ColumnDefault("0")
private Long myTotalConcepts;
@Column(name = "TOTAL_CONCEPT_DESIGNATIONS", nullable = false)
@ColumnDefault("0")
private Long myTotalConceptDesignations;
@Enumerated(EnumType.STRING)
@Column(name = "EXPANSION_STATUS", nullable = false, length = MAX_EXPANSION_STATUS_LENGTH)
private TermValueSetPreExpansionStatusEnum myExpansionStatus;
@ -76,6 +85,8 @@ public class TermValueSet implements Serializable {
public TermValueSet() {
super();
myExpansionStatus = TermValueSetPreExpansionStatusEnum.NOT_EXPANDED;
myTotalConcepts = 0L;
myTotalConceptDesignations = 0L;
}
public Long getId() {
@ -120,6 +131,48 @@ public class TermValueSet implements Serializable {
return myConcepts;
}
public Long getTotalConcepts() {
return myTotalConcepts;
}
public TermValueSet setTotalConcepts(Long theTotalConcepts) {
myTotalConcepts = theTotalConcepts;
return this;
}
public TermValueSet decrementTotalConcepts() {
if (myTotalConcepts > 0) {
myTotalConcepts--;
}
return this;
}
public TermValueSet incrementTotalConcepts() {
myTotalConcepts++;
return this;
}
public Long getTotalConceptDesignations() {
return myTotalConceptDesignations;
}
public TermValueSet setTotalConceptDesignations(Long theTotalConceptDesignations) {
myTotalConceptDesignations = theTotalConceptDesignations;
return this;
}
public TermValueSet decrementTotalConceptDesignations() {
if (myTotalConceptDesignations > 0) {
myTotalConceptDesignations--;
}
return this;
}
public TermValueSet incrementTotalConceptDesignations() {
myTotalConceptDesignations++;
return this;
}
public TermValueSetPreExpansionStatusEnum getExpansionStatus() {
return myExpansionStatus;
}
@ -157,6 +210,8 @@ public class TermValueSet implements Serializable {
.append("myResourcePid", myResourcePid)
.append("myName", myName)
.append(myConcepts != null ? ("myConcepts - size=" + myConcepts.size()) : ("myConcepts=(null)"))
.append("myTotalConcepts", myTotalConcepts)
.append("myTotalConceptDesignations", myTotalConceptDesignations)
.append("myExpansionStatus", myExpansionStatus)
.toString();
}

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

@ -29,26 +29,32 @@ import java.util.Map;
* an expanded ValueSet has its included concepts stored in the terminology tables as well.
*/
public enum TermValueSetPreExpansionStatusEnum {
/**
/*
* Sorting agnostic.
*/
NOT_EXPANDED("notExpanded"),
EXPANSION_IN_PROGRESS("expansionInProgress"),
EXPANDED("expanded"),
FAILED_TO_EXPAND("failedToExpand");
NOT_EXPANDED("notExpanded", "The ValueSet is waiting to be picked up and pre-expanded by a scheduled task."),
EXPANSION_IN_PROGRESS("expansionInProgress", "The ValueSet has been picked up by a scheduled task and pre-expansion is in progress."),
EXPANDED("expanded", "The ValueSet has been picked up by a scheduled task and pre-expansion is complete."),
FAILED_TO_EXPAND("failedToExpand", "The ValueSet has been picked up by a scheduled task and pre-expansion has failed.");
private static Map<String, TermValueSetPreExpansionStatusEnum> ourValues;
private String myCode;
private String myDescription;
TermValueSetPreExpansionStatusEnum(String theCode) {
TermValueSetPreExpansionStatusEnum(String theCode, String theDescription) {
myCode = theCode;
myDescription = theDescription;
}
public String getCode() {
return myCode;
}
public String getDescription() {
return myDescription;
}
public static TermValueSetPreExpansionStatusEnum fromCode(String theCode) {
if (ourValues == null) {
HashMap<String, TermValueSetPreExpansionStatusEnum> values = new HashMap<String, TermValueSetPreExpansionStatusEnum>();

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaProvider.java
View File

@ -44,13 +44,19 @@ import java.util.TreeSet;
public class BaseJpaProvider {
public static final String REMOTE_ADDR = "req.remoteAddr";
public static final String REMOTE_UA = "req.userAgent";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaProvider.class);
@Autowired
protected DaoConfig myDaoConfig;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaProvider.class);
private FhirContext myContext;
public BaseJpaProvider() {
super();
}
public void setDaoConfigForUnitTest(DaoConfig theDaoConfig) {
myDaoConfig = theDaoConfig;
}
protected ExpungeOptions createExpungeOptions(IPrimitiveType<? extends Integer> theLimit, IPrimitiveType<? extends Boolean> theExpungeDeletedResources, IPrimitiveType<? extends Boolean> theExpungeOldVersions, IPrimitiveType<? extends Boolean> theExpungeEverything) {
ExpungeOptions options = new ExpungeOptions();
if (theLimit != null && theLimit.getValue() != null) {

203
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -55,6 +56,7 @@ import org.hibernate.search.query.dsl.BooleanJunction;
import org.hibernate.search.query.dsl.QueryBuilder;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.*;
@ -145,6 +147,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Autowired
private PlatformTransactionManager myTransactionMgr;
private IFhirResourceDaoCodeSystem<?, ?, ?> myCodeSystemResourceDao;
private IFhirResourceDaoValueSet<?, ?, ?> myValueSetResourceDao;
private Cache<TranslationQuery, List<TermConceptMapGroupElementTarget>> myTranslationCache;
private Cache<TranslationQuery, List<TermConceptMapGroupElement>> myTranslationWithReverseCache;
private int myFetchSize = DEFAULT_FETCH_SIZE;
@ -370,13 +373,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
myConceptMapDao.deleteTermConceptMapById(existingTermConceptMap.getId());
ourLog.info("Done deleting existing TermConceptMap[{}] and its children.", existingTermConceptMap.getId());
ourLog.info("Flushing...");
myConceptMapGroupElementTargetDao.flush();
myConceptMapGroupElementDao.flush();
myConceptMapGroupDao.flush();
myConceptMapDao.flush();
ourLog.info("Done flushing.");
}
}
@ -398,12 +394,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
myValueSetConceptDao.deleteByTermValueSetId(existingTermValueSet.getId());
myValueSetDao.deleteByTermValueSetId(existingTermValueSet.getId());
ourLog.info("Done deleting existing TermValueSet[{}] and its children.", existingTermValueSet.getId());
ourLog.info("Flushing...");
myValueSetConceptDesignationDao.flush();
myValueSetConceptDao.flush();
myValueSetDao.flush();
ourLog.info("Done flushing.");
}
}
@ -486,7 +476,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
Optional<TermValueSet> optionalTermValueSet;
if (theValueSetToExpand.hasId()) {
optionalTermValueSet = myValueSetDao.findByResourcePid(theValueSetToExpand.getIdElement().getIdPartAsLong());
Long valueSetResourcePid = getValueSetResourcePid(theValueSetToExpand.getIdElement());
optionalTermValueSet = myValueSetDao.findByResourcePid(valueSetResourcePid);
} else if (theValueSetToExpand.hasUrl()) {
optionalTermValueSet = myValueSetDao.findByUrl(theValueSetToExpand.getUrl());
} else {
@ -494,12 +485,18 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
if (!optionalTermValueSet.isPresent()) {
throw new InvalidRequestException("ValueSet is not present in terminology tables: " + theValueSetToExpand.getUrl());
ourLog.warn("ValueSet is not present in terminology tables. Will perform in-memory expansion without parameters. Will schedule this ValueSet for pre-expansion. {}", getValueSetInfo(theValueSetToExpand));
myDeferredValueSets.add(theValueSetToExpand);
return expandValueSet(theValueSetToExpand); // In-memory expansion.
}
TermValueSet termValueSet = optionalTermValueSet.get();
validatePreExpansionStatusOfValueSetOrThrowException(termValueSet.getExpansionStatus());
if (termValueSet.getExpansionStatus() != TermValueSetPreExpansionStatusEnum.EXPANDED) {
ourLog.warn("{} is present in terminology tables but not ready for persistence-backed invocation of operation $expand. Will perform in-memory expansion without parameters. Current status: {} | {}",
getValueSetInfo(theValueSetToExpand), termValueSet.getExpansionStatus().name(), termValueSet.getExpansionStatus().getDescription());
return expandValueSet(theValueSetToExpand); // In-memory expansion.
}
ValueSet.ValueSetExpansionComponent expansionComponent = new ValueSet.ValueSetExpansionComponent();
expansionComponent.setIdentifier(UUID.randomUUID().toString());
@ -514,22 +511,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
return valueSet;
}
private void validatePreExpansionStatusOfValueSetOrThrowException(TermValueSetPreExpansionStatusEnum thePreExpansionStatus) {
if (TermValueSetPreExpansionStatusEnum.EXPANDED != thePreExpansionStatus) {
String statusMsg = myContext.getLocalizer().getMessage(
TermValueSetPreExpansionStatusEnum.class,
thePreExpansionStatus.getCode());
String msg = myContext.getLocalizer().getMessage(
BaseHapiTerminologySvcImpl.class,
"valueSetNotReadyForExpand",
thePreExpansionStatus.name(),
statusMsg);
throw new UnprocessableEntityException(msg);
}
}
private void populateExpansionComponent(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
int total = myValueSetConceptDao.countByTermValueSetId(theTermValueSet.getId());
int total = theTermValueSet.getTotalConcepts().intValue();
theExpansionComponent.setTotal(total);
theExpansionComponent.setOffset(theOffset);
theExpansionComponent.addParameter().setName("offset").setValue(new IntegerType(theOffset));
@ -544,72 +527,58 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
private void expandConcepts(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
int conceptsExpanded = 0;
for (int i = theOffset; i < (theOffset + theCount); i++) {
final int page = i;
Supplier<Slice<TermValueSetConcept>> loader = () -> myValueSetConceptDao.findByTermValueSetId(PageRequest.of(page, 1), theTermValueSet.getId());
int toIndex = theOffset + theCount;
Slice<TermValueSetConcept> slice = myValueSetConceptDao.findByTermValueSetIdAndPreFetchDesignations(SearchCoordinatorSvcImpl.toPage(theOffset, toIndex), theTermValueSet.getId());
if (!slice.hasContent()) {
logConceptsExpanded(theTermValueSet, conceptsExpanded);
return;
}
Slice<TermValueSetConcept> slice = loader.get();
if (!slice.hasContent()) {
break;
}
for (TermValueSetConcept concept : slice.getContent()) {
ValueSet.ValueSetExpansionContainsComponent containsComponent = theExpansionComponent.addContains();
containsComponent.setSystem(concept.getSystem());
containsComponent.setCode(concept.getCode());
containsComponent.setDisplay(concept.getDisplay());
for (TermValueSetConcept concept : slice.getContent()) {
ValueSet.ValueSetExpansionContainsComponent containsComponent = theExpansionComponent.addContains();
containsComponent.setSystem(concept.getSystem());
containsComponent.setCode(concept.getCode());
containsComponent.setDisplay(concept.getDisplay());
// TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to make this optional.
expandDesignations(theTermValueSet, concept, containsComponent);
// TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to make this optional.
expandDesignations(theTermValueSet, concept, containsComponent);
if (++conceptsExpanded % 250 == 0) {
ourLog.info("Have expanded {} concepts in ValueSet[{}]", conceptsExpanded, theTermValueSet.getUrl());
}
}
if (!slice.hasNext()) {
break;
if (++conceptsExpanded % 250 == 0) {
logConceptsExpanded(theTermValueSet, conceptsExpanded);
}
}
if (conceptsExpanded > 0) {
ourLog.info("Have expanded {} concepts in ValueSet[{}]", conceptsExpanded, theTermValueSet.getUrl());
logConceptsExpanded(theTermValueSet, conceptsExpanded);
}
private void logConceptsExpanded(TermValueSet theTermValueSet, int theConceptsExpanded) {
if (theConceptsExpanded > 0) {
ourLog.info("Have expanded {} concepts in ValueSet[{}]", theConceptsExpanded, theTermValueSet.getUrl());
}
}
private void expandDesignations(TermValueSet theValueSet, TermValueSetConcept theConcept, ValueSet.ValueSetExpansionContainsComponent theContainsComponent) {
int designationsExpanded = 0;
int index = 0;
while (true) {
final int page = index++;
Supplier<Slice<TermValueSetConceptDesignation>> loader = () -> myValueSetConceptDesignationDao.findByTermValueSetConceptId(PageRequest.of(page, 1000), theConcept.getId());
for (TermValueSetConceptDesignation designation : theConcept.getDesignations()) {
ValueSet.ConceptReferenceDesignationComponent designationComponent = theContainsComponent.addDesignation();
designationComponent.setLanguage(designation.getLanguage());
designationComponent.setUse(new Coding(
designation.getUseSystem(),
designation.getUseCode(),
designation.getUseDisplay()));
designationComponent.setValue(designation.getValue());
Slice<TermValueSetConceptDesignation> slice = loader.get();
if (!slice.hasContent()) {
break;
}
for (TermValueSetConceptDesignation designation : slice.getContent()) {
ValueSet.ConceptReferenceDesignationComponent designationComponent = theContainsComponent.addDesignation();
designationComponent.setLanguage(designation.getLanguage());
designationComponent.setUse(new Coding(
designation.getUseSystem(),
designation.getUseCode(),
designation.getUseDisplay()));
designationComponent.setValue(designation.getValue());
if (++designationsExpanded % 250 == 0) {
ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", designationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
}
}
if (!slice.hasNext()) {
break;
if (++designationsExpanded % 250 == 0) {
logDesignationsExpanded(theValueSet, theConcept, designationsExpanded);
}
}
if (designationsExpanded > 0) {
ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", designationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
logDesignationsExpanded(theValueSet, theConcept, designationsExpanded);
}
private void logDesignationsExpanded(TermValueSet theValueSet, TermValueSetConcept theConcept, int theDesignationsExpanded) {
if (theDesignationsExpanded > 0) {
ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", theDesignationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
}
}
@ -960,28 +929,49 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
@Override
public boolean isValueSetPreExpandedForCodeValidation(ValueSet theValueSet) {
Long valueSetResourcePid = getValueSetResourcePid(theValueSet.getIdElement());
Optional<TermValueSet> optionalTermValueSet = myValueSetDao.findByResourcePid(valueSetResourcePid);
if (!optionalTermValueSet.isPresent()) {
ourLog.warn("ValueSet is not present in terminology tables. Will perform in-memory code validation. Will schedule this ValueSet for pre-expansion. {}", getValueSetInfo(theValueSet));
myDeferredValueSets.add(theValueSet);
return false;
}
TermValueSet termValueSet = optionalTermValueSet.get();
if (termValueSet.getExpansionStatus() != TermValueSetPreExpansionStatusEnum.EXPANDED) {
ourLog.warn("{} is present in terminology tables but not ready for persistence-backed invocation of operation $validation-code. Will perform in-memory code validation. Current status: {} | {}",
getValueSetInfo(theValueSet), termValueSet.getExpansionStatus().name(), termValueSet.getExpansionStatus().getDescription());
return false;
}
return true;
}
protected ValidateCodeResult validateCodeIsInPreExpandedValueSet(
ValueSet theValueSet, String theSystem, String theCode, String theDisplay, Coding theCoding, CodeableConcept theCodeableConcept) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet.hasId(), "ValueSet.id is required");
Long valueSetId = theValueSet.getIdElement().toUnqualifiedVersionless().getIdPartAsLong();
Long valueSetResourcePid = getValueSetResourcePid(theValueSet.getIdElement());
List<TermValueSetConcept> concepts = new ArrayList<>();
if (isNotBlank(theCode)) {
if (isNotBlank(theSystem)) {
concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, theSystem, theCode);
concepts.addAll(findByValueSetResourcePidSystemAndCode(valueSetResourcePid, theSystem, theCode));
} else {
concepts = myValueSetConceptDao.findOneByValueSetIdAndCode(valueSetId, theCode);
concepts.addAll(myValueSetConceptDao.findByValueSetResourcePidAndCode(valueSetResourcePid, theCode));
}
} else if (theCoding != null) {
if (theCoding.hasSystem() && theCoding.hasCode()) {
concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, theCoding.getSystem(), theCoding.getCode());
concepts.addAll(findByValueSetResourcePidSystemAndCode(valueSetResourcePid, theCoding.getSystem(), theCoding.getCode()));
}
} else if (theCodeableConcept != null){
for (Coding coding : theCodeableConcept.getCoding()) {
if (coding.hasSystem() && coding.hasCode()) {
concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, coding.getSystem(), coding.getCode());
concepts.addAll(findByValueSetResourcePidSystemAndCode(valueSetResourcePid, coding.getSystem(), coding.getCode()));
if (!concepts.isEmpty()) {
break;
}
@ -1002,6 +992,15 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
return null;
}
private List<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(Long theResourcePid, String theSystem, String theCode) {
List<TermValueSetConcept> retVal = new ArrayList<>();
Optional<TermValueSetConcept> optionalTermValueSetConcept = myValueSetConceptDao.findByValueSetResourcePidSystemAndCode(theResourcePid, theSystem, theCode);
if (optionalTermValueSetConcept.isPresent()) {
retVal.add(optionalTermValueSetConcept.get());
}
return retVal;
}
private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
TermConcept nextChild = nextChildLink.getChild();
@ -1134,6 +1133,27 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
protected abstract CodeSystem getCodeSystemFromContext(String theSystem);
private Long getCodeSystemResourcePid(IIdType theIdType) {
return getCodeSystemResourcePid(theIdType, null);
}
private Long getCodeSystemResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
return getResourcePid(myCodeSystemResourceDao, theIdType, theRequestDetails);
}
private Long getValueSetResourcePid(IIdType theIdType) {
return getValueSetResourcePid(theIdType, null);
}
private Long getValueSetResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
return getResourcePid(myValueSetResourceDao, theIdType, theRequestDetails);
}
private Long getResourcePid(IFhirResourceDao<? extends IBaseResource> theResourceDao, IIdType theIdType, RequestDetails theRequestDetails) {
ResourceTable resourceTable = (ResourceTable) theResourceDao.readEntity(theIdType, theRequestDetails);
return resourceTable.getId();
}
private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack, int theTotalConcepts) {
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
return;
@ -1467,6 +1487,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@PostConstruct
public void start() {
myCodeSystemResourceDao = myApplicationContext.getBean(IFhirResourceDaoCodeSystem.class);
myValueSetResourceDao = myApplicationContext.getBean(IFhirResourceDaoValueSet.class);
myTxTemplate = new TransactionTemplate(myTransactionManager);
}
@ -1600,7 +1621,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.COMPLETE || theCodeSystem.getContent() == null || theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", theResourceEntity.getIdDt().getValue(), theCodeSystem.getContentElement().getValueAsString());
Long codeSystemResourcePid = IDao.RESOURCE_PID.get(theCodeSystem);
Long codeSystemResourcePid = getCodeSystemResourcePid(theCodeSystem.getIdElement());
TermCodeSystemVersion persCs = myCodeSystemVersionDao.findCurrentVersionForCodeSystemResourcePid(codeSystemResourcePid);
if (persCs != null) {
ourLog.info("Code system version already exists in database");
@ -1799,7 +1820,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Scheduled(fixedDelay = 600000) // 10 minutes.
@Override
public synchronized void preExpandValueSetToTerminologyTables() {
public synchronized void preExpandDeferredValueSetsToTerminologyTables() {
if (isNotSafeToPreExpandValueSets()) {
ourLog.info("Skipping scheduled pre-expansion of ValueSets while deferred entities are being loaded.");
return;
@ -1827,7 +1848,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
TermValueSet refreshedValueSetToExpand = myValueSetDao.findById(valueSetToExpand.getId()).get();
return getValueSetFromResourceTable(refreshedValueSetToExpand.getResource());
});
expandValueSet(valueSet, new ValueSetConceptAccumulator(valueSetToExpand, myValueSetConceptDao, myValueSetConceptDesignationDao));
expandValueSet(valueSet, new ValueSetConceptAccumulator(valueSetToExpand, myValueSetDao, myValueSetConceptDao, myValueSetConceptDesignationDao));
// We are done with this ValueSet.
txTemplate.execute(t -> {

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java
View File

@ -26,7 +26,9 @@ import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
@ -153,4 +155,9 @@ public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
throw new UnsupportedOperationException();
}
@Override
public boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet) {
throw new UnsupportedOperationException();
}
}

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
View File

@ -9,6 +9,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.util.ValidateUtil;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
@ -364,24 +365,33 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
@Override
public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
Coding coding = (Coding) theCoding;
org.hl7.fhir.r4.model.Coding codingR4 = null;
if (coding != null) {
codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
}
CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
try {
org.hl7.fhir.r4.model.ValueSet valueSetR4;
valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
org.hl7.fhir.r4.model.Coding codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
org.hl7.fhir.r4.model.CodeableConcept codeableConceptR4 = new org.hl7.fhir.r4.model.CodeableConcept();
org.hl7.fhir.r4.model.CodeableConcept codeableConceptR4 = null;
if (codeableConcept != null) {
codeableConceptR4 = new org.hl7.fhir.r4.model.CodeableConcept();
for (Coding nestedCoding : codeableConcept.getCoding()) {
codeableConceptR4.addCoding(new org.hl7.fhir.r4.model.Coding(nestedCoding.getSystem(), nestedCoding.getCode(), nestedCoding.getDisplay()));
}
return super.validateCodeIsInPreExpandedValueSet(valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConceptR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
return super.validateCodeIsInPreExpandedValueSet(valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConceptR4);
}
@Override
public boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
return super.isValueSetPreExpandedForCodeValidation(valueSetR4);
}
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java
View File

@ -284,4 +284,10 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
return super.validateCodeIsInPreExpandedValueSet(valueSet, theSystem, theCode, theDisplay, coding, codeableConcept);
}
@Override
public boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet) {
ValueSet valueSet = (ValueSet) theValueSet;
return super.isValueSetPreExpandedForCodeValidation(valueSet);
}
}

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java
View File

@ -7,11 +7,12 @@ import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.util.ValidateUtil;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander;
@ -291,17 +292,33 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
@Override
public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
org.hl7.fhir.r4.model.ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theValueSet);
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet);
Coding coding = (Coding) theCoding;
org.hl7.fhir.r4.model.Coding codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
org.hl7.fhir.r4.model.Coding codingR4 = null;
if (coding != null) {
codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
}
CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
org.hl7.fhir.r4.model.CodeableConcept codeableConceptR4 = new org.hl7.fhir.r4.model.CodeableConcept();
for (Coding nestedCoding : codeableConcept.getCoding()) {
codeableConceptR4.addCoding(new org.hl7.fhir.r4.model.Coding(nestedCoding.getSystem(), nestedCoding.getCode(), nestedCoding.getDisplay()));
org.hl7.fhir.r4.model.CodeableConcept codeableConceptR4 = null;
if (codeableConcept != null) {
codeableConceptR4 = new org.hl7.fhir.r4.model.CodeableConcept();
for (Coding nestedCoding : codeableConcept.getCoding()) {
codeableConceptR4.addCoding(new org.hl7.fhir.r4.model.Coding(nestedCoding.getSystem(), nestedCoding.getCode(), nestedCoding.getDisplay()));
}
}
return super.validateCodeIsInPreExpandedValueSet(valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConceptR4);
}
@Override
public boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet);
return super.isValueSetPreExpandedForCodeValidation(valueSetR4);
}
}

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

@ -6,7 +6,9 @@ import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import javax.annotation.Nullable;
import java.util.List;
@ -111,10 +113,17 @@ public interface IHapiTerminologySvc {
AtomicInteger applyDeltaCodesystemsRemove(String theSystem, CodeSystem theDelta);
void preExpandValueSetToTerminologyTables();
void preExpandDeferredValueSetsToTerminologyTables();
/**
* Version independent
*/
ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept);
boolean isValueSetPreExpandedForCodeValidation(ValueSet theValueSet);
/**
* Version independent
*/
boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet);
}

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
@ -38,13 +39,15 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValueSetConceptAccumulator.class);
private TermValueSet myTermValueSet;
private ITermValueSetDao myValueSetDao;
private ITermValueSetConceptDao myValueSetConceptDao;
private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
private int myConceptsSaved;
private int myDesignationsSaved;
public ValueSetConceptAccumulator(@Nonnull TermValueSet theTermValueSet, @Nonnull ITermValueSetConceptDao theValueSetConceptDao, @Nonnull ITermValueSetConceptDesignationDao theValueSetConceptDesignationDao) {
public ValueSetConceptAccumulator(@Nonnull TermValueSet theTermValueSet, @Nonnull ITermValueSetDao theValueSetDao, @Nonnull ITermValueSetConceptDao theValueSetConceptDao, @Nonnull ITermValueSetConceptDesignationDao theValueSetConceptDesignationDao) {
myTermValueSet = theTermValueSet;
myValueSetDao = theValueSetDao;
myValueSetConceptDao = theValueSetConceptDao;
myValueSetConceptDesignationDao = theValueSetConceptDesignationDao;
myConceptsSaved = 0;
@ -79,14 +82,12 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
ourLog.info("Excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
for (TermValueSetConceptDesignation designation : concept.getDesignations()) {
myValueSetConceptDesignationDao.deleteById(designation.getId());
myTermValueSet.decrementTotalConceptDesignations();
}
myValueSetConceptDao.deleteById(concept.getId());
myTermValueSet.decrementTotalConcepts();
myValueSetDao.save(myTermValueSet);
ourLog.info("Done excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
ourLog.info("Flushing...");
myValueSetConceptDesignationDao.flush();
myValueSetConceptDao.flush();
ourLog.info("Done flushing.");
}
}
@ -102,6 +103,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
concept.setDisplay(theDisplay);
}
myValueSetConceptDao.save(concept);
myValueSetDao.save(myTermValueSet.incrementTotalConcepts());
if (myConceptsSaved++ % 250 == 0) { // TODO: DM 2019-08-23 - This message never appears in the log. Fix it!
ourLog.info("Have pre-expanded {} concepts in ValueSet[{}]", myConceptsSaved, myTermValueSet.getUrl());
@ -126,6 +128,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
}
designation.setValue(theDesignation.getValue());
myValueSetConceptDesignationDao.save(designation);
myValueSetDao.save(myTermValueSet.incrementTotalConceptDesignations());
if (myDesignationsSaved++ % 250 == 0) { // TODO: DM 2019-08-23 - This message never appears in the log. Fix it!
ourLog.info("Have pre-expanded {} designations for Concept[{}|{}] in ValueSet[{}]", myDesignationsSaved, theConcept.getSystem(), theConcept.getCode(), myTermValueSet.getUrl());

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SourceTest.java
View File

@ -37,7 +37,7 @@ public class FhirResourceDaoDstu3SourceTest extends BaseJpaDstu3Test {
@Before
public void before() {
myDaoConfig.setStoreMetaSourceInformation(DaoConfig.StoreMetaSourceInformation.SOURCE_URI_AND_REQUEST_ID);
myDaoConfig.setStoreMetaSourceInformation(DaoConfig.StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID);
}
@Test
@ -184,7 +184,7 @@ public class FhirResourceDaoDstu3SourceTest extends BaseJpaDstu3Test {
@Test
public void testSourceDisabled() {
myDaoConfig.setStoreMetaSourceInformation(DaoConfig.StoreMetaSourceInformation.NONE);
myDaoConfig.setStoreMetaSourceInformation(DaoConfig.StoreMetaSourceInformationEnum.NONE);
when(mySrd.getRequestId()).thenReturn("0000000000000000");
Patient pt0 = new Patient();

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SourceTest.java
View File

@ -18,8 +18,6 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import java.util.UUID;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.matchesPattern;
import static org.junit.Assert.assertEquals;
@ -37,7 +35,7 @@ public class FhirResourceDaoR4SourceTest extends BaseJpaR4Test {
@Before
public void before() {
myDaoConfig.setStoreMetaSourceInformation(DaoConfig.StoreMetaSourceInformation.SOURCE_URI_AND_REQUEST_ID);
myDaoConfig.setStoreMetaSourceInformation(DaoConfig.StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID);
}
@Test
@ -184,7 +182,7 @@ public class FhirResourceDaoR4SourceTest extends BaseJpaR4Test {
@Test
public void testSourceDisabled() {
myDaoConfig.setStoreMetaSourceInformation(DaoConfig.StoreMetaSourceInformation.NONE);
myDaoConfig.setStoreMetaSourceInformation(DaoConfig.StoreMetaSourceInformationEnum.NONE);
when(mySrd.getRequestId()).thenReturn("0000000000000000");
Patient pt0 = new Patient();

63
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValueSetTest.java
View File

@ -1,14 +1,12 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.*;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.*;
import org.springframework.transaction.annotation.Transactional;
import java.io.IOException;
@ -22,6 +20,10 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
private IIdType myExtensionalVsId;
@After
public void after() {
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
}
@AfterClass
public static void afterClassClearContext() {
@ -124,6 +126,33 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@Test
public void testValidateCodeOperationByResourceIdAndCodeableConceptWithExistingValueSetAndPreExpansionEnabled() {
myDaoConfig.setPreExpandValueSetsExperimental(true);
UriType valueSetIdentifier = null;
IIdType id = myExtensionalVsId;
CodeType code = null;
UriType system = null;
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = new CodeableConcept();
codeableConcept.addCoding().setSystem("http://acme.org").setCode("11378-7");
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
myTermSvc.saveDeferred();
result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@Test
public void testValidateCodeOperationByResourceIdAndCodeAndSystem() {
UriType valueSetIdentifier = null;
@ -138,6 +167,32 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@Test
public void testValidateCodeOperationByResourceIdAndCodeAndSystemWithExistingValueSetAndPreExpansionEnabled() {
myDaoConfig.setPreExpandValueSetsExperimental(true);
UriType valueSetIdentifier = null;
IIdType id = myExtensionalVsId;
CodeType code = new CodeType("11378-7");
UriType system = new UriType("http://acme.org");
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
myTermSvc.saveDeferred();
result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@Test
public void testExpandById() throws IOException {
String resp;

21
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/entity/TermValueSetPreExpansionStatusEnumTest.java
View File

@ -1,21 +0,0 @@
package ca.uhn.fhir.jpa.entity;
import ca.uhn.fhir.i18n.HapiLocalizer;
import org.junit.Test;
import static org.junit.Assert.fail;
public class TermValueSetPreExpansionStatusEnumTest {
@Test
public void testHaveDescriptions() {
HapiLocalizer localizer = new HapiLocalizer();
for (TermValueSetPreExpansionStatusEnum next : TermValueSetPreExpansionStatusEnum.values()) {
String key = "ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum." + next.getCode();
String msg = localizer.getMessage(key);
if (msg.equals(HapiLocalizer.UNKNOWN_I18N_KEY_MESSAGE)) {
fail("No value for key: " + key);
}
}
}
}

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

@ -319,6 +319,7 @@ public class SearchCoordinatorSvcImplTest {
public void testGetPage() {
Pageable page = SearchCoordinatorSvcImpl.toPage(50, 73);
assertEquals(50, page.getOffset());
assertEquals(23, page.getPageSize());
}
@Test

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
View File

@ -600,7 +600,9 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
TermCodeSystem codeSystem = myTermCodeSystemDao.findByResourcePid(codeSystemId.getIdPartAsLong());
ResourceTable resourceTable = (ResourceTable) myCodeSystemDao.readEntity(codeSystemResource.getIdElement(), null);
Long codeSystemResourcePid = resourceTable.getId();
TermCodeSystem codeSystem = myTermCodeSystemDao.findByResourcePid(codeSystemResourcePid);
assertEquals(CS_URL, codeSystem.getCodeSystemUri());
assertEquals("SYSTEM NAME", codeSystem.getName());

1271
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
View File

File diff suppressed because it is too large Load Diff

6
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -90,6 +90,12 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
// Drop HFJ_SEARCH_RESULT foreign keys
version.onTable("HFJ_SEARCH_RESULT").dropForeignKey("FK_SEARCHRES_RES");
version.onTable("HFJ_SEARCH_RESULT").dropForeignKey("FK_SEARCHRES_SEARCH");
// TermValueSet
version.startSectionWithMessage("Processing table: TRM_VALUESET");
Builder.BuilderWithTableName termValueSetTable = version.onTable("TRM_VALUESET");
termValueSetTable.addColumn("TOTAL_CONCEPTS").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetTable.addColumn("TOTAL_CONCEPT_DESIGNATIONS").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
}
protected void init400() {

20
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryProvenanceEntity.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.model.entity;
/*-
* #%L
* HAPI FHIR Model
* %%
* Copyright (C) 2014 - 2019 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 ca.uhn.fhir.rest.api.Constants;
import javax.persistence.*;

16
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ISearchParamExtractor.java
View File

@ -29,20 +29,20 @@ import java.util.Set;
public interface ISearchParamExtractor {
public abstract Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IBaseResource theResource);
Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IBaseResource theResource);
public abstract Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource);
Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource);
public abstract Set<ResourceIndexedSearchParamNumber> extractSearchParamNumber(ResourceTable theEntity, IBaseResource theResource);
Set<ResourceIndexedSearchParamNumber> extractSearchParamNumber(ResourceTable theEntity, IBaseResource theResource);
public abstract Set<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(ResourceTable theEntity, IBaseResource theResource);
Set<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(ResourceTable theEntity, IBaseResource theResource);
public abstract Set<ResourceIndexedSearchParamString> extractSearchParamStrings(ResourceTable theEntity, IBaseResource theResource);
Set<ResourceIndexedSearchParamString> extractSearchParamStrings(ResourceTable theEntity, IBaseResource theResource);
public abstract Set<BaseResourceIndexedSearchParam> extractSearchParamTokens(ResourceTable theEntity, IBaseResource theResource);
Set<BaseResourceIndexedSearchParam> extractSearchParamTokens(ResourceTable theEntity, IBaseResource theResource);
public abstract Set<ResourceIndexedSearchParamUri> extractSearchParamUri(ResourceTable theEntity, IBaseResource theResource);
Set<ResourceIndexedSearchParamUri> extractSearchParamUri(ResourceTable theEntity, IBaseResource theResource);
public abstract List<PathAndRef> extractResourceLinks(IBaseResource theResource, RuntimeSearchParam theNextSpDef);
List<PathAndRef> extractResourceLinks(IBaseResource theResource, RuntimeSearchParam theNextSpDef);
}

18
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4.java
View File

@ -39,6 +39,7 @@ import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.context.IWorkerContext;
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Enumeration;
@ -48,6 +49,7 @@ import org.hl7.fhir.r4.model.Patient.PatientCommunicationComponent;
import org.hl7.fhir.r4.utils.FHIRPathEngine;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.PostConstruct;
import javax.measure.unit.NonSI;
import javax.measure.unit.Unit;
import java.math.BigDecimal;
@ -79,6 +81,8 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
@Autowired
private org.hl7.fhir.r4.hapi.ctx.IValidationSupport myValidationSupport;
private FHIRPathEngine myFhirPathEngine;
/**
* Constructor
*/
@ -91,6 +95,14 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
public SearchParamExtractorR4(ModelConfig theModelConfig, FhirContext theCtx, IValidationSupport theValidationSupport, ISearchParamRegistry theSearchParamRegistry) {
super(theCtx, theSearchParamRegistry);
myValidationSupport = theValidationSupport;
initFhirPath();
}
@PostConstruct
public void initFhirPath() {
IWorkerContext worker = new HapiWorkerContext(getContext(), myValidationSupport);
myFhirPathEngine = new FHIRPathEngine(worker);
myFhirPathEngine.setHostServices(new SearchParamExtractorR4HostServices());
}
private void addQuantity(ResourceTable theEntity, HashSet<ResourceIndexedSearchParamQuantity> retVal, String resourceName, Quantity nextValue) {
@ -751,16 +763,12 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
*/
@Override
protected List<Object> extractValues(String thePaths, IBaseResource theResource) {
IWorkerContext worker = new org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext(getContext(), myValidationSupport);
FHIRPathEngine fp = new FHIRPathEngine(worker);
fp.setHostServices(new SearchParamExtractorR4HostServices());
List<Object> values = new ArrayList<>();
String[] nextPathsSplit = SPLIT_R4.split(thePaths);
for (String nextPath : nextPathsSplit) {
List<Base> allValues;
try {
allValues = fp.evaluate((Base) theResource, nextPath);
allValues = myFhirPathEngine.evaluate((Base) theResource, nextPath);
} catch (FHIRException e) {
String msg = getContext().getLocalizer().getMessage(BaseSearchParamExtractor.class, "failedToExtractPaths", nextPath, e.toString());
throw new InternalErrorException(msg, e);

15
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR5.java
View File

@ -21,12 +21,10 @@ package ca.uhn.fhir.jpa.searchparam.extractor;
*/
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.util.StringNormalizer;
import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import com.google.common.annotations.VisibleForTesting;
@ -39,6 +37,7 @@ import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Enumeration;
@ -48,6 +47,7 @@ import org.hl7.fhir.r5.model.Patient.PatientCommunicationComponent;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.PostConstruct;
import javax.measure.unit.NonSI;
import javax.measure.unit.Unit;
import java.math.BigDecimal;
@ -78,6 +78,7 @@ public class SearchParamExtractorR5 extends BaseSearchParamExtractor implements
@Autowired
private IValidationSupport myValidationSupport;
private FHIRPathEngine myFhirPathEngine;
/**
* Constructor
@ -86,11 +87,11 @@ public class SearchParamExtractorR5 extends BaseSearchParamExtractor implements
super();
}
// This constructor is used by tests
@VisibleForTesting
public SearchParamExtractorR5(ModelConfig theModelConfig, FhirContext theCtx, IValidationSupport theValidationSupport, ISearchParamRegistry theSearchParamRegistry) {
super(theCtx, theSearchParamRegistry);
myValidationSupport = theValidationSupport;
@PostConstruct
public void initFhirPath() {
IWorkerContext worker = new HapiWorkerContext(getContext(), myValidationSupport);
myFhirPathEngine = new FHIRPathEngine(worker);
myFhirPathEngine.setHostServices(new SearchParamExtractorR5HostServices());
}
private void addQuantity(ResourceTable theEntity, HashSet<ResourceIndexedSearchParamQuantity> retVal, String resourceName, Quantity nextValue) {

34
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/module/subscriber/SubscriptionMatchingSubscriber.java
View File

@ -163,14 +163,7 @@ public class SubscriptionMatchingSubscriber implements MessageHandler {
return;
}
ResourceDeliveryJsonMessage wrappedMsg = new ResourceDeliveryJsonMessage(deliveryMsg);
MessageChannel deliveryChannel = nextActiveSubscription.getSubscribableChannel();
if (deliveryChannel != null) {
resourceMatched = true;
deliveryChannel.send(wrappedMsg);
} else {
ourLog.warn("Do not have delivery channel for subscription {}", nextActiveSubscription.getIdElement(myFhirContext));
}
resourceMatched |= sendToDeliveryChannel(nextActiveSubscription, deliveryMsg);
}
if (!resourceMatched) {
@ -181,6 +174,31 @@ public class SubscriptionMatchingSubscriber implements MessageHandler {
}
}
private boolean sendToDeliveryChannel(ActiveSubscription nextActiveSubscription, ResourceDeliveryMessage theDeliveryMsg) {
boolean retval = false;
ResourceDeliveryJsonMessage wrappedMsg = new ResourceDeliveryJsonMessage(theDeliveryMsg);
MessageChannel deliveryChannel = nextActiveSubscription.getSubscribableChannel();
if (deliveryChannel != null) {
retval = true;
trySendToDeliveryChannel(wrappedMsg, deliveryChannel);
} else {
ourLog.warn("Do not have delivery channel for subscription {}", nextActiveSubscription.getIdElement(myFhirContext));
}
return retval;
}
private void trySendToDeliveryChannel(ResourceDeliveryJsonMessage theWrappedMsg, MessageChannel theDeliveryChannel) {
try {
boolean success = theDeliveryChannel.send(theWrappedMsg);
if (!success) {
ourLog.warn("Failed to send message to Delivery Channel.");
}
} catch (RuntimeException e) {
ourLog.error("Failed to send message to Delivery Channel", e);
throw new RuntimeException("Failed to send message to Delivery Channel", e);
}
}
private String getId(ActiveSubscription theActiveSubscription) {
return theActiveSubscription.getIdElement(myFhirContext).toUnqualifiedVersionless().getValue();
}

4
pom.xml
View File

@ -547,6 +547,10 @@
<id>nickrobison-usds</id>
<name>Nick Robison</name>
</developer>
<developer>
<id>fitzoh</id>
<name>Andrew Fitzgerald</name>
</developer>
</developers>
<licenses>

13
src/changes/changes.xml
View File

@ -77,6 +77,15 @@
Two foreign keys have been dropped from the HFJ_SEARCH_RESULT table used by the FHIR search query cache. These
constraints did not add value and caused unneccessary contention when used under high load.
</action>
<action type="change">
An inefficient regex expression in UrlUtil was replaced with a much more efficient hand-written
checker. This regex was causing a noticable performance drop when feeding large numbers of transactions
into the JPA server at the same time (i.e. when loading Synthea data).
</action>
<action type="fix">
The FHIRPath engine used to parse search parameters in the JPA R4/R5 server is now reused across
requests, as it is somewhat expensive to create and is thread safe.
</action>
<action type="add">
It is now possible to submit a PATCH request as a part of a FHIR transaction in DSTU3 (previously this
was only supported in R4+). This is not officially part of the DSTU3 spec, but it can now be performed by
@ -97,6 +106,10 @@
identifies the LOINC CodeSystem in <![CDATA[<code>ValueSet.compose.include.system</code>]]>. This ValueSet
includes all LOINC codes.
</action>
<action type="add" issue="1461">
A note has been added to the downloads page explaning the removal of the hapi-fhir-utilities
module. Thanks to Andrew Fitzgerald for the PR!
</action>
</release>
<release version="4.0.0" date="2019-08-14" description="Igloo">
<action type="add">

3287
tmp2.txt Normal file
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