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hapi-fhir
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Merge branch 'master' into batch-empi-job

This commit is contained in:
Tadgh 2020-07-16 11:00:32 -07:00
parent 31e9f140ad 49c08f31d8
commit 6bb92717f5
132 changed files with 3458 additions and 1475 deletions
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10
azure-pipelines.yml
View File

@ -25,16 +25,6 @@ jobs:
inputs:
targetType: 'inline'
script: mkdir -p $(MAVEN_CACHE_FOLDER); pwd; ls -al $(MAVEN_CACHE_FOLDER)
# - task: Maven@3
#env:
# JAVA_HOME_11_X64: /usr/local/openjdk-11
# inputs:
# goals: 'dependency:go-offline'
# # These are Maven CLI options (and show up in the build logs) - "-nsu"=Don't update snapshots. We can remove this when Maven OSS is more healthy
# options: '-P ALLMODULES,JACOCO,CI,ERRORPRONE -e -B -Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
# # These are JVM options (and don't show up in the build logs)
# mavenOptions: '-Xmx1024m $(MAVEN_OPTS) -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS -Duser.timezone=America/Toronto'
# jdkVersionOption: 1.11
- task: Maven@3
env:
JAVA_HOME_11_X64: /usr/local/openjdk-11

37
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/phonetic/ApacheEncoder.java
View File

@ -22,9 +22,12 @@ package ca.uhn.fhir.context.phonetic;
import org.apache.commons.codec.EncoderException;
import org.apache.commons.codec.StringEncoder;
import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.StringJoiner;
public class ApacheEncoder implements IPhoneticEncoder {
private static final Logger ourLog = LoggerFactory.getLogger(ApacheEncoder.class);
@ -44,10 +47,44 @@ public class ApacheEncoder implements IPhoneticEncoder {
@Override
public String encode(String theString) {
try {
// If the string contains a space, encode alpha parts separately so, for example, numbers are preserved in address lines.
if (theString.contains(" ")) {
return encodeStringWithSpaces(theString);
}
return myStringEncoder.encode(theString);
} catch (EncoderException e) {
ourLog.error("Failed to encode string " + theString, e);
return theString;
}
}
private String encodeStringWithSpaces(String theString) throws EncoderException {
StringJoiner joiner = new StringJoiner(" ");
// This sub-stack holds the alpha parts
StringJoiner alphaJoiner = new StringJoiner(" ");
for (String part : theString.split("[\\s\\W]+")) {
if (StringUtils.isAlpha(part)) {
alphaJoiner.add(part);
} else {
// Once we hit a non-alpha part, encode all the alpha parts together as a single string
// This is to allow encoders like METAPHONE to match Hans Peter to Hanspeter
alphaJoiner = encodeAlphaParts(joiner, alphaJoiner);
joiner.add(part);
}
}
encodeAlphaParts(joiner, alphaJoiner);
return joiner.toString();
}
private StringJoiner encodeAlphaParts(StringJoiner theJoiner, StringJoiner theAlphaJoiner) throws EncoderException {
// Encode the alpha parts as a single string and then flush the alpha encoder
if (theAlphaJoiner.length() > 0) {
theJoiner.add(myStringEncoder.encode(theAlphaJoiner.toString()));
theAlphaJoiner = new StringJoiner(" ");
}
return theAlphaJoiner;
}
}

14
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/ConceptValidationOptions.java
View File

@ -25,6 +25,9 @@ import org.apache.commons.lang3.builder.ToStringStyle;
public class ConceptValidationOptions {
private boolean myValidateDisplay;
private boolean myInferSystem;
public boolean isInferSystem() {
return myInferSystem;
}
@ -34,12 +37,19 @@ public class ConceptValidationOptions {
return this;
}
private boolean myInferSystem;
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("inferSystem", myInferSystem)
.toString();
}
public boolean isValidateDisplay() {
return myValidateDisplay;
}
public ConceptValidationOptions setValidateDisplay(boolean theValidateDisplay) {
myValidateDisplay = theValidateDisplay;
return this;
}
}

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/ValidationSupportContext.java
View File

@ -20,6 +20,8 @@ package ca.uhn.fhir.context.support;
* #L%
*/
import org.thymeleaf.util.Validate;
import java.util.HashSet;
import java.util.Set;
@ -29,6 +31,7 @@ public class ValidationSupportContext {
private final Set<String> myCurrentlyGeneratingSnapshots = new HashSet<>();
public ValidationSupportContext(IValidationSupport theRootValidationSupport) {
Validate.notNull(theRootValidationSupport, "theRootValidationSupport musty not be null");
myRootValidationSupport = theRootValidationSupport;
}

51
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
View File

@ -854,6 +854,21 @@ public enum Pointcut {
*/
SUBSCRIPTION_AFTER_ACTIVE_SUBSCRIPTION_REGISTERED(void.class, "ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription"),
/**
* <b>Subscription Hook:</b>
* Invoked immediately after an active subscription is "registered". In HAPI FHIR, when
* a subscription
* <p>
* Hooks may make changes to the canonicalized subscription and this will have an effect
* on processing across this server. Note however that timing issues may occur, since the
* subscription is already technically live by the time this hook is called.
* </p>
* No parameters are currently supported.
* <p>
* Hooks should return <code>void</code>.
* </p>
*/
SUBSCRIPTION_AFTER_ACTIVE_SUBSCRIPTION_UNREGISTERED(void.class),
/**
* <b>Storage Hook:</b>
@ -1562,6 +1577,42 @@ public enum Pointcut {
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails"
),
/**
* <b>Storage Hook:</b>
* Invoked when a transaction has been rolled back as a result of a {@link ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException},
* meaning that a database constraint has been violated. This pointcut allows an interceptor to specify a resolution strategy
* other than simply returning the error to the client. This interceptor will be fired after the database transaction rollback
* has been completed.
* <p>
* Hooks may accept the following parameters:
* </p>
* <ul>
* <li>
* ca.uhn.fhir.rest.api.server.RequestDetails - A bean containing details about the request that is about to be processed, including details such as the
* resource type and logical ID (if any) and other FHIR-specific aspects of the request which have been
* pulled out of the servlet request. Note that the bean
* properties are not all guaranteed to be populated, depending on how early during processing the
* exception occurred. <b>Note that this parameter may be null in contexts where the request is not
* known, such as while processing searches</b>
* </li>
* <li>
* ca.uhn.fhir.rest.server.servlet.ServletRequestDetails - A bean containing details about the request that is about to be processed, including details such as the
* resource type and logical ID (if any) and other FHIR-specific aspects of the request which have been
* pulled out of the servlet request. This parameter is identical to the RequestDetails parameter above but will
* only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
* </li>
* </ul>
* <p>
* Hooks should return <code>ca.uhn.fhir.jpa.api.model.ResourceVersionConflictResolutionStrategy</code>. Hooks should not
* throw any exception.
* </p>
*/
STORAGE_VERSION_CONFLICT(
"ca.uhn.fhir.jpa.api.model.ResourceVersionConflictResolutionStrategy",
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails"
),
/**
* <b>EMPI Hook:</b>
* Invoked whenever a persisted Patient/Practitioner resource (a resource that has just been stored in the

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/GraphQL.java
View File

@ -20,6 +20,9 @@ package ca.uhn.fhir.rest.annotation;
* #L%
*/
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
@ -32,4 +35,5 @@ import java.lang.annotation.Target;
@Retention(RetentionPolicy.RUNTIME)
@Target(value= ElementType.METHOD)
public @interface GraphQL {
RequestTypeEnum type() default RequestTypeEnum.GET;
}

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/GraphQLQuery.java → hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/GraphQLQueryBody.java
View File

@ -37,6 +37,6 @@ import java.lang.annotation.Target;
*/
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.PARAMETER)
public @interface GraphQLQuery {
public @interface GraphQLQueryBody {
// ignore
}

42
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/GraphQLQueryUrl.java Normal file
View File

@ -0,0 +1,42 @@
package ca.uhn.fhir.rest.annotation;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* 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 LBoicense.
* #L%
*/
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
/**
* This annotation should be placed on the parameter of a
* {@link GraphQL @GraphQL} annotated method. The given
* parameter will be populated with the specific graphQL
* query being requested.
*
* <p>
* This parameter should be of type {@link String}
* </p>
*/
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.PARAMETER)
public @interface GraphQLQueryUrl {
// ignore
}

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
View File

@ -66,6 +66,7 @@ public class Constants {
public static final String CT_HTML = "text/html";
public static final String CT_HTML_WITH_UTF8 = "text/html" + CHARSET_UTF8_CTSUFFIX;
public static final String CT_JSON = "application/json";
public static final String CT_GRAPHQL = "application/graphql";
public static final String CT_JSON_PATCH = "application/json-patch+json";
public static final String CT_OCTET_STREAM = "application/octet-stream";
public static final String CT_TEXT = "text/plain";

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/exceptions/ResourceVersionConflictException.java
View File

@ -37,6 +37,9 @@ public class ResourceVersionConflictException extends BaseServerResponseExceptio
public static final int STATUS_CODE = Constants.STATUS_HTTP_409_CONFLICT;
private static final long serialVersionUID = 1L;
/**
* Constructor
*/
public ResourceVersionConflictException(String error) {
super(STATUS_CODE, error);
}

33
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
View File

@ -13,6 +13,8 @@ import ca.uhn.fhir.context.RuntimeExtensionDtDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IElement;
import ca.uhn.fhir.model.api.IIdentifiableElement;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
import ca.uhn.fhir.model.base.composite.BaseContainedDt;
@ -21,6 +23,7 @@ import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.parser.DataFormatException;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseElement;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions;
@ -128,6 +131,28 @@ public class FhirTerser {
Validate.notNull(theSource, "theSource must not be null");
Validate.notNull(theTarget, "theTarget must not be null");
// DSTU3+
if (theSource instanceof IBaseElement) {
IBaseElement source = (IBaseElement) theSource;
IBaseElement target = (IBaseElement) theTarget;
target.setId(source.getId());
}
// DSTU2 only
if (theSource instanceof IIdentifiableElement) {
IIdentifiableElement source = (IIdentifiableElement) theSource;
IIdentifiableElement target = (IIdentifiableElement) theTarget;
target.setElementSpecificId(source.getElementSpecificId());
}
// DSTU2 only
if (theSource instanceof IResource) {
IResource source = (IResource) theSource;
IResource target = (IResource) theTarget;
target.setId(source.getId());
target.getResourceMetadata().putAll(source.getResourceMetadata());
}
if (theSource instanceof IPrimitiveType<?>) {
if (theTarget instanceof IPrimitiveType<?>) {
((IPrimitiveType<?>) theTarget).setValueAsString(((IPrimitiveType<?>) theSource).getValueAsString());
@ -159,7 +184,13 @@ public class FhirTerser {
}
BaseRuntimeElementDefinition<?> element = myContext.getElementDefinition(nextValue.getClass());
IBase target = element.newInstance();
Object instanceConstructorArg = targetChild.getInstanceConstructorArguments();
IBase target;
if (instanceConstructorArg != null) {
target = element.newInstance(instanceConstructorArg);
} else {
target = element.newInstance();
}
targetChild.getMutator().addValue(theTarget, target);
cloneInto(nextValue, target, theIgnoreMissingFields);

29
hapi-fhir-base/src/test/java/ca/uhn/fhir/context/phonetic/PhoneticEncoderTest.java Normal file
View File

@ -0,0 +1,29 @@
package ca.uhn.fhir.context.phonetic;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.EnumSource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static org.hamcrest.Matchers.startsWith;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.endsWith;
class PhoneticEncoderTest {
private static final Logger ourLog = LoggerFactory.getLogger(PhoneticEncoderTest.class);
private static final String NUMBER = "123";
private static final String STREET = "Nohili St, Suite";
private static final String SUITE = "456";
private static final String ADDRESS_LINE = NUMBER + " " + STREET + " " + SUITE;
@ParameterizedTest
@EnumSource(PhoneticEncoderEnum.class)
public void testEncodeAddress(PhoneticEncoderEnum thePhoneticEncoderEnum) {
String encoded = thePhoneticEncoderEnum.getPhoneticEncoder().encode(ADDRESS_LINE);
ourLog.info("{}: {}", thePhoneticEncoderEnum.name(), encoded);
assertThat(encoded, startsWith(NUMBER + " "));
assertThat(encoded, endsWith(" " + SUITE));
}
}

16
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/CreatePackageCommand.java
View File

@ -134,14 +134,16 @@ public class CreatePackageCommand extends BaseCommand {
}
String[] dependencies = theCommandLine.getOptionValues(DEPENDENCY_OPT);
for (String nextDependencyString : dependencies) {
int colonIdx = nextDependencyString.indexOf(":");
if (colonIdx == -1) {
throw new ParseException("Invalid dependency spec: " + nextDependencyString);
if (dependencies != null) {
for (String nextDependencyString : dependencies) {
int colonIdx = nextDependencyString.indexOf(":");
if (colonIdx == -1) {
throw new ParseException("Invalid dependency spec: " + nextDependencyString);
}
String depName = nextDependencyString.substring(0, colonIdx);
String depVersion = nextDependencyString.substring(colonIdx + 1);
manifestGenerator.dependency(depName, depVersion);
}
String depName = nextDependencyString.substring(0, colonIdx);
String depVersion = nextDependencyString.substring(colonIdx+1);
manifestGenerator.dependency(depName, depVersion);
}
myWorkDirectory = Files.createTempDir();

48
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/CreatePackageCommandTest.java
View File

@ -113,6 +113,54 @@ public class CreatePackageCommandTest extends BaseTest {
}
@Test
public void testCreatePackage_NoDependencies() throws IOException {
StructureDefinition sd = new StructureDefinition();
sd.setUrl("http://foo/1");
writeFile(sd, "foo1.json");
ValueSet vs = new ValueSet();
vs.setUrl("http://foo/2");
writeFile(vs, "foo2.json");
App.main(new String[]{
"create-package",
"--fhir-version", "R4",
"--name", "com.example.ig",
"--version", "1.0.1",
"--include-package", myWorkDirectory.getAbsolutePath() + "/*.json",
"--target-directory", myTargetDirectory.getAbsolutePath()
});
Archiver archiver = ArchiverFactory.createArchiver("tar", "gz");
File igArchive = new File(myTargetDirectory, "com.example.ig-1.0.1.tgz");
archiver.extract(igArchive, myExtractDirectory);
List<String> allFiles = FileUtils.listFiles(myExtractDirectory, TrueFileFilter.INSTANCE, TrueFileFilter.INSTANCE)
.stream()
.map(t -> t.getPath())
.sorted()
.collect(Collectors.toList());
ourLog.info("Archive contains files:\n * {}", allFiles.stream().collect(Collectors.joining("\n * ")));
// Verify package.json
String packageJsonContents = IOUtils.toString(new FileInputStream(new File(myExtractDirectory, "package/package.json")), Charsets.UTF_8);
ourLog.info("Package.json:\n{}", packageJsonContents);
String expectedPackageJson = "{\n" +
" \"name\": \"com.example.ig\",\n" +
" \"version\": \"1.0.1\"\n" +
"}";
assertEquals(expectedPackageJson, packageJsonContents);
// Try parsing the module again to make sure we can
NpmPackage loadedPackage = NpmPackage.fromPackage(new FileInputStream(igArchive));
assertEquals("com.example.ig", loadedPackage.name());
}
public void writeFile(IBaseResource theResource, String theFileName) throws IOException {
try (FileWriter w = new FileWriter(new File(myWorkDirectory, theFileName), false)) {
myContext.newJsonParser().encodeResourceToWriter(theResource, w);

6
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ServerOperations.java
View File

@ -53,9 +53,9 @@ public class ServerOperations {
ourLog.info("Received call with content type {} and {} bytes", contentType, bytes.length);
theServletResponse.setContentType(contentType);
theServletResponse.getOutputStream().write(bytes);
theServletResponse.getOutputStream().close();
theServletResponse.setContentType("text/plain");
theServletResponse.getWriter().write("hello");
theServletResponse.getWriter().close();
}
//END SNIPPET: manualInputAndOutput

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1896-add-support-for-graphql-body.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 1896
title: "Support has been added for GraphQL querying using an HTTP POST (with the query in the body). Thanks to
Ibrohim Kholilul Islam for the pull request implementing this new feature!"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1966-allow-graphql-or-list.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 1966
title: "The GraphQL module can now accept arrays of arguments as input to searches, and will treat them as
OR'ed parameters. Thanks to Ibrohim Kholilul Isla for the pull request!"

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1971-avoid-concurrent-write-errors.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: add
issue: 1971
title: "A new interceptor called `UserRequestRetryVersionConflictsInterceptor` has been added to the JPA server. This interceptor
allows clients to instruct the server to attempt to avoid returning an HTTP 409 (Version Conflict) if two concurrent client
requests try to update the same resource at the same time."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1971-create-package-no-dependencies.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
issue: 1971
title: The create-package CLI command failed with a NPE if no package dependencies were specified. This has been corrected.

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1982-fix-validation-for-enumerated-valuesets.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: add
issue: 1982
title: The validator will now accept codes that are defined in a ValueSet where the valueset contains an enumeration of
codes, and the CodeSystem URL refers to an unknown CodeSystem. This allows successful validation of ValueSets in several
IGs that rely on the existence of grammar based systems.

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1983-allow-conceptmap-with-no-group-source_or_target.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 1983
title: "ConceptMap resources were blocked from uploading into the JPA server if the ConceptMap had a source
and/or target URL defined at the ConceptMap level but not at the group level. This prevented some US Core
resources from being successfully uploaded. This has been corrected."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/interceptors/built_in_server_interceptors.md
View File

@ -178,3 +178,10 @@ The ResponseSizeCapturingInterceptor can be used to capture the number of charac
* [ResponseSizeCapturingInterceptor JavaDoc](/apidocs/hapi-fhir-server/ca/uhn/fhir/rest/server/interceptor/ResponseSizeCapturingInterceptor.html)
* [ResponseSizeCapturingInterceptor Source](https://github.com/jamesagnew/hapi-fhir/blob/master/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/ResponseSizeCapturingInterceptor.java)
# JPA Server: Allow Cascading Deletes
The CascadingDeleteInterceptor allows clients to request deletes be cascaded to other resources that contain incoming references. See [Cascading Deletes](/docs/server_jpa/configuration.html#cascading-deletes) for more information.
# JPA Server: Retry on Version Conflicts
The UserRequestRetryVersionConflictsInterceptor allows clients to request that the server avoid version conflicts (HTTP 409) when two concurrent client requests attempt to modify the same resource. See [Version Conflicts](/docs/server_jpa/configuration.html#retry-on-version-conflict) for more information.

18
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/configuration.md
View File

@ -103,10 +103,26 @@ Cache-Control: no-store, max-results=20
* [This page](https://www.openhealthhub.org/t/hapi-terminology-server-uk-snomed-ct-import/592) has information on loading national editions (UK specifically) of SNOMED CT files into the database.
<a name="cascading-deletes"/>
# Cascading Deletes
An interceptor called `CascadingDeleteInterceptor` may be registered against the Server. When this interceptor is enabled, cascading deletes may be performed using either of the following:
An interceptor called `CascadingDeleteInterceptor` may be registered against the server. When this interceptor is enabled, cascading deletes may be performed using either of the following:
* The request may include the following parameter: `_cascade=delete`
* The request may include the following header: `X-Cascade: delete`
<a name="retry-on-version-conflict"/>
# Version Conflicts
If a server is serving multiple concurrent requests against the same resource, a [ResourceVersionConflictException](/hapi-fhir/apidocs/hapi-fhir-base/ca/uhn/fhir/rest/server/exceptions/ResourceVersionConflictException.html) may be thrown (resulting in an **HTTP 409 Version Conflict** being returned to the client). For example, if two client requests attempt to update the same resource at the exact same time, this exception will be thrown for one of the requests. This exception is not a bug in the server itself, but instead is a defense against client updates accidentally being lost because of concurrency issues. When this occurs, it is important to consider what the root cause might be, since concurrent writes against the same resource are often indicative of a deeper application design issue.
An interceptor called `UserRequestRetryVersionConflictsInterceptor` may be registered against the server. When this interceptor is enabled, requests may include an optional header requesting for the server to try to avoid returning an error due to concurrent writes. The server will then try to avoid version conflict errors by automatically retrying requests that would have otherwise failed due to a version conflict.
With this interceptor in place, the following header can be added to individual HTTP requests to instruct the server to avoid version conflict errors:
```http
X-Retry-On-Version-Conflict: retry; max-retries=100
```

28
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoValueSet.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.api.dao;
* #L%
*/
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -41,31 +42,6 @@ public interface IFhirResourceDaoValueSet<T extends IBaseResource, CD, CC> exten
void purgeCaches();
ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CD theCoding, CC theCodeableConcept, RequestDetails theRequestDetails);
class ValidateCodeResult {
private String myDisplay;
private String myMessage;
private boolean myResult;
public ValidateCodeResult(boolean theResult, String theMessage, String theDisplay) {
super();
myResult = theResult;
myMessage = theMessage;
myDisplay = theDisplay;
}
public String getDisplay() {
return myDisplay;
}
public String getMessage() {
return myMessage;
}
public boolean isResult() {
return myResult;
}
}
IValidationSupport.CodeValidationResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CD theCoding, CC theCodeableConcept, RequestDetails theRequestDetails);
}

49
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/model/ResourceVersionConflictResolutionStrategy.java Normal file
View File

@ -0,0 +1,49 @@
package ca.uhn.fhir.jpa.api.model;
/*-
* #%L
* HAPI FHIR JPA API
* %%
* 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 org.apache.commons.lang3.Validate;
/**
* @since 5.1.0
*/
public class ResourceVersionConflictResolutionStrategy {
private int myMaxRetries;
private boolean myRetry;
public int getMaxRetries() {
return myMaxRetries;
}
public void setMaxRetries(int theMaxRetries) {
Validate.isTrue(theMaxRetries >= 0, "theRetryUpToMillis must not be negative");
myMaxRetries = theMaxRetries;
}
public boolean isRetry() {
return myRetry;
}
public void setRetry(boolean theRetry) {
myRetry = theRetry;
}
}

14
hapi-fhir-jpaserver-base/pom.xml
View File

@ -163,8 +163,6 @@
</exclusions>
</dependency>
<dependency>
<groupId>net.ttddyy</groupId>
<artifactId>datasource-proxy</artifactId>
@ -734,7 +732,8 @@
<version>dstu2</version>
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
<packageBase>ca.uhn.fhir.jpa.rp.dstu2</packageBase>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-dstu2.xml</targetResourceSpringBeansFile>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-dstu2.xml
</targetResourceSpringBeansFile>
<baseResourceNames/>
<excludeResourceNames>
<!-- <excludeResourceName>OperationDefinition</excludeResourceName> <excludeResourceName>OperationOutcome</excludeResourceName> -->
@ -750,7 +749,8 @@
<version>dstu3</version>
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
<packageBase>ca.uhn.fhir.jpa.rp.dstu3</packageBase>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-dstu3.xml</targetResourceSpringBeansFile>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-dstu3.xml
</targetResourceSpringBeansFile>
<baseResourceNames></baseResourceNames>
<excludeResourceNames>
</excludeResourceNames>
@ -765,7 +765,8 @@
<version>r4</version>
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
<packageBase>ca.uhn.fhir.jpa.rp.r4</packageBase>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-r4.xml</targetResourceSpringBeansFile>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-r4.xml
</targetResourceSpringBeansFile>
<baseResourceNames></baseResourceNames>
<excludeResourceNames>
</excludeResourceNames>
@ -780,7 +781,8 @@
<version>r5</version>
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
<packageBase>ca.uhn.fhir.jpa.rp.r5</packageBase>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-r5.xml</targetResourceSpringBeansFile>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-r5.xml
</targetResourceSpringBeansFile>
<baseResourceNames></baseResourceNames>
</configuration>
</execution>

70
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BulkExportJobParameterValidator.java
View File

@ -28,6 +28,8 @@ import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.batch.core.JobParametersValidator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionTemplate;
import java.util.Arrays;
import java.util.Optional;
@ -38,6 +40,8 @@ import java.util.Optional;
public class BulkExportJobParameterValidator implements JobParametersValidator {
@Autowired
private IBulkExportJobDao myBulkExportJobDao;
@Autowired
private PlatformTransactionManager myTransactionManager;
@Override
public void validate(JobParameters theJobParameters) throws JobParametersInvalidException {
@ -45,41 +49,45 @@ public class BulkExportJobParameterValidator implements JobParametersValidator {
throw new JobParametersInvalidException("This job needs Parameters: [readChunkSize], [jobUUID], [filters], [outputFormat], [resourceTypes]");
}
StringBuilder errorBuilder = new StringBuilder();
Long readChunkSize = theJobParameters.getLong("readChunkSize");
if (readChunkSize == null || readChunkSize < 1) {
errorBuilder.append("There must be a valid number for readChunkSize, which is at least 1. ");
}
String jobUUID = theJobParameters.getString("jobUUID");
Optional<BulkExportJobEntity> oJob = myBulkExportJobDao.findByJobId(jobUUID);
if (!StringUtils.isBlank(jobUUID) && !oJob.isPresent()) {
errorBuilder.append("There is no persisted job that exists with UUID: " + jobUUID + ". ");
}
boolean hasExistingJob = oJob.isPresent();
//Check for to-be-created parameters.
if (!hasExistingJob) {
String resourceTypes = theJobParameters.getString("resourceTypes");
if (StringUtils.isBlank(resourceTypes)) {
errorBuilder.append("You must include [resourceTypes] as a Job Parameter");
} else {
String[] resourceArray = resourceTypes.split(",");
Arrays.stream(resourceArray).filter(resourceType -> resourceType.equalsIgnoreCase("Binary"))
.findFirst()
.ifPresent(resourceType -> {
errorBuilder.append("Bulk export of Binary resources is forbidden");
});
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
String errorMessage = txTemplate.execute(tx -> {
StringBuilder errorBuilder = new StringBuilder();
Long readChunkSize = theJobParameters.getLong("readChunkSize");
if (readChunkSize == null || readChunkSize < 1) {
errorBuilder.append("There must be a valid number for readChunkSize, which is at least 1. ");
}
String outputFormat = theJobParameters.getString("outputFormat");
if (!StringUtils.isBlank(outputFormat) && !Constants.CT_FHIR_NDJSON.equals(outputFormat)) {
errorBuilder.append("The only allowed format for Bulk Export is currently " + Constants.CT_FHIR_NDJSON);
String jobUUID = theJobParameters.getString("jobUUID");
Optional<BulkExportJobEntity> oJob = myBulkExportJobDao.findByJobId(jobUUID);
if (!StringUtils.isBlank(jobUUID) && !oJob.isPresent()) {
errorBuilder.append("There is no persisted job that exists with UUID: " + jobUUID + ". ");
}
}
String errorMessage = errorBuilder.toString();
boolean hasExistingJob = oJob.isPresent();
//Check for to-be-created parameters.
if (!hasExistingJob) {
String resourceTypes = theJobParameters.getString("resourceTypes");
if (StringUtils.isBlank(resourceTypes)) {
errorBuilder.append("You must include [resourceTypes] as a Job Parameter");
} else {
String[] resourceArray = resourceTypes.split(",");
Arrays.stream(resourceArray).filter(resourceType -> resourceType.equalsIgnoreCase("Binary"))
.findFirst()
.ifPresent(resourceType -> {
errorBuilder.append("Bulk export of Binary resources is forbidden");
});
}
String outputFormat = theJobParameters.getString("outputFormat");
if (!StringUtils.isBlank(outputFormat) && !Constants.CT_FHIR_NDJSON.equals(outputFormat)) {
errorBuilder.append("The only allowed format for Bulk Export is currently " + Constants.CT_FHIR_NDJSON);
}
}
return errorBuilder.toString();
});
if (!StringUtils.isEmpty(errorMessage)) {
throw new JobParametersInvalidException(errorMessage);
}

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

@ -21,6 +21,7 @@ import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.dao.index.DaoResourceLinkResolver;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
import ca.uhn.fhir.jpa.interceptor.JpaConsentContextServices;
@ -304,6 +305,11 @@ public abstract class BaseConfig {
return new PersistenceExceptionTranslationPostProcessor();
}
@Bean
public HapiTransactionService hapiTransactionService() {
return new HapiTransactionService();
}
@Bean
public IInterceptorService jpaInterceptorService() {
return new InterceptorService();

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

@ -26,7 +26,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import org.hibernate.HibernateException;
import org.hibernate.StaleStateException;
import org.hibernate.PessimisticLockException;
import org.hibernate.exception.ConstraintViolationException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -35,6 +35,7 @@ import org.springframework.orm.jpa.vendor.HibernateJpaDialect;
import javax.persistence.PersistenceException;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class HapiFhirHibernateJpaDialect extends HibernateJpaDialect {
@ -76,13 +77,14 @@ public class HapiFhirHibernateJpaDialect extends HibernateJpaDialect {
* will return it as lowercase even though the definition is in caps.
*/
if (isNotBlank(constraintName)) {
if (constraintName.toUpperCase().contains(ResourceHistoryTable.IDX_RESVER_ID_VER)) {
constraintName = constraintName.toUpperCase();
if (constraintName.contains(ResourceHistoryTable.IDX_RESVER_ID_VER)) {
throw new ResourceVersionConflictException(messageToPrepend + myLocalizer.getMessage(HapiFhirHibernateJpaDialect.class, "resourceVersionConstraintFailure"));
}
if (constraintName.toUpperCase().contains(ResourceIndexedCompositeStringUnique.IDX_IDXCMPSTRUNIQ_STRING)) {
if (constraintName.contains(ResourceIndexedCompositeStringUnique.IDX_IDXCMPSTRUNIQ_STRING)) {
throw new ResourceVersionConflictException(messageToPrepend + myLocalizer.getMessage(HapiFhirHibernateJpaDialect.class, "resourceIndexedCompositeStringUniqueConstraintFailure"));
}
if (constraintName.toUpperCase().contains(ForcedId.IDX_FORCEDID_TYPE_FID)) {
if (constraintName.contains(ForcedId.IDX_FORCEDID_TYPE_FID)) {
throw new ResourceVersionConflictException(messageToPrepend + myLocalizer.getMessage(HapiFhirHibernateJpaDialect.class, "forcedIdConstraintFailure"));
}
}
@ -102,10 +104,18 @@ public class HapiFhirHibernateJpaDialect extends HibernateJpaDialect {
* class in a method called "checkBatched" currently. This can all be tested using the
* StressTestR4Test method testMultiThreadedUpdateSameResourceInTransaction()
*/
if (theException instanceof StaleStateException) {
if (theException instanceof org.hibernate.StaleStateException) {
String msg = messageToPrepend + myLocalizer.getMessage(HapiFhirHibernateJpaDialect.class, "resourceVersionConstraintFailure");
throw new ResourceVersionConflictException(msg);
}
if (theException instanceof org.hibernate.PessimisticLockException) {
PessimisticLockException ex = (PessimisticLockException) theException;
String sql = defaultString(ex.getSQL()).toUpperCase();
if (sql.contains(ResourceHistoryTable.HFJ_RES_VER)) {
String msg = messageToPrepend + myLocalizer.getMessage(HapiFhirHibernateJpaDialect.class, "resourceVersionConstraintFailure");
throw new ResourceVersionConflictException(msg);
}
}
return super.convertHibernateAccessException(theException);
}

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

@ -79,6 +79,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -113,8 +114,10 @@ import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.stereotype.Repository;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionSynchronizationAdapter;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;

587
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -33,10 +33,9 @@ import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.patch.FhirPatch;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
import ca.uhn.fhir.jpa.model.entity.BaseTag;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
@ -46,15 +45,15 @@ import ca.uhn.fhir.jpa.model.entity.TagDefinition;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.patch.FhirPatch;
import ca.uhn.fhir.jpa.patch.JsonPatchUtils;
import ca.uhn.fhir.jpa.patch.XmlPatchUtils;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.jpa.patch.JsonPatchUtils;
import ca.uhn.fhir.jpa.patch.XmlPatchUtils;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.CacheControlDirective;
@ -70,6 +69,8 @@ import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
@ -108,6 +109,7 @@ import org.springframework.transaction.support.TransactionSynchronizationAdapter
import org.springframework.transaction.support.TransactionSynchronizationManager;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import javax.annotation.PostConstruct;
import javax.persistence.NoResultException;
import javax.persistence.TypedQuery;
@ -124,7 +126,6 @@ import java.util.UUID;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@Transactional(propagation = Propagation.REQUIRED)
public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends BaseHapiFhirDao<T> implements IFhirResourceDao<T> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirResourceDao.class);
@ -151,8 +152,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
private IRequestPartitionHelperSvc myRequestPartitionHelperService;
@Autowired
private PartitionSettings myPartitionSettings;
@Autowired
private HapiTransactionService myTransactionService;
@Override
@Transactional
public void addTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel, RequestDetails theRequest) {
StopWatch w = new StopWatch();
BaseHasResource entity = readEntity(theId, theRequest);
@ -197,8 +201,20 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return create(theResource, theIfNoneExist, null);
}
@Override
public DaoMethodOutcome create(final T theResource, String theIfNoneExist, RequestDetails theRequestDetails) {
return create(theResource, theIfNoneExist, true, new TransactionDetails(), theRequestDetails);
}
@Override
public DaoMethodOutcome create(T theResource, String theIfNoneExist, boolean thePerformIndexing, TransactionDetails theTransactionDetails, RequestDetails theRequestDetails) {
return myTransactionService.execute(theRequestDetails, tx -> doCreateForPost(theResource, theIfNoneExist, thePerformIndexing, theTransactionDetails, theRequestDetails));
}
/**
* Called for FHIR create (POST) operations
*/
private DaoMethodOutcome doCreateForPost(T theResource, String theIfNoneExist, boolean thePerformIndexing, TransactionDetails theTransactionDetails, RequestDetails theRequestDetails) {
if (theResource == null) {
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "missingBody");
throw new InvalidRequestException(msg);
@ -220,241 +236,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineCreatePartitionForRequest(theRequestDetails, theResource, getResourceName());
return doCreate(theResource, theIfNoneExist, thePerformIndexing, theTransactionDetails, theRequestDetails, requestPartitionId);
}
@Override
public DaoMethodOutcome create(final T theResource, String theIfNoneExist, RequestDetails theRequestDetails) {
return create(theResource, theIfNoneExist, true, new TransactionDetails(), theRequestDetails);
}
private IInstanceValidatorModule getInstanceValidator() {
return myInstanceValidator;
}
@Override
public DaoMethodOutcome delete(IIdType theId) {
return delete(theId, null);
}
@Override
public DaoMethodOutcome delete(IIdType theId, DeleteConflictList theDeleteConflicts, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
validateIdPresentForDelete(theId);
validateDeleteEnabled();
final ResourceTable entity = readEntityLatestVersion(theId, theRequest);
if (theId.hasVersionIdPart() && Long.parseLong(theId.getVersionIdPart()) != entity.getVersion()) {
throw new ResourceVersionConflictException("Trying to delete " + theId + " but this is not the current version");
}
// Don't delete again if it's already deleted
if (entity.getDeleted() != null) {
DaoMethodOutcome outcome = new DaoMethodOutcome();
outcome.setEntity(entity);
IIdType id = getContext().getVersion().newIdType();
id.setValue(entity.getIdDt().getValue());
outcome.setId(id);
IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", 1, 0);
String severity = "information";
String code = "informational";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
outcome.setOperationOutcome(oo);
return outcome;
}
StopWatch w = new StopWatch();
T resourceToDelete = toResource(myResourceType, entity, null, false);
theDeleteConflicts.setResourceIdMarkedForDeletion(theId);
// Notify IServerOperationInterceptors about pre-action call
HookParams hook = new HookParams()
.add(IBaseResource.class, resourceToDelete)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(TransactionDetails.class, theTransactionDetails);
doCallHooks(theRequest, Pointcut.STORAGE_PRESTORAGE_RESOURCE_DELETED, hook);
myDeleteConflictService.validateOkToDelete(theDeleteConflicts, entity, false, theRequest, theTransactionDetails);
preDelete(resourceToDelete, entity);
// Notify interceptors
if (theRequest != null) {
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequest, getContext(), theId.getResourceType(), theId);
notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails);
}
ResourceTable savedEntity = updateEntityForDelete(theRequest, theTransactionDetails, entity);
resourceToDelete.setId(entity.getIdDt());
// Notify JPA interceptors
TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronizationAdapter() {
@Override
public void beforeCommit(boolean readOnly) {
HookParams hookParams = new HookParams()
.add(IBaseResource.class, resourceToDelete)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(TransactionDetails.class, theTransactionDetails);
doCallHooks(theRequest, Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);
}
});
DaoMethodOutcome outcome = toMethodOutcome(theRequest, savedEntity, resourceToDelete).setCreated(true);
IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", 1, w.getMillis());
String severity = "information";
String code = "informational";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
outcome.setOperationOutcome(oo);
return outcome;
}
@Override
public DaoMethodOutcome delete(IIdType theId, RequestDetails theRequestDetails) {
validateIdPresentForDelete(theId);
validateDeleteEnabled();
DeleteConflictList deleteConflicts = new DeleteConflictList();
if (isNotBlank(theId.getValue())) {
deleteConflicts.setResourceIdMarkedForDeletion(theId);
}
StopWatch w = new StopWatch();
DaoMethodOutcome retVal = delete(theId, deleteConflicts, theRequestDetails, new TransactionDetails());
DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
ourLog.debug("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
return retVal;
return doCreateForPostOrPut(theResource, theIfNoneExist, thePerformIndexing, theTransactionDetails, theRequestDetails, requestPartitionId);
}
/**
* This method gets called by {@link #deleteByUrl(String, DeleteConflictList, RequestDetails)} as well as by
* transaction processors
* Called both for FHIR create (POST) operations (via {@link #doCreateForPost(IBaseResource, String, boolean, TransactionDetails, RequestDetails)}
* as well as for FHIR update (PUT) where we're doing a create-with-client-assigned-ID (via {@link #doUpdate(IBaseResource, String, boolean, boolean, RequestDetails, TransactionDetails)}.
*/
@Override
public DeleteMethodOutcome deleteByUrl(String theUrl, DeleteConflictList deleteConflicts, RequestDetails theRequest) {
validateDeleteEnabled();
StopWatch w = new StopWatch();
Set<ResourcePersistentId> resourceIds = myMatchResourceUrlService.processMatchUrl(theUrl, myResourceType, theRequest);
if (resourceIds.size() > 1) {
if (myDaoConfig.isAllowMultipleDelete() == false) {
throw new PreconditionFailedException(getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "DELETE", theUrl, resourceIds.size()));
}
}
TransactionDetails transactionDetails = new TransactionDetails();
List<ResourceTable> deletedResources = new ArrayList<>();
for (ResourcePersistentId pid : resourceIds) {
ResourceTable entity = myEntityManager.find(ResourceTable.class, pid.getId());
deletedResources.add(entity);
T resourceToDelete = toResource(myResourceType, entity, null, false);
// Notify IServerOperationInterceptors about pre-action call
HookParams hooks = new HookParams()
.add(IBaseResource.class, resourceToDelete)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(TransactionDetails.class, transactionDetails);
doCallHooks(theRequest, Pointcut.STORAGE_PRESTORAGE_RESOURCE_DELETED, hooks);
myDeleteConflictService.validateOkToDelete(deleteConflicts, entity, false, theRequest, transactionDetails);
// Notify interceptors
IdDt idToDelete = entity.getIdDt();
if (theRequest != null) {
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequest, idToDelete.getResourceType(), idToDelete);
notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails);
}
// Perform delete
updateEntityForDelete(theRequest, transactionDetails, entity);
resourceToDelete.setId(entity.getIdDt());
// Notify JPA interceptors
TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronizationAdapter() {
@Override
public void beforeCommit(boolean readOnly) {
HookParams hookParams = new HookParams()
.add(IBaseResource.class, resourceToDelete)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(TransactionDetails.class, transactionDetails);
doCallHooks(theRequest, Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);
}
});
}
IBaseOperationOutcome oo;
if (deletedResources.isEmpty()) {
oo = OperationOutcomeUtil.newInstance(getContext());
String message = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "unableToDeleteNotFound", theUrl);
String severity = "warning";
String code = "not-found";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
} else {
oo = OperationOutcomeUtil.newInstance(getContext());
String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", deletedResources.size(), w.getMillis());
String severity = "information";
String code = "informational";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
}
ourLog.debug("Processed delete on {} (matched {} resource(s)) in {}ms", theUrl, deletedResources.size(), w.getMillis());
DeleteMethodOutcome retVal = new DeleteMethodOutcome();
retVal.setDeletedEntities(deletedResources);
retVal.setOperationOutcome(oo);
return retVal;
}
@Override
public DeleteMethodOutcome deleteByUrl(String theUrl, RequestDetails theRequestDetails) {
validateDeleteEnabled();
DeleteConflictList deleteConflicts = new DeleteConflictList();
DeleteMethodOutcome outcome = deleteByUrl(theUrl, deleteConflicts, theRequestDetails);
DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
return outcome;
}
private void validateDeleteEnabled() {
if (!myDaoConfig.isDeleteEnabled()) {
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "deleteBlockedBecauseDisabled");
throw new PreconditionFailedException(msg);
}
}
private void validateIdPresentForDelete(IIdType theId) {
if (theId == null || !theId.hasIdPart()) {
throw new InvalidRequestException("Can not perform delete, no ID provided");
}
}
@PostConstruct
public void detectSearchDaoDisabled() {
if (mySearchDao != null && mySearchDao.isDisabled()) {
mySearchDao = null;
}
}
private DaoMethodOutcome doCreate(T theResource, String theIfNoneExist, boolean thePerformIndexing, TransactionDetails theTransactionDetails, RequestDetails theRequest, RequestPartitionId theRequestPartitionId) {
private DaoMethodOutcome doCreateForPostOrPut(T theResource, String theIfNoneExist, boolean thePerformIndexing, TransactionDetails theTransactionDetails, RequestDetails theRequest, RequestPartitionId theRequestPartitionId) {
StopWatch w = new StopWatch();
preProcessResourceForStorage(theResource);
@ -579,6 +368,239 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return outcome;
}
private IInstanceValidatorModule getInstanceValidator() {
return myInstanceValidator;
}
@Override
public DaoMethodOutcome delete(IIdType theId) {
return delete(theId, null);
}
@Override
public DaoMethodOutcome delete(IIdType theId, RequestDetails theRequestDetails) {
validateIdPresentForDelete(theId);
validateDeleteEnabled();
return myTransactionService.execute(theRequestDetails, tx -> {
DeleteConflictList deleteConflicts = new DeleteConflictList();
if (isNotBlank(theId.getValue())) {
deleteConflicts.setResourceIdMarkedForDeletion(theId);
}
StopWatch w = new StopWatch();
DaoMethodOutcome retVal = delete(theId, deleteConflicts, theRequestDetails, new TransactionDetails());
DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
ourLog.debug("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
return retVal;
});
}
@Override
public DaoMethodOutcome delete(IIdType theId, DeleteConflictList theDeleteConflicts, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails) {
validateIdPresentForDelete(theId);
validateDeleteEnabled();
final ResourceTable entity = readEntityLatestVersion(theId, theRequestDetails);
if (theId.hasVersionIdPart() && Long.parseLong(theId.getVersionIdPart()) != entity.getVersion()) {
throw new ResourceVersionConflictException("Trying to delete " + theId + " but this is not the current version");
}
// Don't delete again if it's already deleted
if (entity.getDeleted() != null) {
DaoMethodOutcome outcome = new DaoMethodOutcome();
outcome.setEntity(entity);
IIdType id = getContext().getVersion().newIdType();
id.setValue(entity.getIdDt().getValue());
outcome.setId(id);
IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", 1, 0);
String severity = "information";
String code = "informational";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
outcome.setOperationOutcome(oo);
return outcome;
}
StopWatch w = new StopWatch();
T resourceToDelete = toResource(myResourceType, entity, null, false);
theDeleteConflicts.setResourceIdMarkedForDeletion(theId);
// Notify IServerOperationInterceptors about pre-action call
HookParams hook = new HookParams()
.add(IBaseResource.class, resourceToDelete)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(TransactionDetails.class, theTransactionDetails);
doCallHooks(theRequestDetails, Pointcut.STORAGE_PRESTORAGE_RESOURCE_DELETED, hook);
myDeleteConflictService.validateOkToDelete(theDeleteConflicts, entity, false, theRequestDetails, theTransactionDetails);
preDelete(resourceToDelete, entity);
// Notify interceptors
if (theRequestDetails != null) {
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getContext(), theId.getResourceType(), theId);
notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails);
}
ResourceTable savedEntity = updateEntityForDelete(theRequestDetails, theTransactionDetails, entity);
resourceToDelete.setId(entity.getIdDt());
// Notify JPA interceptors
TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronizationAdapter() {
@Override
public void beforeCommit(boolean readOnly) {
HookParams hookParams = new HookParams()
.add(IBaseResource.class, resourceToDelete)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(TransactionDetails.class, theTransactionDetails);
doCallHooks(theRequestDetails, Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);
}
});
DaoMethodOutcome outcome = toMethodOutcome(theRequestDetails, savedEntity, resourceToDelete).setCreated(true);
IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", 1, w.getMillis());
String severity = "information";
String code = "informational";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
outcome.setOperationOutcome(oo);
return outcome;
}
@Override
public DeleteMethodOutcome deleteByUrl(String theUrl, RequestDetails theRequestDetails) {
validateDeleteEnabled();
return myTransactionService.execute(theRequestDetails, tx -> {
DeleteConflictList deleteConflicts = new DeleteConflictList();
DeleteMethodOutcome outcome = deleteByUrl(theUrl, deleteConflicts, theRequestDetails);
DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
return outcome;
});
}
/**
* This method gets called by {@link #deleteByUrl(String, RequestDetails)} as well as by
* transaction processors
*/
@Override
public DeleteMethodOutcome deleteByUrl(String theUrl, DeleteConflictList deleteConflicts, RequestDetails theRequestDetails) {
validateDeleteEnabled();
return myTransactionService.execute(theRequestDetails, tx -> doDeleteByUrl(theUrl, deleteConflicts, theRequestDetails));
}
@Nonnull
private DeleteMethodOutcome doDeleteByUrl(String theUrl, DeleteConflictList deleteConflicts, RequestDetails theRequest) {
StopWatch w = new StopWatch();
Set<ResourcePersistentId> resourceIds = myMatchResourceUrlService.processMatchUrl(theUrl, myResourceType, theRequest);
if (resourceIds.size() > 1) {
if (myDaoConfig.isAllowMultipleDelete() == false) {
throw new PreconditionFailedException(getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "DELETE", theUrl, resourceIds.size()));
}
}
TransactionDetails transactionDetails = new TransactionDetails();
List<ResourceTable> deletedResources = new ArrayList<>();
for (ResourcePersistentId pid : resourceIds) {
ResourceTable entity = myEntityManager.find(ResourceTable.class, pid.getId());
deletedResources.add(entity);
T resourceToDelete = toResource(myResourceType, entity, null, false);
// Notify IServerOperationInterceptors about pre-action call
HookParams hooks = new HookParams()
.add(IBaseResource.class, resourceToDelete)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(TransactionDetails.class, transactionDetails);
doCallHooks(theRequest, Pointcut.STORAGE_PRESTORAGE_RESOURCE_DELETED, hooks);
myDeleteConflictService.validateOkToDelete(deleteConflicts, entity, false, theRequest, transactionDetails);
// Notify interceptors
IdDt idToDelete = entity.getIdDt();
if (theRequest != null) {
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequest, idToDelete.getResourceType(), idToDelete);
notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails);
}
// Perform delete
updateEntityForDelete(theRequest, transactionDetails, entity);
resourceToDelete.setId(entity.getIdDt());
// Notify JPA interceptors
TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronizationAdapter() {
@Override
public void beforeCommit(boolean readOnly) {
HookParams hookParams = new HookParams()
.add(IBaseResource.class, resourceToDelete)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(TransactionDetails.class, transactionDetails);
doCallHooks(theRequest, Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED, hookParams);
}
});
}
IBaseOperationOutcome oo;
if (deletedResources.isEmpty()) {
oo = OperationOutcomeUtil.newInstance(getContext());
String message = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "unableToDeleteNotFound", theUrl);
String severity = "warning";
String code = "not-found";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
} else {
oo = OperationOutcomeUtil.newInstance(getContext());
String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", deletedResources.size(), w.getMillis());
String severity = "information";
String code = "informational";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
}
ourLog.debug("Processed delete on {} (matched {} resource(s)) in {}ms", theUrl, deletedResources.size(), w.getMillis());
DeleteMethodOutcome retVal = new DeleteMethodOutcome();
retVal.setDeletedEntities(deletedResources);
retVal.setOperationOutcome(oo);
return retVal;
}
private void validateDeleteEnabled() {
if (!myDaoConfig.isDeleteEnabled()) {
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "deleteBlockedBecauseDisabled");
throw new PreconditionFailedException(msg);
}
}
private void validateIdPresentForDelete(IIdType theId) {
if (theId == null || !theId.hasIdPart()) {
throw new InvalidRequestException("Can not perform delete, no ID provided");
}
}
@PostConstruct
public void detectSearchDaoDisabled() {
if (mySearchDao != null && mySearchDao.isDisabled()) {
mySearchDao = null;
}
}
private <MT extends IBaseMetaType> void doMetaAdd(MT theMetaAdd, BaseHasResource entity) {
List<TagDefinition> tags = toTagList(theMetaAdd);
@ -647,7 +669,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
@Transactional(propagation = Propagation.SUPPORTS)
public ExpungeOutcome forceExpungeInExistingTransaction(IIdType theId, ExpungeOptions theExpungeOptions, RequestDetails theRequest) {
TransactionTemplate txTemplate = new TransactionTemplate(myPlatformTransactionManager);
@ -694,6 +715,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
@Transactional
public IBundleProvider history(Date theSince, Date theUntil, RequestDetails theRequestDetails) {
// Notify interceptors
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails);
@ -706,10 +728,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
@Transactional
public IBundleProvider history(final IIdType theId, final Date theSince, Date theUntil, RequestDetails theRequest) {
// Notify interceptors
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequest, getResourceName(), theId);
notifyInterceptors(RestOperationTypeEnum.HISTORY_INSTANCE, requestDetails);
if (theRequest != null) {
// Notify interceptors
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequest, getResourceName(), theId);
notifyInterceptors(RestOperationTypeEnum.HISTORY_INSTANCE, requestDetails);
}
StopWatch w = new StopWatch();
@ -755,6 +780,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
@Transactional
public <MT extends IBaseMetaType> MT metaAddOperation(IIdType theResourceId, MT theMetaAdd, RequestDetails theRequest) {
// Notify interceptors
if (theRequest != null) {
@ -787,6 +813,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
@Transactional
public <MT extends IBaseMetaType> MT metaDeleteOperation(IIdType theResourceId, MT theMetaDel, RequestDetails theRequest) {
// Notify interceptors
if (theRequest != null) {
@ -821,6 +848,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
@Transactional
public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, IIdType theId, RequestDetails theRequest) {
// Notify interceptors
if (theRequest != null) {
@ -842,6 +870,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
@Transactional
public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, RequestDetails theRequestDetails) {
// Notify interceptors
if (theRequestDetails != null) {
@ -859,7 +888,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Override
public DaoMethodOutcome patch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, IBaseParameters theFhirPatchBody, RequestDetails theRequest) {
return myTransactionService.execute(theRequest, tx -> doPatch(theId, theConditionalUrl, thePatchType, thePatchBody, theFhirPatchBody, theRequest));
}
private DaoMethodOutcome doPatch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, IBaseParameters theFhirPatchBody, RequestDetails theRequest) {
ResourceTable entityToUpdate;
if (isNotBlank(theConditionalUrl)) {
@ -890,10 +922,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
IBaseResource destination;
switch (thePatchType) {
case JSON_PATCH:
destination = JsonPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
destination = JsonPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
break;
case XML_PATCH:
destination = XmlPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
destination = XmlPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
break;
case FHIR_PATCH_XML:
case FHIR_PATCH_JSON:
@ -932,6 +964,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
@Transactional
public T readByPid(ResourcePersistentId thePid) {
StopWatch w = new StopWatch();
@ -950,16 +983,19 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
@Transactional
public T read(IIdType theId) {
return read(theId, null);
}
@Override
@Transactional
public T read(IIdType theId, RequestDetails theRequestDetails) {
return read(theId, theRequestDetails, false);
}
@Override
@Transactional
public T read(IIdType theId, RequestDetails theRequest, boolean theDeletedOk) {
validateResourceTypeAndThrowInvalidRequestException(theId);
@ -1012,11 +1048,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
@Transactional
public BaseHasResource readEntity(IIdType theId, RequestDetails theRequest) {
return readEntity(theId, true, theRequest);
}
@Override
@Transactional
public BaseHasResource readEntity(IIdType theId, boolean theCheckForForcedId, RequestDetails theRequest) {
validateResourceTypeAndThrowInvalidRequestException(theId);
@ -1099,6 +1137,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Override
public void reindex(T theResource, ResourceTable theEntity) {
assert TransactionSynchronizationManager.isActualTransactionActive();
ourLog.debug("Indexing resource {} - PID {}", theEntity.getIdDt().getValue(), theEntity.getId());
if (theResource != null) {
CURRENTLY_REINDEXING.put(theResource, Boolean.TRUE);
@ -1111,11 +1151,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
}
@Transactional
@Override
public void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm) {
removeTag(theId, theTagType, theScheme, theTerm, null);
}
@Transactional
@Override
public void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, RequestDetails theRequest) {
// Notify interceptors
@ -1216,26 +1258,28 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Override
public Set<ResourcePersistentId> searchForIds(SearchParameterMap theParams, RequestDetails theRequest) {
theParams.setLoadSynchronousUpTo(10000);
return myTransactionService.execute(theRequest, tx -> {
theParams.setLoadSynchronousUpTo(10000);
ISearchBuilder builder = mySearchBuilderFactory.newSearchBuilder(this, getResourceName(), getResourceType());
ISearchBuilder builder = mySearchBuilderFactory.newSearchBuilder(this, getResourceName(), getResourceType());
HashSet<ResourcePersistentId> retVal = new HashSet<>();
HashSet<ResourcePersistentId> retVal = new HashSet<>();
String uuid = UUID.randomUUID().toString();
SearchRuntimeDetails searchRuntimeDetails = new SearchRuntimeDetails(theRequest, uuid);
String uuid = UUID.randomUUID().toString();
SearchRuntimeDetails searchRuntimeDetails = new SearchRuntimeDetails(theRequest, uuid);
RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequest(theRequest, getResourceName());
try (IResultIterator iter = builder.createQuery(theParams, searchRuntimeDetails, theRequest, requestPartitionId)) {
while (iter.hasNext()) {
retVal.add(iter.next());
RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequest(theRequest, getResourceName());
try (IResultIterator iter = builder.createQuery(theParams, searchRuntimeDetails, theRequest, requestPartitionId)) {
while (iter.hasNext()) {
retVal.add(iter.next());
}
} catch (IOException e) {
ourLog.error("IO failure during database access", e);
}
} catch (IOException e) {
ourLog.error("IO failure during database access", e);
}
return retVal;
return retVal;
});
}
protected <MT extends IBaseMetaType> MT toMetaDt(Class<MT> theType, Collection<TagDefinition> tagDefinitions) {
@ -1303,10 +1347,21 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "missingBody");
throw new InvalidRequestException(msg);
}
assert theResource.getIdElement().hasIdPart() || isNotBlank(theMatchUrl);
return myTransactionService.execute(theRequest, tx -> doUpdate(theResource, theMatchUrl, thePerformIndexing, theForceUpdateVersion, theRequest, theTransactionDetails));
}
private DaoMethodOutcome doUpdate(T theResource, String theMatchUrl, boolean thePerformIndexing, boolean theForceUpdateVersion, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
StopWatch w = new StopWatch();
preProcessResourceForStorage(theResource);
T resource = theResource;
if (JpaInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_VERSION_CONFLICT, myInterceptorBroadcaster, theRequest)) {
resource = (T) getContext().getResourceDefinition(theResource).newInstance();
getContext().newTerser().cloneInto(theResource, resource, false);
}
preProcessResourceForStorage(resource);
final ResourceTable entity;
@ -1321,7 +1376,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
entity = myEntityManager.find(ResourceTable.class, pid.getId());
resourceId = entity.getIdDt();
} else {
return create(theResource, null, thePerformIndexing, theTransactionDetails, theRequest);
return create(resource, null, thePerformIndexing, theTransactionDetails, theRequest);
}
} else {
/*
@ -1330,13 +1385,15 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
* BaseOutcomeReturningMethodBindingWithResourceParam
*/
resourceId = theResource.getIdElement();
assert resourceId != null;
assert resourceId.hasIdPart();
RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequest(theRequest, getResourceName());
try {
entity = readEntityLatestVersion(resourceId, requestPartitionId);
} catch (ResourceNotFoundException e) {
requestPartitionId = myRequestPartitionHelperService.determineCreatePartitionForRequest(theRequest, theResource, getResourceName());
return doCreate(theResource, null, thePerformIndexing, theTransactionDetails, theRequest, requestPartitionId);
return doCreateForPostOrPut(resource, null, thePerformIndexing, theTransactionDetails, theRequest, requestPartitionId);
}
}
@ -1372,8 +1429,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
* directly. So we just bail now.
*/
if (!thePerformIndexing) {
theResource.setId(entity.getIdDt().getValue());
DaoMethodOutcome outcome = toMethodOutcome(theRequest, entity, theResource).setCreated(wasDeleted);
resource.setId(entity.getIdDt().getValue());
DaoMethodOutcome outcome = toMethodOutcome(theRequest, entity, resource).setCreated(wasDeleted);
outcome.setPreviousResource(oldResource);
return outcome;
}
@ -1381,11 +1438,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
/*
* Otherwise, we're not in a transaction
*/
ResourceTable savedEntity = updateInternal(theRequest, theResource, thePerformIndexing, theForceUpdateVersion, entity, resourceId, oldResource, theTransactionDetails);
DaoMethodOutcome outcome = toMethodOutcome(theRequest, savedEntity, theResource).setCreated(wasDeleted);
ResourceTable savedEntity = updateInternal(theRequest, resource, thePerformIndexing, theForceUpdateVersion, entity, resourceId, oldResource, theTransactionDetails);
DaoMethodOutcome outcome = toMethodOutcome(theRequest, savedEntity, resource).setCreated(wasDeleted);
if (!thePerformIndexing) {
outcome.setId(theResource.getIdElement());
IIdType id = getContext().getVersion().newIdType();
id.setValue(entity.getIdDt().getValue());
outcome.setId(id);
}
String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "successfulUpdate", outcome.getId(), w.getMillisAndRestart());

17
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
View File

@ -32,6 +32,7 @@ import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.model.DeleteConflict;
import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@ -64,7 +65,6 @@ import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ResourceReferenceInfo;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
import com.google.common.collect.ArrayListMultimap;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.dstu3.model.Bundle;
@ -83,6 +83,7 @@ import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct;
@ -121,6 +122,8 @@ public abstract class BaseTransactionProcessor {
private IInterceptorBroadcaster myInterceptorBroadcaster;
@Autowired
private MatchResourceUrlService myMatchResourceUrlService;
@Autowired
private HapiTransactionService myHapiTransactionService;
@PostConstruct
public void start() {
@ -344,9 +347,6 @@ public abstract class BaseTransactionProcessor {
final TransactionDetails transactionDetails = new TransactionDetails();
final StopWatch transactionStopWatch = new StopWatch();
final Set<IIdType> allIds = new LinkedHashSet<>();
final Map<IIdType, IIdType> idSubstitutions = new HashMap<>();
final Map<IIdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<>();
List<IBase> requestEntries = myVersionAdapter.getEntries(theRequest);
// Do all entries have a verb?
@ -403,13 +403,16 @@ public abstract class BaseTransactionProcessor {
* heavy load with lots of concurrent transactions using all available
* database connections.
*/
TransactionTemplate txManager = new TransactionTemplate(myTxManager);
Map<IBase, IBasePersistedResource> entriesToProcess = txManager.execute(status -> {
TransactionCallback<Map<IBase, IBasePersistedResource>> txCallback = status -> {
final Set<IIdType> allIds = new LinkedHashSet<>();
final Map<IIdType, IIdType> idSubstitutions = new HashMap<>();
final Map<IIdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<>();
Map<IBase, IBasePersistedResource> retVal = doTransactionWriteOperations(theRequestDetails, theActionName, transactionDetails, allIds, idSubstitutions, idToPersistedOutcome, response, originalRequestOrder, entries, transactionStopWatch);
transactionStopWatch.startTask("Commit writes to database");
return retVal;
});
};
Map<IBase, IBasePersistedResource> entriesToProcess = myHapiTransactionService.execute(theRequestDetails, txCallback);
transactionStopWatch.endCurrentTask();
for (Map.Entry<IBase, IBasePersistedResource> nextEntry : entriesToProcess.entrySet()) {

96
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
View File

@ -57,6 +57,8 @@ import java.util.Collections;
import java.util.List;
import java.util.Set;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoValueSetDstu3.vsValidateCodeOptions;
import static ca.uhn.fhir.jpa.util.LogicUtil.multiXor;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -291,102 +293,14 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
// nothing
}
private String toStringOrNull(IPrimitiveType<String> thePrimitive) {
public static String toStringOrNull(IPrimitiveType<String> thePrimitive) {
return thePrimitive != null ? thePrimitive.getValue() : null;
}
@Override
public ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
public IValidationSupport.CodeValidationResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CodingDt theCoding, CodeableConceptDt theCodeableConcept, RequestDetails theRequest) {
List<IIdType> valueSetIds;
boolean haveCodeableConcept = theCodeableConcept != null && theCodeableConcept.getCoding().size() > 0;
boolean haveCoding = theCoding != null && theCoding.isEmpty() == false;
boolean haveCode = theCode != null && theCode.isEmpty() == false;
if (!haveCodeableConcept && !haveCoding && !haveCode) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
if (!multiXor(haveCodeableConcept, haveCoding, haveCode)) {
throw new InvalidRequestException("$validate-code can only validate (system AND code) OR (coding) OR (codeableConcept)");
}
boolean haveIdentifierParam = theValueSetIdentifier != null && theValueSetIdentifier.isEmpty() == false;
if (theId != null) {
valueSetIds = Collections.singletonList(theId);
} else if (haveIdentifierParam) {
Set<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(ValueSet.SP_IDENTIFIER, new TokenParam(null, theValueSetIdentifier.getValue())), theRequest);
valueSetIds = new ArrayList<>();
for (ResourcePersistentId next : ids) {
IIdType id = myIdHelperService.translatePidIdToForcedId(myFhirContext, "ValueSet", next);
valueSetIds.add(id);
}
} else {
if (theCode == null || theCode.isEmpty()) {
throw new InvalidRequestException("Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.");
}
String code = theCode.getValue();
String system = toStringOrNull(theSystem);
valueSetIds = findCodeSystemIdsContainingSystemAndCode(code, system, theRequest);
}
for (IIdType nextId : valueSetIds) {
ValueSet expansion = expand(nextId, null, theRequest);
List<ExpansionContains> contains = expansion.getExpansion().getContains();
ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
if (result != null) {
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
if (!theDisplay.getValue().equals(result.getDisplay())) {
return new ValidateCodeResult(false, "Display for code does not match", result.getDisplay());
}
}
return result;
}
}
return new ValidateCodeResult(false, "Code not found", null);
}
private ValidateCodeResult validateCodeIsInContains(List<ExpansionContains> contains, String theSystem, String theCode, CodingDt theCoding,
CodeableConceptDt theCodeableConcept) {
for (ExpansionContains nextCode : contains) {
ValidateCodeResult result = validateCodeIsInContains(nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
if (result != null) {
return result;
}
String system = nextCode.getSystem();
String code = nextCode.getCode();
if (isNotBlank(theCode)) {
if (theCode.equals(code) && (isBlank(theSystem) || theSystem.equals(system))) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
} else if (theCoding != null) {
if (StringUtils.equals(system, theCoding.getSystem()) && StringUtils.equals(code, theCoding.getCode())) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
} else {
for (CodingDt next : theCodeableConcept.getCoding()) {
if (StringUtils.equals(system, next.getSystem()) && StringUtils.equals(code, next.getCode())) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
}
}
}
return null;
}
private static boolean multiXor(boolean... theValues) {
int count = 0;
for (int i = 0; i < theValues.length; i++) {
if (theValues[i]) {
count++;
}
}
return count == 1;
return myTerminologySvc.validateCode(vsValidateCodeOptions(), theId, toStringOrNull(theValueSetIdentifier), toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
}
}

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
@ -73,7 +74,6 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
@ -109,14 +109,13 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
private DaoRegistry myDaoRegistry;
@Autowired
private MatchResourceUrlService myMatchResourceUrlService;
@Autowired
private HapiTransactionService myHapiTransactionalService;
private Bundle batch(final RequestDetails theRequestDetails, Bundle theRequest) {
ourLog.info("Beginning batch with {} resources", theRequest.getEntry().size());
long start = System.currentTimeMillis();
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
Bundle resp = new Bundle();
resp.setType(BundleTypeEnum.BATCH_RESPONSE);
@ -144,7 +143,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
// create their own
nextResponseBundle = callback.doInTransaction(null);
} else {
nextResponseBundle = txTemplate.execute(callback);
nextResponseBundle = myHapiTransactionalService.execute(theRequestDetails, callback);
}
caughtEx = null;

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

@ -90,6 +90,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import javax.annotation.Nonnull;
import javax.persistence.EntityManager;
@ -245,6 +246,7 @@ public class SearchBuilder implements ISearchBuilder {
@Override
public Iterator<Long> createCountQuery(SearchParameterMap theParams, String theSearchUuid, RequestDetails theRequest, @Nonnull RequestPartitionId theRequestPartitionId) {
assert theRequestPartitionId != null;
assert TransactionSynchronizationManager.isActualTransactionActive();
init(theParams, theSearchUuid, theRequestPartitionId);
@ -263,6 +265,7 @@ public class SearchBuilder implements ISearchBuilder {
@Override
public IResultIterator createQuery(SearchParameterMap theParams, SearchRuntimeDetails theSearchRuntimeDetails, RequestDetails theRequest, @Nonnull RequestPartitionId theRequestPartitionId) {
assert theRequestPartitionId != null;
assert TransactionSynchronizationManager.isActualTransactionActive();
init(theParams, theSearchRuntimeDetails.getSearchUuid(), theRequestPartitionId);

120
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* #L%
*/
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
@ -29,14 +30,12 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ElementUtil;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
@ -50,15 +49,14 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import static ca.uhn.fhir.jpa.dao.FhirResourceDaoValueSetDstu2.toStringOrNull;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoValueSetR4.validateHaveExpansionOrThrowInternalErrorException;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -81,7 +79,7 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
@Override
public void start() {
super.start();
myValidationSupport = getApplicationContext().getBean(IValidationSupport.class,"myJpaValidationSupportChain" );
myValidationSupport = getApplicationContext().getBean(IValidationSupport.class, "myJpaValidationSupportChain");
}
@Override
@ -264,108 +262,10 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
}
@Override
public IFhirResourceDaoValueSet.ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding,
CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
List<IIdType> valueSetIds = Collections.emptyList();
boolean haveCodeableConcept = theCodeableConcept != null && theCodeableConcept.getCoding().size() > 0;
boolean haveCoding = theCoding != null && theCoding.isEmpty() == false;
boolean haveCode = theCode != null && theCode.isEmpty() == false;
if (!haveCodeableConcept && !haveCoding && !haveCode) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
if (!LogicUtil.multiXor(haveCodeableConcept, haveCoding, haveCode)) {
throw new InvalidRequestException("$validate-code can only validate (system AND code) OR (coding) OR (codeableConcept)");
}
boolean haveIdentifierParam = theValueSetIdentifier != null && theValueSetIdentifier.isEmpty() == false;
ValueSet vs = null;
boolean isBuiltInValueSet = false;
if (theId != null) {
vs = read(theId, theRequestDetails);
} else if (haveIdentifierParam) {
vs = (ValueSet) myDefaultProfileValidationSupport.fetchValueSet(theValueSetIdentifier.getValue());
if (vs == null) {
vs = (ValueSet) myValidationSupport.fetchValueSet(theValueSetIdentifier.getValue());
if (vs == null) {
throw new InvalidRequestException("Unknown ValueSet identifier: " + theValueSetIdentifier.getValue());
}
} else {
isBuiltInValueSet = true;
}
} else {
if (theCode == null || theCode.isEmpty()) {
throw new InvalidRequestException("Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.");
}
// String code = theCode.getValue();
// String system = toStringOrNull(theSystem);
IValidationSupport.LookupCodeResult result = myCodeSystemDao.lookupCode(theCode, theSystem, null, null);
if (result != null && result.isFound()) {
IFhirResourceDaoValueSet.ValidateCodeResult retVal = new ValidateCodeResult(true, "Found code", result.getCodeDisplay());
return retVal;
}
}
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSets() && !isBuiltInValueSet && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(new ValidationOptions(), vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
}
if (result != null) {
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
if (!theDisplay.getValue().equals(result.getDisplay())) {
return new ValidateCodeResult(false, "Display for code does not match", result.getDisplay());
}
}
return result;
}
}
return new ValidateCodeResult(false, "Code not found", null);
}
private String toStringOrNull(IPrimitiveType<String> thePrimitive) {
return thePrimitive != null ? thePrimitive.getValue() : null;
}
private IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInContains(List<ValueSetExpansionContainsComponent> contains, String theSystem, String theCode,
Coding theCoding, CodeableConcept theCodeableConcept) {
for (ValueSetExpansionContainsComponent nextCode : contains) {
IFhirResourceDaoValueSet.ValidateCodeResult result = validateCodeIsInContains(nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
if (result != null) {
return result;
}
String system = nextCode.getSystem();
String code = nextCode.getCode();
if (isNotBlank(theCode)) {
if (theCode.equals(code) && (isBlank(theSystem) || theSystem.equals(system))) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
} else if (theCoding != null) {
if (StringUtils.equals(system, theCoding.getSystem()) && StringUtils.equals(code, theCoding.getCode())) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
} else {
for (Coding next : theCodeableConcept.getCoding()) {
if (StringUtils.equals(system, next.getSystem()) && StringUtils.equals(code, next.getCode())) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
}
}
}
return null;
public IValidationSupport.CodeValidationResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding,
CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
return myTerminologySvc.validateCode(vsValidateCodeOptions(), theId, toStringOrNull(theValueSetIdentifier), toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
}
@Override
@ -395,4 +295,8 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
return retVal;
}
public static ConceptValidationOptions vsValidateCodeOptions() {
return new ConceptValidationOptions().setValidateDisplay(true);
}
}

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

@ -133,6 +133,8 @@ public class IdHelperService {
*/
@Nonnull
public ResourcePersistentId resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theId) {
Validate.notNull(theId, "theId must not be null");
Long retVal;
if (myDaoConfig.getResourceClientIdStrategy() == DaoConfig.ClientIdStrategyEnum.ANY || !isValidPid(theId)) {
if (myDaoConfig.isDeleteEnabled()) {

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

@ -497,11 +497,6 @@ class PredicateBuilderReference extends BasePredicateBuilder {
}
}
// one value
if (path.size() == 1) {
return myCriteriaBuilder.equal(from.get("mySourcePath").as(String.class), path.get(0));
}
// multiple values
return from.get("mySourcePath").in(path);
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderToken.java
View File

@ -366,12 +366,12 @@ class PredicateBuilderToken extends BasePredicateBuilder implements IPredicateBu
break;
}
Predicate predicate;
if (values.size() == 1) {
predicate = myCriteriaBuilder.equal(hashField, values.get(0));
} else {
predicate = hashField.in(values);
}
/*
* Note: At one point we had an IF-ELSE here that did an equals if there was only 1 value, and an IN if there
* was more than 1. This caused a performance regression for some reason in Postgres though. So maybe simpler
* is better..
*/
Predicate predicate = hashField.in(values);
if (theModifier == TokenParamModifier.NOT) {
Predicate identityPredicate = theBuilder.equal(theFrom.get("myHashIdentity").as(Long.class), BaseResourceIndexedSearchParam.calculateHashIdentity(getPartitionSettings(), theRequestPartitionId, theResourceName, theParamName));

110
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
View File

@ -31,7 +31,6 @@ import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -49,13 +48,13 @@ import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r4.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import static ca.uhn.fhir.jpa.dao.FhirResourceDaoValueSetDstu2.toStringOrNull;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoValueSetDstu3.vsValidateCodeOptions;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -243,108 +242,11 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
}
@Override
public ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding,
CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
public IValidationSupport.CodeValidationResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding,
CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
List<IIdType> valueSetIds = Collections.emptyList();
boolean haveCodeableConcept = theCodeableConcept != null && theCodeableConcept.getCoding().size() > 0;
boolean haveCoding = theCoding != null && !theCoding.isEmpty();
boolean haveCode = theCode != null && !theCode.isEmpty();
if (!haveCodeableConcept && !haveCoding && !haveCode) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
if (!LogicUtil.multiXor(haveCodeableConcept, haveCoding, haveCode)) {
throw new InvalidRequestException("$validate-code can only validate (system AND code) OR (coding) OR (codeableConcept)");
}
boolean haveIdentifierParam = theValueSetIdentifier != null && !theValueSetIdentifier.isEmpty();
ValueSet vs = null;
boolean isBuiltInValueSet = false;
if (theId != null) {
vs = read(theId, theRequestDetails);
} else if (haveIdentifierParam) {
vs = (ValueSet) myDefaultProfileValidationSupport.fetchValueSet(theValueSetIdentifier.getValue());
if (vs == null) {
vs = (ValueSet) myValidationSupport.fetchValueSet(theValueSetIdentifier.getValue());
if (vs == null) {
throw new InvalidRequestException("Unknown ValueSet identifier: " + theValueSetIdentifier.getValue());
}
} else {
isBuiltInValueSet = true;
}
} else {
if (theCode == null || theCode.isEmpty()) {
throw new InvalidRequestException("Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.");
}
// String code = theCode.getValue();
// String system = toStringOrNull(theSystem);
IValidationSupport.LookupCodeResult result = myCodeSystemDao.lookupCode(theCode, theSystem, null, null);
if (result.isFound()) {
ValidateCodeResult retVal = new ValidateCodeResult(true, "Found code", result.getCodeDisplay());
return retVal;
}
}
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSets() && !isBuiltInValueSet && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(new ValidationOptions(), vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
}
if (result != null) {
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
if (!theDisplay.getValue().equals(result.getDisplay())) {
return new ValidateCodeResult(false, "Display for code does not match", result.getDisplay());
}
}
return result;
}
}
return new ValidateCodeResult(false, "Code not found", null);
}
private String toStringOrNull(IPrimitiveType<String> thePrimitive) {
return thePrimitive != null ? thePrimitive.getValue() : null;
}
private ValidateCodeResult validateCodeIsInContains(List<ValueSetExpansionContainsComponent> contains, String theSystem, String theCode,
Coding theCoding, CodeableConcept theCodeableConcept) {
for (ValueSetExpansionContainsComponent nextCode : contains) {
ValidateCodeResult result = validateCodeIsInContains(nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
if (result != null) {
return result;
}
String system = nextCode.getSystem();
String code = nextCode.getCode();
if (isNotBlank(theCode)) {
if (theCode.equals(code) && (isBlank(theSystem) || theSystem.equals(system))) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
} else if (theCoding != null) {
if (StringUtils.equals(system, theCoding.getSystem()) && StringUtils.equals(code, theCoding.getCode())) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
} else {
for (Coding next : theCodeableConcept.getCoding()) {
if (StringUtils.equals(system, next.getSystem()) && StringUtils.equals(code, next.getCode())) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
}
}
}
return null;
return myTerminologySvc.validateCode(vsValidateCodeOptions(), theId, toStringOrNull(theValueSetIdentifier), toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
}
@Override

109
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.r5;
* #L%
*/
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
@ -55,6 +56,8 @@ import java.util.Collections;
import java.util.Date;
import java.util.List;
import static ca.uhn.fhir.jpa.dao.FhirResourceDaoValueSetDstu2.toStringOrNull;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoValueSetDstu3.vsValidateCodeOptions;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoValueSetR4.validateHaveExpansionOrThrowInternalErrorException;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -245,108 +248,10 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
}
@Override
public ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding,
CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
List<IIdType> valueSetIds = Collections.emptyList();
boolean haveCodeableConcept = theCodeableConcept != null && theCodeableConcept.getCoding().size() > 0;
boolean haveCoding = theCoding != null && theCoding.isEmpty() == false;
boolean haveCode = theCode != null && theCode.isEmpty() == false;
if (!haveCodeableConcept && !haveCoding && !haveCode) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
if (!LogicUtil.multiXor(haveCodeableConcept, haveCoding, haveCode)) {
throw new InvalidRequestException("$validate-code can only validate (system AND code) OR (coding) OR (codeableConcept)");
}
boolean haveIdentifierParam = theValueSetIdentifier != null && theValueSetIdentifier.isEmpty() == false;
ValueSet vs = null;
boolean isBuiltInValueSet = false;
if (theId != null) {
vs = read(theId, theRequestDetails);
} else if (haveIdentifierParam) {
vs = (ValueSet) myDefaultProfileValidationSupport.fetchValueSet(theValueSetIdentifier.getValue());
if (vs == null) {
vs = (ValueSet) myValidationSupport.fetchValueSet(theValueSetIdentifier.getValue());
if (vs == null) {
throw new InvalidRequestException("Unknown ValueSet identifier: " + theValueSetIdentifier.getValue());
}
} else {
isBuiltInValueSet = true;
}
} else {
if (theCode == null || theCode.isEmpty()) {
throw new InvalidRequestException("Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.");
}
// String code = theCode.getValue();
// String system = toStringOrNull(theSystem);
IValidationSupport.LookupCodeResult result = myCodeSystemDao.lookupCode(theCode, theSystem, null, null);
if (result.isFound()) {
ValidateCodeResult retVal = new ValidateCodeResult(true, "Found code", result.getCodeDisplay());
return retVal;
}
}
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSets() && !isBuiltInValueSet && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(new ValidationOptions(), vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
}
if (result != null) {
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
if (!theDisplay.getValue().equals(result.getDisplay())) {
return new ValidateCodeResult(false, "Display for code does not match", result.getDisplay());
}
}
return result;
}
}
return new ValidateCodeResult(false, "Code not found", null);
}
private String toStringOrNull(IPrimitiveType<String> thePrimitive) {
return thePrimitive != null ? thePrimitive.getValue() : null;
}
private ValidateCodeResult validateCodeIsInContains(List<ValueSetExpansionContainsComponent> contains, String theSystem, String theCode,
Coding theCoding, CodeableConcept theCodeableConcept) {
for (ValueSetExpansionContainsComponent nextCode : contains) {
ValidateCodeResult result = validateCodeIsInContains(nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
if (result != null) {
return result;
}
String system = nextCode.getSystem();
String code = nextCode.getCode();
if (isNotBlank(theCode)) {
if (theCode.equals(code) && (isBlank(theSystem) || theSystem.equals(system))) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
} else if (theCoding != null) {
if (StringUtils.equals(system, theCoding.getSystem()) && StringUtils.equals(code, theCoding.getCode())) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
} else {
for (Coding next : theCodeableConcept.getCoding()) {
if (StringUtils.equals(system, next.getSystem()) && StringUtils.equals(code, next.getCode())) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
}
}
}
return null;
public IValidationSupport.CodeValidationResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding,
CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
return myTerminologySvc.validateCode(vsValidateCodeOptions(), theId, toStringOrNull(theValueSetIdentifier), toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
}
@Override

103
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionService.java Normal file
View File

@ -0,0 +1,103 @@
package ca.uhn.fhir.jpa.dao.tx;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* 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.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.model.ResourceVersionConflictResolutionStrategy;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct;
public class HapiTransactionService {
private static final Logger ourLog = LoggerFactory.getLogger(HapiTransactionService.class);
@Autowired
private IInterceptorBroadcaster myInterceptorBroadcaster;
@Autowired
private PlatformTransactionManager myTransactionManager;
private TransactionTemplate myTxTemplate;
@PostConstruct
public void start() {
myTxTemplate = new TransactionTemplate(myTransactionManager);
}
public <T> T execute(RequestDetails theRequestDetails, TransactionCallback<T> theCallback) {
for (int i = 0; ; i++) {
try {
try {
return myTxTemplate.execute(theCallback);
} catch (MyException e) {
if (e.getCause() instanceof RuntimeException) {
throw (RuntimeException) e.getCause();
} else {
throw new InternalErrorException(e);
}
}
} catch (ResourceVersionConflictException e) {
ourLog.debug("Version conflict detected: {}", e.toString());
HookParams params = new HookParams()
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
ResourceVersionConflictResolutionStrategy conflictResolutionStrategy = (ResourceVersionConflictResolutionStrategy) JpaInterceptorBroadcaster.doCallHooksAndReturnObject(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_VERSION_CONFLICT, params);
if (conflictResolutionStrategy != null && conflictResolutionStrategy.isRetry()) {
if (i <= conflictResolutionStrategy.getMaxRetries()) {
continue;
}
ourLog.info("Max retries ({}) exceeded for version conflict", conflictResolutionStrategy.getMaxRetries());
}
throw e;
}
}
}
/**
* This is just an unchecked exception so that we can catch checked exceptions inside TransactionTemplate
* and rethrow them outside of it
*/
static class MyException extends RuntimeException {
public MyException(Throwable theThrowable) {
super(theThrowable);
}
}
}

37
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactional.java Normal file
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@ -0,0 +1,37 @@
package ca.uhn.fhir.jpa.dao.tx;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* 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 java.lang.annotation.Retention;
import java.lang.annotation.Target;
import static java.lang.annotation.ElementType.METHOD;
import static java.lang.annotation.ElementType.TYPE;
import static java.lang.annotation.RetentionPolicy.RUNTIME;
/**
* @see HapiTransactionalAspect
* @since 5.1.0
*/
@Retention(RUNTIME)
@Target({METHOD, TYPE})
public @interface HapiTransactional {
}

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

@ -44,6 +44,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import java.util.List;

99
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/JpaStorageServices.java
View File

@ -25,15 +25,24 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateOrListParam;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.NumberOrListParam;
import ca.uhn.fhir.rest.param.NumberParam;
import ca.uhn.fhir.rest.param.QuantityOrListParam;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.SpecialOrListParam;
import ca.uhn.fhir.rest.param.SpecialParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
@ -56,6 +65,7 @@ import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import static ca.uhn.fhir.rest.api.Constants.PARAM_FILTER;
@ -111,42 +121,63 @@ public class JpaStorageServices extends BaseHapiFhirDao<IBaseResource> implement
throw new InvalidRequestException(msg);
}
for (Value nextValue : nextArgument.getValues()) {
String value = nextValue.getValue();
IQueryParameterOr<?> queryParam;
IQueryParameterType param = null;
switch (searchParam.getParamType()) {
case NUMBER:
param = new NumberParam(value);
break;
case DATE:
param = new DateParam(value);
break;
case STRING:
param = new StringParam(value);
break;
case TOKEN:
param = new TokenParam(null, value);
break;
case REFERENCE:
param = new ReferenceParam(value);
break;
case COMPOSITE:
throw new InvalidRequestException("Composite parameters are not yet supported in GraphQL");
case QUANTITY:
param = new QuantityParam(value);
break;
case SPECIAL:
param = new SpecialParam().setValue(value);
break;
case URI:
break;
case HAS:
break;
}
params.add(searchParamName, param);
switch (searchParam.getParamType()) {
case NUMBER:
NumberOrListParam numberOrListParam = new NumberOrListParam();
for (Value value: nextArgument.getValues()) {
numberOrListParam.addOr(new NumberParam(value.getValue()));
}
queryParam = numberOrListParam;
break;
case DATE:
DateOrListParam dateOrListParam = new DateOrListParam();
for (Value value: nextArgument.getValues()) {
dateOrListParam.addOr(new DateParam(value.getValue()));
}
queryParam = dateOrListParam;
break;
case STRING:
StringOrListParam stringOrListParam = new StringOrListParam();
for (Value value: nextArgument.getValues()) {
stringOrListParam.addOr(new StringParam(value.getValue()));
}
queryParam = stringOrListParam;
break;
case TOKEN:
TokenOrListParam tokenOrListParam = new TokenOrListParam();
for (Value value: nextArgument.getValues()) {
tokenOrListParam.addOr(new TokenParam(value.getValue()));
}
queryParam = tokenOrListParam;
break;
case REFERENCE:
ReferenceOrListParam referenceOrListParam = new ReferenceOrListParam();
for (Value value: nextArgument.getValues()) {
referenceOrListParam.addOr(new ReferenceParam(value.getValue()));
}
queryParam = referenceOrListParam;
break;
case QUANTITY:
QuantityOrListParam quantityOrListParam = new QuantityOrListParam();
for (Value value: nextArgument.getValues()) {
quantityOrListParam.addOr(new QuantityParam(value.getValue()));
}
queryParam = quantityOrListParam;
break;
case SPECIAL:
SpecialOrListParam specialOrListParam = new SpecialOrListParam();
for (Value value: nextArgument.getValues()) {
specialOrListParam.addOr(new SpecialParam().setValue(value.getValue()));
}
queryParam = specialOrListParam;
break;
default:
throw new InvalidRequestException(String.format("%s parameters are not yet supported in GraphQL", searchParam.getParamType()));
}
params.add(searchParamName, queryParam);
}
RequestDetails requestDetails = (RequestDetails) theAppInfo;

82
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/UserRequestRetryVersionConflictsInterceptor.java Normal file
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@ -0,0 +1,82 @@
package ca.uhn.fhir.jpa.interceptor;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* 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.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Interceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.model.ResourceVersionConflictResolutionStrategy;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import java.util.StringTokenizer;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
/**
* This interceptor looks for a header on incoming requests called <code>X-Retry-On-Version-Conflict</code> and
* if present, it will instruct the server to automatically retry JPA server operations that would have
* otherwise failed with a {@link ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException} (HTTP 409).
* <p>
* The format of the header is:<br/>
* <code>X-Retry-On-Version-Conflict: retry; max-retries=100</code>
* </p>
*/
@Interceptor
public class UserRequestRetryVersionConflictsInterceptor {
public static final String HEADER_NAME = "X-Retry-On-Version-Conflict";
public static final String MAX_RETRIES = "max-retries";
public static final String RETRY = "retry";
@Hook(value = Pointcut.STORAGE_VERSION_CONFLICT, order = 100)
public ResourceVersionConflictResolutionStrategy check(RequestDetails theRequestDetails) {
ResourceVersionConflictResolutionStrategy retVal = new ResourceVersionConflictResolutionStrategy();
if (theRequestDetails != null) {
for (String headerValue : theRequestDetails.getHeaders(HEADER_NAME)) {
if (isNotBlank(headerValue)) {
StringTokenizer tok = new StringTokenizer(headerValue, ";");
while (tok.hasMoreTokens()) {
String next = trim(tok.nextToken());
if (next.equals(RETRY)) {
retVal.setRetry(true);
} else if (next.startsWith(MAX_RETRIES + "=")) {
String val = trim(next.substring((MAX_RETRIES + "=").length()));
int maxRetries = Integer.parseInt(val);
maxRetries = Math.min(100, maxRetries);
retVal.setMaxRetries(maxRetries);
}
}
}
}
}
return retVal;
}
}

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

@ -297,7 +297,8 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
}
myPackageVersionResourceDao.save(resourceEntity);
String msg = "Indexing Resource[" + dirName + '/' + nextFile + "] with URL: " + defaultString(url) + "|" + defaultString(version);
String resType = packageContext.getResourceType(resource);
String msg = "Indexing " + resType + " Resource[" + dirName + '/' + nextFile + "] with URL: " + defaultString(url) + "|" + defaultString(version);
getProcessingMessages(npmPackage).add(msg);
ourLog.info("Package[{}#{}] " + msg, thePackageId, packageVersionId);
}

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

@ -31,6 +31,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
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.util.FhirTerser;
import com.google.common.collect.Lists;
import com.google.gson.Gson;
@ -258,13 +259,14 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
return Collections.EMPTY_LIST;
}
ArrayList<IBaseResource> resources = new ArrayList<>();
for (String file : pkg.getFolders().get("package").listFiles()) {
if (file.contains(type)) {
List<String> filesForType = pkg.getFolders().get("package").getTypes().get(type);
if (filesForType != null) {
for (String file : filesForType) {
try {
byte[] content = pkg.getFolders().get("package").fetchFile(file);
resources.add(fhirContext.newJsonParser().parseResource(new String(content)));
} catch (IOException e) {
ourLog.error("Cannot install resource of type {}: Could not fetch file {}", type, file);
throw new InternalErrorException("Cannot install resource of type "+type+": Could not fetch file "+ file, e);
}
}
}

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

@ -35,9 +35,11 @@ import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.transaction.Transactional;
import java.util.HashSet;
import static ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster.doCallHooks;

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderValueSetDstu2.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.provider;
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
@ -39,6 +40,8 @@ import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.ParametersUtil;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import javax.servlet.http.HttpServletRequest;
@ -142,21 +145,27 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt> dao = (IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt>) getDao();
IFhirResourceDaoValueSet.ValidateCodeResult result = dao.validateCode(theValueSetIdentifier, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
Parameters retVal = new Parameters();
retVal.addParameter().setName("result").setValue(new BooleanDt(result.isResult()));
if (isNotBlank(result.getMessage())) {
retVal.addParameter().setName("message").setValue(new StringDt(result.getMessage()));
}
if (isNotBlank(result.getDisplay())) {
retVal.addParameter().setName("display").setValue(new StringDt(result.getDisplay()));
}
return retVal;
IValidationSupport.CodeValidationResult result = dao.validateCode(theValueSetIdentifier, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
return (Parameters) toValidateCodeResult(getContext(), result);
} finally {
endRequest(theServletRequest);
}
}
public static IBaseParameters toValidateCodeResult(FhirContext theContext, IValidationSupport.CodeValidationResult theResult) {
IBaseParameters retVal = ParametersUtil.newInstance(theContext);
ParametersUtil.addParameterToParametersBoolean(theContext, retVal, "result", theResult.isOk());
if (isNotBlank(theResult.getMessage())) {
ParametersUtil.addParameterToParametersString(theContext, retVal, "message", theResult.getMessage());
}
if (isNotBlank(theResult.getDisplay())) {
ParametersUtil.addParameterToParametersString(theContext, retVal, "display", theResult.getDisplay());
}
return retVal;
}
private static boolean moreThanOneTrue(boolean... theBooleans) {
boolean haveOne = false;
for (boolean next : theBooleans) {

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/GraphQLProvider.java
View File

@ -25,9 +25,12 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.rest.annotation.GraphQL;
import ca.uhn.fhir.rest.annotation.GraphQLQuery;
import ca.uhn.fhir.rest.annotation.GraphQLQueryBody;
import ca.uhn.fhir.rest.annotation.GraphQLQueryUrl;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Initialize;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -107,9 +110,23 @@ public class GraphQLProvider {
myStorageServices = theStorageServices;
}
@GraphQL
public String processGraphQlRequest(ServletRequestDetails theRequestDetails, @IdParam IIdType theId, @GraphQLQuery String theQuery) {
@GraphQL(type=RequestTypeEnum.GET)
public String processGraphQlGetRequest(ServletRequestDetails theRequestDetails, @IdParam IIdType theId, @GraphQLQueryUrl String queryUrl) {
if (queryUrl != null) {
return processGraphQLRequest(theRequestDetails, theId, queryUrl);
}
throw new InvalidRequestException("Unable to parse empty GraphQL expression");
}
@GraphQL(type=RequestTypeEnum.POST)
public String processGraphQlPostRequest(ServletRequestDetails theRequestDetails, @IdParam IIdType theId, @GraphQLQueryBody String queryBody) {
if (queryBody != null) {
return processGraphQLRequest(theRequestDetails, theId, queryBody);
}
throw new InvalidRequestException("Unable to parse empty GraphQL expression");
}
public String processGraphQLRequest(ServletRequestDetails theRequestDetails, IIdType theId, String theQuery) {
IGraphQLEngine engine = engineFactory.get();
engine.setAppInfo(theRequestDetails);
engine.setServices(myStorageServices);

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java
View File

@ -20,8 +20,10 @@ package ca.uhn.fhir.jpa.provider.dstu3;
* #L%
*/
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
@ -148,16 +150,8 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
IFhirResourceDaoValueSet.ValidateCodeResult result = dao.validateCode(url, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
Parameters retVal = new Parameters();
retVal.addParameter().setName("result").setValue(new BooleanType(result.isResult()));
if (isNotBlank(result.getMessage())) {
retVal.addParameter().setName("message").setValue(new StringType(result.getMessage()));
}
if (isNotBlank(result.getDisplay())) {
retVal.addParameter().setName("display").setValue(new StringType(result.getDisplay()));
}
return retVal;
IValidationSupport.CodeValidationResult result = dao.validateCode(url, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
return (Parameters) BaseJpaResourceProviderValueSetDstu2.toValidateCodeResult(getContext(), result);
} finally {
endRequest(theServletRequest);
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderValueSetR4.java
View File

@ -20,8 +20,10 @@ package ca.uhn.fhir.jpa.provider.r4;
* #L%
*/
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
@ -134,16 +136,8 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
IFhirResourceDaoValueSet.ValidateCodeResult result = dao.validateCode(theValueSetUrl, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
Parameters retVal = new Parameters();
retVal.addParameter().setName("result").setValue(new BooleanType(result.isResult()));
if (isNotBlank(result.getMessage())) {
retVal.addParameter().setName("message").setValue(new StringType(result.getMessage()));
}
if (isNotBlank(result.getDisplay())) {
retVal.addParameter().setName("display").setValue(new StringType(result.getDisplay()));
}
return retVal;
IValidationSupport.CodeValidationResult result = dao.validateCode(theValueSetUrl, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
return (Parameters) BaseJpaResourceProviderValueSetDstu2.toValidateCodeResult(getContext(), result);
} finally {
endRequest(theServletRequest);
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderValueSetR5.java
View File

@ -20,8 +20,10 @@ package ca.uhn.fhir.jpa.provider.r5;
* #L%
*/
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
@ -134,16 +136,8 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
IFhirResourceDaoValueSet.ValidateCodeResult result = dao.validateCode(theValueSetUrl, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
Parameters retVal = new Parameters();
retVal.addParameter().setName("result").setValue(new BooleanType(result.isResult()));
if (isNotBlank(result.getMessage())) {
retVal.addParameter().setName("message").setValue(new StringType(result.getMessage()));
}
if (isNotBlank(result.getDisplay())) {
retVal.addParameter().setName("display").setValue(new StringType(result.getDisplay()));
}
return retVal;
IValidationSupport.CodeValidationResult result = dao.validateCode(theValueSetUrl, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
return (Parameters) BaseJpaResourceProviderValueSetDstu2.toValidateCodeResult(getContext(), result);
} finally {
endRequest(theServletRequest);
}

199
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

@ -30,7 +30,6 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.api.model.TranslationQuery;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@ -73,6 +72,7 @@ import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
@ -81,6 +81,7 @@ 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.util.CoverageIgnore;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.util.ValidateUtil;
@ -105,10 +106,14 @@ import org.hibernate.search.jpa.FullTextEntityManager;
import org.hibernate.search.jpa.FullTextQuery;
import org.hibernate.search.query.dsl.BooleanJunction;
import org.hibernate.search.query.dsl.QueryBuilder;
import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService;
import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.CodeSystem;
@ -169,6 +174,7 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNoneBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.isNotEmpty;
public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
public static final int DEFAULT_FETCH_SIZE = 250;
@ -653,16 +659,21 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
includedConcepts = theIncludeOrExclude
.getConcept()
.stream()
.map(t->new VersionIndependentConcept(theIncludeOrExclude.getSystem(), t.getCode()))
.map(t -> new VersionIndependentConcept(theIncludeOrExclude.getSystem(), t.getCode()))
.collect(Collectors.toList());
}
if (includedConcepts != null) {
int foundCount = 0;
for (VersionIndependentConcept next : includedConcepts) {
LookupCodeResult lookup = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), next.getSystem(), next.getCode());
String nextSystem = next.getSystem();
if (nextSystem == null) {
nextSystem = system;
}
LookupCodeResult lookup = myValidationSupport.lookupCode(new ValidationSupportContext(provideValidationSupport()), nextSystem, next.getCode());
if (lookup != null && lookup.isFound()) {
addOrRemoveCode(theValueSetCodeAccumulator, theAddedCodes, theAdd, next.getSystem(), next.getCode(), lookup.getCodeDisplay());
addOrRemoveCode(theValueSetCodeAccumulator, theAddedCodes, theAdd, nextSystem, next.getCode(), lookup.getCodeDisplay());
foundCount++;
}
}
@ -1244,8 +1255,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
return true;
}
protected IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInPreExpandedValueSet(
ValidationOptions theValidationOptions,
protected IValidationSupport.CodeValidationResult validateCodeIsInPreExpandedValueSet(
ConceptValidationOptions theValidationOptions,
ValueSet theValueSet, String theSystem, String theCode, String theDisplay, Coding theCoding, CodeableConcept theCodeableConcept) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet.hasId(), "ValueSet.id is required");
@ -1253,7 +1264,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
List<TermValueSetConcept> concepts = new ArrayList<>();
if (isNotBlank(theCode)) {
if (theValidationOptions.isGuessSystem()) {
if (theValidationOptions.isInferSystem()) {
concepts.addAll(myValueSetConceptDao.findByValueSetResourcePidAndCode(valueSetResourcePid.getIdAsLong(), theCode));
} else if (isNotBlank(theSystem)) {
concepts.addAll(findByValueSetResourcePidSystemAndCode(valueSetResourcePid, theSystem, theCode));
@ -1271,19 +1282,40 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
}
}
} else {
return null;
}
for (TermValueSetConcept concept : concepts) {
if (isNotBlank(theDisplay) && theDisplay.equals(concept.getDisplay())) {
return new IFhirResourceDaoValueSet.ValidateCodeResult(true, "Validation succeeded", concept.getDisplay());
if (theValidationOptions.isValidateDisplay() && concepts.size() > 0) {
for (TermValueSetConcept concept : concepts) {
if (isBlank(theDisplay) || isBlank(concept.getDisplay()) || theDisplay.equals(concept.getDisplay())) {
return new IValidationSupport.CodeValidationResult()
.setCode(concept.getCode())
.setDisplay(concept.getDisplay());
}
}
return createFailureCodeValidationResult(theSystem, theCode, " - Concept Display \"" + theDisplay + "\" does not match expected \"" + concepts.get(0).getDisplay() + "\"").setDisplay(concepts.get(0).getDisplay());
}
if (!concepts.isEmpty()) {
return new IFhirResourceDaoValueSet.ValidateCodeResult(true, "Validation succeeded", concepts.get(0).getDisplay());
return new IValidationSupport.CodeValidationResult()
.setCode(concepts.get(0).getCode())
.setDisplay(concepts.get(0).getDisplay());
}
return null;
return createFailureCodeValidationResult(theSystem, theCode);
}
private CodeValidationResult createFailureCodeValidationResult(String theSystem, String theCode) {
String append = "";
return createFailureCodeValidationResult(theSystem, theCode, append);
}
private CodeValidationResult createFailureCodeValidationResult(String theSystem, String theCode, String theAppend) {
return new CodeValidationResult()
.setSeverity(IssueSeverity.ERROR)
.setMessage("Unknown code {" + theSystem + "}" + theCode + theAppend);
}
private List<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(ResourcePersistentId theResourcePid, String theSystem, String theCode) {
@ -1499,6 +1531,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
return;
}
if (source == null && theConceptMap.hasSourceCanonicalType()) {
source = theConceptMap.getSourceCanonicalType().getValueAsString();
}
if (target == null && theConceptMap.hasTargetCanonicalType()) {
target = theConceptMap.getTargetCanonicalType().getValueAsString();
}
/*
* For now we always delete old versions. At some point, it would be nice to allow configuration to keep old versions.
*/
@ -1526,17 +1565,28 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
if (theConceptMap.hasGroup()) {
TermConceptMapGroup termConceptMapGroup;
for (ConceptMap.ConceptMapGroupComponent group : theConceptMap.getGroup()) {
if (isBlank(group.getSource())) {
String groupSource = group.getSource();
if (isBlank(groupSource)) {
groupSource = source;
}
if (isBlank(groupSource)) {
throw new UnprocessableEntityException("ConceptMap[url='" + theConceptMap.getUrl() + "'] contains at least one group without a value in ConceptMap.group.source");
}
if (isBlank(group.getTarget())) {
String groupTarget = group.getTarget();
if (isBlank(groupTarget)) {
groupTarget = target;
}
if (isBlank(groupTarget)) {
throw new UnprocessableEntityException("ConceptMap[url='" + theConceptMap.getUrl() + "'] contains at least one group without a value in ConceptMap.group.target");
}
termConceptMapGroup = new TermConceptMapGroup();
termConceptMapGroup.setConceptMap(termConceptMap);
termConceptMapGroup.setSource(group.getSource());
termConceptMapGroup.setSource(groupSource);
termConceptMapGroup.setSourceVersion(group.getSourceVersion());
termConceptMapGroup.setTarget(group.getTarget());
termConceptMapGroup.setTarget(groupTarget);
termConceptMapGroup.setTargetVersion(group.getTargetVersion());
myConceptMapGroupDao.save(termConceptMapGroup);
@ -1636,6 +1686,58 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
}
@Override
public CodeValidationResult validateCode(ConceptValidationOptions theOptions, IIdType theValueSetId, String theValueSetUrl, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
CodeableConcept codeableConcept = toCanonicalCodeableConcept(theCodeableConcept);
boolean haveCodeableConcept = codeableConcept != null && codeableConcept.getCoding().size() > 0;
Coding coding = toCanonicalCoding(theCoding);
boolean haveCoding = coding != null && coding.isEmpty() == false;
boolean haveCode = theCode != null && theCode.isEmpty() == false;
if (!haveCodeableConcept && !haveCoding && !haveCode) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
if (!LogicUtil.multiXor(haveCodeableConcept, haveCoding, haveCode)) {
throw new InvalidRequestException("$validate-code can only validate (system AND code) OR (coding) OR (codeableConcept)");
}
boolean haveIdentifierParam = isNotBlank(theValueSetUrl);
String valueSetUrl;
if (theValueSetId != null) {
IBaseResource valueSet = myDaoRegistry.getResourceDao("ValueSet").read(theValueSetId);
valueSetUrl = CommonCodeSystemsTerminologyService.getValueSetUrl(valueSet);
} else if (haveIdentifierParam) {
valueSetUrl = theValueSetUrl;
} else {
throw new InvalidRequestException("Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.");
}
ValidationSupportContext validationContext = new ValidationSupportContext(provideValidationSupport());
String code = theCode;
String system = theSystem;
String display = theDisplay;
if (haveCodeableConcept) {
for (int i = 0; i < codeableConcept.getCoding().size(); i++) {
Coding nextCoding = codeableConcept.getCoding().get(i);
CodeValidationResult nextValidation = validateCode(validationContext, theOptions, nextCoding.getSystem(), nextCoding.getCode(), nextCoding.getDisplay(), valueSetUrl);
if (nextValidation.isOk() || i == codeableConcept.getCoding().size() - 1) {
return nextValidation;
}
}
} else if (haveCoding) {
system = coding.getSystem();
code = coding.getCode();
display = coding.getDisplay();
}
return validateCode(validationContext, theOptions, system, code, display, valueSetUrl);
}
private boolean isNotSafeToPreExpandValueSets() {
return myDeferredStorageSvc != null && !myDeferredStorageSvc.isStorageQueueEmpty();
}
@ -1997,7 +2099,36 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
return null;
}
Optional<VersionIndependentConcept> validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theValidationOptions, String theValueSetUrl, String theCodeSystem, String theCode) {
@CoverageIgnore
@Override
public IValidationSupport.CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
invokeRunnableForUnitTest();
if (isNotBlank(theValueSetUrl)) {
return validateCodeInValueSet(theValidationSupportContext, theOptions, theValueSetUrl, theCodeSystem, theCode, theDisplay);
}
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
Optional<VersionIndependentConcept> codeOpt = txTemplate.execute(t -> findCode(theCodeSystem, theCode).map(c -> new VersionIndependentConcept(theCodeSystem, c.getCode())));
if (codeOpt != null && codeOpt.isPresent()) {
VersionIndependentConcept code = codeOpt.get();
if (!theOptions.isValidateDisplay() || (isNotBlank(code.getDisplay()) && isNotBlank(theDisplay) && code.getDisplay().equals(theDisplay))) {
return new CodeValidationResult()
.setCode(code.getCode())
.setDisplay(code.getDisplay());
} else {
return createFailureCodeValidationResult(theCodeSystem, theCode, " - Concept Display \"" + code.getDisplay() + "\" does not match expected \"" + code.getDisplay() + "\"").setDisplay(code.getDisplay());
}
}
return createFailureCodeValidationResult(theCodeSystem, theCode);
}
IValidationSupport.CodeValidationResult validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theValidationOptions, String theValueSetUrl, String theCodeSystem, String theCode, String theDisplay) {
IBaseResource valueSet = theValidationSupportContext.getRootValidationSupport().fetchValueSet(theValueSetUrl);
// If we don't have a PID, this came from some source other than the JPA
@ -2006,24 +2137,26 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
Long pid = IDao.RESOURCE_PID.get((IAnyResource) valueSet);
if (pid != null) {
if (isValueSetPreExpandedForCodeValidation(valueSet)) {
IFhirResourceDaoValueSet.ValidateCodeResult outcome = validateCodeIsInPreExpandedValueSet(new ValidationOptions(), valueSet, theCodeSystem, theCode, null, null, null);
if (outcome != null && outcome.isResult()) {
return Optional.of(new VersionIndependentConcept(theCodeSystem, theCode));
}
return validateCodeIsInPreExpandedValueSet(theValidationOptions, valueSet, theCodeSystem, theCode, null, null, null);
}
}
}
ValueSet canonicalValueSet = toCanonicalValueSet(valueSet);
VersionIndependentConcept wantConcept = new VersionIndependentConcept(theCodeSystem, theCode);
ValueSetExpansionOptions expansionOptions = new ValueSetExpansionOptions()
.setFailOnMissingCodeSystem(false);
CodeValidationResult retVal = null;
if (valueSet != null) {
retVal = new InMemoryTerminologyServerValidationSupport(myContext).validateCodeInValueSet(theValidationSupportContext, theValidationOptions, theCodeSystem, theCode, theDisplay, valueSet);
} else {
String append = " - Unable to locate ValueSet[" + theValueSetUrl + "]";
retVal = createFailureCodeValidationResult(theCodeSystem, theCode, append);
}
if (retVal == null) {
String append = " - Unable to expand ValueSet[" + theValueSetUrl + "]";
retVal = createFailureCodeValidationResult(theCodeSystem, theCode, append);
}
return retVal;
List<VersionIndependentConcept> expansionOutcome = expandValueSetAndReturnVersionIndependentConcepts(expansionOptions, canonicalValueSet, wantConcept);
return expansionOutcome
.stream()
.filter(t -> (theValidationOptions.isInferSystem() || t.getSystem().equals(theCodeSystem)) && t.getCode().equals(theCode))
.findFirst();
}
@Override
@ -2148,6 +2281,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
return false;
}
@Nullable
protected abstract Coding toCanonicalCoding(@Nullable IBaseDatatype theCoding);
@Nullable
protected abstract CodeableConcept toCanonicalCodeableConcept(@Nullable IBaseDatatype theCodeableConcept);
public static class Job implements HapiJob {
@Autowired
private ITermReadSvc myTerminologySvc;

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu2.java
View File

@ -20,18 +20,23 @@ package ca.uhn.fhir.jpa.term;
* #L%
*/
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.util.VersionIndependentConcept;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nullable;
import java.util.ArrayList;
import java.util.List;
@ -132,8 +137,34 @@ public class TermReadSvcDstu2 extends BaseTermReadSvcImpl {
return retVal;
}
@Nullable
@Override
public IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInPreExpandedValueSet(ValidationOptions theOptions, IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
protected Coding toCanonicalCoding(@Nullable IBaseDatatype theCoding) {
Coding retVal = null;
if (theCoding != null) {
CodingDt coding = (CodingDt) theCoding;
retVal = new Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
}
return retVal;
}
@Nullable
@Override
protected CodeableConcept toCanonicalCodeableConcept(@Nullable IBaseDatatype theCodeableConcept) {
CodeableConcept outcome = null;
if (theCodeableConcept != null) {
outcome = new CodeableConcept();
CodeableConceptDt cc = (CodeableConceptDt) theCodeableConcept;
outcome.setText(cc.getText());
for (CodingDt next : cc.getCoding()) {
outcome.addCoding(toCanonicalCoding(next));
}
}
return outcome;
}
@Override
public CodeValidationResult validateCodeIsInPreExpandedValueSet(ConceptValidationOptions theOptions, IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
throw new UnsupportedOperationException();
}

48
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java
View File

@ -12,6 +12,8 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.ValidateUtil;
import ca.uhn.fhir.util.VersionIndependentConcept;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.conv30_40.CodeSystem30_40;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeableConcept;
@ -26,6 +28,7 @@ import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nullable;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -103,6 +106,20 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
return CodeSystem30_40.convertCodeSystem((CodeSystem)theCodeSystem);
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseDatatype theCoding) {
return VersionConvertor_30_40.convertCoding((org.hl7.fhir.dstu3.model.Coding) theCoding);
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.CodeableConcept toCanonicalCodeableConcept(IBaseDatatype theCoding) {
return VersionConvertor_30_40.convertCodeableConcept((org.hl7.fhir.dstu3.model.CodeableConcept) theCoding);
}
@Override
public void expandValueSet(ValueSetExpansionOptions theExpansionOptions, IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
ValueSet valueSetToExpand = (ValueSet) theValueSetToExpand;
@ -130,35 +147,6 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
return valueSetR4;
}
@CoverageIgnore
@Override
public IValidationSupport.CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
Optional<VersionIndependentConcept> codeOpt = Optional.empty();
boolean haveValidated = false;
if (isNotBlank(theValueSetUrl)) {
codeOpt = super.validateCodeInValueSet(theValidationSupportContext, theOptions, theValueSetUrl, theCodeSystem, theCode);
haveValidated = true;
}
if (!haveValidated) {
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
codeOpt = txTemplate.execute(t -> findCode(theCodeSystem, theCode).map(c -> new VersionIndependentConcept(theCodeSystem, c.getCode())));
}
if (codeOpt != null && codeOpt.isPresent()) {
VersionIndependentConcept code = codeOpt.get();
IValidationSupport.CodeValidationResult retVal = new IValidationSupport.CodeValidationResult()
.setCode(code.getCode());
return retVal;
}
return new IValidationSupport.CodeValidationResult()
.setSeverity(IssueSeverity.ERROR)
.setMessage("Unknown code {" + theCodeSystem + "}" + theCode);
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return super.lookupCode(theSystem, theCode);
@ -170,7 +158,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
}
@Override
public IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInPreExpandedValueSet(ValidationOptions theOptions, IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
public IValidationSupport.CodeValidationResult validateCodeIsInPreExpandedValueSet(ConceptValidationOptions theOptions, IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = convertValueSet(valueSet);

56
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR4.java
View File

@ -5,28 +5,19 @@ import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.VersionIndependentConcept;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.support.TransactionTemplate;
import javax.transaction.Transactional;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
* #%L
@ -98,50 +89,29 @@ public class TermReadSvcR4 extends BaseTermReadSvcImpl implements ITermReadSvcR4
return (CodeSystem) theCodeSystem;
}
@CoverageIgnore
@Override
public IValidationSupport.CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
invokeRunnableForUnitTest();
Optional<VersionIndependentConcept> codeOpt = Optional.empty();
boolean haveValidated = false;
if (isNotBlank(theValueSetUrl)) {
codeOpt = super.validateCodeInValueSet(theValidationSupportContext, theOptions, theValueSetUrl, theCodeSystem, theCode);
haveValidated = true;
}
if (!haveValidated) {
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
codeOpt = txTemplate.execute(t -> findCode(theCodeSystem, theCode).map(c -> new VersionIndependentConcept(theCodeSystem, c.getCode())));
}
if (codeOpt != null && codeOpt.isPresent()) {
VersionIndependentConcept code = codeOpt.get();
IValidationSupport.CodeValidationResult retVal = new IValidationSupport.CodeValidationResult()
.setCode(code.getCode());
return retVal;
}
return new IValidationSupport.CodeValidationResult()
.setSeverity(IssueSeverity.ERROR)
.setMessage("Unknown code {" + theCodeSystem + "}" + theCode);
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return super.lookupCode(theSystem, theCode);
}
@Override
public IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInPreExpandedValueSet(ValidationOptions theOptions, IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
public IValidationSupport.CodeValidationResult validateCodeIsInPreExpandedValueSet(ConceptValidationOptions theOptions, IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
ValueSet valueSet = (ValueSet) theValueSet;
Coding coding = (Coding) theCoding;
CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
Coding coding = toCanonicalCoding(theCoding);
CodeableConcept codeableConcept = toCanonicalCodeableConcept(theCodeableConcept);
return super.validateCodeIsInPreExpandedValueSet(theOptions, valueSet, theSystem, theCode, theDisplay, coding, codeableConcept);
}
@Override
protected Coding toCanonicalCoding(IBaseDatatype theCoding) {
return (Coding) theCoding;
}
@Override
protected CodeableConcept toCanonicalCodeableConcept(IBaseDatatype theCodeableConcept) {
return (CodeableConcept) theCodeableConcept;
}
@Override
public boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet) {
ValueSet valueSet = (ValueSet) theValueSet;

68
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR5.java
View File

@ -6,17 +6,15 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
import ca.uhn.fhir.util.ValidateUtil;
import ca.uhn.fhir.util.VersionIndependentConcept;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.conv40_50.CodeSystem40_50;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ValueSet;
@ -24,13 +22,9 @@ import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nullable;
import javax.transaction.Transactional;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
* #%L
@ -86,57 +80,18 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR5);
}
@Override
public IValidationSupport.CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
Optional<VersionIndependentConcept> codeOpt = Optional.empty();
boolean haveValidated = false;
if (isNotBlank(theValueSetUrl)) {
codeOpt = super.validateCodeInValueSet(theValidationSupportContext, theOptions, theValueSetUrl, theCodeSystem, theCode);
haveValidated = true;
}
if (!haveValidated) {
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
codeOpt = txTemplate.execute(t -> findCode(theCodeSystem, theCode).map(c -> new VersionIndependentConcept(theCodeSystem, c.getCode())));
}
if (codeOpt != null && codeOpt.isPresent()) {
VersionIndependentConcept code = codeOpt.get();
ConceptDefinitionComponent def = new ConceptDefinitionComponent();
def.setCode(code.getCode());
IValidationSupport.CodeValidationResult retVal = new IValidationSupport.CodeValidationResult()
.setCode(code.getCode());
return retVal;
}
return new IValidationSupport.CodeValidationResult()
.setSeverity(IssueSeverity.ERROR)
.setCode("Unknown code {" + theCodeSystem + "}" + theCode);
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return super.lookupCode(theSystem, theCode);
}
@Override
public FhirContext getFhirContext() {
return myContext;
}
@Override
public IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInPreExpandedValueSet(ValidationOptions theOptions, IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
public CodeValidationResult validateCodeIsInPreExpandedValueSet(ConceptValidationOptions theOptions, IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = toCanonicalValueSet(valueSet);
Coding coding = (Coding) theCoding;
org.hl7.fhir.r4.model.Coding codingR4 = null;
if (coding != null) {
codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
}
org.hl7.fhir.r4.model.Coding codingR4 = toCanonicalCoding(theCoding);
CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
org.hl7.fhir.r4.model.CodeableConcept codeableConceptR4 = null;
@ -147,9 +102,22 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
}
}
return super.validateCodeIsInPreExpandedValueSet(new TerminologyServiceOptions(), valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConceptR4);
return super.validateCodeIsInPreExpandedValueSet(theOptions, valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConceptR4);
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseDatatype theCoding) {
return VersionConvertor_40_50.convertCoding((Coding) theCoding);
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.CodeableConcept toCanonicalCodeableConcept(IBaseDatatype theCoding) {
return VersionConvertor_40_50.convertCodeableConcept((CodeableConcept) theCoding);
}
@Override
protected org.hl7.fhir.r4.model.ValueSet toCanonicalValueSet(IBaseResource theValueSet) throws org.hl7.fhir.exceptions.FHIRException {
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet((ValueSet) theValueSet);

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

@ -1,19 +1,22 @@
package ca.uhn.fhir.jpa.term.api;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IValueSetConceptAccumulator;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.util.VersionIndependentConcept;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
@ -105,7 +108,12 @@ public interface ITermReadSvc extends IValidationSupport {
/**
* Version independent
*/
IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInPreExpandedValueSet(ValidationOptions theOptions, IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept);
CodeValidationResult validateCode(ConceptValidationOptions theOptions, IIdType theValueSetId, String theValueSetUrl, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept);
/**
* Version independent
*/
CodeValidationResult validateCodeIsInPreExpandedValueSet(ConceptValidationOptions theOptions, IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept);
boolean isValueSetPreExpandedForCodeValidation(ValueSet theValueSet);
@ -114,5 +122,4 @@ public interface ITermReadSvc extends IValidationSupport {
*/
boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet);
}

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

@ -66,13 +66,13 @@ public class JpaValidationSupportChain extends ValidationSupportChain {
@PostConstruct
public void postConstruct() {
addValidationSupport(new CommonCodeSystemsTerminologyService(myFhirContext));
addValidationSupport(myDefaultProfileValidationSupport);
addValidationSupport(myJpaValidationSupport);
addValidationSupport(myTerminologyService);
addValidationSupport(new SnapshotGeneratingValidationSupport(myFhirContext));
addValidationSupport(new InMemoryTerminologyServerValidationSupport(myFhirContext));
addValidationSupport(myNpmJpaValidationSupport);
addValidationSupport(new CommonCodeSystemsTerminologyService(myFhirContext));
}
}

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java
View File

@ -7,6 +7,7 @@ import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import net.ttddyy.dsproxy.listener.ThreadQueryCountHolder;
import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hibernate.dialect.H2Dialect;

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
View File

@ -56,6 +56,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
private Exception myLastStackTrace;
@Override
@Bean
public IBatchJobSubmitter batchJobSubmitter() {
return new BatchJobSubmitterImpl();
@ -118,7 +119,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
retVal.setDriver(new org.h2.Driver());
retVal.setUrl("jdbc:h2:mem:testdb_r4");
retVal.setMaxWaitMillis(10000);
retVal.setMaxWaitMillis(30000);
retVal.setUsername("");
retVal.setPassword("");
retVal.setMaxTotal(ourMaxThreads);
@ -126,7 +127,8 @@ public class TestR4Config extends BaseJavaConfigR4 {
SLF4JLogLevel level = SLF4JLogLevel.INFO;
DataSource dataSource = ProxyDataSourceBuilder
.create(retVal)
.logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
// .logQueryBySlf4j(level)
.logSlowQueryBySlf4j(10, TimeUnit.SECONDS, level)
.beforeQuery(new BlockLargeNumbersOfParamsListener())
.afterQuery(captureQueriesListener())
.afterQuery(new CurrentThreadCaptureQueriesListener())

27
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -9,8 +9,8 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
@ -22,6 +22,8 @@ import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionLoader;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
@ -29,6 +31,7 @@ import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.test.BaseTest;
import ca.uhn.fhir.test.utilities.LoggingExtension;
@ -59,7 +62,6 @@ import org.mockito.Mock;
import org.mockito.MockitoAnnotations;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.annotation.Bean;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.test.context.TestPropertySource;
import org.springframework.transaction.PlatformTransactionManager;
@ -128,6 +130,10 @@ public abstract class BaseJpaTest extends BaseTest {
@Autowired
protected IPartitionLookupSvc myPartitionConfigSvc;
@Autowired
protected SubscriptionRegistry mySubscriptionRegistry;
@Autowired
protected SubscriptionLoader mySubscriptionLoader;
@Autowired
private IdHelperService myIdHelperService;
@Autowired
private MemoryCacheService myMemoryCacheService;
@ -419,6 +425,23 @@ public abstract class BaseJpaTest extends BaseTest {
return retVal.toArray(new String[0]);
}
protected void waitForActivatedSubscriptionCount(int theSize) throws Exception {
for (int i = 0; ; i++) {
if (i == 10) {
fail("Failed to init subscriptions");
}
try {
mySubscriptionLoader.doSyncSubscriptionsForUnitTest();
break;
} catch (ResourceVersionConflictException e) {
Thread.sleep(250);
}
}
TestUtil.waitForSize(theSize, () -> mySubscriptionRegistry.size());
Thread.sleep(500);
}
@BeforeAll
public static void beforeClassRandomizeLocale() {
randomizeLocale();

28
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java
View File

@ -590,19 +590,27 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
@Test
public void testDeleteFailsIfIncomingLinks() {
String methodName = "testDeleteFailsIfIncomingLinks";
SearchParameterMap map;
List<IIdType> found;
Organization org = new Organization();
org.setName(methodName);
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
map = SearchParameterMap.newSynchronous();
map.add("_id", new StringParam(orgId.getIdPart()));
map.addRevInclude(new Include("*"));
found = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));
assertThat(found, contains(orgId));
Patient patient = new Patient();
patient.addName().addFamily(methodName);
patient.getManagingOrganization().setReference(orgId);
IIdType patId = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap map = new SearchParameterMap();
map.add("_id", new StringParam(orgId.getIdPart()));
map.addRevInclude(new Include("*"));
List<IIdType> found = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));
found = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));
assertThat(found, contains(orgId, patId));
try {
@ -613,9 +621,21 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
}
map = SearchParameterMap.newSynchronous();
map.add("_id", new StringParam(orgId.getIdPart()));
map.addRevInclude(new Include("*"));
ourLog.info("***** About to perform search");
found = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));
runInTransaction(()->{
ourLog.info("Resources:\n * {}", myResourceTableDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
});
assertThat(found.toString(), found, contains(orgId, patId));
myPatientDao.delete(patId, mySrd);
map = new SearchParameterMap();
map = SearchParameterMap.newSynchronous();
map.add("_id", new StringParam(orgId.getIdPart()));
map.addRevInclude(new Include("*"));
found = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));
@ -623,7 +643,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
myOrganizationDao.delete(orgId, mySrd);
map = new SearchParameterMap();
map = SearchParameterMap.newSynchronous();
map.add("_id", new StringParam(orgId.getIdPart()));
map.addRevInclude(new Include("*"));
found = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));

55
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoValueSetDstu2Test.java
View File

@ -1,6 +1,6 @@
package ca.uhn.fhir.jpa.dao.dstu2;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.model.dstu2.resource.ValueSet;
@ -8,9 +8,7 @@ import ca.uhn.fhir.model.primitive.CodeDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.transaction.annotation.Transactional;
@ -40,30 +38,42 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
}
@Test
public void testValidateCodeOperationByCodeAndSystemBad() {
UriDt valueSetIdentifier = null;
public void testValidateCodeOperationByCodeAndSystemBadCode() {
UriDt valueSetIdentifier = new UriDt("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
IdDt id = null;
CodeDt code = new CodeDt("8450-9-XXX");
UriDt system = new UriDt("http://loinc.org");
StringDt display = null;
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isOk());
}
@Test
public void testValidateCodeOperationByCodeAndSystemGood() {
UriDt valueSetIdentifier = null;
public void testValidateCodeOperationByCodeAndSystemBadSystem() {
UriDt valueSetIdentifier = new UriDt("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
IdDt id = null;
CodeDt code = new CodeDt("8450-9-XXX");
UriDt system = new UriDt("http://zzz");
StringDt display = null;
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isOk());
}
@Test
public void testValidateCodeOperationByIdentifierCodeInCsButNotInVs() {
UriDt valueSetIdentifier = new UriDt("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
IdDt id = null;
CodeDt code = new CodeDt("8450-9");
UriDt system = new UriDt("http://loinc.org");
StringDt display = null;
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure--expiration", result.getDisplay());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isOk());
}
@Test
@ -75,8 +85,8 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = null;
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -89,9 +99,10 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = new StringDt("Systolic blood pressure at First encounterXXXX");
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
assertEquals("Concept Display \"Systolic blood pressure at First encounterXXXX\" does not match expected \"Systolic blood pressure at First encounter\"", result.getMessage());
}
@Test
@ -103,8 +114,8 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = new StringDt("Systolic blood pressure at First encounter");
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -117,8 +128,8 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = null;
CodingDt coding = null;
CodeableConceptDt codeableConcept = new CodeableConceptDt("http://loinc.org", "11378-7");
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -131,8 +142,8 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = null;
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptMapDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptMapGroupElementTargetDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
@ -340,6 +341,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
private IValidationSupport myJpaValidationSupportChainDstu3;
@Autowired
private IBulkDataExportSvc myBulkDataExportSvc;
@Autowired
protected ITermValueSetDao myTermValueSetDao;
@AfterEach()
public void afterCleanupDao() {

102
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValueSetTest.java
View File

@ -1,9 +1,9 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.CodeableConcept;
@ -14,7 +14,6 @@ import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@ -52,6 +51,51 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
}
@Test
public void testExpandValueSetWithIso3166() throws IOException {
ValueSet vs = loadResourceFromClasspath(ValueSet.class, "/dstu3/nl/LandISOCodelijst-2.16.840.1.113883.2.4.3.11.60.40.2.20.5.2--20171231000000.json");
myValueSetDao.create(vs);
runInTransaction(() -> {
TermValueSet vsEntity = myTermValueSetDao.findByUrl("http://decor.nictiz.nl/fhir/ValueSet/2.16.840.1.113883.2.4.3.11.60.40.2.20.5.2--20171231000000").orElseThrow(() -> new IllegalStateException());
assertEquals(TermValueSetPreExpansionStatusEnum.NOT_EXPANDED, vsEntity.getExpansionStatus());
});
IValidationSupport.CodeValidationResult validationOutcome;
UriType vsIdentifier = new UriType("http://decor.nictiz.nl/fhir/ValueSet/2.16.840.1.113883.2.4.3.11.60.40.2.20.5.2--20171231000000");
CodeType code = new CodeType();
CodeType system = new CodeType("urn:iso:std:iso:3166");
// Validate good
code.setValue("NL");
validationOutcome = myValueSetDao.validateCode(vsIdentifier, null, code, system, null, null, null, mySrd);
assertEquals(true, validationOutcome.isOk());
// Validate bad
code.setValue("QQ");
validationOutcome = myValueSetDao.validateCode(vsIdentifier, null, code, system, null, null, null, mySrd);
assertEquals(false, validationOutcome.isOk());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
runInTransaction(() -> {
TermValueSet vsEntity = myTermValueSetDao.findByUrl("http://decor.nictiz.nl/fhir/ValueSet/2.16.840.1.113883.2.4.3.11.60.40.2.20.5.2--20171231000000").orElseThrow(() -> new IllegalStateException());
assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, vsEntity.getExpansionStatus());
});
// Validate good
code.setValue("NL");
validationOutcome = myValueSetDao.validateCode(vsIdentifier, null, code, system, null, null, null, mySrd);
assertEquals(true, validationOutcome.isOk());
// Validate bad
code.setValue("QQ");
validationOutcome = myValueSetDao.validateCode(vsIdentifier, null, code, system, null, null, null, mySrd);
assertEquals(false, validationOutcome.isOk());
}
@Test
@Disabled
public void testBuiltInValueSetFetchAndExpand() {
@ -144,33 +188,6 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
assertThat(resp, not(containsString("<code value=\"8450-9\"/>")));
}
@Test
public void testValidateCodeOperationByCodeAndSystemBad() {
UriType valueSetIdentifier = null;
IdType id = null;
CodeType code = new CodeType("8450-9-XXX");
UriType system = new UriType("http://acme.org");
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isResult());
}
@Test
public void testValidateCodeOperationByCodeAndSystemGood() {
UriType valueSetIdentifier = null;
IdType id = null;
CodeType code = new CodeType("8450-9");
UriType system = new UriType("http://acme.org");
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure--expiration", result.getDisplay());
}
@Test
public void testValidateCodeOperationByIdentifierAndCodeAndSystem() {
UriType valueSetIdentifier = new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
@ -180,8 +197,8 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -194,8 +211,8 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
StringType display = new StringType("Systolic blood pressure at First encounterXXXX");
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -208,8 +225,8 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
StringType display = new StringType("Systolic blood pressure at First encounter");
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -222,8 +239,8 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -237,8 +254,8 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
Coding coding = null;
CodeableConcept codeableConcept = new CodeableConcept();
codeableConcept.addCoding().setSystem("http://acme.org").setCode("11378-7");
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -250,13 +267,12 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
StringType vsIdentifier = new StringType("http://hl7.org/fhir/ValueSet/administrative-gender");
StringType code = new StringType("male");
StringType system = new StringType("http://hl7.org/fhir/administrative-gender");
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(vsIdentifier, null, code, system, display, coding, codeableConcept, mySrd);
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(vsIdentifier, null, code, system, display, coding, codeableConcept, mySrd);
ourLog.info(result.getMessage());
assertTrue(result.isResult(), result.getMessage());
assertTrue(result.isOk(), result.getMessage());
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -447,8 +447,6 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
protected ITermConceptMapGroupElementTargetDao myTermConceptMapGroupElementTargetDao;
@Autowired
protected ICacheWarmingSvc myCacheWarmingSvc;
@Autowired
protected SubscriptionRegistry mySubscriptionRegistry;
protected IServerInterceptor myInterceptor;
@Autowired
protected DaoRegistry myDaoRegistry;

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseR4SearchLastN.java
View File

@ -163,7 +163,7 @@ public class BaseR4SearchLastN extends BaseJpaTest {
}
private Date calculateObservationDateFromOffset(Integer theTimeOffset, Integer theObservationIndex) {
int milliSecondsPerHour = 3600 * 1000;
long milliSecondsPerHour = 3600L * 1000L;
// Generate a Date by subtracting a calculated number of hours from the static observationDate property.
return new Date(observationDate.getTimeInMillis() - (milliSecondsPerHour * (theTimeOffset + theObservationIndex)));
}

44
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java
View File

@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.api.model.TranslationResult;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
@ -1042,6 +1043,49 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
});
}
/**
* Some US core ConceptMaps use this style, e.g:
*
* http://hl7.org/fhir/us/core/ConceptMap/ndc-cvx
*/
@Test
public void testUploadConceptMapWithOnlyCanonicalSourceAtConceptMapLevel() {
ConceptMap cm = new ConceptMap();
cm.setUrl("http://foo");
cm.setSource(new CanonicalType("http://source"));
cm.setTarget(new CanonicalType("http://target"));
cm.addGroup().addElement().setCode("source1").addTarget().setCode("target1").setEquivalence(ConceptMapEquivalence.EQUAL);
myConceptMapDao.create(cm);
runInTransaction(()->{
TranslationRequest translationRequest = new TranslationRequest();
translationRequest.getCodeableConcept().addCoding()
.setSystem("http://source")
.setCode("source1");
translationRequest.setTarget(new UriType("http://target"));
ourLog.info("*** About to translate");
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
ourLog.info("*** Done translating");
assertTrue(translationResult.getResult().booleanValue());
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
assertEquals(1, translationResult.getMatches().size());
TranslationMatch translationMatch = translationResult.getMatches().get(0);
assertEquals("equal", translationMatch.getEquivalence().getCode());
Coding concept = translationMatch.getConcept();
assertEquals("target1", concept.getCode());
assertEquals(null, concept.getDisplay());
assertEquals("http://target", concept.getSystem());
});
}
@Test
public void testUploadAndApplyR4DemoConceptMap() throws IOException {

442
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConcurrentWriteTest.java Normal file
View File

@ -0,0 +1,442 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.interceptor.executor.InterceptorService;
import ca.uhn.fhir.jpa.interceptor.UserRequestRetryVersionConflictsInterceptor;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.HapiExtensions;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.SearchParameter;
import org.hl7.fhir.r4.model.StringType;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.greaterThanOrEqualTo;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
@SuppressWarnings({"unchecked", "deprecation", "Duplicates"})
public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ConcurrentWriteTest.class);
private ExecutorService myExecutor;
private UserRequestRetryVersionConflictsInterceptor myRetryInterceptor;
@BeforeEach
public void before() {
myExecutor = Executors.newFixedThreadPool(10);
myRetryInterceptor = new UserRequestRetryVersionConflictsInterceptor();
RestfulServer server = new RestfulServer(myFhirCtx);
when(mySrd.getServer()).thenReturn(server);
}
@AfterEach
public void after() {
myExecutor.shutdown();
myInterceptorRegistry.unregisterInterceptor(myRetryInterceptor);
}
@Test
public void testCreateWithClientAssignedId() {
myInterceptorRegistry.registerInterceptor(myRetryInterceptor);
String value = UserRequestRetryVersionConflictsInterceptor.RETRY + "; " + UserRequestRetryVersionConflictsInterceptor.MAX_RETRIES + "=10";
when(mySrd.getHeaders(eq(UserRequestRetryVersionConflictsInterceptor.HEADER_NAME))).thenReturn(Collections.singletonList(value));
List<Future<?>> futures = new ArrayList<>();
for (int i = 0; i < 5; i++) {
Patient p = new Patient();
p.setId("ABC");
p.setActive(true);
p.addIdentifier().setValue("VAL" + i);
Runnable task = () -> myPatientDao.update(p, mySrd);
Future<?> future = myExecutor.submit(task);
futures.add(future);
}
// Look for failures
for (Future<?> next : futures) {
try {
next.get();
ourLog.info("Future produced success");
} catch (Exception e) {
ourLog.info("Future produced exception: {}", e.toString());
throw new AssertionError("Failed with message: " + e.toString(), e);
}
}
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
@Test
public void testCreateWithUniqueConstraint() {
SearchParameter sp = new SearchParameter();
sp.setId("SearchParameter/patient-gender");
sp.setType(Enumerations.SearchParamType.TOKEN);
sp.setCode("gender");
sp.setExpression("Patient.gender");
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.addBase("Patient");
mySearchParameterDao.update(sp);
sp = new SearchParameter();
sp.setId("SearchParameter/patient-gender-unique");
sp.setType(Enumerations.SearchParamType.COMPOSITE);
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.addBase("Patient");
sp.addComponent()
.setExpression("Patient")
.setDefinition("SearchParameter/patient-gender");
sp.addExtension()
.setUrl(HapiExtensions.EXT_SP_UNIQUE)
.setValue(new BooleanType(true));
mySearchParameterDao.update(sp);
mySearchParamRegistry.forceRefresh();
List<Future<?>> futures = new ArrayList<>();
for (int i = 0; i < 5; i++) {
Patient p = new Patient();
p.setGender(Enumerations.AdministrativeGender.MALE);
p.addIdentifier().setValue("VAL" + i);
Runnable task = () -> {
try {
myPatientDao.create(p);
} catch (PreconditionFailedException e) {
// expected - This is as a result of the unique SP
assertThat(e.getMessage(), containsString("duplicate index matching query: Patient?gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale"));
} catch (ResourceVersionConflictException e) {
// expected - This is as a result of the unique SP
assertThat(e.getMessage(), containsString("would have resulted in a duplicate value for a unique index"));
}
};
Future<?> future = myExecutor.submit(task);
futures.add(future);
}
// Look for failures
for (Future<?> next : futures) {
try {
next.get();
ourLog.info("Future produced success");
} catch (Exception e) {
ourLog.info("Future produced exception: {}", e.toString());
throw new AssertionError("Failed with message: " + e.toString(), e);
}
}
runInTransaction(() -> {
ourLog.info("Uniques:\n * " + myResourceIndexedCompositeStringUniqueDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
});
// Make sure we saved the object
myCaptureQueriesListener.clear();
IBundleProvider search = myPatientDao.search(SearchParameterMap.newSynchronous("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male")));
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(1, search.sizeOrThrowNpe());
}
@Test
public void testDelete() {
myInterceptorRegistry.registerInterceptor(myRetryInterceptor);
String value = UserRequestRetryVersionConflictsInterceptor.RETRY + "; " + UserRequestRetryVersionConflictsInterceptor.MAX_RETRIES + "=100";
when(mySrd.getHeaders(eq(UserRequestRetryVersionConflictsInterceptor.HEADER_NAME))).thenReturn(Collections.singletonList(value));
IIdType patientId = runInTransaction(() -> {
Patient p = new Patient();
p.setActive(true);
return myPatientDao.create(p).getId().toUnqualifiedVersionless();
});
List<Future<?>> futures = new ArrayList<>();
for (int i = 0; i < 5; i++) {
// Submit an update
Patient p = new Patient();
p.setId(patientId);
p.addIdentifier().setValue("VAL" + i);
Runnable task = () -> myPatientDao.update(p, mySrd);
Future<?> future = myExecutor.submit(task);
futures.add(future);
// Submit a delete
task = () -> myPatientDao.delete(patientId, mySrd);
future = myExecutor.submit(task);
futures.add(future);
}
// Look for failures
for (Future<?> next : futures) {
try {
next.get();
ourLog.info("Future produced success");
} catch (Exception e) {
ourLog.info("Future produced exception: {}", e.toString());
throw new AssertionError("Failed with message: " + e.toString(), e);
}
}
// Make sure we saved the object
IBundleProvider patient = myPatientDao.history(patientId, null, null, null);
assertThat(patient.sizeOrThrowNpe(), greaterThanOrEqualTo(3));
}
@Test
public void testNoRetryRequest() {
myInterceptorRegistry.registerInterceptor(myRetryInterceptor);
when(mySrd.getHeaders(eq(UserRequestRetryVersionConflictsInterceptor.HEADER_NAME))).thenReturn(Collections.emptyList());
List<Future<?>> futures = new ArrayList<>();
for (int i = 0; i < 5; i++) {
Patient p = new Patient();
p.setId("ABC");
p.setActive(true);
p.addIdentifier().setValue("VAL" + i);
Runnable task = () -> myPatientDao.update(p, mySrd);
Future<?> future = myExecutor.submit(task);
futures.add(future);
}
// Look for failures
for (Future<?> next : futures) {
try {
next.get();
ourLog.info("Future produced success");
} catch (ExecutionException | InterruptedException e) {
if (e.getCause() instanceof ResourceVersionConflictException) {
// this is expected since we're not retrying
ourLog.info("Version conflict (expected): {}", e.getCause().toString());
} else {
ourLog.info("Future produced exception: {}", e.toString());
throw new AssertionError("Failed with message: " + e.toString(), e);
}
}
}
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
@Test
public void testNoRetryInterceptor() {
List<Future<?>> futures = new ArrayList<>();
for (int i = 0; i < 5; i++) {
Patient p = new Patient();
p.setId("ABC");
p.setActive(true);
p.addIdentifier().setValue("VAL" + i);
Runnable task = () -> myPatientDao.update(p, mySrd);
Future<?> future = myExecutor.submit(task);
futures.add(future);
}
// Look for failures
for (Future<?> next : futures) {
try {
next.get();
ourLog.info("Future produced success");
} catch (ExecutionException | InterruptedException e) {
if (e.getCause() instanceof ResourceVersionConflictException) {
// this is expected since we're not retrying
ourLog.info("Version conflict (expected): {}", e.getCause().toString());
} else {
ourLog.info("Future produced exception: {}", e.toString());
throw new AssertionError("Failed with message: " + e.toString(), e);
}
}
}
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
@Test
public void testNoRequestDetails() {
myInterceptorRegistry.registerInterceptor(myRetryInterceptor);
when(mySrd.getHeaders(eq(UserRequestRetryVersionConflictsInterceptor.HEADER_NAME))).thenReturn(Collections.emptyList());
List<Future<?>> futures = new ArrayList<>();
for (int i = 0; i < 5; i++) {
Patient p = new Patient();
p.setId("ABC");
p.setActive(true);
p.addIdentifier().setValue("VAL" + i);
Runnable task = () -> myPatientDao.update(p);
Future<?> future = myExecutor.submit(task);
futures.add(future);
}
// Look for failures
for (Future<?> next : futures) {
try {
next.get();
ourLog.info("Future produced success");
} catch (ExecutionException | InterruptedException e) {
if (e.getCause() instanceof ResourceVersionConflictException) {
// this is expected since we're not retrying
ourLog.info("Version conflict (expected): {}", e.getCause().toString());
} else {
ourLog.info("Future produced exception: {}", e.toString());
throw new AssertionError("Failed with message: " + e.toString(), e);
}
}
}
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
@Test
public void testPatch() {
myInterceptorRegistry.registerInterceptor(myRetryInterceptor);
String value = UserRequestRetryVersionConflictsInterceptor.RETRY + "; " + UserRequestRetryVersionConflictsInterceptor.MAX_RETRIES + "=10";
when(mySrd.getHeaders(eq(UserRequestRetryVersionConflictsInterceptor.HEADER_NAME))).thenReturn(Collections.singletonList(value));
Patient p = new Patient();
p.addName().setFamily("FAMILY");
IIdType pId = myPatientDao.create(p).getId().toUnqualifiedVersionless();
List<Future<?>> futures = new ArrayList<>();
for (int i = 0; i < 5; i++) {
Parameters patch = new Parameters();
Parameters.ParametersParameterComponent operation = patch.addParameter();
operation.setName("operation");
operation
.addPart()
.setName("type")
.setValue(new CodeType("replace"));
operation
.addPart()
.setName("path")
.setValue(new StringType("Patient.name[0].family"));
operation
.addPart()
.setName("value")
.setValue(new StringType("FAMILY-" + i));
Runnable task = () -> myPatientDao.patch(pId, null, PatchTypeEnum.FHIR_PATCH_JSON, null, patch, mySrd);
Future<?> future = myExecutor.submit(task);
futures.add(future);
}
// Look for failures
for (Future<?> next : futures) {
try {
next.get();
ourLog.info("Future produced success");
} catch (Exception e) {
ourLog.info("Future produced exception: {}", e.toString());
throw new AssertionError("Failed with message: " + e.toString(), e);
}
}
// Make sure we saved the object
Patient patient = myPatientDao.read(pId);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals("6", patient.getMeta().getVersionId());
}
@Test
public void testTransactionWithCreate() {
myInterceptorRegistry.registerInterceptor(myRetryInterceptor);
ServletRequestDetails srd = mock(ServletRequestDetails.class);
String value = UserRequestRetryVersionConflictsInterceptor.RETRY + "; " + UserRequestRetryVersionConflictsInterceptor.MAX_RETRIES + "=10";
when(srd.getHeaders(eq(UserRequestRetryVersionConflictsInterceptor.HEADER_NAME))).thenReturn(Collections.singletonList(value));
when(srd.getUserData()).thenReturn(new HashMap<>());
when(srd.getServer()).thenReturn(new RestfulServer(myFhirCtx));
when(srd.getInterceptorBroadcaster()).thenReturn(new InterceptorService());
List<Future<?>> futures = new ArrayList<>();
for (int i = 0; i < 5; i++) {
Patient p = new Patient();
p.setId("ABC");
p.setActive(true);
p.addIdentifier().setValue("VAL" + i);
Bundle bundle = new Bundle();
bundle.setType(Bundle.BundleType.TRANSACTION);
bundle
.addEntry()
.setResource(p)
.getRequest()
.setMethod(Bundle.HTTPVerb.PUT)
.setUrl("Patient/ABC");
Runnable task = () -> mySystemDao.transaction(srd, bundle);
Future<?> future = myExecutor.submit(task);
futures.add(future);
}
// Look for failures
for (Future<?> next : futures) {
try {
next.get();
ourLog.info("Future produced success");
} catch (Exception e) {
ourLog.info("Future produced exception: {}", e.toString());
throw new AssertionError("Failed with message: " + e.toString(), e);
}
}
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
View File

@ -441,7 +441,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
Observation obs = new Observation();
obs.getSubject().setReference("Patient/P");
myObservationDao.update(obs);
myObservationDao.create(obs);
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);
@ -482,7 +482,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
Observation obs = new Observation();
obs.getSubject().setReference("Patient/P");
myObservationDao.update(obs);
myObservationDao.create(obs);
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java
View File

@ -697,7 +697,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
myCaptureQueriesListener.logSelectQueries();
String selectQuery = myCaptureQueriesListener.getSelectQueries().get(1).getSql(true, true);
assertThat(selectQuery, containsString("HASH_VALUE="));
assertThat(selectQuery, containsString("HASH_VALUE"));
assertThat(selectQuery, not(containsString("HASH_SYS")));
}

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java
View File

@ -398,7 +398,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
unformattedSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
assertThat(unformattedSql, stringContainsInOrder(
"IDX_STRING='Patient?identifier=urn%7C111'",
"HASH_SYS_AND_VALUE='-3122824860083758210'"
"HASH_SYS_AND_VALUE in ('-3122824860083758210')"
));
assertThat(unformattedSql, not(containsString(("RES_DELETED_AT"))));
assertThat(unformattedSql, not(containsString(("RES_TYPE"))));
@ -535,7 +535,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
unformattedSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
assertThat(unformattedSql, stringContainsInOrder(
"IDX_STRING='ServiceRequest?identifier=sys%7C111&patient=Patient%2F" + ptId.getIdPart() + "&performer=Practitioner%2F" + practId.getIdPart() + "'",
"HASH_SYS_AND_VALUE='6795110643554413877'"
"HASH_SYS_AND_VALUE in ('6795110643554413877')"
));
assertThat(unformattedSql, not(containsString(("RES_DELETED_AT"))));
assertThat(unformattedSql, not(containsString(("RES_TYPE"))));
@ -556,8 +556,8 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
assertThat(toUnqualifiedVersionlessIdValues(outcome), containsInAnyOrder(srId));
unformattedSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
assertThat(unformattedSql, stringContainsInOrder(
"SRC_PATH='ServiceRequest.subject.where(resolve() is Patient)'",
"SRC_PATH='ServiceRequest.performer'"
"SRC_PATH in ('ServiceRequest.subject.where(resolve() is Patient)')",
"SRC_PATH in ('ServiceRequest.performer')"
));
assertThat(unformattedSql, not(containsString(("RES_DELETED_AT"))));
assertThat(unformattedSql, not(containsString(("RES_TYPE"))));

195
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
View File

@ -9,7 +9,10 @@ import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcLoincTest;
import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
@ -36,9 +39,11 @@ import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Condition;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.ElementDefinition;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.IdType;
@ -49,11 +54,13 @@ import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Questionnaire;
import org.hl7.fhir.r4.model.QuestionnaireResponse;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.junit.jupiter.api.AfterEach;
@ -73,6 +80,7 @@ import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.mock;
@ -95,6 +103,105 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
@Autowired
private ValidationSettings myValidationSettings;
@Test
public void testValidateCodeInValueSetWithUnknownCodeSystem() {
myValidationSupport.fetchCodeSystem("http://not-exist"); // preload DefaultProfileValidationSupport
ValueSet vs = new ValueSet();
vs.setUrl("http://vs");
vs
.getCompose()
.addInclude()
.setSystem("http://cs")
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code1")))
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code2")));
myValueSetDao.create(vs);
StructureDefinition sd = new StructureDefinition();
sd.setDerivation(StructureDefinition.TypeDerivationRule.CONSTRAINT);
sd.setType("Observation");
sd.setUrl("http://sd");
sd.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/Observation");
sd.getDifferential()
.addElement()
.setPath("Observation.value[x]")
.addType(new ElementDefinition.TypeRefComponent(new UriType("Quantity")))
.setBinding(new ElementDefinition.ElementDefinitionBindingComponent().setStrength(Enumerations.BindingStrength.REQUIRED).setValueSet("http://vs"))
.setId("Observation.value[x]");
myStructureDefinitionDao.create(sd);
Observation obs = new Observation();
obs.getMeta().addProfile("http://sd");
obs.getText().setDivAsString("<div>Hello</div>");
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
obs.getCategoryFirstRep().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs");
obs.getCode().setText("hello");
obs.setSubject(new Reference("Patient/123"));
obs.addPerformer(new Reference("Practitioner/123"));
obs.setEffective(DateTimeType.now());
obs.setStatus(ObservationStatus.FINAL);
OperationOutcome oo;
// Valid code
obs.setValue(new Quantity().setSystem("http://cs").setCode("code1").setValue(123));
oo = validateAndReturnOutcome(obs);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals("No issues detected during validation", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
// Invalid code
obs.setValue(new Quantity().setSystem("http://cs").setCode("code99").setValue(123));
oo = validateAndReturnOutcome(obs);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals("Could not confirm that the codes provided are in the value set http://vs, and a code from this value set is required", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
}
@Test
public void testGenerateSnapshotOnStructureDefinitionWithNoBase() {
// No base populated here, which isn't valid
StructureDefinition sd = new StructureDefinition();
sd.setDerivation(StructureDefinition.TypeDerivationRule.CONSTRAINT);
sd.setUrl("http://sd");
sd.getDifferential()
.addElement()
.setPath("Observation.value[x]")
.addType(new ElementDefinition.TypeRefComponent(new UriType("string")))
.setId("Observation.value[x]");
try {
myStructureDefinitionDao.generateSnapshot(sd, null, null, null);
fail();
} catch (PreconditionFailedException e) {
assertEquals("StructureDefinition[id=null, url=http://sd] has no base", e.getMessage());
}
myStructureDefinitionDao.create(sd);
Observation obs = new Observation();
obs.getMeta().addProfile("http://sd");
obs.getText().setDivAsString("<div>Hello</div>");
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
obs.getCategoryFirstRep().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs");
obs.getCode().setText("hello");
obs.setSubject(new Reference("Patient/123"));
obs.addPerformer(new Reference("Practitioner/123"));
obs.setEffective(DateTimeType.now());
obs.setStatus(ObservationStatus.FINAL);
OperationOutcome oo;
// Valid code
obs.setValue(new Quantity().setSystem("http://cs").setCode("code1").setValue(123));
try {
myObservationDao.validate(obs, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
assertEquals("StructureDefinition[id=null, url=http://sd] has no base", e.getMessage());
}
}
/**
* Use a valueset that explicitly brings in some UCUM codes
*/
@ -505,6 +612,64 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
}
@Test
public void testValidateValueSet() {
String input = "{\n" +
" \"resourceType\": \"ValueSet\",\n" +
" \"meta\": {\n" +
" \"profile\": [\n" +
" \"https://foo\"\n" +
" ]\n" +
" },\n" +
" \"text\": {\n" +
" \"status\": \"generated\",\n" +
" \"div\": \"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\"></div>\"\n" +
" },\n" +
" \"url\": \"https://foo/bb\",\n" +
" \"name\": \"BBBehaviourType\",\n" +
" \"title\": \"BBBehaviour\",\n" +
" \"status\": \"draft\",\n" +
" \"version\": \"20190731\",\n" +
" \"experimental\": false,\n" +
" \"description\": \"alcohol habits.\",\n" +
" \"publisher\": \"BB\",\n" +
" \"immutable\": false,\n" +
" \"compose\": {\n" +
" \"include\": [\n" +
" {\n" +
" \"system\": \"https://bb\",\n" +
" \"concept\": [\n" +
" {\n" +
" \"code\": \"123\",\n" +
" \"display\": \"Current drinker\"\n" +
" },\n" +
" {\n" +
" \"code\": \"456\",\n" +
" \"display\": \"Ex-drinker\"\n" +
" },\n" +
" {\n" +
" \"code\": \"789\",\n" +
" \"display\": \"Lifetime non-drinker (finding)\"\n" +
" }\n" +
" ]\n" +
" }\n" +
" ]\n" +
" }\n" +
"}";
ValueSet vs = myFhirCtx.newJsonParser().parseResource(ValueSet.class, input);
OperationOutcome oo = validateAndReturnOutcome(vs);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals("The code 123 is not valid in the system https://bb", oo.getIssue().get(0).getDiagnostics());
}
/**
* Per: https://chat.fhir.org/#narrow/stream/179166-implementers/topic/Handling.20incomplete.20CodeSystems
* <p>
@ -533,16 +698,10 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
obs.getCode().getCodingFirstRep().setSystem("http://example.com/codesystem");
obs.getCode().getCodingFirstRep().setCode("foo-foo");
obs.getCode().getCodingFirstRep().setDisplay("Some Code");
try {
outcome = (OperationOutcome) myObservationDao.validate(obs, null, null, null, ValidationModeEnum.CREATE, "http://example.com/structuredefinition", mySrd).getOperationOutcome();
ourLog.info("Outcome: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
fail();
} catch (PreconditionFailedException e) {
OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals("None of the codes provided are in the value set http://example.com/valueset (http://example.com/valueset), and a code from this value set is required) (codes = http://example.com/codesystem#foo-foo)", oo.getIssueFirstRep().getDiagnostics());
assertEquals(OperationOutcome.IssueSeverity.ERROR, oo.getIssueFirstRep().getSeverity());
}
outcome = (OperationOutcome) myObservationDao.validate(obs, null, null, null, ValidationModeEnum.CREATE, "http://example.com/structuredefinition", mySrd).getOperationOutcome();
ourLog.info("Outcome: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
assertEquals("Unknown code in fragment CodeSystem 'http://example.com/codesystem#foo-foo'", outcome.getIssueFirstRep().getDiagnostics());
assertEquals(OperationOutcome.IssueSeverity.WARNING, outcome.getIssueFirstRep().getSeverity());
// Correct codesystem, Code in codesystem
obs.getCode().getCodingFirstRep().setSystem("http://example.com/codesystem");
@ -1442,4 +1601,20 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
}
@Test
public void testKnownCodeSystemUnknownValueSetUri() {
CodeSystem cs = new CodeSystem();
cs.setUrl(ITermLoaderSvc.LOINC_URI);
cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
cs.addConcept().setCode("10013-1");
myCodeSystemDao.create(cs);
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(new UriType("http://fooVs"), null, new StringType("10013-1"), new StringType(ITermLoaderSvc.LOINC_URI), null, null, null, mySrd);
assertFalse(result.isOk());
assertEquals("Unknown code {http://loinc.org}10013-1 - Unable to locate ValueSet[http://fooVs]", result.getMessage());
}
}

90
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValueSetTest.java
View File

@ -1,10 +1,10 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.CodeSystem;
@ -15,7 +15,6 @@ 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.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
@ -49,14 +48,14 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
public void before02() throws IOException {
ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
CodeSystem upload2 = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
myCodeSystemDao.create(upload2, mySrd).getId().toUnqualifiedVersionless();
}
@Test
public void testValidateCodeOperationByCodeAndSystemBad() {
public void testValidateCodeOperationNoValueSet() {
UriType valueSetIdentifier = null;
IdType id = null;
CodeType code = new CodeType("8450-9-XXX");
@ -64,22 +63,12 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isResult());
}
@Test
public void testValidateCodeOperationByCodeAndSystemGood() {
UriType valueSetIdentifier = null;
IdType id = null;
CodeType code = new CodeType("8450-9");
UriType system = new UriType("http://acme.org");
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure--expiration", result.getDisplay());
try {
myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
fail();
} catch (InvalidRequestException e) {
assertEquals("Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.", e.getMessage());
}
}
@Test
@ -91,8 +80,8 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -105,9 +94,10 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
StringType display = new StringType("Systolic blood pressure at First encounterXXXX");
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
assertEquals("Concept Display \"Systolic blood pressure at First encounterXXXX\" does not match expected \"Systolic blood pressure at First encounter\"", result.getMessage());
}
@Test
@ -119,8 +109,8 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
StringType display = new StringType("Systolic blood pressure at First encounter");
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -134,8 +124,8 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
Coding coding = null;
CodeableConcept codeableConcept = new CodeableConcept();
codeableConcept.addCoding().setSystem("http://acme.org").setCode("11378-7");
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -151,18 +141,18 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
Coding coding = null;
CodeableConcept codeableConcept = new CodeableConcept();
codeableConcept.addCoding().setSystem("http://acme.org").setCode("11378-7");
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
myTerminologyDeferredStorageSvc.saveDeferred();
result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -175,8 +165,8 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -191,18 +181,18 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
myTerminologyDeferredStorageSvc.saveDeferred();
result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -213,17 +203,17 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
ValueSet expanded = myValueSetDao.expand(myExtensionalVsId, null, mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
assertThat(resp, containsString("<expansion>"));
assertThat(resp, containsString("<contains>"));
assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
assertThat(resp, containsString("<code value=\"8450-9\"/>"));
assertThat(resp, containsString("<display value=\"Systolic blood pressure--expiration\"/>"));
assertThat(resp, containsString("<display value=\"Systolic blood pressure--expiration\"/>"));
assertThat(resp, containsString("</contains>"));
assertThat(resp, containsString("<contains>"));
assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
assertThat(resp, containsString("<code value=\"11378-7\"/>"));
assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
assertThat(resp, containsString("</contains>"));
assertThat(resp, containsString("</expansion>"));
@ -236,12 +226,12 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
ourLog.info(resp);
//@formatter:off
assertThat(resp, stringContainsInOrder(
"<code value=\"11378-7\"/>",
"<display value=\"Systolic blood pressure at First encounter\"/>"));
"<code value=\"11378-7\"/>",
"<display value=\"Systolic blood pressure at First encounter\"/>"));
//@formatter:on
}
@Test
public void testExpandByValueSet_ExceedsMaxSize() {
// Add a bunch of codes
@ -265,7 +255,7 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
}
}
@Test
public void testValidateCodeAgainstBuiltInValueSetAndCodeSystemWithValidCode() {
IPrimitiveType<String> display = null;
@ -274,14 +264,14 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
StringType vsIdentifier = new StringType("http://hl7.org/fhir/ValueSet/administrative-gender");
StringType code = new StringType("male");
StringType system = new StringType("http://hl7.org/fhir/administrative-gender");
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(vsIdentifier, null, code, system, display, coding, codeableConcept, mySrd);
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(vsIdentifier, null, code, system, display, coding, codeableConcept, mySrd);
ourLog.info(result.getMessage());
assertTrue( result.isResult(), result.getMessage());
assertTrue(result.isOk(), result.getMessage());
assertEquals("Male", result.getDisplay());
}
}

33
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningR4Test.java
View File

@ -1704,15 +1704,14 @@ public class PartitioningR4Test extends BaseJpaR4SystemTest {
@Test
public void testSearch_TagNotParam_SearchAllPartitions() {
IIdType patientIdNull = createPatient(withPartition(null), withActiveTrue(), withTag("http://system", "code"));
IIdType patientId1 = createPatient(withPartition(1), withActiveTrue(), withTag("http://system", "code"));
IIdType patientIdNull = createPatient(withPartition(null), withActiveTrue(), withTag("http://system", "code"), withIdentifier("http://foo", "bar"));
IIdType patientId1 = createPatient(withPartition(1), withActiveTrue(), withTag("http://system", "code"), withIdentifier("http://foo", "bar"));
IIdType patientId2 = createPatient(withPartition(2), withActiveTrue(), withTag("http://system", "code"));
createPatient(withPartition(null), withActiveTrue(), withTag("http://system", "code2"));
createPatient(withPartition(1), withActiveTrue(), withTag("http://system", "code2"));
createPatient(withPartition(2), withActiveTrue(), withTag("http://system", "code2"));
addReadAllPartitions();
myCaptureQueriesListener.clear();
SearchParameterMap map = new SearchParameterMap();
map.add(Constants.PARAM_TAG, new TokenParam("http://system", "code2").setModifier(TokenParamModifier.NOT));
@ -1725,6 +1724,26 @@ public class PartitioningR4Test extends BaseJpaR4SystemTest {
ourLog.info("Search SQL:\n{}", searchSql);
assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"));
assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM='http://system'"));
// And with another param
addReadAllPartitions();
myCaptureQueriesListener.clear();
map = new SearchParameterMap();
map.add(Constants.PARAM_TAG, new TokenParam("http://system", "code2").setModifier(TokenParamModifier.NOT));
map.add(Patient.SP_IDENTIFIER, new TokenParam("http://foo", "bar"));
map.setLoadSynchronous(true);
results = myPatientDao.search(map);
ids = toUnqualifiedVersionlessIds(results);
assertThat(ids, Matchers.contains(patientIdNull, patientId1));
searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
ourLog.info("Search SQL:\n{}", searchSql);
assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"));
assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM='http://system'"));
assertEquals(1, StringUtils.countMatches(searchSql, "myparamsto1_.HASH_SYS_AND_VALUE in"));
}
@Test
@ -1947,10 +1966,10 @@ public class PartitioningR4Test extends BaseJpaR4SystemTest {
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(ids, Matchers.contains(observationId));
String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
ourLog.info("Search SQL:\n{}", searchSql);
assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.PARTITION_ID='1'"));
assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.SRC_PATH='Observation.subject'"));
assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.SRC_PATH in ('Observation.subject')"));
assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.TARGET_RESOURCE_ID='" + patientId.getIdPartAsLong() + "'"));
assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));
@ -1985,10 +2004,10 @@ public class PartitioningR4Test extends BaseJpaR4SystemTest {
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(ids, Matchers.contains(observationId));
String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
ourLog.info("Search SQL:\n{}", searchSql);
assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.PARTITION_ID is null"));
assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.SRC_PATH='Observation.subject'"));
assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.SRC_PATH in ('Observation.subject')"));
assertEquals(1, StringUtils.countMatches(searchSql, "myresource1_.TARGET_RESOURCE_ID='" + patientId.getIdPartAsLong() + "'"));
assertEquals(1, StringUtils.countMatches(searchSql, "PARTITION_ID"));

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchWithInterceptorR4Test.java
View File

@ -68,7 +68,7 @@ public class SearchWithInterceptorR4Test extends BaseJpaR4Test {
String query = list.get(0).getSql(true, false);
ourLog.info("Query: {}", query);
assertThat(query, containsString("HASH_SYS_AND_VALUE='3788488238034018567'"));
assertThat(query, containsString("HASH_SYS_AND_VALUE in ('3788488238034018567')"));
} finally {
myInterceptorRegistry.unregisterInterceptor(interceptor);

27
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/graphql/JpaStorageServicesTest.java
View File

@ -9,6 +9,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Appointment;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.utilities.graphql.Argument;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.hl7.fhir.utilities.graphql.StringValue;
@ -22,6 +23,7 @@ import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
@ -94,4 +96,29 @@ public class JpaStorageServicesTest extends BaseJpaR4Test {
assertEquals("Unknown GraphQL argument \"test\". Value GraphQL argument for this type are: [_id, _language, actor, appointment_type, based_on, date, identifier, location, part_status, patient, practitioner, reason_code, reason_reference, service_category, service_type, slot, specialty, status, supporting_info]", e.getMessage());
}
}
private void createSomePatientWithId(String id) {
Patient somePatient = new Patient();
somePatient.setId(id);
myPatientDao.update(somePatient);
}
@Test
public void testListResourceGraphqlArrayOfArgument() {
createSomePatientWithId("hapi-123");
createSomePatientWithId("hapi-124");
Argument argument = new Argument();
argument.setName("_id");
argument.addValue(new StringValue("hapi-123"));
argument.addValue(new StringValue("hapi-124"));
List<IBaseResource> result = new ArrayList<>();
mySvc.listResources(mySrd, "Patient", Collections.singletonList(argument), result);
assertFalse(result.isEmpty());
List<String> expectedId = Arrays.asList("hapi-123", "hapi-124");
assertTrue(result.stream().allMatch((it) -> expectedId.contains(it.getIdElement().getIdPart())));
}
}

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/IgInstallerDstu3Test.java
View File

@ -98,12 +98,12 @@ public class IgInstallerDstu3Test extends BaseJpaDstu3Test {
PackageInstallationSpec spec = new PackageInstallationSpec()
.setName("nictiz.fhir.nl.stu3.questionnaires")
.setVersion("1.0.2")
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL)
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_ONLY)
.setFetchDependencies(true)
.addDependencyExclude("hl7\\.fhir\\.[a-zA-Z0-9]+\\.core");
PackageInstallOutcomeJson outcome = igInstaller.install(spec);
ourLog.info("Install messages:\n * {}", outcome.getMessage().stream().collect(Collectors.joining("\n * ")));
assertThat(outcome.getMessage(), hasItem("Indexing Resource[package/vl-QuestionnaireProvisioningTask.json] with URL: http://nictiz.nl/fhir/StructureDefinition/vl-QuestionnaireProvisioningTask|1.0.1"));
assertThat(outcome.getMessage(), hasItem("Indexing StructureDefinition Resource[package/vl-QuestionnaireProvisioningTask.json] with URL: http://nictiz.nl/fhir/StructureDefinition/vl-QuestionnaireProvisioningTask|1.0.1"));
runInTransaction(() -> {
assertTrue(myPackageVersionDao.findByPackageIdAndVersion("nictiz.fhir.nl.stu3.questionnaires", "1.0.2").isPresent());
@ -207,6 +207,6 @@ public class IgInstallerDstu3Test extends BaseJpaDstu3Test {
byte[] bytes = loadResourceAsByteArray("/packages/basisprofil.de.tar.gz");
myFakeNpmServlet.getResponses().put("/basisprofil.de/0.2.40", bytes);
igInstaller.install(new PackageInstallationSpec().setName("basisprofil.de").setVersion("0.2.40").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL));
igInstaller.install(new PackageInstallationSpec().setName("basisprofil.de").setVersion("0.2.40").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_ONLY));
}
}

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmTestR4.java
View File

@ -94,6 +94,7 @@ public class NpmTestR4 extends BaseJpaR4Test {
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
}
@Test
public void testCacheDstu3Package() throws Exception {
byte[] bytes = loadClasspathBytes("/packages/nictiz.fhir.nl.stu3.questionnaires-1.0.2.tgz");
@ -215,6 +216,10 @@ public class NpmTestR4 extends BaseJpaR4Test {
NpmPackage pkg = myPackageCacheManager.loadPackage("UK.Core.r4", "1.1.0");
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
@ -262,7 +267,7 @@ public class NpmTestR4 extends BaseJpaR4Test {
PackageInstallOutcomeJson outcome = igInstaller.install(spec);
ourLog.info("Install messages:\n * {}", outcome.getMessage().stream().collect(Collectors.joining("\n * ")));
assertThat(outcome.getMessage(), hasItem("Marking package hl7.fhir.uv.shorthand#0.12.0 as current version"));
assertThat(outcome.getMessage(), hasItem("Indexing Resource[package/CodeSystem-shorthand-code-system.json] with URL: http://hl7.org/fhir/uv/shorthand/CodeSystem/shorthand-code-system|0.12.0"));
assertThat(outcome.getMessage(), hasItem("Indexing CodeSystem Resource[package/CodeSystem-shorthand-code-system.json] with URL: http://hl7.org/fhir/uv/shorthand/CodeSystem/shorthand-code-system|0.12.0"));
spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.11.1").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_ONLY);
outcome = igInstaller.install(spec);

79
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/JpaGraphQLR4ProviderTest.java
View File

@ -31,6 +31,7 @@ import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.utilities.graphql.Argument;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.hl7.fhir.utilities.graphql.Value;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
@ -38,8 +39,11 @@ import org.junit.jupiter.api.Test;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.LinkedList;
import java.util.List;
import java.util.concurrent.TimeUnit;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.startsWith;
@ -158,7 +162,38 @@ public class JpaGraphQLR4ProviderTest {
" }]\n" +
" },{\n" +
" \"name\":[{\n" +
" \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
" \"given\":[\"pet\",\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
" }]\n" +
" }]\n" +
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
} finally {
IOUtils.closeQuietly(status.getEntity().getContent());
}
}
@Test
public void testGraphSystemArrayArgumentList() throws Exception {
String query = "{PatientList(id:[\"hapi-123\",\"hapi-124\"]){id,name{family}}}";
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
CloseableHttpResponse status = ourClient.execute(httpGet);
try {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
" \"PatientList\":[{\n" +
" \"id\":\"Patient/hapi-123/_history/2\",\n" +
" \"name\":[{\n" +
" \"family\":\"FAMILY 123\"\n" +
" }]\n" +
" },{\n" +
" \"id\":\"Patient/hapi-124/_history/1\",\n" +
" \"name\":[{\n" +
" \"family\":\"FAMILY 124\"\n" +
" }]\n" +
" }]\n" +
"}" + DATA_SUFFIX), TestUtil.stripWhitespace(responseContent));
@ -230,24 +265,46 @@ public class JpaGraphQLR4ProviderTest {
ourLog.info("listResources of {} - {}", theType, theSearchParams);
if (theSearchParams.size() == 1) {
String name = theSearchParams.get(0).getName();
if ("name".equals(name)) {
Patient p = new Patient();
p.addName()
.setFamily(theSearchParams.get(0).getValues().get(0).toString())
Argument argument = theSearchParams.get(0);
String name = argument.getName();
List<String> value = argument.getValues().stream()
.map((it) -> it.getValue())
.collect(Collectors.toList());
if ("name".equals(name) && "pet".equals(value.get(0))) {
Patient patient1 = new Patient();
patient1.addName()
.setFamily("pet")
.addGiven("GIVEN1")
.addGiven("GIVEN2");
p.addName()
patient1.addName()
.addGiven("GivenOnly1")
.addGiven("GivenOnly2");
theMatches.add(p);
p = new Patient();
p.addName()
Patient patient2 = new Patient();
patient2.addName()
.addGiven("pet")
.addGiven("GivenOnlyB1")
.addGiven("GivenOnlyB2");
theMatches.add(p);
theMatches.add(patient1);
theMatches.add(patient2);
}
if ("id".equals(name) && Arrays.asList("hapi-123", "hapi-124").containsAll(value)) {
Patient patient1 = new Patient();
patient1.setId("Patient/hapi-123/_history/2");
patient1.addName()
.setFamily("FAMILY 123");
Patient patient2 = new Patient();
patient2.setId("Patient/hapi-124/_history/1");
patient2.addName()
.setFamily("FAMILY 124");
theMatches.add(patient1);
theMatches.add(patient2);
}
}
}

18
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2ValueSetTest.java
View File

@ -45,23 +45,7 @@ public class ResourceProviderDstu2ValueSetTest extends BaseResourceProviderDstu2
.operation()
.onInstance(myExtensionalVsId)
.named("validate-code")
.withParameter(Parameters.class, "code", new CodeDt("8495-4"))
.andParameter("system", new UriDt("http://loinc.org"))
.execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(new BooleanDt(true), respParam.getParameter().get(0).getValue());
}
@Test
public void testValidateCodeOperationByCodeAndSystemType() {
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("validate-code")
.withParameter(Parameters.class, "code", new CodeDt("8450-9"))
.withParameter(Parameters.class, "code", new CodeDt("11378-7"))
.andParameter("system", new UriDt("http://loinc.org"))
.execute();

15
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
View File

@ -749,6 +749,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
.named("validate-code")
.withParameter(Parameters.class, "code", new CodeType("8450-9"))
.andParameter("system", new UriType("http://acme.org"))
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
.execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
@ -780,11 +781,8 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
assertEquals("result", respParam.getParameter().get(0).getName());
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("message", respParam.getParameter().get(1).getName());
assertThat(((StringType) respParam.getParameter().get(1).getValue()).getValue(), Matchers.containsStringIgnoringCase("succeeded"));
assertEquals("display", respParam.getParameter().get(2).getName());
assertEquals("Male", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(1).getName());
assertEquals("Male", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
}
/**
@ -810,11 +808,8 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
assertEquals("result", respParam.getParameter().get(0).getName());
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("message", respParam.getParameter().get(1).getName());
assertThat(((StringType) respParam.getParameter().get(1).getValue()).getValue(), Matchers.containsStringIgnoringCase("succeeded"));
assertEquals("display", respParam.getParameter().get(2).getName());
assertEquals("Male", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(1).getName());
assertEquals("Male", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
}
@AfterEach

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java
View File

@ -202,10 +202,6 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
return names;
}
protected void waitForActivatedSubscriptionCount(int theSize) throws Exception {
TestUtil.waitForSize(theSize, () -> mySubscriptionRegistry.size());
Thread.sleep(500);
}
@AfterAll
public static void afterClassClearContextBaseResourceProviderR4Test() throws Exception {

67
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
View File

@ -10,9 +10,9 @@ import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -54,6 +54,7 @@ import java.util.Optional;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_VALUE_SET;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.containsStringIgnoringCase;
import static org.hamcrest.Matchers.not;
@ -61,7 +62,6 @@ import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertSame;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ -98,11 +98,11 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
private void persistCodeSystem(CodeSystem theCodeSystem) {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(@Nonnull TransactionStatus theStatus) {
myExtensionalCsId = myCodeSystemDao.create(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
}
});
@Override
protected void doInTransactionWithoutResult(@Nonnull TransactionStatus theStatus) {
myExtensionalCsId = myCodeSystemDao.create(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
}
});
myCodeSystemDao.readEntity(myExtensionalCsId, null).getId();
}
@ -156,7 +156,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
createLocalVsWithUnknownCode(codeSystem);
}
private void createLocalCsAndVs() {
private void createLocalCs() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
@ -671,8 +671,8 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
.named("$expand")
.withNoParameters(Parameters.class)
.returnResourceType(ValueSet.class)
.execute();
ourLog.info("Expanded: {}",myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
.execute();
ourLog.info("Expanded: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
assertEquals(1, expanded.getExpansion().getContains().size());
// Update the CodeSystem URL and Codes
@ -696,12 +696,11 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
.withNoParameters(Parameters.class)
.returnResourceType(ValueSet.class)
.execute();
ourLog.info("Expanded: {}",myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
ourLog.info("Expanded: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
assertEquals(1, expanded.getExpansion().getContains().size());
}
/**
* #516
*/
@ -796,7 +795,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
private void validateTermValueSetNotExpanded(String theValueSetName) {
runInTransaction(()->{
runInTransaction(() -> {
Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable);
assertTrue(optionalValueSetByResourcePid.isPresent());
@ -814,7 +813,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
private void validateTermValueSetExpandedAndChildren(String theValueSetName, CodeSystem theCodeSystem) {
runInTransaction(()->{
runInTransaction(() -> {
Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable);
assertTrue(optionalValueSetByResourcePid.isPresent());
@ -906,10 +905,11 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
@Test
public void testValidateCodeOperationByCodeAndSystemInstanceOnType() throws IOException {
createLocalCsAndVs();
createLocalCs();
createLocalVsWithIncludeConcept();
String url = ourServerBase +
"/ValueSet/$validate-code?system=" +
"/ValueSet/" + myLocalValueSetId.getIdPart() + "/$validate-code?system=" +
UrlUtil.escapeUrlParam(URL_MY_CODE_SYSTEM) +
"&code=AA";
@ -926,7 +926,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
@Test
public void testValidateCodeOperationByCodeAndSystemInstanceOnInstance() throws IOException {
createLocalCsAndVs();
createLocalCs();
createLocalVsWithIncludeConcept();
String url = ourServerBase +
@ -953,7 +953,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
Parameters respParam = myClient
.operation()
.onType(ValueSet.class)
.onInstance(myExtensionalVsId)
.named("validate-code")
.withParameter(Parameters.class, "code", new CodeType("8450-9"))
.andParameter("system", new UriType("http://acme.org"))
@ -965,6 +965,24 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
}
@Test
public void testValidateCodeOperationNoValueSetProvided() throws Exception {
loadAndPersistCodeSystemAndValueSet();
try {
myClient
.operation()
.onType(ValueSet.class)
.named("validate-code")
.withParameter(Parameters.class, "code", new CodeType("8450-9"))
.andParameter("system", new UriType("http://acme.org"))
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.", e.getMessage());
}
}
@Test
public void testValidateCodeAgainstBuiltInSystem() {
Parameters respParam = myClient
@ -983,11 +1001,8 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
assertEquals("result", respParam.getParameter().get(0).getName());
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("message", respParam.getParameter().get(1).getName());
assertThat(((StringType) respParam.getParameter().get(1).getValue()).getValue(), containsStringIgnoringCase("succeeded"));
assertEquals("display", respParam.getParameter().get(2).getName());
assertEquals("Male", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(1).getName());
assertEquals("Male", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
}
@Test
@ -1018,7 +1033,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
ourLog.info("Response: {}", response);
}
HttpGet validateCodeGet = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?code=ChildAA&_pretty=true");
HttpGet validateCodeGet = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?system=http://mycs&code=ChildAA&_pretty=true");
try (CloseableHttpResponse status = ourHttpClient.execute(validateCodeGet)) {
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
ourLog.info("Response: {}", response);
@ -1026,7 +1041,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
assertEquals(true, output.getParameterBool("result"));
}
HttpGet validateCodeGet2 = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?code=FOO&_pretty=true");
HttpGet validateCodeGet2 = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?system=http://mycs&code=FOO&_pretty=true");
try (CloseableHttpResponse status = ourHttpClient.execute(validateCodeGet2)) {
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
ourLog.info("Response: {}", response);
@ -1070,7 +1085,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
cs.getConcepts().add(parentB);
theTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
theTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
return codeSystem;
}

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/BaseResourceProviderR5Test.java
View File

@ -205,23 +205,6 @@ public abstract class BaseResourceProviderR5Test extends BaseJpaR5Test {
return names;
}
protected void waitForActivatedSubscriptionCount(int theSize) throws Exception {
for (int i = 0; ; i++) {
if (i == 10) {
fail("Failed to init subscriptions");
}
try {
mySubscriptionLoader.doSyncSubscriptionsForUnitTest();
break;
} catch (ResourceVersionConflictException e) {
Thread.sleep(250);
}
}
TestUtil.waitForSize(theSize, () -> mySubscriptionRegistry.size());
Thread.sleep(500);
}
@AfterAll
public static void afterClassClearContextBaseResourceProviderR5Test() throws Exception {
JettyUtil.closeServer(ourServer);

62
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ValueSetTest.java
View File

@ -10,10 +10,10 @@ import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -53,6 +53,7 @@ import java.util.Optional;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_VALUE_SET;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.containsStringIgnoringCase;
import static org.hamcrest.Matchers.not;
@ -60,7 +61,6 @@ import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertSame;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ -983,8 +983,8 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
.named("$expand")
.withNoParameters(Parameters.class)
.returnResourceType(ValueSet.class)
.execute();
ourLog.info("Expanded: {}",myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
.execute();
ourLog.info("Expanded: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
assertEquals(1, expanded.getExpansion().getContains().size());
// Update the CodeSystem URL and Codes
@ -1008,12 +1008,11 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
.withNoParameters(Parameters.class)
.returnResourceType(ValueSet.class)
.execute();
ourLog.info("Expanded: {}",myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
ourLog.info("Expanded: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
assertEquals(1, expanded.getExpansion().getContains().size());
}
/**
* #516
*/
@ -1108,7 +1107,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
}
private void validateTermValueSetNotExpanded(String theValueSetName) {
runInTransaction(()->{
runInTransaction(() -> {
Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable);
assertTrue(optionalValueSetByResourcePid.isPresent());
@ -1126,7 +1125,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
}
private void validateTermValueSetExpandedAndChildren(String theValueSetName, CodeSystem theCodeSystem) {
runInTransaction(()->{
runInTransaction(() -> {
Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable);
assertTrue(optionalValueSetByResourcePid.isPresent());
@ -1219,9 +1218,10 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
@Test
public void testValidateCodeOperationByCodeAndSystemInstanceOnType() throws IOException {
createLocalCsAndVs();
createLocalVsWithIncludeConcept();
String url = ourServerBase +
"/ValueSet/$validate-code?system=" +
"/ValueSet/" + myLocalValueSetId.getIdPart() + "/$validate-code?system=" +
UrlUtil.escapeUrlParam(URL_MY_CODE_SYSTEM) +
"&code=AA";
@ -1265,7 +1265,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
Parameters respParam = myClient
.operation()
.onType(ValueSet.class)
.onInstance(myExtensionalVsId)
.named("validate-code")
.withParameter(Parameters.class, "code", new CodeType("8450-9"))
.andParameter("system", new UriType("http://acme.org"))
@ -1297,12 +1297,10 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
assertEquals("result", respParam.getParameter().get(0).getName());
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("message", respParam.getParameter().get(1).getName());
assertThat(((StringType) respParam.getParameter().get(1).getValue()).getValue(), containsStringIgnoringCase("succeeded"));
assertEquals("display", respParam.getParameter().get(2).getName());
assertEquals("Male", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(1).getName());
assertEquals("Male", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
}
// Good code and system, but not in specified valueset
{
Parameters respParam = myClient
@ -1322,7 +1320,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
assertEquals(false, ((BooleanType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("message", respParam.getParameter().get(1).getName());
assertThat(((StringType) respParam.getParameter().get(1).getValue()).getValue(), containsStringIgnoringCase("Code not found"));
assertEquals("Unknown code 'http://hl7.org/fhir/administrative-gender#male'", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
}
}
@ -1352,9 +1350,10 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
try (CloseableHttpResponse status = ourHttpClient.execute(expandGet)) {
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
ourLog.info("Response: {}", response);
assertThat(response, containsString("<display value=\"Child AA\"/>"));
}
HttpGet validateCodeGet = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?code=ChildAA&_pretty=true");
HttpGet validateCodeGet = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?system=http://mycs&code=ChildAA&_pretty=true");
try (CloseableHttpResponse status = ourHttpClient.execute(validateCodeGet)) {
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
ourLog.info("Response: {}", response);
@ -1362,7 +1361,32 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
assertEquals(true, output.getParameterBool("result"));
}
HttpGet validateCodeGet2 = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?code=FOO&_pretty=true");
HttpGet validateCodeGet2 = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?system=http://mycs&code=FOO&_pretty=true");
try (CloseableHttpResponse status = ourHttpClient.execute(validateCodeGet2)) {
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
ourLog.info("Response: {}", response);
Parameters output = myFhirCtx.newXmlParser().parseResource(Parameters.class, response);
assertEquals(false, output.getParameterBool("result"));
}
// Now do a pre-expansion
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
expandGet = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$expand?_pretty=true");
try (CloseableHttpResponse status = ourHttpClient.execute(expandGet)) {
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
ourLog.info("Response: {}", response);
}
validateCodeGet = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?system=http://mycs&code=ChildAA&_pretty=true");
try (CloseableHttpResponse status = ourHttpClient.execute(validateCodeGet)) {
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
ourLog.info("Response: {}", response);
Parameters output = myFhirCtx.newXmlParser().parseResource(Parameters.class, response);
assertEquals(true, output.getParameterBool("result"));
}
validateCodeGet2 = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?system=http://mycs&code=FOO&_pretty=true");
try (CloseableHttpResponse status = ourHttpClient.execute(validateCodeGet2)) {
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
ourLog.info("Response: {}", response);
@ -1407,7 +1431,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
cs.getConcepts().add(parentB);
theTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
theTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
return codeSystem;
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcMultipleObservationsIT.java
View File

@ -508,7 +508,7 @@ public class LastNElasticsearchSvcMultipleObservationsIT {
for (int entryCount = 0; entryCount < 10; entryCount++) {
ObservationJson observationJson = new ObservationJson();
String identifier = String.valueOf((entryCount + patientCount * 10));
String identifier = String.valueOf((entryCount + patientCount * 10L));
observationJson.setIdentifier(identifier);
observationJson.setSubject(subject);
@ -524,7 +524,7 @@ public class LastNElasticsearchSvcMultipleObservationsIT {
assertTrue(elasticsearchSvc.createOrUpdateObservationCodeIndex(codeableConceptId2, codeJson2));
}
Date effectiveDtm = new Date(baseObservationDate.getTimeInMillis() - ((10 - entryCount) * 3600 * 1000));
Date effectiveDtm = new Date(baseObservationDate.getTimeInMillis() - ((10L - entryCount) * 3600L * 1000L));
observationJson.setEffectiveDtm(effectiveDtm);
assertTrue(elasticsearchSvc.createOrUpdateObservationIndex(identifier, observationJson));

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

@ -86,4 +86,7 @@ public class SubscriptionTestUtil {
subscriber.setEmailSender(myEmailSender);
}
public int getActiveSubscriptionCount() {
return mySubscriptionRegistry.size();
}
}

11
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestDstu2Test.java
View File

@ -157,6 +157,7 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
Subscription subscription1 = createSubscription(criteria1, payload, ourListenerServerBase);
Subscription subscription2 = createSubscription(criteria2, payload, ourListenerServerBase);
waitForActivatedSubscriptionCount(2);
Observation observation1 = sendObservation(code, "SNOMED-CT");
@ -169,7 +170,6 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
ourLog.info("Current interceptors:\n * {}", allInterceptors);
// Should see 1 subscription notification
waitForQueueToDrain();
waitForSize(0, ourCreatedObservations);
waitForSize(1, ourUpdatedObservations);
@ -181,20 +181,21 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
ourClient.update().resource(subscriptionTemp).withId(subscriptionTemp.getIdElement()).execute();
waitForQueueToDrain();
ourLog.info("Have {} updates and {} subscriptions - sending observation", ourUpdatedObservations.size(), mySubscriptionTestUtil.getActiveSubscriptionCount());
Observation observation2 = sendObservation(code, "SNOMED-CT");
waitForQueueToDrain();
// Should see one subscription notification
waitForSize(0, ourCreatedObservations);
waitForSize(3, ourUpdatedObservations);
// Delet one subscription
// Delete one subscription
ourClient.delete().resourceById(new IdDt("Subscription/" + subscription2.getId())).execute();
waitForActivatedSubscriptionCount(1);
ourLog.info("Have {} updates and {} subscriptions - sending observation", ourUpdatedObservations.size(), mySubscriptionTestUtil.getActiveSubscriptionCount());
Observation observationTemp3 = sendObservation(code, "SNOMED-CT");
// Should see only one subscription notification
waitForQueueToDrain();
waitForSize(0, ourCreatedObservations);
waitForSize(4, ourUpdatedObservations);
@ -204,6 +205,7 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
CodingDt coding = codeableConcept.addCoding();
coding.setCode(code + "111");
coding.setSystem("SNOMED-CT");
ourLog.info("Have {} updates and {} subscriptions - sending observation", ourUpdatedObservations.size(), mySubscriptionTestUtil.getActiveSubscriptionCount());
ourClient.update().resource(observation3).withId(observation3.getIdElement()).execute();
// Should see no subscription notification
@ -218,6 +220,7 @@ public class RestHookTestDstu2Test extends BaseResourceProviderDstu2Test {
CodingDt coding1 = codeableConcept1.addCoding();
coding1.setCode(code);
coding1.setSystem("SNOMED-CT");
ourLog.info("Have {} updates and {} subscriptions - sending observation", ourUpdatedObservations.size(), mySubscriptionTestUtil.getActiveSubscriptionCount());
ourClient.update().resource(observation3a).withId(observation3a.getIdElement()).execute();
// Should see only one subscription notification

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestR4Test.java
View File

@ -7,6 +7,7 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.*;
@ -250,7 +251,7 @@ public class RestHookTestR4Test extends BaseSubscriptionsR4Test {
// Manually unregister all subscriptions
mySubscriptionRegistry.unregisterAllSubscriptions();
waitForActivatedSubscriptionCount(0);
assertEquals(0, mySubscriptionRegistry.size());
// Force a reload
mySubscriptionLoader.doSyncSubscriptionsForUnitTest();

24
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestWithInterceptorRegisteredToDaoConfigDstu2Test.java
View File

@ -21,9 +21,7 @@ import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.collect.Lists;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
@ -42,7 +40,6 @@ import java.util.stream.Collectors;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.fail;
/**
* Test the rest-hook subscriptions
@ -90,23 +87,6 @@ public class RestHookTestWithInterceptorRegisteredToDaoConfigDstu2Test extends B
mySubscriptionTestUtil.waitForQueueToDrain();
}
protected void waitForActivatedSubscriptionCount(int theSize) throws Exception {
for (int i = 0; ; i++) {
if (i == 10) {
fail("Failed to init subscriptions");
}
try {
mySubscriptionLoader.doSyncSubscriptionsForUnitTest();
break;
} catch (ResourceVersionConflictException e) {
Thread.sleep(250);
}
}
TestUtil.waitForSize(theSize, () -> mySubscriptionRegistry.size());
Thread.sleep(500);
}
private Subscription createSubscription(String criteria, String payload, String endpoint) throws InterruptedException {
Subscription subscription = new Subscription();
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
@ -232,8 +212,8 @@ public class RestHookTestWithInterceptorRegisteredToDaoConfigDstu2Test extends B
Subscription subscription2 = createSubscription(criteria2, payload, ourListenerServerBase);
runInTransaction(()->{
ourLog.info("All token indexes:\n * {}", myResourceIndexedSearchParamTokenDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
runInTransaction(() -> {
ourLog.info("All token indexes:\n * {}", myResourceIndexedSearchParamTokenDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
});
myCaptureQueriesListener.clear();

22
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcIntegrationDstu3Test.java
View File

@ -2,10 +2,8 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.collect.Lists;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.Coding;
@ -13,10 +11,10 @@ import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.PrimitiveType;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.Type;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
@ -30,12 +28,12 @@ import java.util.Set;
import java.util.stream.Collectors;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.greaterThan;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
@ -228,11 +226,13 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
ZipCollectionBuilder files = new ZipCollectionBuilder();
TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesToZip(files);
myLoader.loadLoinc(files.getFiles(), mySrd);
myTerminologyDeferredStorageSvc.saveDeferred();
myTerminologyDeferredStorageSvc.saveDeferred();
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(null, null, new StringType("10013-1"), new StringType(ITermLoaderSvc.LOINC_URI), null, null, null, mySrd);
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(new UriType("http://loinc.org/vs"), null, new StringType("10013-1"), new StringType(ITermLoaderSvc.LOINC_URI), null, null, null, mySrd);
assertTrue(result.isResult());
assertEquals("Found code", result.getMessage());
assertTrue(result.isOk());
assertEquals("R' wave amplitude in lead I", result.getDisplay());
}
@Test
@ -240,11 +240,13 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
ZipCollectionBuilder files = new ZipCollectionBuilder();
TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesToZip(files);
myLoader.loadLoinc(files.getFiles(), mySrd);
myTerminologyDeferredStorageSvc.saveDeferred();
myTerminologyDeferredStorageSvc.saveDeferred();
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(null, null, new StringType("10013-1-9999999999"), new StringType(ITermLoaderSvc.LOINC_URI), null, null, null, mySrd);
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(new UriType("http://loinc.org/vs"), null, new StringType("10013-1-9999999999"), new StringType(ITermLoaderSvc.LOINC_URI), null, null, null, mySrd);
assertFalse(result.isResult());
assertEquals("Code not found", result.getMessage());
assertFalse(result.isOk());
assertEquals("Unknown code {http://loinc.org}10013-1-9999999999 - Unable to expand ValueSet[http://loinc.org/vs]", result.getMessage());
}
private Set<String> toExpandedCodes(ValueSet theExpanded) {

47
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
View File

@ -3,7 +3,6 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.entity.TermConceptMap;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
@ -43,8 +42,8 @@ import static org.junit.jupiter.api.Assertions.fail;
public class TerminologySvcImplR4Test extends BaseTermR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(TerminologySvcImplR4Test.class);
ValidationOptions optsNoGuess = new ValidationOptions();
ValidationOptions optsGuess = new ValidationOptions().guessSystem();
ConceptValidationOptions optsNoGuess = new ConceptValidationOptions();
ConceptValidationOptions optsGuess = new ConceptValidationOptions().setInferSystem(true);
private IIdType myConceptMapId;
private void createAndPersistConceptMap() {
@ -1799,42 +1798,37 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
IFhirResourceDaoValueSet.ValidateCodeResult result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, null, null, null, null);
IValidationSupport.CodeValidationResult result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, null, null, null, null);
assertNull(result);
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, "BOGUS", null, null, null);
assertNull(result);
assertFalse(result.isOk());
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, "11378-7", null, null, null);
assertNull(result);
assertFalse(result.isOk());
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsGuess, valueSet, null, "11378-7", null, null, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsGuess, valueSet, null, "11378-7", "Systolic blood pressure at First encounter", null, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, "http://acme.org", "11378-7", null, null, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
Coding coding = new Coding("http://acme.org", "11378-7", "Systolic blood pressure at First encounter");
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, null, null, coding, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
CodeableConcept codeableConcept = new CodeableConcept();
codeableConcept.addCoding(new Coding("BOGUS", "BOGUS", "BOGUS"));
codeableConcept.addCoding(coding);
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, null, null, null, codeableConcept);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -1852,43 +1846,38 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
IFhirResourceDaoValueSet.ValidateCodeResult result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, null, null, null, null);
IValidationSupport.CodeValidationResult result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, null, null, null, null);
assertNull(result);
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, "BOGUS", null, null, null);
assertNull(result);
assertFalse(result.isOk());
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, "11378-7", null, null, null);
assertNull(result);
assertFalse(result.isOk());
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsGuess, valueSet, null, "11378-7", null, null, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsGuess, valueSet, null, "11378-7", "Systolic blood pressure at First encounter", null, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, "http://acme.org", "11378-7", null, null, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
Coding coding = new Coding("http://acme.org", "11378-7", "Systolic blood pressure at First encounter");
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, null, null, coding, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
CodeableConcept codeableConcept = new CodeableConcept();
codeableConcept.addCoding(new Coding("BOGUS", "BOGUS", "BOGUS"));
codeableConcept.addCoding(coding);
result = myTermSvc.validateCodeIsInPreExpandedValueSet(optsNoGuess, valueSet, null, null, null, null, codeableConcept);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertTrue(result.isOk());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
}

55
hapi-fhir-jpaserver-base/src/test/resources/dstu3/nl/LandISOCodelijst-2.16.840.1.113883.2.4.3.11.60.40.2.20.5.2--20171231000000.json Executable file
View File

@ -0,0 +1,55 @@
{
"resourceType": "ValueSet",
"id": "2.16.840.1.113883.2.4.3.11.60.40.2.20.5.2--20171231000000",
"meta": {
"profile": [
"http://hl7.org/fhir/StructureDefinition/shareablevalueset"
]
},
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/resource-effectivePeriod",
"valuePeriod": {
"start": "2017-12-31T00:00:00+02:00"
}
}
],
"url": "http://decor.nictiz.nl/fhir/ValueSet/2.16.840.1.113883.2.4.3.11.60.40.2.20.5.2--20171231000000",
"identifier": [
{
"use": "official",
"system": "http://art-decor.org/ns/oids/vs",
"value": "2.16.840.1.113883.2.4.3.11.60.40.2.20.5.2"
}
],
"version": "2017-12-31T00:00:00",
"name": "LandISOCodelijst",
"title": "LandISOCodelijst",
"status": "active",
"experimental": false,
"publisher": "Registratie aan de bron",
"contact": [
{
"name": "Registratie aan de bron",
"telecom": [
{
"system": "url",
"value": "https://www.registratieaandebron.nl"
},
{
"system": "url",
"value": "https://zibs.nl"
}
]
}
],
"description": "ISO 3166-1 (alpha-2) - Alle waarden",
"immutable": false,
"compose": {
"include": [
{
"system": "urn:iso:std:iso:3166"
}
]
}
}

6
hapi-fhir-jpaserver-base/src/test/resources/extensional-case-2.xml
View File

@ -26,6 +26,10 @@
<code value="8450-9" />
<display value="Systolic blood pressure--expiration" />
</concept>
<concept>
<code value="11378-7" />
<display value="Systolic blood pressure at First encounter" />
</concept>
</codeSystem>
<compose>
<include>
@ -124,4 +128,4 @@
</concept>
</include>
</compose>
</ValueSet>
</ValueSet>

6
hapi-fhir-jpaserver-empi/src/main/java/ca/uhn/fhir/jpa/empi/svc/EmpiResourceDaoSvc.java
View File

@ -74,7 +74,11 @@ public class EmpiResourceDaoSvc {
}
public DaoMethodOutcome updatePerson(IAnyResource thePerson) {
return myPersonDao.update(thePerson);
if (thePerson.getIdElement().hasIdPart()) {
return myPersonDao.update(thePerson);
} else {
return myPersonDao.create(thePerson);
}
}
public IAnyResource readPersonByPid(ResourcePersistentId thePersonPid) {

10
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/BaseMigrator.java
View File

@ -35,6 +35,7 @@ public abstract class BaseMigrator implements IMigrator {
private boolean myDryRun;
private boolean myNoColumnShrink;
private boolean myOutOfOrderPermitted;
private boolean mySchemaWasInitialized;
private DriverTypeEnum myDriverType;
private DataSource myDataSource;
private List<BaseTask.ExecutedStatement> myExecutedStatements = new ArrayList<>();
@ -111,4 +112,13 @@ public abstract class BaseMigrator implements IMigrator {
}
return statementBuilder;
}
public boolean isSchemaWasInitialized() {
return mySchemaWasInitialized;
}
public BaseMigrator setSchemaWasInitialized(boolean theSchemaWasInitialized) {
mySchemaWasInitialized = theSchemaWasInitialized;
return this;
}
}

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