honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

2564 contained resource validation flag (#3225) 

* First cut at multithreading bundle validation

* javadoc

* change test to a red-green test

* add daoconfig

* move bundle concurrency config from validationsupport to request validator

* Moved concurrent details from ValidationOptions to FhirValidator

* Remove bundleValidationThreadCount (it's set by creating an appropriate executor)

* validate threadpool prefixes

* FIXME cleanup

* reassign FIXMEs to JB

* only create the threadpool if it will be used

* Add the MdcTaskDectorator to all threadpools

* Add bundle path to concurrently validated bundle resource validation messages.

* Add test to check bundle entry path being added to validation messages

* Threaded validation of contained resources initial checkin

* FHIR validator refactored to maintain correct bundle path and async validation task

* Refactored to use validation complete invoke callback to support raw string resource or resource object

* switch from XML to JSON

* # Conflicts:
#	hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/FhirValidator.java
#	hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

* Updated to use new HAPI-FHIR version

* merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation

* Updated to use new HAPI-FHIR version

* Revert "Updated to use new HAPI-FHIR version"

This reverts commit 910b7f676b.

* Revert "merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation"

This reverts commit c7d60fc3e6.

* Revert "Updated to use new HAPI-FHIR version"

This reverts commit aa8a7af455.

# Conflicts:
#	hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

* Fix Test dependencies after reverting changes.

* merge 'validate_contains_change' to 2564-contained-resource-validation-flag

* Disable threadpool prefix name validate check.

* merge master

* fix thread regexp

* pre-review cleanup

* change log

* fix test

* revert to XML as default validation serialization

* fix test

* fix test

Co-authored-by: Jaison B <jaisonb@gmail.com>
This commit is contained in:
Ken Stevens 2021-12-08 15:18:54 -05:00 committed by GitHub
parent d481896d9b
commit 9753b66610
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
116 changed files with 726 additions and 279 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
hapi-deployable-pom/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

18
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
View File

@ -127,6 +127,7 @@ public class FhirContext {
private volatile Boolean myFormatJsonSupported;
private volatile Boolean myFormatNDJsonSupported;
private volatile Boolean myFormatRdfSupported;
private IFhirValidatorFactory myFhirValidatorFactory = fhirContext -> new FhirValidator(fhirContext);
/**
* @deprecated It is recommended that you use one of the static initializer methods instead
@ -908,7 +909,7 @@ public class FhirContext {
* </p>
*/
public FhirValidator newValidator() {
return new FhirValidator(this);
return myFhirValidatorFactory.newFhirValidator(this);
}
public ViewGenerator newViewGenerator() {
@ -1072,9 +1073,22 @@ public class FhirContext {
*
* @param theParserErrorHandler The error handler
*/
public void setParserErrorHandler(final IParserErrorHandler theParserErrorHandler) {
public FhirContext setParserErrorHandler(final IParserErrorHandler theParserErrorHandler) {
Validate.notNull(theParserErrorHandler, "theParserErrorHandler must not be null");
myParserErrorHandler = theParserErrorHandler;
return this;
}
/**
* Set the factory method used to create FhirValidator instances
*
* @param theFhirValidatorFactory
* @return this
* @since 5.6.0
*/
public FhirContext setFhirValidatorFactory(IFhirValidatorFactory theFhirValidatorFactory) {
myFhirValidatorFactory = theFhirValidatorFactory;
return this;
}
@SuppressWarnings({"cast"})

27
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/IFhirValidatorFactory.java Normal file
View File

@ -0,0 +1,27 @@
package ca.uhn.fhir.context;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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.validation.FhirValidator;
public interface IFhirValidatorFactory {
FhirValidator newFhirValidator(FhirContext theFhirContext);
}

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/DefaultProfileValidationSupport.java
View File

@ -380,5 +380,4 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
ArrayList<IBaseResource> retVal = new ArrayList<>(theMap.values());
return (List<T>) Collections.unmodifiableList(retVal);
}
}

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java
View File

@ -36,7 +36,6 @@ import javax.annotation.Nullable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.function.Supplier;
@ -340,7 +339,6 @@ public interface IValidationSupport {
return null;
}
enum IssueSeverity {
/**
* The issue caused the action to fail, and no further checking could be performed.

165
hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/FhirValidator.java
View File

@ -24,13 +24,25 @@ import ca.uhn.fhir.context.FhirContext;
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.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.validation.schematron.SchematronProvider;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Future;
import java.util.function.Consumer;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
/**
@ -46,6 +58,7 @@ import java.util.List;
* </p>
*/
public class FhirValidator {
private static final Logger ourLog = LoggerFactory.getLogger(FhirValidator.class);
private static final String I18N_KEY_NO_PH_ERROR = FhirValidator.class.getName() + ".noPhError";
@ -53,6 +66,9 @@ public class FhirValidator {
private final FhirContext myContext;
private List<IValidatorModule> myValidators = new ArrayList<>();
private IInterceptorBroadcaster myInterceptorBroadcaster;
private boolean myConcurrentBundleValidation;
private ExecutorService myExecutorService;
/**
* Constructor (this should not be called directly, but rather {@link FhirContext#newValidator()} should be called to obtain an instance of {@link FhirValidator})
@ -72,8 +88,7 @@ public class FhirValidator {
registerValidatorModule(theInstance);
}
} else {
for (Iterator<IValidatorModule> iter = myValidators.iterator(); iter.hasNext(); ) {
IValidatorModule next = iter.next();
for (IValidatorModule next : myValidators) {
if (next.getClass().equals(type)) {
unregisterValidatorModule(next);
}
@ -86,6 +101,7 @@ public class FhirValidator {
for (IValidatorModule next : myValidators) {
if (next.getClass().equals(type)) {
found = true;
break;
}
}
return found;
@ -202,6 +218,21 @@ public class FhirValidator {
return validateWithResult(theResource, null);
}
/**
* Validates a resource instance returning a {@link ValidationResult} which contains the results.
*
* @param theResource the resource to validate
* @param theOptions Optionally provides options to the validator
* @return the results of validation
* @since 4.0.0
*/
public ValidationResult validateWithResult(String theResource, ValidationOptions theOptions) {
Validate.notNull(theResource, "theResource must not be null");
IValidationContext<IBaseResource> validationContext = ValidationContext.forText(myContext, theResource, theOptions);
Function<ValidationResult, ValidationResult> callback = result -> invokeValidationCompletedHooks(null, theResource, result);
return doValidate(validationContext, theOptions, callback);
}
/**
* Validates a resource instance returning a {@link ValidationResult} which contains the results.
*
@ -212,18 +243,65 @@ public class FhirValidator {
*/
public ValidationResult validateWithResult(IBaseResource theResource, ValidationOptions theOptions) {
Validate.notNull(theResource, "theResource must not be null");
IValidationContext<IBaseResource> validationContext = ValidationContext.forResource(myContext, theResource, theOptions);
Function<ValidationResult, ValidationResult> callback = result -> invokeValidationCompletedHooks(theResource, null, result);
return doValidate(validationContext, theOptions, callback);
}
private ValidationResult doValidate(IValidationContext<IBaseResource> theValidationContext, ValidationOptions theOptions,
Function<ValidationResult, ValidationResult> theValidationCompletionCallback) {
applyDefaultValidators();
IValidationContext<IBaseResource> ctx = ValidationContext.forResource(myContext, theResource, theOptions);
for (IValidatorModule next : myValidators) {
next.validateResource(ctx);
ValidationResult result;
if (myConcurrentBundleValidation && theValidationContext.getResource() instanceof IBaseBundle
&& myExecutorService != null) {
result = validateBundleEntriesConcurrently(theValidationContext, theOptions);
} else {
result = validateResource(theValidationContext);
}
ValidationResult result = ctx.toResult();
result = invokeValidationCompletedHooks(theResource, null, result);
return result;
return theValidationCompletionCallback.apply(result);
}
private ValidationResult validateBundleEntriesConcurrently(IValidationContext<IBaseResource> theValidationContext, ValidationOptions theOptions) {
List<IBaseResource> entries = BundleUtil.toListOfResources(myContext, (IBaseBundle) theValidationContext.getResource());
// Async validation tasks
List<ConcurrentValidationTask> validationTasks = IntStream.range(0, entries.size())
.mapToObj(index -> {
IBaseResource entry = entries.get(index);
String entryPathPrefix = String.format("Bundle.entry[%d].resource.ofType(%s)", index, entry.fhirType());
Future<ValidationResult> future = myExecutorService.submit(() -> {
IValidationContext<IBaseResource> entryValidationContext = ValidationContext.forResource(theValidationContext.getFhirContext(), entry, theOptions);
return validateResource(entryValidationContext);
});
return new ConcurrentValidationTask(entryPathPrefix, future);
}).collect(Collectors.toList());
List<SingleValidationMessage> validationMessages = new ArrayList<>();
try {
for (ConcurrentValidationTask validationTask : validationTasks) {
ValidationResult result = validationTask.getFuture().get();
final String bundleEntryPathPrefix = validationTask.getResourcePathPrefix();
List<SingleValidationMessage> messages = result.getMessages().stream()
.map(message -> {
String currentPath = message.getLocationString().substring(message.getLocationString().indexOf('.'));
message.setLocationString(bundleEntryPathPrefix + currentPath);
return message;
})
.collect(Collectors.toList());
validationMessages.addAll(messages);
}
} catch (InterruptedException | ExecutionException exp) {
throw new InternalErrorException(exp);
}
return new ValidationResult(myContext, new ArrayList<>(validationMessages));
}
private ValidationResult validateResource(IValidationContext<IBaseResource> theValidationContext) {
for (IValidatorModule next : myValidators) {
next.validateResource(theValidationContext);
}
return theValidationContext.toResult();
}
private ValidationResult invokeValidationCompletedHooks(IBaseResource theResourceParsed, String theResourceRaw, ValidationResult theValidationResult) {
@ -242,30 +320,6 @@ public class FhirValidator {
return theValidationResult;
}
/**
* Validates a resource instance returning a {@link ValidationResult} which contains the results.
*
* @param theResource the resource to validate
* @param theOptions Optionally provides options to the validator
* @return the results of validation
* @since 4.0.0
*/
public ValidationResult validateWithResult(String theResource, ValidationOptions theOptions) {
Validate.notNull(theResource, "theResource must not be null");
applyDefaultValidators();
IValidationContext<IBaseResource> ctx = ValidationContext.forText(myContext, theResource, theOptions);
for (IValidatorModule next : myValidators) {
next.validateResource(ctx);
}
ValidationResult result = ctx.toResult();
result = invokeValidationCompletedHooks(null, theResource, result);
return result;
}
/**
* Optionally supplies an interceptor broadcaster that will be used to invoke validation related Pointcut events
*
@ -274,4 +328,47 @@ public class FhirValidator {
public void setInterceptorBroadcaster(IInterceptorBroadcaster theInterceptorBraodcaster) {
myInterceptorBroadcaster = theInterceptorBraodcaster;
}
public FhirValidator setExecutorService(ExecutorService theExecutorService) {
myExecutorService = theExecutorService;
return this;
}
/**
* If this is true, bundles will be validated in parallel threads. The bundle structure itself will not be validated,
* only the resources in its entries.
*/
public boolean isConcurrentBundleValidation() {
return myConcurrentBundleValidation;
}
/**
* If this is true, bundles will be validated in parallel threads. The bundle structure itself will not be validated,
* only the resources in its entries.
*/
public FhirValidator setConcurrentBundleValidation(boolean theConcurrentBundleValidation) {
myConcurrentBundleValidation = theConcurrentBundleValidation;
return this;
}
// Simple Tuple to keep track of bundle path and associate aync future task
private static class ConcurrentValidationTask {
private final String myResourcePathPrefix;
private final Future<ValidationResult> myFuture;
private ConcurrentValidationTask(String theResourcePathPrefix, Future<ValidationResult> theFuture) {
myResourcePathPrefix = theResourcePathPrefix;
myFuture = theFuture;
}
public String getResourcePathPrefix() {
return myResourcePathPrefix;
}
public Future<ValidationResult> getFuture() {
return myFuture;
}
}
}

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/ValidationOptions.java
View File

@ -33,6 +33,9 @@ public class ValidationOptions {
private static ValidationOptions ourEmpty;
private Set<String> myProfiles;
public ValidationOptions() {
}
public Set<String> getProfiles() {
return myProfiles != null ? Collections.unmodifiableSet(myProfiles) : Collections.emptySet();
}

2
hapi-fhir-batch/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-bom/pom.xml
View File

@ -10,7 +10,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

3
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiFlywayMigrateDatabaseCommandTest.java
View File

@ -13,6 +13,7 @@ import org.springframework.jdbc.core.support.AbstractLobCreatingPreparedStatemen
import org.springframework.jdbc.support.lob.DefaultLobHandler;
import org.springframework.jdbc.support.lob.LobCreator;
import javax.annotation.Nonnull;
import javax.validation.constraints.NotNull;
import java.io.File;
import java.io.IOException;
@ -278,7 +279,7 @@ public class HapiFlywayMigrateDatabaseCommandTest {
assertTrue(JdbcUtils.getTableNames(connectionProperties).contains("HFJ_BLK_EXPORT_JOB")); // Late table
}
@NotNull
@Nonnull
private File getLocation(String theDatabaseName) throws IOException {
File directory = new File(DB_DIRECTORY);
if (directory.exists()) {

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-dist/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/2564-skip-contained-multithreaded-validation.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: add
title: "New configuration option added to validate bundle resources concurrently.
Also new configuration added to skip validation of contained resources."

2
hapi-fhir-jacoco/pom.xml
View File

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpa/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.binstore;
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IIdType;

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

@ -125,7 +125,6 @@ import ca.uhn.fhir.jpa.search.cache.DatabaseSearchResultCacheSvcImpl;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
import ca.uhn.fhir.jpa.search.reindex.BlockPolicy;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.search.reindex.ResourceReindexer;
import ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl;
@ -151,6 +150,7 @@ import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
import ca.uhn.fhir.rest.server.provider.DeleteExpungeProvider;
import ca.uhn.fhir.rest.server.provider.ReindexProvider;
import ca.uhn.fhir.util.ThreadPoolUtil;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -181,7 +181,6 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.scheduling.TaskScheduler;
import org.springframework.scheduling.concurrent.ConcurrentTaskScheduler;
import org.springframework.scheduling.concurrent.ScheduledExecutorFactoryBean;
import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
@ -426,18 +425,9 @@ public abstract class BaseConfig {
@Bean(name= BatchConstants.JOB_LAUNCHING_TASK_EXECUTOR)
public TaskExecutor jobLaunchingTaskExecutor() {
ThreadPoolTaskExecutor asyncTaskExecutor = new ThreadPoolTaskExecutor();
asyncTaskExecutor.setCorePoolSize(0);
asyncTaskExecutor.setMaxPoolSize(10);
asyncTaskExecutor.setQueueCapacity(0);
asyncTaskExecutor.setAllowCoreThreadTimeOut(true);
asyncTaskExecutor.setThreadNamePrefix("JobLauncher-");
asyncTaskExecutor.setRejectedExecutionHandler(new BlockPolicy());
asyncTaskExecutor.initialize();
return asyncTaskExecutor;
return ThreadPoolUtil.newThreadPool(0, 10, "job-launcher-");
}
@Bean
public IResourceReindexingSvc resourceReindexingSvc() {
return new ResourceReindexingSvcImpl();

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfigDstu3Plus.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.JpaPersistedResourceValidationSupport;
import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
@ -66,7 +67,7 @@ public abstract class BaseConfigDstu3Plus extends BaseConfig {
public abstract ITermVersionAdapterSvc terminologyVersionAdapterSvc();
@Bean(name = "myDefaultProfileValidationSupport")
public DefaultProfileValidationSupport defaultProfileValidationSupport() {
public DefaultProfileValidationSupport defaultProfileValidationSupport(DaoConfig theDaoConfig) {
return new DefaultProfileValidationSupport(fhirContext());
}

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

@ -86,7 +86,6 @@ import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
@ -1776,7 +1775,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
FhirValidator validator = getContext().newValidator();
validator.setInterceptorBroadcaster(CompositeInterceptorBroadcaster.newCompositeBroadcaster(myInterceptorBroadcaster, theRequest));
validator.registerValidatorModule(getInstanceValidator());
validator.registerValidatorModule(new IdChecker(theMode));

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
View File

@ -40,7 +40,6 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.ListMultimap;
import com.google.common.collect.MultimapBuilder;
import org.apache.commons.lang3.Functions;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IAnyResource;

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

@ -27,7 +27,12 @@ import ca.uhn.fhir.jpa.model.search.ExtendedLuceneIndexData;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
import org.jetbrains.annotations.NotNull;
import java.util.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
/**
* Extract search params for advanced lucene indexing.

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

@ -23,7 +23,18 @@ package ca.uhn.fhir.jpa.entity;
import ca.uhn.fhir.util.ValidateUtil;
import javax.annotation.Nonnull;
import javax.persistence.*;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.ForeignKey;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.Index;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import java.io.Serializable;
import static org.apache.commons.lang3.StringUtils.left;

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

@ -22,7 +22,20 @@ package ca.uhn.fhir.jpa.entity;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
import javax.persistence.*;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.EnumType;
import javax.persistence.Enumerated;
import javax.persistence.FetchType;
import javax.persistence.ForeignKey;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.Index;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import java.io.Serializable;
@Entity

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -41,15 +41,10 @@ import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
import ca.uhn.fhir.util.VersionEnum;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import static java.util.stream.Collectors.toSet;
@SuppressWarnings({"SqlNoDataSourceInspection", "SpellCheckingInspection"})
public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {

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

@ -390,21 +390,9 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
return Optional.empty();
}
@NotNull
@Nonnull
private PersistedJpaSearchFirstPageBundleProvider submitSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails, String theSearchUuid, ISearchBuilder theSb, String theQueryString, RequestPartitionId theRequestPartitionId, Search theSearch) {
StopWatch w = new StopWatch();
// Search search = new Search();
//TODO GGG MOVE THIS POPULATE AND ALSO THE HOOK CALL HIGHER UP IN THE STACK.
// populateSearchEntity(theParams, theResourceType, theSearchUuid, theQueryString, search, theRequestPartitionId);
// Interceptor call: STORAGE_PRESEARCH_REGISTERED
// HookParams params = new HookParams()
// .add(ICachedSearchDetails.class, search)
// .add(RequestDetails.class, theRequestDetails)
// .addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
// .add(SearchParameterMap.class, theParams);
// CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_PRESEARCH_REGISTERED, params);
SearchTask task = new SearchTask(theSearch, theCallingDao, theParams, theResourceType, theRequestDetails, theRequestPartitionId);
myIdToSearchTask.put(theSearch.getUuid(), task);
task.call();
@ -841,7 +829,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(@Nonnull @NotNull TransactionStatus theArg0) {
protected void doInTransactionWithoutResult(@Nonnull TransactionStatus theArg0) {
doSaveSearch();
}
@ -853,7 +841,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(@Nonnull @NotNull TransactionStatus theArg0) {
protected void doInTransactionWithoutResult(@Nonnull TransactionStatus theArg0) {
if (mySearch.getId() == null) {
doSaveSearch();
}

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

@ -2266,7 +2266,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
@Nullable
protected abstract CodeableConcept toCanonicalCodeableConcept(@Nullable IBaseDatatype theCodeableConcept);
@NotNull
@Nonnull
private FhirVersionIndependentConcept toConcept(IPrimitiveType<String> theCodeType, IPrimitiveType<String> theCodeSystemIdentifierType, IBaseCoding theCodingType) {
String code = theCodeType != null ? theCodeType.getValueAsString() : null;
String system = theCodeSystemIdentifierType != null ? getUrlFromIdentifier(theCodeSystemIdentifierType.getValueAsString()) : null;

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

@ -413,7 +413,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
}
@VisibleForTesting
@NotNull
@Nonnull
Properties getProperties(LoadedFileDescriptors theDescriptors, String thePropertiesFile) {
Properties retVal = new Properties();

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermCodeSystemStorageSvc.java
View File

@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.term.api;
* #L%
*/
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermDeferredStorageSvc.java
View File

@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.term.api;
* #L%
*/
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/BatchTermCodeSystemVersionDeleteWriter.java
View File

@ -22,10 +22,6 @@ package ca.uhn.fhir.jpa.term.job;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptPropertyDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import org.slf4j.Logger;
@ -34,7 +30,6 @@ import org.springframework.batch.item.ItemWriter;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import java.text.DecimalFormat;
import java.util.List;
import java.util.Optional;

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/TermCodeSystemDeleteTasklet.java
View File

@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.term.job;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/TermConceptDeleteTasklet.java
View File

@ -32,6 +32,8 @@ import org.springframework.batch.repeat.RepeatStatus;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import javax.annotation.Nonnull;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_ID;
/**
@ -49,7 +51,7 @@ public class TermConceptDeleteTasklet implements Tasklet {
private ITermCodeSystemVersionDao myCodeSystemVersionDao;
@Override
public RepeatStatus execute(@NotNull StepContribution contribution, ChunkContext context) throws Exception {
public RepeatStatus execute(@Nonnull StepContribution contribution, ChunkContext context) throws Exception {
long codeSystemPid = (Long) context.getStepContext().getJobParameters().get(JOB_PARAM_CODE_SYSTEM_ID);
ourLog.info("Deleting code system {}", codeSystemPid);

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincLinguisticVariantsHandler.java
View File

@ -5,6 +5,7 @@ import static org.apache.commons.lang3.StringUtils.trim;
import java.util.List;
import javax.annotation.Nonnull;
import javax.validation.constraints.NotNull;
import org.apache.commons.csv.CSVRecord;
@ -73,7 +74,7 @@ public class LoincLinguisticVariantsHandler implements IZipContentsHandlerCsv {
private String myIsoCountry;
private String myLanguageName;
public LinguisticVariant(@NotNull String theId, @NotNull String theIsoLanguage, @NotNull String theIsoCountry, @NotNull String theLanguageName) {
public LinguisticVariant(@Nonnull String theId, @Nonnull String theIsoLanguage, @Nonnull String theIsoCountry, @Nonnull String theLanguageName) {
this.myId = theId;
this.myIsoLanguage = theIsoLanguage;
this.myIsoCountry = theIsoCountry;

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

@ -615,7 +615,7 @@ public abstract class BaseJpaTest extends BaseTest {
}
}
@NotNull
@Nonnull
public static Map<String, String> buildHibernateSearchProperties(boolean enableLucene) {
Map<String, String> hibernateSearchProperties;
if (enableLucene) {

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -16,7 +16,6 @@ import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.validation.FhirValidator;

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -60,7 +60,6 @@ import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import ca.uhn.fhir.jpa.interceptor.PerformanceTracingLoggingInterceptor;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
@ -93,8 +92,6 @@ import ca.uhn.fhir.util.ClasspathUtil;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;
import org.hibernate.search.mapper.orm.Search;
import org.hibernate.search.mapper.orm.session.SearchSession;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.instance.model.api.IBaseResource;

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LuceneDisabledStandardQueries.java
View File

@ -20,8 +20,6 @@ import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.springframework.transaction.PlatformTransactionManager;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ExtendWith(SpringExtension.class)
@ContextConfiguration(classes = {TestR4WithLuceneDisabledConfig.class})
@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
View File

@ -15,7 +15,6 @@ import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.validation.FhirValidator;

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
View File

@ -130,7 +130,6 @@ import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.apache.commons.lang3.StringUtils.countMatches;
import static org.apache.commons.lang3.StringUtils.defaultString;

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java
View File

@ -49,7 +49,6 @@ import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import ca.uhn.fhir.jpa.interceptor.PerformanceTracingLoggingInterceptor;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.provider.r5.JpaSystemProviderR5;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
@ -76,8 +75,6 @@ import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;
import org.apache.commons.io.IOUtils;
import org.hibernate.search.mapper.orm.Search;
import org.hibernate.search.mapper.orm.session.SearchSession;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ExpungeR4Test.java
View File

@ -32,7 +32,6 @@ import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.DecimalType;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.MedicationRequest;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestDstu2Test.java
View File

@ -34,6 +34,7 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
import javax.validation.constraints.NotNull;
import java.util.ArrayList;
import java.util.List;
@ -109,7 +110,7 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
return subscription;
}
@NotNull
@Nonnull
private Subscription newSubscription(String criteria, String payload, String endpoint) {
Subscription subscription = new Subscription();
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestDstu3Test.java
View File

@ -41,6 +41,7 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
import javax.servlet.http.HttpServletRequest;
import javax.validation.constraints.NotNull;
import java.util.ArrayList;
@ -136,7 +137,7 @@ public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
return (Subscription) methodOutcome.getResource();
}
@NotNull
@Nonnull
private Subscription newSubscription(String theCriteria, String thePayload, String theEndpoint, List<StringType> headers) {
Subscription subscription = new Subscription();
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");

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

@ -14,9 +14,7 @@ import org.springframework.batch.core.JobExecution;
import org.springframework.test.util.ReflectionTestUtils;
import org.springframework.transaction.PlatformTransactionManager;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import static org.junit.jupiter.api.Assertions.assertFalse;

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

@ -13,7 +13,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplCurrentVersionR4Test.java
View File

@ -27,7 +27,6 @@ import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.mockito.Answers;
@ -36,7 +35,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.util.ResourceUtils;
import javax.persistence.EntityManager;

2
hapi-fhir-jpaserver-cql/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-mdm/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvc.java
View File

@ -155,7 +155,7 @@ public class MdmLinkDaoSvc {
return getMdmLinkWithMatchResult(theSourceResource, MdmMatchResultEnum.POSSIBLE_MATCH);
}
@NotNull
@Nonnull
private Optional<MdmLink> getMdmLinkWithMatchResult(IBaseResource theSourceResource, MdmMatchResultEnum theMatchResult) {
Long pid = myIdHelperService.getPidOrNull(theSourceResource);
if (pid == null) {

1
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/BaseProviderR4Test.java
View File

@ -3,7 +3,6 @@ package ca.uhn.fhir.jpa.mdm.provider;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.mdm.api.IMdmClearJobSubmitter;
import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
import ca.uhn.fhir.mdm.provider.MdmControllerHelper;
import ca.uhn.fhir.mdm.provider.MdmProviderDstu3Plus;

2
hapi-fhir-jpaserver-model/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

8
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/BinaryStorageEntity.java
View File

@ -20,7 +20,13 @@ package ca.uhn.fhir.jpa.model.entity;
* #L%
*/
import javax.persistence.*;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Lob;
import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import java.sql.Blob;
import java.util.Date;

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

@ -21,11 +21,9 @@ package ca.uhn.fhir.jpa.model.search;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.param.TokenParam;
import com.google.common.collect.HashMultimap;
import com.google.common.collect.SetMultimap;
import org.apache.commons.lang3.StringUtils;
import org.hibernate.search.engine.backend.document.DocumentElement;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

2
hapi-fhir-jpaserver-searchparam/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java
View File

@ -290,7 +290,7 @@ public class SearchParamExtractorService {
theEntity.setHasLinks(theParams.myLinks.size() > 0);
}
private void extractResourceLinks(@NotNull RequestPartitionId theRequestPartitionId, ResourceIndexedSearchParams theParams, ResourceTable theEntity, TransactionDetails theTransactionDetails, RuntimeSearchParam theRuntimeSearchParam, PathAndRef thePathAndRef, boolean theFailOnInvalidReference, RequestDetails theRequest) {
private void extractResourceLinks(@Nonnull RequestPartitionId theRequestPartitionId, ResourceIndexedSearchParams theParams, ResourceTable theEntity, TransactionDetails theTransactionDetails, RuntimeSearchParam theRuntimeSearchParam, PathAndRef thePathAndRef, boolean theFailOnInvalidReference, RequestDetails theRequest) {
IBaseReference nextReference = thePathAndRef.getRef();
IIdType nextId = nextReference.getReferenceElement();
String path = thePathAndRef.getPath();

2
hapi-fhir-jpaserver-subscription/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/websocket/WebsocketConnectionValidator.java
View File

@ -29,6 +29,8 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
public class WebsocketConnectionValidator {
private static Logger ourLog = LoggerFactory.getLogger(WebsocketConnectionValidator.class);
@ -43,7 +45,7 @@ public class WebsocketConnectionValidator {
super();
}
public WebsocketValidationResponse validate(@NotNull IdType id) {
public WebsocketValidationResponse validate(@Nonnull IdType id) {
if (!id.hasIdPart() || !id.isIdPartValid()) {
return WebsocketValidationResponse.INVALID_RESPONSE("Invalid bind request - No ID included: " + id.getValue());
}

2
hapi-fhir-jpaserver-test-utilities/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/config/TestJpaDstu3Config.java
View File

@ -22,8 +22,6 @@ package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.binstore.MemoryBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;

2
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-server-mdm/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

12
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmProviderDstu3Plus.java
View File

@ -22,10 +22,8 @@ package ca.uhn.fhir.mdm.provider;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
import ca.uhn.fhir.mdm.api.MatchedTarget;
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.mdm.api.MdmLinkJson;
import ca.uhn.fhir.mdm.api.paging.MdmPageRequest;
@ -39,30 +37,20 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.BundleBuilder;
import ca.uhn.fhir.util.ParametersUtil;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import javax.annotation.Nonnull;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.Date;
import java.util.List;
import java.util.UUID;
import java.util.stream.Collectors;
import static ca.uhn.fhir.rest.api.Constants.PARAM_OFFSET;

1
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmProviderLoader.java
View File

@ -23,7 +23,6 @@ package ca.uhn.fhir.mdm.provider;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;

2
hapi-fhir-server-openapi/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

11
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/ResponseValidatingInterceptor.java
View File

@ -20,20 +20,19 @@ package ca.uhn.fhir.rest.server.interceptor;
* #L%
*/
import java.util.HashSet;
import java.util.Set;
import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Pointcut;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import ca.uhn.fhir.validation.ValidationResult;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.util.HashSet;
import java.util.Set;
/**
* This interceptor intercepts each outgoing response and if it contains a FHIR resource, validates that resource. The interceptor may be configured to run any validator modules, and will then add

6
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/GraphQLQueryBodyParameter.java
View File

@ -21,21 +21,15 @@ package ca.uhn.fhir.rest.server.method;
*/
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.parser.json.JsonLikeObject;
import ca.uhn.fhir.parser.json.JsonLikeStructure;
import ca.uhn.fhir.parser.json.JsonLikeValue;
import ca.uhn.fhir.parser.json.jackson.JacksonStructure;
import ca.uhn.fhir.rest.annotation.Count;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.fasterxml.jackson.core.JsonFactory;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.io.IOUtils;
import javax.annotation.Nullable;
import java.io.IOException;
import java.io.Reader;
import java.lang.reflect.Method;

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-sql-migrate/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-storage/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

24
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
View File

@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.validation.FhirValidator;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.StringUtils;
@ -286,6 +287,12 @@ public class DaoConfig {
*/
private int myInlineResourceTextBelowSize = 0;
/**
* @see FhirValidator#isConcurrentBundleValidation()
* @since 5.7.0
*/
private boolean myConcurrentBundleValidation;
/**
* Constructor
*/
@ -2724,6 +2731,23 @@ public class DaoConfig {
this.myAdvancedLuceneIndexing = theAdvancedLuceneIndexing;
}
/**
* @see FhirValidator#isConcurrentBundleValidation()
* @since 5.7.0
*/
public boolean isConcurrentBundleValidation() {
return myConcurrentBundleValidation;
}
/**
* @see FhirValidator#isConcurrentBundleValidation()
* @since 5.7.0
*/
public DaoConfig setConcurrentBundleValidation(boolean theConcurrentBundleValidation) {
myConcurrentBundleValidation = theConcurrentBundleValidation;
return this;
}
public enum StoreMetaSourceInformationEnum {
NONE(false, false),
SOURCE_URI(true, false),

2
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java
View File

@ -431,7 +431,7 @@ public abstract class BaseStorageDao {
return oo;
}
@NotNull
@Nonnull
protected ResourceGoneException createResourceGoneException(IBasePersistedResource theResourceEntity) {
StringBuilder b = new StringBuilder();
b.append("Resource was deleted at ");

10
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
View File

@ -80,6 +80,7 @@ import ca.uhn.fhir.util.ElementUtil;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ResourceReferenceInfo;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.ThreadPoolUtil;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.ArrayListMultimap;
@ -102,7 +103,6 @@ import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.task.SyncTaskExecutor;
import org.springframework.core.task.TaskExecutor;
import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.support.TransactionCallback;
@ -193,13 +193,7 @@ public abstract class BaseTransactionProcessor {
private TaskExecutor getTaskExecutor() {
if (myExecutor == null) {
if (myDaoConfig.getBundleBatchPoolSize() > 1) {
ThreadPoolTaskExecutor executor = new ThreadPoolTaskExecutor();
executor.setThreadNamePrefix("bundle_batch_");
executor.setCorePoolSize(myDaoConfig.getBundleBatchPoolSize());
executor.setMaxPoolSize(myDaoConfig.getBundleBatchMaxPoolSize());
executor.initialize();
myExecutor = executor;
myExecutor = ThreadPoolUtil.newThreadPool(myDaoConfig.getBundleBatchPoolSize(), myDaoConfig.getBundleBatchMaxPoolSize(), "bundle-batch-");
} else {
SyncTaskExecutor executor = new SyncTaskExecutor();
myExecutor = executor;

47
hapi-fhir-storage/src/main/java/ca/uhn/fhir/util/ThreadPoolUtil.java Normal file
View File

@ -0,0 +1,47 @@
package ca.uhn.fhir.util;
/*-
* #%L
* HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.search.reindex.BlockPolicy;
import org.apache.commons.lang3.Validate;
import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import javax.annotation.Nonnull;
public final class ThreadPoolUtil {
private ThreadPoolUtil() {
}
@Nonnull
public static ThreadPoolTaskExecutor newThreadPool(int theCorePoolSize, int theMaxPoolSize, String theThreadNamePrefix) {
Validate.isTrue(theThreadNamePrefix.endsWith("-"), "Thread pool prefix name must end with a hyphen");
ThreadPoolTaskExecutor asyncTaskExecutor = new ThreadPoolTaskExecutor();
asyncTaskExecutor.setCorePoolSize(theCorePoolSize);
asyncTaskExecutor.setMaxPoolSize(theMaxPoolSize);
asyncTaskExecutor.setQueueCapacity(0);
asyncTaskExecutor.setAllowCoreThreadTimeOut(true);
asyncTaskExecutor.setThreadNamePrefix(theThreadNamePrefix);
asyncTaskExecutor.setRejectedExecutionHandler(new BlockPolicy());
asyncTaskExecutor.initialize();
return asyncTaskExecutor;
}
}

2
hapi-fhir-structures-dstu2.1/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-hl7org-dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-test-utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-testpage-overlay/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu2.1/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE4-SNAPSHOT</version>
<version>5.7.0-PRE5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

Some files were not shown because too many files have changed in this diff Show More