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Merge remote-tracking branch 'origin/master' into feature_2020_09_02_term_multi_version_support

This commit is contained in:
ianmarshall 2020-09-25 08:54:17 -04:00
parent 404abb2dcb ecc09889cb
commit 6f9874468a
54 changed files with 1048 additions and 452 deletions
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4
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
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@ -1620,7 +1620,7 @@ public enum Pointcut {
* <p>
* Hooks may accept the following parameters:
* <ul>
* <li>ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage - This parameter should not be modified as processing is complete when this hook is invoked.</li>
* <li>ca.uhn.fhir.rest.server.messaging.ResourceOperationMessage - This parameter should not be modified as processing is complete when this hook is invoked.</li>
* <li>ca.uhn.fhir.empi.model.TransactionLogMessages - This parameter is for informational messages provided by the EMPI module during EMPI procesing. .</li>
* </ul>
* </p>
@ -1628,7 +1628,7 @@ public enum Pointcut {
* Hooks should return <code>void</code>.
* </p>
*/
EMPI_AFTER_PERSISTED_RESOURCE_CHECKED(void.class, "ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage", "ca.uhn.fhir.rest.server.TransactionLogMessages"),
EMPI_AFTER_PERSISTED_RESOURCE_CHECKED(void.class, "ca.uhn.fhir.rest.server.messaging.ResourceOperationMessage", "ca.uhn.fhir.rest.server.TransactionLogMessages"),
/**
* <b>Performance Tracing Hook:</b>

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2083-search-coordinator-threads-use-threadpoolexecutor.yaml Normal file
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@ -0,0 +1,6 @@
---
type: add
issue: 2083
title: "The JPA search coordinator will now use worker threads sourced from a ThreadPoolTaskExecutor, in order to simplify
the addition of decorators to those threads. Thanks to Tue Toft Nørgård for the pull requets!"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2087-limit-transaction-size-config.yaml Normal file
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@ -0,0 +1,5 @@
---
type: add
issue: 2087
title: "Added new DaoConfig parameter called maximumTransactionBundleSize that if not-null will throw a
PayloadTooLarge exception when the number of resources in a transaction bundle exceeds this size."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2097-avoid-crash-on-double-chained-date.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 2097
title: "A crash in the JPA server was fixed when performing a search containined two chained search parameters to
date target types."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2099-dont-install-draft-package-contents.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 2099
title: "When using an NPM package spec in STORE_AND_INSTALL mode, conformance resources will only be stored if they
have a status of `active`. This fixes a bug wgere installing the US Core IG caused searches to stop working due to
draft Search Parameters."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2099-dont-override-sps-with-draft.yaml Normal file
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@ -0,0 +1,6 @@
---
type: add
issue: 2099
title: "Stored SearchParameter resources with a status of DRAFT will no longer override and disable existing built-in
search parameters. This is done in order to avoid issues caused by uploading NPM packages such as US Core that
contain a large number of draft parameters."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2101-avoid-dupe-params-in-cs.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 2101
title: "In some circumstances when using a Plain Server, the generated CapabilityStatement could have duplciate
Search Parameter definitions. This has been corrected."

28
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
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@ -80,6 +80,7 @@ public class DaoConfig {
* @see #setMaximumSearchResultCountInTransaction(Integer)
*/
private static final Integer DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = null;
private static final Integer DEFAULT_MAXIMUM_TRANSACTION_BUNDLE_SIZE = null;
private static final Logger ourLog = LoggerFactory.getLogger(DaoConfig.class);
private static final int DEFAULT_EXPUNGE_BATCH_SIZE = 800;
private IndexEnabledEnum myIndexMissingFieldsEnabled = IndexEnabledEnum.DISABLED;
@ -126,6 +127,8 @@ public class DaoConfig {
private boolean myIndexContainedResources = true;
private int myMaximumExpansionSize = DEFAULT_MAX_EXPANSION_SIZE;
private Integer myMaximumSearchResultCountInTransaction = DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION;
private Integer myMaximumTransactionBundleSize = DEFAULT_MAXIMUM_TRANSACTION_BUNDLE_SIZE;
private ResourceEncodingEnum myResourceEncoding = ResourceEncodingEnum.JSONC;
/**
* update setter javadoc if default changes
@ -655,6 +658,31 @@ public class DaoConfig {
myMaximumSearchResultCountInTransaction = theMaximumSearchResultCountInTransaction;
}
/**
* Specifies the maximum number of resources permitted within a single transaction bundle.
* If a transaction bundle is submitted with more than this number of resources, it will be
* rejected with a PayloadTooLarge exception.
* <p>
* The default value is <code>null</code>, which means that there is no limit.
* </p>
*/
public Integer getMaximumTransactionBundleSize() {
return myMaximumTransactionBundleSize;
}
/**
* Specifies the maximum number of resources permitted within a single transaction bundle.
* If a transaction bundle is submitted with more than this number of resources, it will be
* rejected with a PayloadTooLarge exception.
* <p>
* The default value is <code>null</code>, which means that there is no limit.
* </p>
*/
public DaoConfig setMaximumTransactionBundleSize(Integer theMaximumTransactionBundleSize) {
myMaximumTransactionBundleSize = theMaximumTransactionBundleSize;
return this;
}
/**
* This setting controls the number of threads allocated to resource reindexing
* (which is only ever used if SearchParameters change, or a manual reindex is

15
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/model/DaoMethodOutcome.java
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@ -28,6 +28,7 @@ public class DaoMethodOutcome extends MethodOutcome {
private IBasePersistedResource myEntity;
private IBaseResource myPreviousResource;
private boolean myNop;
/**
* Constructor
@ -36,6 +37,20 @@ public class DaoMethodOutcome extends MethodOutcome {
super();
}
/**
* Was this a NO-OP - Typically because of an update to a resource that already matched the contents provided
*/
public boolean isNop() {
return myNop;
}
/**
* Was this a NO-OP - Typically because of an update to a resource that already matched the contents provided
*/
public void setNop(boolean theNop) {
myNop = theNop;
}
public IBasePersistedResource getEntity() {
return myEntity;
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -262,6 +262,14 @@ public abstract class BaseConfig {
return new DatabaseSearchResultCacheSvcImpl();
}
@Bean
public ThreadPoolTaskExecutor searchCoordinatorThreadFactory() {
final ThreadPoolTaskExecutor threadPoolTaskExecutor = new ThreadPoolTaskExecutor();
threadPoolTaskExecutor.setThreadNamePrefix("search_coord_");
threadPoolTaskExecutor.initialize();
return threadPoolTaskExecutor;
}
@Bean
public TaskScheduler taskScheduler() {
ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();

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

@ -29,6 +29,7 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
@ -128,6 +129,12 @@ public abstract class BaseStorageDao {
protected DaoMethodOutcome toMethodOutcome(RequestDetails theRequest, @Nonnull final IBasePersistedResource theEntity, @Nonnull IBaseResource theResource) {
DaoMethodOutcome outcome = new DaoMethodOutcome();
if (theEntity instanceof ResourceTable) {
if (((ResourceTable) theEntity).isUnchangedInCurrentOperation()) {
outcome.setNop(true);
}
}
IIdType id = null;
if (theResource.getIdElement().getValue() != null) {
id = theResource.getIdElement();

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
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@ -25,6 +25,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IJpaDao;
@ -54,6 +55,7 @@ import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.NotModifiedException;
import ca.uhn.fhir.rest.server.exceptions.PayloadTooLargeException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
import ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding;
@ -124,6 +126,8 @@ public abstract class BaseTransactionProcessor {
private MatchResourceUrlService myMatchResourceUrlService;
@Autowired
private HapiTransactionService myHapiTransactionService;
@Autowired
private DaoConfig myDaoConfig;
@PostConstruct
public void start() {
@ -342,7 +346,15 @@ public abstract class BaseTransactionProcessor {
throw new InvalidRequestException("Unable to process transaction where incoming Bundle.type = " + transactionType);
}
ourLog.debug("Beginning {} with {} resources", theActionName, myVersionAdapter.getEntries(theRequest).size());
int numberOfEntries = myVersionAdapter.getEntries(theRequest).size();
if (myDaoConfig.getMaximumTransactionBundleSize() != null && numberOfEntries > myDaoConfig.getMaximumTransactionBundleSize()) {
throw new PayloadTooLargeException("Transaction Bundle Too large. Transaction bundle contains " +
numberOfEntries +
" which exceedes the maximum permitted transaction bundle size of " + myDaoConfig.getMaximumTransactionBundleSize());
}
ourLog.debug("Beginning {} with {} resources", theActionName, numberOfEntries);
final TransactionDetails transactionDetails = new TransactionDetails();
final StopWatch transactionStopWatch = new StopWatch();
@ -350,7 +362,7 @@ public abstract class BaseTransactionProcessor {
List<IBase> requestEntries = myVersionAdapter.getEntries(theRequest);
// Do all entries have a verb?
for (int i = 0; i < myVersionAdapter.getEntries(theRequest).size(); i++) {
for (int i = 0; i < numberOfEntries; i++) {
IBase nextReqEntry = requestEntries.get(i);
String verb = myVersionAdapter.getEntryRequestVerb(myContext, nextReqEntry);
if (verb == null || !isValidVerb(verb)) {

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderDate.java
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@ -49,7 +49,6 @@ import java.util.Map;
public class PredicateBuilderDate extends BasePredicateBuilder implements IPredicateBuilder {
private static final Logger ourLog = LoggerFactory.getLogger(PredicateBuilderDate.class);
private Map<String, From<?, ResourceIndexedSearchParamDate>> myJoinMap;
PredicateBuilderDate(SearchBuilder theSearchBuilder) {
super(theSearchBuilder);
@ -64,15 +63,15 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
String paramName = theSearchParam.getName();
boolean newJoin = false;
if (myJoinMap == null) {
myJoinMap = new HashMap<>();
}
Map<String, From<?, ResourceIndexedSearchParamDate>> joinMap = myQueryStack.getJoinMap();
String key = theResourceName + " " + paramName;
From<?, ResourceIndexedSearchParamDate> join = myJoinMap.get(key);
From<?, ResourceIndexedSearchParamDate> join = joinMap.get(key);
if (join == null) {
join = myQueryStack.createJoin(SearchBuilderJoinEnum.DATE, paramName);
myJoinMap.put(key, join);
joinMap.put(key, join);
newJoin = true;
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootEntry.java
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@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.dao.predicate.querystack;
import ca.uhn.fhir.jpa.dao.predicate.IndexJoins;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinEnum;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinKey;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
import javax.persistence.criteria.AbstractQuery;
import javax.persistence.criteria.CriteriaBuilder;
@ -37,7 +38,9 @@ import javax.persistence.criteria.Subquery;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
abstract class QueryRootEntry {
@ -45,6 +48,7 @@ abstract class QueryRootEntry {
private final IndexJoins myIndexJoins = new IndexJoins();
private final CriteriaBuilder myCriteriaBuilder;
private boolean myHasImplicitTypeSelection;
private Map<String, From<?, ResourceIndexedSearchParamDate>> myJoinMap;
QueryRootEntry(CriteriaBuilder theCriteriaBuilder) {
myCriteriaBuilder = theCriteriaBuilder;
@ -108,6 +112,15 @@ abstract class QueryRootEntry {
return getQueryRoot();
}
public Map<String, From<?, ResourceIndexedSearchParamDate>> getJoinMap() {
Map<String, From<?, ResourceIndexedSearchParamDate>> retVal = myJoinMap;
if (retVal==null) {
retVal = new HashMap<>();
myJoinMap = retVal;
}
return retVal;
}
abstract void orderBy(List<Order> theOrders);
abstract Expression<Date> getLastUpdatedColumn();

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryStack.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.dao.predicate.querystack;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinEnum;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinKey;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import org.apache.commons.lang3.Validate;
@ -38,6 +39,7 @@ import javax.persistence.criteria.Root;
import javax.persistence.criteria.Subquery;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Stack;
@ -281,4 +283,9 @@ public class QueryStack {
public Predicate addNeverMatchingPredicate() {
return top().addNeverMatchingPredicate();
}
public Map<String, From<?, ResourceIndexedSearchParamDate>> getJoinMap() {
return top().getJoinMap();
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImpl.java
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@ -26,6 +26,7 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -35,7 +36,6 @@ import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.SearchParameterUtil;
import com.google.common.annotations.VisibleForTesting;
@ -208,6 +208,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
count[i] = resources.size();
for (IBaseResource next : resources) {
try {
next = isStructureDefinitionWithoutSnapshot(next) ? generateSnapshot(next) : next;
create(next, theOutcome);
@ -215,6 +216,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
ourLog.warn("Failed to upload resource of type {} with ID {} - Error: {}", myFhirContext.getResourceType(next), next.getIdElement().getValue(), e.toString());
throw new ImplementationGuideInstallationException(String.format("Error installing IG %s#%s: %s", name, version, e.toString()), e);
}
}
}
@ -321,10 +323,11 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
} else {
ourLog.info("Updating existing resource matching {}", map.toNormalizedQueryString(myFhirContext));
theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
theResource.setId(searchResult.getResources(0,1).get(0).getIdElement().toUnqualifiedVersionless());
dao.update(theResource);
theResource.setId(searchResult.getResources(0, 1).get(0).getIdElement().toUnqualifiedVersionless());
DaoMethodOutcome outcome = dao.update(theResource);
if (!outcome.isNop()) {
theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
}
}
}
@ -349,6 +352,13 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
}
}
List<IPrimitiveType> statusTypes = myFhirContext.newFhirPath().evaluate(theResource, "status", IPrimitiveType.class);
if (statusTypes.size() > 0) {
if (!statusTypes.get(0).getValueAsString().equals("active")) {
return false;
}
}
return true;
}

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

@ -37,7 +37,6 @@ import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchInclude;
import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
@ -54,6 +53,7 @@ import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.IPagingProvider;
import ca.uhn.fhir.rest.server.SimpleBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
@ -80,7 +80,7 @@ import org.springframework.data.domain.Sort;
import org.springframework.orm.jpa.JpaDialect;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.vendor.HibernateJpaDialect;
import org.springframework.scheduling.concurrent.CustomizableThreadFactory;
import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import org.springframework.stereotype.Component;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
@ -111,7 +111,6 @@ 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 static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
@ -161,9 +160,9 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
/**
* Constructor
*/
public SearchCoordinatorSvcImpl() {
CustomizableThreadFactory threadFactory = new CustomizableThreadFactory("search_coord_");
myExecutor = Executors.newCachedThreadPool(threadFactory);
@Autowired
public SearchCoordinatorSvcImpl(ThreadPoolTaskExecutor searchCoordinatorThreadFactory) {
myExecutor = searchCoordinatorThreadFactory.getThreadPoolExecutor();
}
@VisibleForTesting

46
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3SearchTest.java
View File

@ -1,46 +0,0 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
import ca.uhn.fhir.util.TestUtil;
public class FhirSystemDaoDstu3SearchTest extends BaseJpaDstu3SystemTest {
@Test
public void testSearchByParans() {
// code to come.. just here to prevent a failure
}
/*//@formatter:off
* [ERROR] Search parameter action has conflicting types token and reference
* [ERROR] Search parameter source has conflicting types token and reference
* [ERROR] Search parameter plan has conflicting types reference and token
* [ERROR] Search parameter version has conflicting types token and string
* [ERROR] Search parameter source has conflicting types reference and uri
* [ERROR] Search parameter location has conflicting types reference and uri
* [ERROR] Search parameter title has conflicting types string and token
* [ERROR] Search parameter manufacturer has conflicting types string and reference
* [ERROR] Search parameter address has conflicting types token and string
* [ERROR] Search parameter source has conflicting types reference and string
* [ERROR] Search parameter destination has conflicting types reference and string
* [ERROR] Search parameter responsible has conflicting types reference and string
* [ERROR] Search parameter value has conflicting types token and string
* [ERROR] Search parameter address has conflicting types token and string
* [ERROR] Search parameter address has conflicting types token and string
* [ERROR] Search parameter address has conflicting types token and string
* [ERROR] Search parameter address has conflicting types token and string
* [ERROR] Search parameter action has conflicting types reference and token
* [ERROR] Search parameter version has conflicting types token and string
* [ERROR] Search parameter address has conflicting types token and string
* [ERROR] Search parameter base has conflicting types reference and token
* [ERROR] Search parameter target has conflicting types reference and token
* [ERROR] Search parameter base has conflicting types reference and uri
* [ERROR] Search parameter contact has conflicting types string and token
* [ERROR] Search parameter substance has conflicting types token and reference
* [ERROR] Search parameter provider has conflicting types reference and token
* [ERROR] Search parameter system has conflicting types token and uri
* [ERROR] Search parameter reference has conflicting types reference and uri
* //@formatter:off
*/
}

102
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java
View File

@ -2888,108 +2888,6 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
assertEquals(1, found.size().intValue());
}
//
//
// /**
// * Issue #55
// */
// @Test
// public void testTransactionWithCidIds() throws Exception {
// Bundle request = new Bundle();
//
// Patient p1 = new Patient();
// p1.setId("cid:patient1");
// p1.addIdentifier().setSystem("system").setValue("testTransactionWithCidIds01");
// res.add(p1);
//
// Observation o1 = new Observation();
// o1.setId("cid:observation1");
// o1.getIdentifier().setSystem("system").setValue("testTransactionWithCidIds02");
// o1.setSubject(new Reference("Patient/cid:patient1"));
// res.add(o1);
//
// Observation o2 = new Observation();
// o2.setId("cid:observation2");
// o2.getIdentifier().setSystem("system").setValue("testTransactionWithCidIds03");
// o2.setSubject(new Reference("Patient/cid:patient1"));
// res.add(o2);
//
// ourSystemDao.transaction(res);
//
// assertTrue(p1.getId().getValue(), p1.getId().getIdPart().matches("^[0-9]+$"));
// assertTrue(o1.getId().getValue(), o1.getId().getIdPart().matches("^[0-9]+$"));
// assertTrue(o2.getId().getValue(), o2.getId().getIdPart().matches("^[0-9]+$"));
//
// assertThat(o1.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
// assertThat(o2.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
//
// }
//
// @Test
// public void testTransactionWithDelete() throws Exception {
// Bundle request = new Bundle();
//
// /*
// * Create 3
// */
//
// List<IResource> res;
// res = new ArrayList<IResource>();
//
// Patient p1 = new Patient();
// p1.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
// res.add(p1);
//
// Patient p2 = new Patient();
// p2.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
// res.add(p2);
//
// Patient p3 = new Patient();
// p3.addIdentifier().setSystem("urn:system").setValue("testTransactionWithDelete");
// res.add(p3);
//
// ourSystemDao.transaction(res);
//
// /*
// * Verify
// */
//
// IBundleProvider results = ourPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam("urn:system",
// "testTransactionWithDelete"));
// assertEquals(3, results.size());
//
// /*
// * Now delete 2
// */
//
// request = new Bundle();
// res = new ArrayList<IResource>();
// List<IResource> existing = results.getResources(0, 3);
//
// p1 = new Patient();
// p1.setId(existing.get(0).getId());
// ResourceMetadataKeyEnum.DELETED_AT.put(p1, InstantDt.withCurrentTime());
// res.add(p1);
//
// p2 = new Patient();
// p2.setId(existing.get(1).getId());
// ResourceMetadataKeyEnum.DELETED_AT.put(p2, InstantDt.withCurrentTime());
// res.add(p2);
//
// ourSystemDao.transaction(res);
//
// /*
// * Verify
// */
//
// IBundleProvider results2 = ourPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam("urn:system",
// "testTransactionWithDelete"));
// assertEquals(1, results2.size());
// List<IResource> existing2 = results2.getResources(0, 1);
// assertEquals(existing2.get(0).getId(), existing.get(2).getId());
//
// }
@Test
public void testTransactionWithRelativeOidIds() {
Bundle res = new Bundle();

78
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoTransactionDstu3Test.java Normal file
View File

@ -0,0 +1,78 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.rest.server.exceptions.PayloadTooLargeException;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
import org.hl7.fhir.dstu3.model.Observation;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
public class FhirSystemDaoTransactionDstu3Test extends BaseJpaDstu3SystemTest {
public static final int TEST_MAXIMUM_TRANSACTION_BUNDLE_SIZE = 5;
@AfterEach
public void after() {
myDaoConfig.setMaximumTransactionBundleSize(new DaoConfig().getMaximumTransactionBundleSize());
}
@BeforeEach
public void beforeDisableResultReuse() {
myDaoConfig.setMaximumTransactionBundleSize(TEST_MAXIMUM_TRANSACTION_BUNDLE_SIZE);
}
private Bundle createInputTransactionWithSize(int theSize) {
Bundle retval = new Bundle();
retval.setType(BundleType.TRANSACTION);
for (int i = 0; i < theSize; ++i) {
Observation obs = new Observation();
obs.setStatus(Observation.ObservationStatus.FINAL);
retval
.addEntry()
.setFullUrl("urn:uuid:000" + i)
.setResource(obs)
.getRequest()
.setMethod(HTTPVerb.POST);
}
return retval;
}
@Test
public void testTransactionTooBig() {
Bundle bundle = createInputTransactionWithSize(TEST_MAXIMUM_TRANSACTION_BUNDLE_SIZE + 1);
try {
mySystemDao.transaction(null, bundle);
fail();
} catch (PayloadTooLargeException e) {
assertThat(e.getMessage(), containsString("Transaction Bundle Too large. Transaction bundle contains " +
(TEST_MAXIMUM_TRANSACTION_BUNDLE_SIZE + 1) +
" which exceedes the maximum permitted transaction bundle size of " + TEST_MAXIMUM_TRANSACTION_BUNDLE_SIZE));
}
}
@Test
public void testTransactionSmallEnough() {
testTransactionBundleSucceedsWithSize(TEST_MAXIMUM_TRANSACTION_BUNDLE_SIZE);
testTransactionBundleSucceedsWithSize(TEST_MAXIMUM_TRANSACTION_BUNDLE_SIZE - 1);
testTransactionBundleSucceedsWithSize(1);
}
private void testTransactionBundleSucceedsWithSize(int theSize) {
Bundle bundle = createInputTransactionWithSize(theSize);
Bundle response = mySystemDao.transaction(null, bundle);
assertEquals(theSize, response.getEntry().size());
assertEquals("201 Created", response.getEntry().get(0).getResponse().getStatus());
assertEquals("201 Created", response.getEntry().get(theSize - 1).getResponse().getStatus());
}
}

19
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java
View File

@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
@ -462,6 +463,24 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
}
@Test
public void testBuiltInSearchParameterNotReplacedByDraftSearchParameter() {
myModelConfig.setDefaultSearchParamsCanBeOverridden(true);
SearchParameter memberSp = new SearchParameter();
memberSp.setCode("family");
memberSp.addBase("Patient");
memberSp.setType(Enumerations.SearchParamType.STRING);
memberSp.setExpression("Patient.name.family");
memberSp.setStatus(Enumerations.PublicationStatus.DRAFT);
mySearchParameterDao.create(memberSp, mySrd);
mySearchParamRegistry.forceRefresh();
RuntimeSearchParam sp = mySearchParamRegistry.getActiveSearchParam("Patient", "family");
assertEquals(RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE, sp.getStatus());
}
@Test

29
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -72,6 +72,7 @@ import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Communication;
import org.hl7.fhir.r4.model.CommunicationRequest;
import org.hl7.fhir.r4.model.Condition;
import org.hl7.fhir.r4.model.ContactPoint.ContactPointSystem;
@ -5080,6 +5081,34 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertThat(toUnqualifiedVersionlessIdValues(outcome), contains(crId));
}
@Test
public void testSearchWithTwoChainedDates() {
// Matches
Encounter e1 = new Encounter();
e1.setPeriod(new Period().setStartElement(new DateTimeType("2020-09-14T12:00:00Z")).setEndElement(new DateTimeType("2020-09-14T12:00:00Z")));
String e1Id = myEncounterDao.create(e1).getId().toUnqualifiedVersionless().getValue();
Communication c1 = new Communication();
c1.getEncounter().setReference(e1Id);
myCommunicationDao.create(c1);
// Doesn't match
Encounter e2 = new Encounter();
e2.setPeriod(new Period().setStartElement(new DateTimeType("2020-02-14T12:00:00Z")).setEndElement(new DateTimeType("2020-02-14T12:00:00Z")));
String e2Id = myEncounterDao.create(e2).getId().toUnqualifiedVersionless().getValue();
Communication c2 = new Communication();
c2.getEncounter().setReference(e2Id);
myCommunicationDao.create(c2);
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add(Communication.SP_ENCOUNTER, new ReferenceParam("ge2020-09-14").setChain("date"));
map.add(Communication.SP_ENCOUNTER, new ReferenceParam("le2020-09-15").setChain("date"));
IBundleProvider outcome = myCommunicationDao.search(map);
assertEquals(1, outcome.sizeOrThrowNpe());
}
@Test
public void testCircularReferencesDontBreakRevIncludes() {

45
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmTestR4.java
View File

@ -49,6 +49,7 @@ import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
@ -114,6 +115,20 @@ public class NpmTestR4 extends BaseJpaR4Test {
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.us.core").setVersion("3.1.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL).setFetchDependencies(true);
igInstaller.install(spec);
runInTransaction(()->{
SearchParameterMap map = SearchParameterMap.newSynchronous(SearchParameter.SP_BASE, new TokenParam("NamingSystem"));
IBundleProvider outcome = mySearchParameterDao.search(map);
List<IBaseResource> resources = outcome.getResources(0, outcome.sizeOrThrowNpe());
for (int i = 0; i < resources.size(); i++) {
ourLog.info("**************************************************************************");
ourLog.info("**************************************************************************");
ourLog.info("Res " + i);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resources.get(i)));
}
});
igInstaller.install(spec);
}
@ -162,7 +177,8 @@ public class NpmTestR4 extends BaseJpaR4Test {
myFakeNpmServlet.myResponses.put("/hl7.fhir.uv.shorthand/0.12.0", bytes);
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.12.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
igInstaller.install(spec);
PackageInstallOutcomeJson outcome = igInstaller.install(spec);
assertEquals(1, outcome.getResourcesInstalled().get("CodeSystem"));
// Be sure no further communication with the server
JettyUtil.closeServer(myServer);
@ -215,11 +231,25 @@ public class NpmTestR4 extends BaseJpaR4Test {
runInTransaction(() -> {
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add(StructureDefinition.SP_URL, new UriParam("http://hl7.org/fhir/uv/shorthand/CodeSystem/shorthand-code-system"));
IBundleProvider outcome = myCodeSystemDao.search(map);
assertEquals(1, outcome.sizeOrThrowNpe());
IBundleProvider result = myCodeSystemDao.search(map);
assertEquals(1, result.sizeOrThrowNpe());
});
}
@Test
public void testInstallR4Package_DraftResourcesNotInstalled() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
byte[] bytes = loadClasspathBytes("/packages/test-draft-sample.tgz");
myFakeNpmServlet.myResponses.put("/hl7.fhir.uv.shorthand/0.11.1", bytes);
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.11.1").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
PackageInstallOutcomeJson outcome = igInstaller.install(spec);
assertEquals(0, outcome.getResourcesInstalled().size(), outcome.getResourcesInstalled().toString());
}
@Test
public void testInstallR4Package_Twice() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
@ -236,6 +266,11 @@ public class NpmTestR4 extends BaseJpaR4Test {
igInstaller.install(spec);
outcome = igInstaller.install(spec);
assertEquals(null, outcome.getResourcesInstalled().get("CodeSystem"));
// Ensure that we loaded the contents
IBundleProvider searchResult = myCodeSystemDao.search(SearchParameterMap.newSynchronous("url", new UriParam("http://hl7.org/fhir/uv/shorthand/CodeSystem/shorthand-code-system")));
assertEquals(1, searchResult.sizeOrThrowNpe());
}
@ -257,9 +292,6 @@ public class NpmTestR4 extends BaseJpaR4Test {
assertEquals(null, pkg.description());
assertEquals("UK.Core.r4", pkg.name());
// Ensure that we loaded the contents
IBundleProvider searchResult = myStructureDefinitionDao.search(SearchParameterMap.newSynchronous("url", new UriParam("https://fhir.nhs.uk/R4/StructureDefinition/UKCore-Patient")));
assertEquals(1, searchResult.sizeOrThrowNpe());
}
@Test
@ -384,6 +416,7 @@ public class NpmTestR4 extends BaseJpaR4Test {
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.12.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_ONLY);
igInstaller.install(spec);
runInTransaction(() -> {
NpmPackageVersionEntity versionEntity = myPackageVersionDao.findByPackageIdAndVersion("hl7.fhir.uv.shorthand", "0.12.0").orElseThrow(() -> new IllegalArgumentException());
assertEquals(true, versionEntity.isCurrentVersion());

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

@ -7,6 +7,7 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.config.dstu3.BaseDstu3Config;
import ca.uhn.fhir.jpa.dao.IResultIterator;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilder;
@ -124,7 +125,7 @@ public class SearchCoordinatorSvcImplTest {
myCurrentSearch = null;
mySvc = new SearchCoordinatorSvcImpl();
mySvc = new SearchCoordinatorSvcImpl(new BaseDstu3Config().searchCoordinatorThreadFactory());
mySvc.setEntityManagerForUnitTest(myEntityManager);
mySvc.setTransactionManagerForUnitTest(myTxManager);
mySvc.setContextForUnitTest(ourCtx);

BIN
hapi-fhir-jpaserver-base/src/test/resources/packages/test-draft-sample.tgz Normal file
View File

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9
hapi-fhir-jpaserver-empi/src/main/java/ca/uhn/fhir/jpa/empi/broker/EmpiMessageHandler.java
View File

@ -33,6 +33,7 @@ import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedJsonMessage;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
import ca.uhn.fhir.rest.server.TransactionLogMessages;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.messaging.ResourceOperationMessage;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
@ -93,16 +94,20 @@ public class EmpiMessageHandler implements MessageHandler {
}catch (Exception e) {
log(empiContext, "Failure during EMPI processing: " + e.getMessage());
} finally {
// Interceptor call: EMPI_AFTER_PERSISTED_RESOURCE_CHECKED
ResourceOperationMessage outgoingMsg = new ResourceOperationMessage(myFhirContext, theMsg.getPayload(myFhirContext), theMsg.getOperationType());
outgoingMsg.setTransactionId(theMsg.getTransactionId());
HookParams params = new HookParams()
.add(ResourceModifiedMessage.class, theMsg)
.add(ResourceOperationMessage.class, outgoingMsg)
.add(TransactionLogMessages.class, empiContext.getTransactionLogMessages());
myInterceptorBroadcaster.callHooks(Pointcut.EMPI_AFTER_PERSISTED_RESOURCE_CHECKED, params);
}
}
private EmpiTransactionContext createEmpiContext(ResourceModifiedMessage theMsg) {
TransactionLogMessages transactionLogMessages = TransactionLogMessages.createFromTransactionGuid(theMsg.getParentTransactionGuid());
TransactionLogMessages transactionLogMessages = TransactionLogMessages.createFromTransactionGuid(theMsg.getTransactionId());
EmpiTransactionContext.OperationType empiOperation;
switch (theMsg.getOperationType()) {
case CREATE:

3
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/registry/SearchParamRegistryImpl.java
View File

@ -291,6 +291,9 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry {
if (runtimeSp == null) {
continue;
}
if (runtimeSp.getStatus() == RuntimeSearchParam.RuntimeSearchParamStatusEnum.DRAFT) {
continue;
}
for (String nextBaseName : SearchParameterUtil.getBaseAsStrings(myFhirContext, nextSp)) {
if (isBlank(nextBaseName)) {

2
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/message/SubscriptionDeliveringMessageSubscriber.java
View File

@ -64,7 +64,7 @@ public class SubscriptionDeliveringMessageSubscriber extends BaseSubscriptionDel
protected void doDelivery(ResourceDeliveryMessage theMsg, CanonicalSubscription theSubscription, IChannelProducer theChannelProducer, IBaseResource thePayloadResource) {
ResourceModifiedMessage payload = new ResourceModifiedMessage(myFhirContext, thePayloadResource, theMsg.getOperationType());
payload.setParentTransactionGuid(theMsg.getParentTransactionGuid());
payload.setTransactionId(theMsg.getTransactionId());
ResourceModifiedJsonMessage message = new ResourceModifiedJsonMessage(payload);
theChannelProducer.send(message);
ourLog.debug("Delivering {} message payload {} for {}", theMsg.getOperationType(), theMsg.getPayloadId(), theSubscription.getIdElement(myFhirContext).toUnqualifiedVersionless().getValue());

5
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/matcher/matching/DaoSubscriptionMatcher.java
View File

@ -37,11 +37,14 @@ import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
public class DaoSubscriptionMatcher implements ISubscriptionMatcher {
private Logger ourLog = LoggerFactory.getLogger(DaoSubscriptionMatcher.class);
@Autowired
DaoRegistry myDaoRegistry;
@Autowired
MatchUrlService myMatchUrlService;
private Logger ourLog = LoggerFactory.getLogger(DaoSubscriptionMatcher.class);
@Autowired
private FhirContext myCtx;

6
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/matcher/subscriber/SubscriptionActivatingSubscriber.java
View File

@ -23,13 +23,13 @@ package ca.uhn.fhir.jpa.subscription.match.matcher.subscriber;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscriptionChannelType;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedJsonMessage;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyEvaluator;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionCanonicalizer;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionConstants;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscriptionChannelType;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedJsonMessage;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.SubscriptionUtil;
import org.hl7.fhir.instance.model.api.IBaseResource;

3
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/matcher/subscriber/SubscriptionMatchingSubscriber.java
View File

@ -86,7 +86,6 @@ public class SubscriptionMatchingSubscriber implements MessageHandler {
ResourceModifiedMessage msg = ((ResourceModifiedJsonMessage) theMessage).getPayload();
matchActiveSubscriptionsAndDeliver(msg);
}
public void matchActiveSubscriptionsAndDeliver(ResourceModifiedMessage theMsg) {
@ -164,7 +163,7 @@ public class SubscriptionMatchingSubscriber implements MessageHandler {
deliveryMsg.setPayload(myFhirContext, payload, encoding);
deliveryMsg.setSubscription(subscription);
deliveryMsg.setOperationType(theMsg.getOperationType());
deliveryMsg.setParentTransactionGuid(theMsg.getParentTransactionGuid());
deliveryMsg.setTransactionId(theMsg.getTransactionId());
deliveryMsg.copyAdditionalPropertiesFrom(theMsg);
// Interceptor call: SUBSCRIPTION_RESOURCE_MATCHED

2
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/matcher/subscriber/SubscriptionRegisteringSubscriber.java
View File

@ -21,10 +21,10 @@ package ca.uhn.fhir.jpa.subscription.match.matcher.subscriber;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionCanonicalizer;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedJsonMessage;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

1
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/model/ResourceDeliveryJsonMessage.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.subscription.model;
* #L%
*/
import ca.uhn.fhir.rest.server.messaging.json.BaseJsonMessage;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;

34
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/model/ResourceDeliveryMessage.java
View File

@ -23,6 +23,8 @@ package ca.uhn.fhir.jpa.subscription.model;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.messaging.BaseResourceMessage;
import ca.uhn.fhir.rest.server.messaging.IResourceMessage;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;
@ -38,22 +40,10 @@ public class ResourceDeliveryMessage extends BaseResourceMessage implements IRes
private CanonicalSubscription mySubscription;
@JsonProperty("payload")
private String myPayloadString;
@JsonIgnore
private transient IBaseResource myPayload;
@JsonProperty("payloadId")
private String myPayloadId;
@JsonProperty("parentTransactionGuid")
private String myParentTransactionGuid;
@JsonProperty("operationType")
private ResourceModifiedMessage.OperationTypeEnum myOperationType;
public String getParentTransactionGuid() {
return myParentTransactionGuid;
}
public void setParentTransactionGuid(String theParentTransactionGuid) {
myParentTransactionGuid = theParentTransactionGuid;
}
@JsonIgnore
private transient IBaseResource myPayloadDecoded;
/**
* Constructor
@ -62,20 +52,12 @@ public class ResourceDeliveryMessage extends BaseResourceMessage implements IRes
super();
}
public ResourceModifiedMessage.OperationTypeEnum getOperationType() {
return myOperationType;
}
public void setOperationType(ResourceModifiedMessage.OperationTypeEnum theOperationType) {
myOperationType = theOperationType;
}
public IBaseResource getPayload(FhirContext theCtx) {
IBaseResource retVal = myPayload;
IBaseResource retVal = myPayloadDecoded;
if (retVal == null && isNotBlank(myPayloadString)) {
IParser parser = EncodingEnum.detectEncoding(myPayloadString).newParser(theCtx);
retVal = parser.parseResource(myPayloadString);
myPayload = retVal;
myPayloadDecoded = retVal;
}
return retVal;
}
@ -133,9 +115,9 @@ public class ResourceDeliveryMessage extends BaseResourceMessage implements IRes
return new ToStringBuilder(this)
.append("mySubscription", mySubscription)
.append("myPayloadString", myPayloadString)
.append("myPayload", myPayload)
.append("myPayload", myPayloadDecoded)
.append("myPayloadId", myPayloadId)
.append("myOperationType", myOperationType)
.append("myOperationType", getOperationType())
.toString();
}

1
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/model/ResourceModifiedJsonMessage.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.subscription.model;
* #L%
*/
import ca.uhn.fhir.rest.server.messaging.json.BaseJsonMessage;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;

136
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/model/ResourceModifiedMessage.java
View File

@ -21,40 +21,24 @@ package ca.uhn.fhir.jpa.subscription.model;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IModelJson;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.util.ResourceReferenceInfo;
import com.fasterxml.jackson.annotation.JsonIgnore;
import ca.uhn.fhir.rest.server.messaging.BaseResourceModifiedMessage;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import java.util.List;
/**
* Most of this class has been moved to ResourceModifiedMessage in the hapi-fhir-server project, for a reusable channel ResourceModifiedMessage
* that doesn't require knowledge of subscriptions.
*/
public class ResourceModifiedMessage extends BaseResourceModifiedMessage {
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class ResourceModifiedMessage extends BaseResourceMessage implements IResourceMessage, IModelJson {
@JsonProperty("resourceId")
private String myId;
@JsonProperty("operationType")
private OperationTypeEnum myOperationType;
/**
* This will only be set if the resource is being triggered for a specific
* subscription
*/
@JsonProperty(value = "subscriptionId", required = false)
private String mySubscriptionId;
@JsonProperty("payload")
private String myPayload;
@JsonProperty("payloadId")
private String myPayloadId;
@JsonProperty("parentTransactionGuid")
private String myParentTransactionGuid;
@JsonIgnore
private transient IBaseResource myPayloadDecoded;
/**
* Constructor
@ -64,25 +48,13 @@ public class ResourceModifiedMessage extends BaseResourceMessage implements IRes
}
public ResourceModifiedMessage(FhirContext theFhirContext, IBaseResource theResource, OperationTypeEnum theOperationType) {
this();
setId(theResource.getIdElement());
setOperationType(theOperationType);
if (theOperationType != OperationTypeEnum.DELETE) {
setNewPayload(theFhirContext, theResource);
}
super(theFhirContext, theResource, theOperationType);
}
public ResourceModifiedMessage(FhirContext theFhirContext, IBaseResource theNewResource, OperationTypeEnum theOperationType, RequestDetails theRequest) {
this(theFhirContext, theNewResource, theOperationType);
if (theRequest != null) {
setParentTransactionGuid(theRequest.getTransactionGuid());
}
super(theFhirContext, theNewResource, theOperationType, theRequest);
}
@Override
public String getPayloadId() {
return myPayloadId;
}
public String getSubscriptionId() {
return mySubscriptionId;
@ -92,98 +64,6 @@ public class ResourceModifiedMessage extends BaseResourceMessage implements IRes
mySubscriptionId = theSubscriptionId;
}
public String getId() {
return myId;
}
public IIdType getId(FhirContext theCtx) {
IIdType retVal = null;
if (myId != null) {
retVal = theCtx.getVersion().newIdType().setValue(myId);
}
return retVal;
}
public IBaseResource getNewPayload(FhirContext theCtx) {
if (myPayloadDecoded == null && isNotBlank(myPayload)) {
myPayloadDecoded = theCtx.newJsonParser().parseResource(myPayload);
}
return myPayloadDecoded;
}
public OperationTypeEnum getOperationType() {
return myOperationType;
}
public void setOperationType(OperationTypeEnum theOperationType) {
myOperationType = theOperationType;
}
public void setId(IIdType theId) {
myId = null;
if (theId != null) {
myId = theId.getValue();
}
}
public String getParentTransactionGuid() {
return myParentTransactionGuid;
}
public void setParentTransactionGuid(String theParentTransactionGuid) {
myParentTransactionGuid = theParentTransactionGuid;
}
private void setNewPayload(FhirContext theCtx, IBaseResource theNewPayload) {
/*
* References with placeholders would be invalid by the time we get here, and
* would be caught before we even get here. This check is basically a last-ditch
* effort to make sure nothing has broken in the various safeguards that
* should prevent this from happening (hence it only being an assert as
* opposed to something executed all the time).
*/
assert payloadContainsNoPlaceholderReferences(theCtx, theNewPayload);
/*
* Note: Don't set myPayloadDecoded in here- This is a false optimization since
* it doesn't actually get used if anyone is doing subscriptions at any
* scale using a queue engine, and not going through the serialize/deserialize
* as we would in a queue engine can mask bugs.
* -JA
*/
myPayload = theCtx.newJsonParser().encodeResourceToString(theNewPayload);
myPayloadId = theNewPayload.getIdElement().toUnqualified().getValue();
}
public enum OperationTypeEnum {
CREATE,
UPDATE,
DELETE,
MANUALLY_TRIGGERED
}
private static boolean payloadContainsNoPlaceholderReferences(FhirContext theCtx, IBaseResource theNewPayload) {
List<ResourceReferenceInfo> refs = theCtx.newTerser().getAllResourceReferences(theNewPayload);
for (ResourceReferenceInfo next : refs) {
String ref = next.getResourceReference().getReferenceElement().getValue();
if (isBlank(ref)) {
IBaseResource resource = next.getResourceReference().getResource();
if (resource != null) {
ref = resource.getIdElement().getValue();
}
}
if (isNotBlank(ref)) {
if (ref.startsWith("#")) {
continue;
}
if (ref.startsWith("urn:uuid:")) {
throw new AssertionError("Reference at " + next.getName() + " is invalid: " + ref);
}
}
}
return true;
}
@Override
public String toString() {
return new ToStringBuilder(this)

2
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/triggering/SubscriptionTriggeringSvcImpl.java
View File

@ -26,7 +26,6 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.sched.HapiJob;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
@ -38,6 +37,7 @@ import ca.uhn.fhir.model.dstu2.valueset.ResourceTypeEnum;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;

2
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/util/SubscriptionDebugLogInterceptor.java
View File

@ -25,8 +25,8 @@ import ca.uhn.fhir.interceptor.api.Interceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryMatchResult;
import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscriptionChannelType;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
import ca.uhn.fhir.jpa.subscription.model.ResourceDeliveryMessage;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
import ca.uhn.fhir.util.StopWatch;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

14
hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/match/deliver/BaseSubscriptionDeliverySubscriberTest.java
View File

@ -3,12 +3,12 @@ package ca.uhn.fhir.jpa.subscription.match.deliver;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.subscription.match.deliver.resthook.SubscriptionDeliveringRestHookSubscriber;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
import ca.uhn.fhir.jpa.subscription.model.ResourceDeliveryJsonMessage;
import ca.uhn.fhir.jpa.subscription.model.ResourceDeliveryMessage;
import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
import ca.uhn.fhir.jpa.subscription.match.deliver.resthook.SubscriptionDeliveringRestHookSubscriber;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.IRestfulClientFactory;
@ -18,18 +18,20 @@ import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Answers;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.mockito.junit.jupiter.MockitoExtension;
import org.springframework.messaging.Message;
import org.springframework.messaging.MessagingException;
import org.springframework.messaging.support.GenericMessage;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.*;
import static org.mockito.Mockito.eq;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
public class BaseSubscriptionDeliverySubscriberTest {

1
hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/cache/SubscriptionRegistrySharedTest.java vendored
View File

@ -33,7 +33,6 @@ public class SubscriptionRegistrySharedTest extends BaseSubscriptionRegistryTest
return "shared";
}
}
}
@Test

23
hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/matcher/InMemorySubscriptionMatcherR3Test.java
View File

@ -10,7 +10,26 @@ import ca.uhn.fhir.jpa.subscription.module.BaseSubscriptionDstu3Test;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.server.SimpleBundleProvider;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.BodySite;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.CommunicationRequest;
import org.hl7.fhir.dstu3.model.DateTimeType;
import org.hl7.fhir.dstu3.model.Dosage;
import org.hl7.fhir.dstu3.model.Enumerations;
import org.hl7.fhir.dstu3.model.EpisodeOfCare;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Location;
import org.hl7.fhir.dstu3.model.MedicationRequest;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Procedure;
import org.hl7.fhir.dstu3.model.ProcedureRequest;
import org.hl7.fhir.dstu3.model.Provenance;
import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.dstu3.model.SearchParameter;
import org.hl7.fhir.dstu3.model.Timing;
import org.hl7.fhir.dstu3.model.codesystems.MedicationRequestCategory;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -89,10 +108,8 @@ public class InMemorySubscriptionMatcherR3Test extends BaseSubscriptionDstu3Test
pr.setSubject(new Reference("Patient/"));
assertMatched(pr, "ProcedureRequest?intent=original-order");
assertNotMatched(pr, "ProcedureRequest?subject=Patient/123");
}
@Test
public void testResourceById() {

2
hapi-fhir-server-empi/src/main/java/ca/uhn/fhir/empi/util/PersonHelper.java
View File

@ -268,7 +268,7 @@ public class PersonHelper {
if (theAllowOverwriting || person.getName().isEmpty()) {
person.setName(patient.getName());
}
if (theAllowOverwriting || person.getName().isEmpty()) {
if (theAllowOverwriting || person.getAddress().isEmpty()) {
person.setAddress(patient.getAddress());
}
if (theAllowOverwriting || person.getTelecom().isEmpty()) {

6
hapi-fhir-server/pom.xml
View File

@ -73,8 +73,12 @@
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-messaging</artifactId>
</dependency>
</dependencies>
</dependencies>
<build>
<plugins>

61
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/model/BaseResourceMessage.java → hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/BaseResourceMessage.java
View File

@ -1,8 +1,8 @@
package ca.uhn.fhir.jpa.subscription.model;
package ca.uhn.fhir.rest.server.messaging;
/*-
* #%L
* HAPI FHIR Subscription Server
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 University Health Network
* %%
@ -20,10 +20,13 @@ package ca.uhn.fhir.jpa.subscription.model;
* #L%
*/
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.Validate;
import javax.annotation.Nullable;
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
@ -31,9 +34,15 @@ import java.util.Optional;
@SuppressWarnings("WeakerAccess")
public abstract class BaseResourceMessage implements IResourceMessage, IModelJson {
@JsonProperty("operationType")
protected BaseResourceModifiedMessage.OperationTypeEnum myOperationType;
@JsonProperty("attributes")
private Map<String, String> myAttributes;
@JsonProperty("transactionId")
private String myTransactionId;
/**
* Returns an attribute stored in this message.
* <p>
@ -94,4 +103,52 @@ public abstract class BaseResourceMessage implements IResourceMessage, IModelJso
myAttributes.putAll(theMsg.myAttributes);
}
}
/**
* Returns the {@link OperationTypeEnum} that is occurring to the Resource of the message
*
* @return the operation type.
*/
public BaseResourceModifiedMessage.OperationTypeEnum getOperationType() {
return myOperationType;
}
/**
* Sets the {@link OperationTypeEnum} occuring to the resource of the message.
*
* @param theOperationType The operation type to set.
*/
public void setOperationType(BaseResourceModifiedMessage.OperationTypeEnum theOperationType) {
myOperationType = theOperationType;
}
/**
* Retrieve the transaction ID related to this message.
*
* @return the transaction ID, or null.
*/
@Nullable
public String getTransactionId() {
return myTransactionId;
}
/**
* Adds a transaction ID to this message. This ID can be used for many purposes. For example, performing tracing
* across asynchronous hooks, tying data together, or downstream logging purposes.
*
* One current internal implementation uses this field to tie back EMPI processing results (which are asynchronous)
* to the original transaction log that caused the EMPI processing to occur.
*
* @param theTransactionId An ID representing a transaction of relevance to this message.
*/
public void setTransactionId(String theTransactionId) {
myTransactionId = theTransactionId;
}
public enum OperationTypeEnum {
CREATE,
UPDATE,
DELETE,
MANUALLY_TRIGGERED
}
}

177
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/BaseResourceModifiedMessage.java Normal file
View File

@ -0,0 +1,177 @@
package ca.uhn.fhir.rest.server.messaging;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 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.FhirContext;
import ca.uhn.fhir.model.api.IModelJson;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.util.ResourceReferenceInfo;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public abstract class BaseResourceModifiedMessage extends BaseResourceMessage implements IResourceMessage, IModelJson {
@JsonProperty("resourceId")
protected String myId;
@JsonProperty("payload")
protected String myPayload;
@JsonProperty("payloadId")
protected String myPayloadId;
@JsonIgnore
protected transient IBaseResource myPayloadDecoded;
/**
* Constructor
*/
public BaseResourceModifiedMessage() {
super();
}
public BaseResourceModifiedMessage(FhirContext theFhirContext, IBaseResource theResource, OperationTypeEnum theOperationType) {
this();
setId(theResource.getIdElement());
setOperationType(theOperationType);
if (theOperationType != OperationTypeEnum.DELETE) {
setNewPayload(theFhirContext, theResource);
}
}
public BaseResourceModifiedMessage(FhirContext theFhirContext, IBaseResource theNewResource, OperationTypeEnum theOperationType, RequestDetails theRequest) {
this(theFhirContext, theNewResource, theOperationType);
if (theRequest != null) {
setTransactionId(theRequest.getTransactionGuid());
}
}
@Override
public String getPayloadId() {
return myPayloadId;
}
public String getId() {
return myId;
}
public IIdType getId(FhirContext theCtx) {
IIdType retVal = null;
if (myId != null) {
retVal = theCtx.getVersion().newIdType().setValue(myId);
}
return retVal;
}
public IBaseResource getNewPayload(FhirContext theCtx) {
if (myPayloadDecoded == null && isNotBlank(myPayload)) {
myPayloadDecoded = theCtx.newJsonParser().parseResource(myPayload);
}
return myPayloadDecoded;
}
public IBaseResource getPayload(FhirContext theCtx) {
IBaseResource retVal = myPayloadDecoded;
if (retVal == null && isNotBlank(myPayload)) {
IParser parser = EncodingEnum.detectEncoding(myPayload).newParser(theCtx);
retVal = parser.parseResource(myPayload);
myPayloadDecoded = retVal;
}
return retVal;
}
public String getPayloadString() {
if (this.myPayload != null) {
return this.myPayload;
}
return "";
}
public void setId(IIdType theId) {
myId = null;
if (theId != null) {
myId = theId.getValue();
}
}
protected void setNewPayload(FhirContext theCtx, IBaseResource theNewPayload) {
/*
* References with placeholders would be invalid by the time we get here, and
* would be caught before we even get here. This check is basically a last-ditch
* effort to make sure nothing has broken in the various safeguards that
* should prevent this from happening (hence it only being an assert as
* opposed to something executed all the time).
*/
assert payloadContainsNoPlaceholderReferences(theCtx, theNewPayload);
/*
* Note: Don't set myPayloadDecoded in here- This is a false optimization since
* it doesn't actually get used if anyone is doing subscriptions at any
* scale using a queue engine, and not going through the serialize/deserialize
* as we would in a queue engine can mask bugs.
* -JA
*/
myPayload = theCtx.newJsonParser().encodeResourceToString(theNewPayload);
myPayloadId = theNewPayload.getIdElement().toUnqualified().getValue();
}
protected static boolean payloadContainsNoPlaceholderReferences(FhirContext theCtx, IBaseResource theNewPayload) {
List<ResourceReferenceInfo> refs = theCtx.newTerser().getAllResourceReferences(theNewPayload);
for (ResourceReferenceInfo next : refs) {
String ref = next.getResourceReference().getReferenceElement().getValue();
if (isBlank(ref)) {
IBaseResource resource = next.getResourceReference().getResource();
if (resource != null) {
ref = resource.getIdElement().getValue();
}
}
if (isNotBlank(ref)) {
if (ref.startsWith("#")) {
continue;
}
if (ref.startsWith("urn:uuid:")) {
throw new AssertionError("Reference at " + next.getName() + " is invalid: " + ref);
}
}
}
return true;
}
@Override
public String toString() {
return new ToStringBuilder(this)
.append("myId", myId)
.append("myOperationType", myOperationType)
// .append("myPayload", myPayload)
.append("myPayloadId", myPayloadId)
// .append("myPayloadDecoded", myPayloadDecoded)
.toString();
}
}

6
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/model/IResourceMessage.java → hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/IResourceMessage.java
View File

@ -1,8 +1,8 @@
package ca.uhn.fhir.jpa.subscription.model;
package ca.uhn.fhir.rest.server.messaging;
/*-
* #%L
* HAPI FHIR Subscription Server
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 University Health Network
* %%
@ -20,6 +20,8 @@ package ca.uhn.fhir.jpa.subscription.model;
* #L%
*/
public interface IResourceMessage {
String getPayloadId();
}

38
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/ResourceOperationMessage.java Normal file
View File

@ -0,0 +1,38 @@
package ca.uhn.fhir.rest.server.messaging;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 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.FhirContext;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
public class ResourceOperationMessage extends BaseResourceModifiedMessage {
public ResourceOperationMessage() {
}
public ResourceOperationMessage(FhirContext theFhirContext, IBaseResource theResource, OperationTypeEnum theOperationType) {
super(theFhirContext, theResource, theOperationType);
}
public ResourceOperationMessage(FhirContext theFhirContext, IBaseResource theNewResource, OperationTypeEnum theOperationType, RequestDetails theRequest) {
super(theFhirContext, theNewResource, theOperationType, theRequest);
}
}

20
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/model/BaseJsonMessage.java → hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/json/BaseJsonMessage.java
View File

@ -1,8 +1,8 @@
package ca.uhn.fhir.jpa.subscription.model;
package ca.uhn.fhir.rest.server.messaging.json;
/*-
* #%L
* HAPI FHIR Subscription Server
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 University Health Network
* %%
@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.subscription.model;
* #L%
*/
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.springframework.messaging.Message;
@ -29,21 +30,32 @@ public abstract class BaseJsonMessage<T> implements Message<T>, IModelJson {
private static final long serialVersionUID = 1L;
@JsonProperty("headers")
private MessageHeaders myHeaders;
private HapiMessageHeaders myHeaders;
/**
* Constructor
*/
public BaseJsonMessage() {
super();
setDefaultRetryHeaders();
}
protected void setDefaultRetryHeaders() {
HapiMessageHeaders messageHeaders = new HapiMessageHeaders();
setHeaders(messageHeaders);
}
@Override
public MessageHeaders getHeaders() {
return myHeaders.toMessageHeaders();
}
public HapiMessageHeaders getHapiHeaders() {
return myHeaders;
}
public void setHeaders(MessageHeaders theHeaders) {
public void setHeaders(HapiMessageHeaders theHeaders) {
myHeaders = theHeaders;
}
}

95
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/json/HapiMessageHeaders.java Normal file
View File

@ -0,0 +1,95 @@
package ca.uhn.fhir.rest.server.messaging.json;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 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.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.springframework.messaging.MessageHeaders;
import java.util.HashMap;
import java.util.Map;
/**
* This class is for holding headers for BaseJsonMessages. Any serializable data can be thrown into
* the header map. There are also three special headers, defined by the constants in this class, which are for use
* in message handling retrying. There are also matching helper functions for fetching those special variables; however
* they can also be accessed in standard map fashion with a `get` on the map.
*/
public class HapiMessageHeaders implements IModelJson {
public static final String RETRY_COUNT_KEY = "retryCount";
public static final String FIRST_FAILURE_KEY = "firstFailureTimestamp";
public static final String LAST_FAILURE_KEY = "lastFailureTimestamp";
@JsonProperty(RETRY_COUNT_KEY)
private Integer myRetryCount = 0;
@JsonProperty(FIRST_FAILURE_KEY)
private Long myFirstFailureTimestamp;
@JsonProperty(LAST_FAILURE_KEY)
private Long myLastFailureTimestamp;
@JsonProperty("customHeaders")
private final Map<String, Object> headers;
public HapiMessageHeaders(Map<String, Object> theHeaders) {
headers = theHeaders;
}
public HapiMessageHeaders() {
headers = new HashMap<>();
}
public Integer getRetryCount() {
return this.myRetryCount;
}
public Long getFirstFailureDate() {
return this.myFirstFailureTimestamp;
}
public Long getLastFailureDate() {
return this.myLastFailureTimestamp;
}
public void setRetryCount(Integer theRetryCount) {
this.myRetryCount = theRetryCount;
}
public void setLastFailureDate(Long theLastFailureDate) {
this.myLastFailureTimestamp = theLastFailureDate;
}
public void setFirstFailureDate(Long theFirstFailureDate) {
this.myFirstFailureTimestamp = theFirstFailureDate;
}
public Map<String, Object> getCustomHeaders() {
return this.headers;
}
public MessageHeaders toMessageHeaders() {
Map<String, Object> returnedHeaders = new HashMap<>(this.headers);
returnedHeaders.put(RETRY_COUNT_KEY, myRetryCount);
returnedHeaders.put(FIRST_FAILURE_KEY, myFirstFailureTimestamp);
returnedHeaders.put(LAST_FAILURE_KEY, myLastFailureTimestamp);
return new MessageHeaders(returnedHeaders);
}
}

69
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/json/ResourceOperationJsonMessage.java Normal file
View File

@ -0,0 +1,69 @@
package ca.uhn.fhir.rest.server.messaging.json;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 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.server.messaging.ResourceOperationMessage;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;
public class ResourceOperationJsonMessage extends BaseJsonMessage<ResourceOperationMessage> {
@JsonProperty("payload")
private ResourceOperationMessage myPayload;
/**
* Constructor
*/
public ResourceOperationJsonMessage() {
super();
}
/**
* Constructor
*/
public ResourceOperationJsonMessage(ResourceOperationMessage thePayload) {
myPayload = thePayload;
setDefaultRetryHeaders();
}
public ResourceOperationJsonMessage(HapiMessageHeaders theRetryMessageHeaders, ResourceOperationMessage thePayload) {
myPayload = thePayload;
setHeaders(theRetryMessageHeaders);
}
@Override
public ResourceOperationMessage getPayload() {
return myPayload;
}
public void setPayload(ResourceOperationMessage thePayload) {
myPayload = thePayload;
}
@Override
public String toString() {
return new ToStringBuilder(this)
.append("myPayload", myPayload)
.toString();
}
}

33
hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/messaging/BaseResourceModifiedMessageTest.java Normal file
View File

@ -0,0 +1,33 @@
package ca.uhn.fhir.rest.server.messaging;
import ca.uhn.fhir.rest.server.messaging.json.ResourceOperationJsonMessage;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.junit.jupiter.api.Test;
import static ca.uhn.fhir.rest.server.messaging.json.HapiMessageHeaders.FIRST_FAILURE_KEY;
import static ca.uhn.fhir.rest.server.messaging.json.HapiMessageHeaders.LAST_FAILURE_KEY;
import static ca.uhn.fhir.rest.server.messaging.json.HapiMessageHeaders.RETRY_COUNT_KEY;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.MatcherAssert.assertThat;
class ResourceOperationMessageTest {
@Test
public void testSerializationAndDeserializationOfResourceModifiedMessage() throws JsonProcessingException {
ResourceOperationJsonMessage jsonMessage = new ResourceOperationJsonMessage();
jsonMessage.setPayload(new ResourceOperationMessage());
ObjectMapper mapper = new ObjectMapper();
String serialized = mapper.writeValueAsString(jsonMessage);
jsonMessage = mapper.readValue(serialized, ResourceOperationJsonMessage.class);
assertThat(jsonMessage.getHapiHeaders().getRetryCount(), is(equalTo(0)));
assertThat(jsonMessage.getHapiHeaders().getFirstFailureDate(), is(equalTo(null)));
assertThat(jsonMessage.getHapiHeaders().getLastFailureDate(), is(equalTo(null)));
assertThat(jsonMessage.getHeaders().get(RETRY_COUNT_KEY), is(equalTo(0)));
assertThat(jsonMessage.getHeaders().get(FIRST_FAILURE_KEY), is(equalTo(null)));
assertThat(jsonMessage.getHeaders().get(LAST_FAILURE_KEY), is(equalTo(null)));
}
}

7
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/rest/server/ServerCapabilityStatementProvider.java
View File

@ -332,6 +332,7 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
sortSearchParameters(searchParameters);
if (!searchParameters.isEmpty()) {
Set<String> paramNames = new HashSet<>();
for (SearchParameter nextParameter : searchParameters) {
if (nextParameter.getParamType() == null) {
@ -346,6 +347,10 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
nextParamUnchainedName = nextParamName.substring(0, nextParamName.indexOf('.'));
}
if (!paramNames.add(nextParamUnchainedName)) {
continue;
}
String nextParamDescription = nextParameter.getDescription();
/*
@ -425,6 +430,8 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
param.setMin(nextParam.isRequired() ? 1 : 0);
param.setMax("1");
param.setName(nextParam.getName());
}
}

221
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/ServerCapabilityStatementProviderR4Test.java
View File

@ -5,11 +5,26 @@ import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.Delete;
import ca.uhn.fhir.rest.annotation.History;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.IncludeParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.OptionalParam;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.annotation.Validate;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
@ -27,7 +42,8 @@ import ca.uhn.fhir.validation.ValidationResult;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.hapi.rest.server.ServerCapabilityStatementProvider;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.CapabilityStatement;
import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestComponent;
import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceComponent;
import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceOperationComponent;
@ -35,10 +51,18 @@ import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResource
import org.hl7.fhir.r4.model.CapabilityStatement.ConditionalDeleteStatus;
import org.hl7.fhir.r4.model.CapabilityStatement.SystemRestfulInteraction;
import org.hl7.fhir.r4.model.CapabilityStatement.TypeRestfulInteraction;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.DiagnosticReport;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.OperationDefinition;
import org.hl7.fhir.r4.model.OperationDefinition.OperationDefinitionParameterComponent;
import org.hl7.fhir.r4.model.OperationDefinition.OperationKind;
import org.hl7.fhir.r4.model.OperationDefinition.OperationParameterUse;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
@ -49,6 +73,7 @@ import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
@ -65,8 +90,12 @@ import static org.mockito.Mockito.when;
public class ServerCapabilityStatementProviderR4Test {
private static FhirContext ourCtx;
public static final String PATIENT_SUB = "PatientSub";
public static final String PATIENT_SUB_SUB = "PatientSubSub";
public static final String PATIENT_SUB_SUB_2 = "PatientSubSub2";
public static final String PATIENT_TRIPLE_SUB = "PatientTripleSub";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ServerCapabilityStatementProviderR4Test.class);
private static FhirContext ourCtx;
private static FhirValidator ourValidator;
static {
@ -259,7 +288,9 @@ public class ServerCapabilityStatementProviderR4Test {
assertNull(res.getConditionalUpdateElement().getValue());
}
/** See #379 */
/**
* See #379
*/
@Test
public void testOperationAcrossMultipleTypes() throws Exception {
RestfulServer rs = new RestfulServer(ourCtx);
@ -513,10 +544,10 @@ public class ServerCapabilityStatementProviderR4Test {
for (ResourceBinding resourceBinding : resourceBindings) {
if (resourceBinding.getResourceName().equals("Patient")) {
List<BaseMethodBinding<?>> methodBindings = resourceBinding.getMethodBindings();
SearchMethodBinding binding = (SearchMethodBinding) methodBindings.get(0);
SearchParameter param = (SearchParameter) binding.getParameters().get(25);
assertEquals("The organization at which this person is a patient", param.getDescription());
found = true;
SearchMethodBinding binding = (SearchMethodBinding) methodBindings.get(0);
SearchParameter param = (SearchParameter) binding.getParameters().get(25);
assertEquals("The organization at which this person is a patient", param.getDescription());
found = true;
}
}
assertTrue(found);
@ -569,7 +600,7 @@ public class ServerCapabilityStatementProviderR4Test {
@Test
public void testSearchReferenceParameterWithList() throws Exception {
RestfulServer rsNoType = new RestfulServer(ourCtx){
RestfulServer rsNoType = new RestfulServer(ourCtx) {
@Override
public RestfulServerConfiguration createConfiguration() {
RestfulServerConfiguration retVal = super.createConfiguration();
@ -586,7 +617,7 @@ public class ServerCapabilityStatementProviderR4Test {
String confNoType = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance);
ourLog.info(confNoType);
RestfulServer rsWithType = new RestfulServer(ourCtx){
RestfulServer rsWithType = new RestfulServer(ourCtx) {
@Override
public RestfulServerConfiguration createConfiguration() {
RestfulServerConfiguration retVal = super.createConfiguration();
@ -645,6 +676,46 @@ public class ServerCapabilityStatementProviderR4Test {
assertThat(conf, containsString("<interaction><code value=\"" + TypeRestfulInteraction.HISTORYTYPE.toCode() + "\"/></interaction>"));
}
@Test
public void testStaticIncludeChains() throws Exception {
class MyProvider implements IResourceProvider {
@Override
public Class<DiagnosticReport> getResourceType() {
return DiagnosticReport.class;
}
@Search
public List<IBaseResource> search(@RequiredParam(name = DiagnosticReport.SP_PATIENT + "." + Patient.SP_FAMILY) StringParam lastName,
@RequiredParam(name = DiagnosticReport.SP_PATIENT + "." + Patient.SP_GIVEN) StringParam firstName,
@RequiredParam(name = DiagnosticReport.SP_PATIENT + "." + Patient.SP_BIRTHDATE) DateParam dob,
@OptionalParam(name = DiagnosticReport.SP_DATE) DateRangeParam range) {
return null;
}
}
RestfulServer rs = new RestfulServer(ourCtx);
rs.setProviders(new MyProvider());
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider() {
};
rs.setServerConformanceProvider(sc);
rs.init(createServletConfig());
CapabilityStatement opDef = sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
String conf = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(opDef);
ourLog.info(conf);
CapabilityStatementRestResourceComponent resource = opDef.getRest().get(0).getResource().get(0);
assertEquals("DiagnosticReport", resource.getType());
List<String> searchParamNames = resource.getSearchParam().stream().map(t -> t.getName()).collect(Collectors.toList());
assertThat(searchParamNames, containsInAnyOrder("patient", "date"));
}
@Test
public void testSystemLevelNamedQueryWithParameters() throws Exception {
RestfulServer rs = new RestfulServer(ourCtx);
@ -729,8 +800,8 @@ public class ServerCapabilityStatementProviderR4Test {
assertThat(param.getUse(), is(OperationParameterUse.IN));
CapabilityStatementRestResourceComponent patientResource = restComponent.getResource().stream()
.filter(r -> patientResourceName.equals(r.getType()))
.findAny().get();
.filter(r -> patientResourceName.equals(r.getType()))
.findAny().get();
assertThat("Named query parameters should not appear in the resource search params", patientResource.getSearchParam(), is(empty()));
}
@ -762,25 +833,25 @@ public class ServerCapabilityStatementProviderR4Test {
assertThat(opDef.getInstance(), is(false));
}
@Test
public void testProfiledResourceStructureDefinitionLinks() throws Exception {
RestfulServer rs = new RestfulServer(ourCtx);
rs.setResourceProviders(new ProfiledPatientProvider(), new MultipleProfilesPatientProvider());
@Test
public void testProfiledResourceStructureDefinitionLinks() throws Exception {
RestfulServer rs = new RestfulServer(ourCtx);
rs.setResourceProviders(new ProfiledPatientProvider(), new MultipleProfilesPatientProvider());
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider();
rs.setServerConformanceProvider(sc);
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider();
rs.setServerConformanceProvider(sc);
rs.init(createServletConfig());
rs.init(createServletConfig());
CapabilityStatement conformance = sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance));
CapabilityStatement conformance = sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance));
List<CapabilityStatementRestResourceComponent> resources = conformance.getRestFirstRep().getResource();
CapabilityStatementRestResourceComponent patientResource = resources.stream()
.filter(resource -> "Patient".equals(resource.getType()))
.findFirst().get();
assertThat(patientResource.getProfile(), containsString(PATIENT_SUB));
}
List<CapabilityStatementRestResourceComponent> resources = conformance.getRestFirstRep().getResource();
CapabilityStatementRestResourceComponent patientResource = resources.stream()
.filter(resource -> "Patient".equals(resource.getType()))
.findFirst().get();
assertThat(patientResource.getProfile(), containsString(PATIENT_SUB));
}
private List<String> toOperationIdParts(List<CapabilityStatementRestResourceOperationComponent> theOperation) {
ArrayList<String> retVal = Lists.newArrayList();
@ -817,11 +888,6 @@ public class ServerCapabilityStatementProviderR4Test {
assertTrue(result.isSuccessful(), outcome);
}
@AfterAll
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@SuppressWarnings("unused")
public static class ConditionalProvider implements IResourceProvider {
@ -866,7 +932,7 @@ public class ServerCapabilityStatementProviderR4Test {
@Search(type = Patient.class)
public Patient findPatient(@Description(shortDefinition = "The patient's identifier") @OptionalParam(name = Patient.SP_IDENTIFIER) TokenParam theIdentifier,
@Description(shortDefinition = "The patient's name") @OptionalParam(name = Patient.SP_NAME) StringParam theName) {
@Description(shortDefinition = "The patient's name") @OptionalParam(name = Patient.SP_NAME) StringParam theName) {
return null;
}
@ -942,7 +1008,7 @@ public class ServerCapabilityStatementProviderR4Test {
@SuppressWarnings("unused")
public static class PlainProviderWithExtendedOperationOnNoType {
@Operation(name = "plain", idempotent = true, returnParameters = { @OperationParam(min = 1, max = 2, name = "out1", type = StringType.class) })
@Operation(name = "plain", idempotent = true, returnParameters = {@OperationParam(min = 1, max = 2, name = "out1", type = StringType.class)})
public IBundleProvider everything(HttpServletRequest theServletRequest, @IdParam IdType theId, @OperationParam(name = "start") DateType theStart,
@OperationParam(name = "end") DateType theEnd) {
return null;
@ -972,8 +1038,8 @@ public class ServerCapabilityStatementProviderR4Test {
@Description(shortDefinition = "This is a search for stuff!")
@Search
public List<DiagnosticReport> findDiagnosticReportsByPatient(@RequiredParam(name = DiagnosticReport.SP_SUBJECT + '.' + Patient.SP_IDENTIFIER) TokenParam thePatientId,
@OptionalParam(name = DiagnosticReport.SP_CODE) TokenOrListParam theNames, @OptionalParam(name = DiagnosticReport.SP_DATE) DateRangeParam theDateRange,
@IncludeParam(allow = { "DiagnosticReport.result" }) Set<Include> theIncludes) throws Exception {
@OptionalParam(name = DiagnosticReport.SP_CODE) TokenOrListParam theNames, @OptionalParam(name = DiagnosticReport.SP_DATE) DateRangeParam theDateRange,
@IncludeParam(allow = {"DiagnosticReport.result"}) Set<Include> theIncludes) throws Exception {
return null;
}
@ -1004,7 +1070,7 @@ public class ServerCapabilityStatementProviderR4Test {
@Search(type = Patient.class)
public Patient findPatient2(
@Description(shortDefinition = "All patients linked to the given patient") @OptionalParam(name = "link", targetTypes = { Patient.class }) ReferenceAndListParam theLink) {
@Description(shortDefinition = "All patients linked to the given patient") @OptionalParam(name = "link", targetTypes = {Patient.class}) ReferenceAndListParam theLink) {
return null;
}
@ -1014,15 +1080,15 @@ public class ServerCapabilityStatementProviderR4Test {
public static class SearchProviderWithWhitelist {
@Search(type = Patient.class)
public Patient findPatient1(@Description(shortDefinition = "The organization at which this person is a patient") @RequiredParam(name = Patient.SP_ORGANIZATION, chainWhitelist = { "foo",
"bar" }) ReferenceAndListParam theIdentifier) {
public Patient findPatient1(@Description(shortDefinition = "The organization at which this person is a patient") @RequiredParam(name = Patient.SP_ORGANIZATION, chainWhitelist = {"foo",
"bar"}) ReferenceAndListParam theIdentifier) {
return null;
}
}
@SuppressWarnings("unused")
public static class SearchProviderWithListNoType implements IResourceProvider {
public static class SearchProviderWithListNoType implements IResourceProvider {
@Override
public Class<? extends IBaseResource> getResourceType() {
@ -1030,7 +1096,6 @@ public class ServerCapabilityStatementProviderR4Test {
}
@Search()
public List<Patient> findPatient1(@Description(shortDefinition = "The organization at which this person is a patient") @RequiredParam(name = Patient.SP_ORGANIZATION) ReferenceAndListParam theIdentifier) {
return null;
@ -1039,7 +1104,7 @@ public class ServerCapabilityStatementProviderR4Test {
}
@SuppressWarnings("unused")
public static class SearchProviderWithListWithType implements IResourceProvider {
public static class SearchProviderWithListWithType implements IResourceProvider {
@Override
public Class<? extends IBaseResource> getResourceType() {
@ -1047,15 +1112,13 @@ public class ServerCapabilityStatementProviderR4Test {
}
@Search(type=Patient.class)
@Search(type = Patient.class)
public List<Patient> findPatient1(@Description(shortDefinition = "The organization at which this person is a patient") @RequiredParam(name = Patient.SP_ORGANIZATION) ReferenceAndListParam theIdentifier) {
return null;
}
}
public static class SystemHistoryProvider {
@History
@ -1140,48 +1203,52 @@ public class ServerCapabilityStatementProviderR4Test {
}
public static class ProfiledPatientProvider implements IResourceProvider {
public static class ProfiledPatientProvider implements IResourceProvider {
@Override
public Class<? extends IBaseResource> getResourceType() {
return PatientSubSub2.class;
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return PatientSubSub2.class;
}
@Search
public List<PatientSubSub2> find() {
return null;
}
}
@Search
public List<PatientSubSub2> find() {
return null;
}
}
public static class MultipleProfilesPatientProvider implements IResourceProvider {
public static class MultipleProfilesPatientProvider implements IResourceProvider {
@Override
public Class<? extends IBaseResource> getResourceType() {
return PatientSubSub.class;
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return PatientSubSub.class;
}
@Read(type = PatientTripleSub.class)
public PatientTripleSub read(@IdParam IdType theId) {
return null;
}
@Read(type = PatientTripleSub.class)
public PatientTripleSub read(@IdParam IdType theId) {
return null;
}
}
}
public static final String PATIENT_SUB = "PatientSub";
public static final String PATIENT_SUB_SUB = "PatientSubSub";
public static final String PATIENT_SUB_SUB_2 = "PatientSubSub2";
public static final String PATIENT_TRIPLE_SUB = "PatientTripleSub";
@ResourceDef(id = PATIENT_SUB)
public static class PatientSub extends Patient {
}
@ResourceDef(id = PATIENT_SUB)
public static class PatientSub extends Patient {}
@ResourceDef(id = PATIENT_SUB_SUB)
public static class PatientSubSub extends PatientSub {
}
@ResourceDef(id = PATIENT_SUB_SUB)
public static class PatientSubSub extends PatientSub {}
@ResourceDef(id = PATIENT_SUB_SUB_2)
public static class PatientSubSub2 extends PatientSub {
}
@ResourceDef(id = PATIENT_SUB_SUB_2)
public static class PatientSubSub2 extends PatientSub {}
@ResourceDef(id = PATIENT_TRIPLE_SUB)
public static class PatientTripleSub extends PatientSubSub {
}
@ResourceDef(id = PATIENT_TRIPLE_SUB)
public static class PatientTripleSub extends PatientSubSub {}
@AfterAll
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

2
pom.xml
View File

@ -1824,7 +1824,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>animal-sniffer-maven-plugin</artifactId>
<version>1.18</version>
<version>1.19</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>