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

Jakarta/Javax Servlet Migration (#5429) 

* Servlet migrsation changes

* Apply spotless

* Work on migration

* Start working on JPA migration

* Test fixes

* Test fixes

* Test fixes

* Work

* Work on servlet migration

* Work on migration

* Work on fixes

* Imports fix

* Work on tests

* Test fix

* All tests passing

* Work on migration

* Schema generator

* Refactor ID strategy

* Some test fixes

* Test fixes

* API additions

* Work on websockets

* Test fixe

* Version bump

* Work on migration

* All tests have passed!

* Work on test fixes

* Fixes

* Work on fixes

* CDR fix

* Work on migration

* Fixes

* Spotless

* Disable onetoone ban

* Adjust migratyions

* Transaction service fix

* Add tinyint to migrator

* Work

* Migration

* Compile fix

* Add license

* Test fix

* Test fix

* Cleanup

* Cleanup attempt

* Test fix

* Reslve fixmes

* Remove legacy lastn implementation

* Test cleanup

* Cleanup

* Remove dead import

* Bad import setups

* Review comments

* Review fixes

* Build fix

* Test fix

* Spotless

* Account for CR changes

* Compile fixes

* Rollback one change

* Test tweak

* License header

* Test fix

* Test fix part 2:

* Clean up tx isolation

* Spotless

* Spotless apply

* Drop min SQL Server level

* Attempted test fix

* Test fix

* Test fix

* Test fix

* Bump hibernate

* Test fix

* Test fixes

* Test fixes

* Test fixes

* Test cleanup

* One more test fix

* Test fix

* Try to fix test

* Clean up expunge

* Test fix

* Remove unneeded task

* Spotless

* Bump compiler plugin

* Spotless

* Compile fix

* Add license headers

* License header

* Test fixes

* Bump animal sniffer

* Spotless

* Bump Jetty version

* Test fix and version bump

* Cleanup

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
This commit is contained in:
James Agnew 2023-12-03 11:15:37 -05:00 committed by GitHub
parent 113cf4002d
commit 6d58df0f44
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
876 changed files with 9407 additions and 17801 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
.mvn/wrapper/MavenWrapperDownloader.java vendored
View File

@ -13,9 +13,16 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
import java.net.*;
import java.io.*;
import java.nio.channels.*;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.net.Authenticator;
import java.net.PasswordAuthentication;
import java.net.URL;
import java.nio.channels.Channels;
import java.nio.channels.ReadableByteChannel;
import java.util.Properties;
public class MavenWrapperDownloader {

11
hapi-deployable-pom/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -45,7 +45,6 @@
<checkRuntimeClasspath>false</checkRuntimeClasspath>
<checkTestClasspath>false</checkTestClasspath>
<skip>false</skip>
<quiet>false</quiet>
<preferLocal>true</preferLocal>
<useResultFile>true</useResultFile>
<resultFileMinClasspathCount>2</resultFileMinClasspathCount>
@ -103,14 +102,6 @@
<groupId>net.bytebuddy</groupId>
<artifactId>byte-buddy</artifactId>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
</dependency>
</ignoredDependencies>
<ignoredResourcePatterns>
<ignoredResourcePattern>.*\.txt$</ignoredResourcePattern>

8
hapi-fhir-android/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -131,12 +131,6 @@
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<configuration>
<classFolders>
<classFolder>${basedir}/target/classes</classFolder>
</classFolders>
<sourceFolders>
<sourceFolder>${basedir}/src/main/java</sourceFolder>
</sourceFolders>
<dumpOnExit>true</dumpOnExit>
</configuration>
<executions>

17
hapi-fhir-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -52,19 +52,13 @@
<!-- Only required for Schematron Validator Support -->
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
<groupId>com.helger.schematron</groupId>
<artifactId>ph-schematron-api</artifactId>
<optional>true</optional>
<exclusions>
<exclusion>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-commons</artifactId>
<groupId>com.helger.schematron</groupId>
<artifactId>ph-schematron-xslt</artifactId>
<optional>true</optional>
</dependency>
@ -221,7 +215,6 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>${maven_checkstyle_version}</version>
<configuration>
<!--suppress UnresolvedMavenProperty -->
<configLocation>${maven.multiModuleProjectDirectory}/hapi-fhir-checkstyle/src/checkstyle/hapi-base-checkstyle.xml</configLocation>

19
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/LookupCodeRequest.java
View File

@ -1,3 +1,22 @@
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2023 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.context.support;
import java.util.Collection;

54
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
View File

@ -158,10 +158,10 @@ public enum Pointcut implements IPointcut {
* Hooks may accept the following parameters:
* <ul>
* <li>
* javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* </li>
* <li>
* javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* </li>
* </ul>
* </p>
@ -171,7 +171,7 @@ public enum Pointcut implements IPointcut {
* no further processing will occur and no further interceptors will be called.
*/
SERVER_INCOMING_REQUEST_PRE_PROCESSED(
boolean.class, "javax.servlet.http.HttpServletRequest", "javax.servlet.http.HttpServletResponse"),
boolean.class, "jakarta.servlet.http.HttpServletRequest", "jakarta.servlet.http.HttpServletResponse"),
/**
* <b>Server Hook:</b>
@ -198,10 +198,10 @@ public enum Pointcut implements IPointcut {
* only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
* </li>
* <li>
* javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* </li>
* <li>
* javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* </li>
* <li>
* ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException - The exception that was thrown
@ -220,8 +220,8 @@ public enum Pointcut implements IPointcut {
boolean.class,
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"javax.servlet.http.HttpServletRequest",
"javax.servlet.http.HttpServletResponse",
"jakarta.servlet.http.HttpServletRequest",
"jakarta.servlet.http.HttpServletResponse",
"ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException"),
/**
@ -244,10 +244,10 @@ public enum Pointcut implements IPointcut {
* only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
* </li>
* <li>
* javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* </li>
* <li>
* javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* </li>
* </ul>
* <p>
@ -268,8 +268,8 @@ public enum Pointcut implements IPointcut {
boolean.class,
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"javax.servlet.http.HttpServletRequest",
"javax.servlet.http.HttpServletResponse"),
"jakarta.servlet.http.HttpServletRequest",
"jakarta.servlet.http.HttpServletResponse"),
/**
* <b>Server Hook:</b>
@ -291,10 +291,10 @@ public enum Pointcut implements IPointcut {
* only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
* </li>
* <li>
* javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* </li>
* <li>
* javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* </li>
* </ul>
* <p>
@ -313,8 +313,8 @@ public enum Pointcut implements IPointcut {
boolean.class,
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"javax.servlet.http.HttpServletRequest",
"javax.servlet.http.HttpServletResponse"),
"jakarta.servlet.http.HttpServletRequest",
"jakarta.servlet.http.HttpServletResponse"),
/**
* <b>Server Hook:</b>
@ -416,10 +416,10 @@ public enum Pointcut implements IPointcut {
* {@link NullPointerException} in the case of a bug being triggered.
* </li>
* <li>
* javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* </li>
* <li>
* javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* </li>
* </ul>
* <p>
@ -434,8 +434,8 @@ public enum Pointcut implements IPointcut {
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"java.lang.Throwable",
"javax.servlet.http.HttpServletRequest",
"javax.servlet.http.HttpServletResponse"),
"jakarta.servlet.http.HttpServletRequest",
"jakarta.servlet.http.HttpServletResponse"),
/**
* <b>Server Hook:</b>
@ -463,10 +463,10 @@ public enum Pointcut implements IPointcut {
* ca.uhn.fhir.rest.api.server.ResponseDetails - This object contains details about the response, including the contents. Hook methods may modify this object to change or replace the response.
* </li>
* <li>
* javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* </li>
* <li>
* javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* </li>
* </ul>
* </p>
@ -487,8 +487,8 @@ public enum Pointcut implements IPointcut {
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"org.hl7.fhir.instance.model.api.IBaseResource",
"ca.uhn.fhir.rest.api.server.ResponseDetails",
"javax.servlet.http.HttpServletRequest",
"javax.servlet.http.HttpServletResponse"),
"jakarta.servlet.http.HttpServletRequest",
"jakarta.servlet.http.HttpServletResponse"),
/**
* <b>Server Hook:</b>
@ -554,10 +554,10 @@ public enum Pointcut implements IPointcut {
* java.lang.String - The GraphQL response
* </li>
* <li>
* javax.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* jakarta.servlet.http.HttpServletRequest - The servlet request, when running in a servlet environment
* </li>
* <li>
* javax.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* jakarta.servlet.http.HttpServletResponse - The servlet response, when running in a servlet environment
* </li>
* </ul>
* </p>
@ -578,8 +578,8 @@ public enum Pointcut implements IPointcut {
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"java.lang.String",
"java.lang.String",
"javax.servlet.http.HttpServletRequest",
"javax.servlet.http.HttpServletResponse"),
"jakarta.servlet.http.HttpServletRequest",
"jakarta.servlet.http.HttpServletResponse"),
/**
* <b>Server Hook:</b>

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BaseElement.java
View File

@ -24,7 +24,11 @@ import ca.uhn.fhir.model.api.annotation.Description;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import java.util.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public abstract class BaseElement implements /*IElement, */ ISupportsUndeclaredExtensions {

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/IFhirVersion.java
View File

@ -19,10 +19,15 @@
*/
package ca.uhn.fhir.model.api;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.fhirpath.IFhirPath;
import ca.uhn.fhir.rest.api.IVersionSpecificBundleFactory;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.instance.model.api.IBase;
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 java.io.InputStream;
import java.util.Date;

11
hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative2/NarrativeTemplateManifest.java
View File

@ -41,9 +41,18 @@ import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Properties;
import java.util.function.Consumer;
import java.util.stream.Collectors;
import java.util.*;
import javax.annotation.Nonnull;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

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

@ -118,7 +118,7 @@ public @interface Operation {
* always the right choice), the framework will not attempt to generate a response to
* this method.
* <p>
* This is useful if you want to include an {@link javax.servlet.http.HttpServletResponse}
* This is useful if you want to include an {@link jakarta.servlet.http.HttpServletResponse}
* in your method parameters and create a response yourself directly from your
* <code>@Operation</code> method.
* </p>
@ -134,7 +134,7 @@ public @interface Operation {
* always the right choice), the framework will not attempt to parse the request body,
* but will instead delegate it to the <code>@Operation</code> method.
* <p>
* This is useful if you want to include an {@link javax.servlet.http.HttpServletRequest}
* This is useful if you want to include an {@link jakarta.servlet.http.HttpServletRequest}
* in your method parameters and parse the request yourself.
* </p>
*/

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Read.java
View File

@ -23,7 +23,10 @@ import ca.uhn.fhir.rest.client.api.IBasicClient;
import ca.uhn.fhir.rest.client.api.IRestfulClient;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.lang.annotation.*;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
/**
* RESTful method annotation to be used for the FHIR <a href="http://hl7.org/implement/standards/fhir/http.html#read">read</a> and <a

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Transaction.java
View File

@ -19,7 +19,10 @@
*/
package ca.uhn.fhir.rest.annotation;
import java.lang.annotation.*;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
/**
* RESTful method annotation to be used for the FHIR <a href="http://hl7.org/implement/standards/fhir/http.html#transaction">transaction</a> method.

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/TransactionParam.java
View File

@ -19,7 +19,10 @@
*/
package ca.uhn.fhir.rest.annotation;
import java.lang.annotation.*;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
import java.util.List;
/**

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Validate.java
View File

@ -22,7 +22,10 @@ package ca.uhn.fhir.rest.annotation;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.lang.annotation.*;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
/**
* RESTful method annotation to be used for the FHIR

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/TokenClientParam.java
View File

@ -23,7 +23,9 @@ import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
import org.apache.commons.lang3.ObjectUtils;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import java.util.*;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.defaultString;

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ParamPrefixEnum.java
View File

@ -19,7 +19,9 @@
*/
package ca.uhn.fhir.rest.param;
import java.util.*;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
/**
* Comparator/qualifier for values used in REST params, such as {@link DateParam}, {@link NumberParam}, and

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/AttachmentUtil.java
View File

@ -19,7 +19,11 @@
*/
package ca.uhn.fhir.util;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.ICompositeType;

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/rdf/RDFUtil.java
View File

@ -24,7 +24,8 @@ import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.riot.Lang;
import org.apache.jena.riot.RDFDataMgr;
import java.io.*;
import java.io.Reader;
import java.io.Writer;
public class RDFUtil {

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/schematron/SchematronBaseValidator.java
View File

@ -37,8 +37,8 @@ import com.helger.commons.io.resource.ClassPathResource;
import com.helger.commons.io.resource.IReadableResource;
import com.helger.schematron.ISchematronResource;
import com.helger.schematron.SchematronHelper;
import com.helger.schematron.sch.SchematronResourceSCH;
import com.helger.schematron.svrl.jaxb.SchematronOutputType;
import com.helger.schematron.xslt.SchematronResourceSCH;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
@ -90,7 +90,12 @@ public class SchematronBaseValidator implements IValidatorModule {
}
StreamSource source = new StreamSource(new StringReader(resourceAsString));
SchematronOutputType results = SchematronHelper.applySchematron(sch, source);
SchematronOutputType results;
try {
results = sch.applySchematronValidationToSVRL(source);
} catch (Exception e) {
throw new InternalErrorException(Msg.code(2433) + e.getMessage(), e);
}
if (results == null) {
return;
}

10
hapi-fhir-base/src/test/java/ca/uhn/fhir/i18n/HapiLocalizerTest.java
View File

@ -1,12 +1,14 @@
package ca.uhn.fhir.i18n;
import static org.hamcrest.Matchers.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.hamcrest.MatcherAssert.assertThat;
import org.junit.jupiter.api.Test;
import java.util.Set;
import org.junit.jupiter.api.Test;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.matchesPattern;
import static org.hamcrest.Matchers.not;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class HapiLocalizerTest {

3
hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnumTest.java
View File

@ -2,7 +2,8 @@ package ca.uhn.fhir.model.api;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
public class ResourceMetadataKeyEnumTest {

5
hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/TagTest.java
View File

@ -5,7 +5,10 @@ import org.junit.jupiter.api.Test;
import java.net.URI;
import java.net.URISyntaxException;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class TagTest {

4
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/api/CacheControlDirectiveTest.java
View File

@ -5,7 +5,9 @@ import org.junit.jupiter.api.Test;
import java.util.Arrays;
import java.util.List;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class CacheControlDirectiveTest {

2
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/api/EncodingEnumTest.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.rest.api;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class EncodingEnumTest {

3
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/api/MethodOutcomeTest.java
View File

@ -7,7 +7,8 @@ import java.util.Arrays;
import java.util.HashMap;
import java.util.Optional;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
class MethodOutcomeTest {

4
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/DateParamTest.java
View File

@ -17,7 +17,9 @@ import static java.util.concurrent.TimeUnit.SECONDS;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.endsWith;
import static org.hamcrest.Matchers.startsWith;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.fail;
public class DateParamTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DateParamTest.class);

3
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/QualifierDetailsTest.java
View File

@ -3,7 +3,8 @@ package ca.uhn.fhir.rest.param;
import com.google.common.collect.Sets;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class QualifierDetailsTest {

12
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/StringParamTest.java
View File

@ -1,14 +1,11 @@
package ca.uhn.fhir.rest.param;
import static ca.uhn.fhir.rest.api.Constants.PARAMQUALIFIER_STRING_TEXT;
import static org.junit.jupiter.api.Assertions.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ch.qos.logback.classic.Level;
import ch.qos.logback.classic.Logger;
import ch.qos.logback.classic.spi.ILoggingEvent;
import ch.qos.logback.core.read.ListAppender;
import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
@ -18,12 +15,17 @@ import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import ch.qos.logback.classic.Logger;
import org.slf4j.LoggerFactory;
import java.util.List;
import java.util.stream.Collectors;
import static ca.uhn.fhir.rest.api.Constants.PARAMQUALIFIER_STRING_TEXT;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
@ExtendWith(MockitoExtension.class)
public class StringParamTest {

2
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/exceptions/BaseServerResponseExceptionTest.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.rest.server.exceptions;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class BaseServerResponseExceptionTest {

5
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/DateRangeUtilTest.java
View File

@ -5,7 +5,6 @@ import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.MethodSource;
@ -19,7 +18,9 @@ import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN_OR_EQUALS;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN;
import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN_OR_EQUALS;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.*;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.notNullValue;
import static org.hamcrest.Matchers.nullValue;
class DateRangeUtilTest {

6
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/LogUtilTest.java
View File

@ -5,7 +5,11 @@ import org.slf4j.Logger;
import org.slf4j.event.Level;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.Mockito.*;
import static org.mockito.Mockito.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.verifyNoMoreInteractions;
public class LogUtilTest {

12
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/ReflectionUtilTest.java
View File

@ -1,15 +1,17 @@
package ca.uhn.fhir.util;
import static org.junit.jupiter.api.Assertions.*;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.i18n.Msg;
import org.junit.jupiter.api.Test;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.List;
import ca.uhn.fhir.i18n.Msg;
import org.junit.jupiter.api.Test;
import ca.uhn.fhir.context.ConfigurationException;
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;
public class ReflectionUtilTest {

4
hapi-fhir-base/src/test/java/ca/uhn/fhir/validation/ResultSeverityEnumTest.java
View File

@ -1,9 +1,9 @@
package ca.uhn.fhir.validation;
import static org.junit.jupiter.api.Assertions.*;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class ResultSeverityEnumTest {
@Test

4
hapi-fhir-bom/pom.xml
View File

@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
@ -12,7 +12,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-checkstyle/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -42,7 +42,6 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>3.2.0</version>
<dependencies>
<dependency>
<groupId>com.puppycrawl.tools</groupId>
@ -109,7 +108,6 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>${maven_checkstyle_version}</version>
<configuration>
<excludes>**/osgi/**/*, **/.mvn/**/*, **/.mvn_/**/*</excludes>
<sourceDirectories>

7
hapi-fhir-checkstyle/src/checkstyle/hapi-base-checkstyle.xml
View File

@ -18,6 +18,13 @@
<property name="format" value="(?i)FIXME"/>
</module>
<!-- Ban star imports - TODO: enable this -->
<!--
<module name="RegexpSinglelineJava">
<property name="format" value="^import .*\*;"/>
</module>
-->
<module name="RegexpSinglelineJava">
<property name="format" value="System\.out\.println"/>
<property name="ignoreComments" value="true"/>

74
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -152,38 +152,25 @@
<artifactId>spring-web</artifactId>
</dependency>
<!-- Web Server -->
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
<groupId>org.eclipse.jetty.ee10.websocket</groupId>
<artifactId>jetty-ee10-websocket-jakarta-client</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<groupId>jakarta.websocket</groupId>
<artifactId>jakarta.websocket-client-api</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-api</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-core-client</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-client</artifactId>
<groupId>org.eclipse.jetty.ee10</groupId>
<artifactId>jetty-ee10-servlet</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
@ -195,39 +182,17 @@
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf-spring5</artifactId>
<artifactId>thymeleaf-spring6</artifactId>
</dependency>
<!-- Dependencies for Schematron -->
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
<exclusions>
<exclusion>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
</exclusion>
<exclusion>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.istack</groupId>
<artifactId>istack-commons-runtime</artifactId>
</exclusion>
</exclusions>
<groupId>com.helger.schematron</groupId>
<artifactId>ph-schematron-api</artifactId>
</dependency>
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-commons</artifactId>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<groupId>com.helger.schematron</groupId>
<artifactId>ph-schematron-xslt</artifactId>
</dependency>
@ -272,6 +237,15 @@
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<parallel>none</parallel>
<reuseForks>false</reuseForks>
<forkCount>1</forkCount>
</configuration>
</plugin>
</plugins>
</build>

12
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BulkImportCommand.java
View File

@ -40,11 +40,12 @@ import org.apache.commons.io.file.PathUtils;
import org.apache.commons.io.filefilter.FileFileFilter;
import org.apache.commons.io.filefilter.IOFileFilter;
import org.apache.commons.io.filefilter.SuffixFileFilter;
import org.apache.commons.lang3.time.DateUtils;
import org.eclipse.jetty.ee10.servlet.ServletContextHandler;
import org.eclipse.jetty.ee10.servlet.ServletHolder;
import org.eclipse.jetty.server.Connector;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.server.ServerConnector;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -234,7 +235,12 @@ public class BulkImportCommand extends BaseCommand {
private List<String> startServer(int thePort, List<File> files) {
List<String> indexes = new ArrayList<>();
myServer = new Server(thePort);
myServer = new Server();
ServerConnector connector = new ServerConnector(myServer);
connector.setIdleTimeout(DateUtils.MILLIS_PER_MINUTE);
connector.setPort(myPort);
myServer.setConnectors(new Connector[] {connector});
myServlet = new BulkImportFileServlet();
for (File t : files) {

3
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ReindexTerminologyCommand.java
View File

@ -24,7 +24,6 @@ import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.util.ParametersUtil;
import joptsimple.internal.Strings;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.ParseException;
import org.hl7.fhir.instance.model.api.IBaseParameters;
@ -111,7 +110,7 @@ public class ReindexTerminologyCommand extends BaseRequestGeneratingCommand {
@Nonnull
private String getResponseMessage(IBaseParameters response) {
List<String> message = ParametersUtil.getNamedParameterValuesAsString(myFhirCtx, response, "message");
return Strings.join(message, NL);
return String.join(NL, message);
}
public static final String NL = System.getProperty("line.separator");

47
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/WebsocketSubscribeCommand.java
View File

@ -21,19 +21,17 @@ package ca.uhn.fhir.cli;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.primitive.IdDt;
import jakarta.websocket.ClientEndpoint;
import jakarta.websocket.ContainerProvider;
import jakarta.websocket.OnClose;
import jakarta.websocket.OnError;
import jakarta.websocket.OnMessage;
import jakarta.websocket.OnOpen;
import jakarta.websocket.Session;
import jakarta.websocket.WebSocketContainer;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.eclipse.jetty.websocket.api.Frame;
import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.api.annotations.OnWebSocketClose;
import org.eclipse.jetty.websocket.api.annotations.OnWebSocketConnect;
import org.eclipse.jetty.websocket.api.annotations.OnWebSocketError;
import org.eclipse.jetty.websocket.api.annotations.OnWebSocketFrame;
import org.eclipse.jetty.websocket.api.annotations.OnWebSocketMessage;
import org.eclipse.jetty.websocket.api.annotations.WebSocket;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
import org.eclipse.jetty.websocket.client.WebSocketClient;
import java.net.URI;
@ -46,6 +44,7 @@ public class WebsocketSubscribeCommand extends BaseCommand {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(WebsocketSubscribeCommand.class);
private boolean myQuit;
private Session mySession;
@Override
public String getCommandDescription() {
@ -75,14 +74,13 @@ public class WebsocketSubscribeCommand extends BaseCommand {
IdDt subsId = new IdDt(theCommandLine.getOptionValue("i"));
WebSocketClient client = new WebSocketClient();
SimpleEchoSocket socket = new SimpleEchoSocket(subsId.getIdPart());
try {
client.start();
URI echoUri = new URI(target);
ClientUpgradeRequest request = new ClientUpgradeRequest();
ourLog.info("Connecting to : {}", echoUri);
client.connect(socket, echoUri, request);
WebSocketContainer container = ContainerProvider.getWebSocketContainer();
mySession = container.connectToServer(socket, echoUri);
while (!myQuit) {
Thread.sleep(500L);
@ -93,7 +91,9 @@ public class WebsocketSubscribeCommand extends BaseCommand {
throw new CommandFailureException(Msg.code(1537) + e);
} finally {
try {
client.stop();
if (mySession != null) {
mySession.close();
}
} catch (Exception e) {
ourLog.error("Failure", e);
}
@ -103,7 +103,7 @@ public class WebsocketSubscribeCommand extends BaseCommand {
/**
* Basic Echo Client Socket
*/
@WebSocket(maxTextMessageSize = 64 * 1024)
@ClientEndpoint
public class SimpleEchoSocket {
private String mySubsId;
@ -115,37 +115,32 @@ public class WebsocketSubscribeCommand extends BaseCommand {
mySubsId = theSubsId;
}
@OnWebSocketClose
@OnClose
public void onClose(int statusCode, String reason) {
ourLog.info("Received CLOSE status={} reason={}", statusCode, reason);
}
@OnWebSocketConnect
@OnOpen
public void onConnect(Session theSession) {
ourLog.info("Successfully connected");
this.session = theSession;
try {
String sending = "bind " + mySubsId;
LOG_SEND.info("{}", sending);
theSession.getRemote().sendString(sending);
theSession.getBasicRemote().sendText(sending);
} catch (Throwable t) {
ourLog.error("Failure", t);
myQuit = true;
}
}
@OnWebSocketError
@OnError
public void onError(Throwable theError) {
ourLog.error("Websocket error: ", theError);
myQuit = true;
}
@OnWebSocketFrame
public void onFrame(Frame theFrame) {
ourLog.debug("Websocket frame: {}", theFrame);
}
@OnWebSocketMessage
@OnMessage
public void onMessage(String theMsg) {
LOG_RECV.info("{}", theMsg);
}

19
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/BulkImportCommandIT.java → hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/BulkImportCommandTest.java
View File

@ -54,9 +54,9 @@ import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
public class BulkImportCommandIT {
public class BulkImportCommandTest {
private static final Logger ourLog = LoggerFactory.getLogger(BulkImportCommandIT.class);
private static final Logger ourLog = LoggerFactory.getLogger(BulkImportCommandTest.class);
static {
HapiSystemProperties.enableTestMode();
@ -64,7 +64,7 @@ public class BulkImportCommandIT {
@RegisterExtension
public HttpClientExtension myHttpClientExtension = new HttpClientExtension();
@Mock
@Mock(strictness = Mock.Strictness.LENIENT)
private IJobCoordinator myJobCoordinator;
private final BulkDataImportProvider myProvider = new BulkDataImportProvider();
private final FhirContext myCtx = FhirContext.forR4Cached();
@ -101,19 +101,12 @@ public class BulkImportCommandIT {
@Test
public void testBulkImport() throws IOException {
JobInstance jobInfo = new JobInstance()
.setStatus(StatusEnum.COMPLETED)
.setCreateTime(parseDate("2022-01-01T12:00:00-04:00"))
.setStartTime(parseDate("2022-01-01T12:10:00-04:00"));
when(myJobCoordinator.getInstance(eq("THE-JOB-ID"))).thenReturn(jobInfo);
String fileContents1 = "{\"resourceType\":\"Observation\"}\n{\"resourceType\":\"Observation\"}";
String fileContents2 = "{\"resourceType\":\"Patient\"}\n{\"resourceType\":\"Patient\"}";
writeNdJsonFileToTempDirectory(fileContents1, "file1.json");
writeNdJsonFileToTempDirectory(fileContents2, "file2.json");
when(myJobCoordinator.startInstance(any())).thenReturn(createJobStartResponse("THE-JOB-ID"));
when(myJobCoordinator.startInstance(any(), any())).thenReturn(createJobStartResponse("THE-JOB-ID"));
// Start the command in a separate thread
new Thread(() -> App.main(new String[]{
@ -154,7 +147,7 @@ public class BulkImportCommandIT {
writeNdJsonFileToTempDirectory(fileContents1, "file1.json.gz");
writeNdJsonFileToTempDirectory(fileContents2, "file2.json.gz");
when(myJobCoordinator.startInstance(any()))
when(myJobCoordinator.startInstance(any(), any()))
.thenReturn(createJobStartResponse("THE-JOB-ID"));
// Start the command in a separate thread
@ -196,7 +189,7 @@ public class BulkImportCommandIT {
writeNdJsonFileToTempDirectory(fileContents1, "file1.json");
writeNdJsonFileToTempDirectory(fileContents2, "file2.json");
when(myJobCoordinator.startInstance(any())).thenReturn(createJobStartResponse("THE-JOB-ID"));
when(myJobCoordinator.startInstance(any(), any())).thenReturn(createJobStartResponse("THE-JOB-ID"));
// Start the command in a separate thread
new Thread(() -> App.main(new String[]{

9
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiClearMigrationLockCommandTest.java
View File

@ -21,14 +21,19 @@ import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.Timestamp;
import java.sql.Types;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import java.util.UUID;
import static ca.uhn.fhir.jpa.migrate.HapiMigrationLock.LOCK_PID;
import static ca.uhn.fhir.jpa.migrate.HapiMigrationStorageSvc.LOCK_TYPE;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
import static org.slf4j.LoggerFactory.getLogger;
public class HapiClearMigrationLockCommandTest extends ConsoleOutputCapturingBaseTest {

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

@ -258,8 +258,9 @@ public class HapiFlywayMigrateDatabaseCommandTest {
private File getLocation(String theDatabaseName) throws IOException {
File directory = new File(myDbDirectory);
if (directory.exists()) {
FileUtils.deleteDirectory(directory);
FileUtils.forceDelete(directory);
}
assertFalse(directory.exists());
return new File(myDbDirectory + "/" + theDatabaseName);
}

39
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HeaderPassthroughOptionTest.java
View File

@ -8,16 +8,19 @@ import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.test.utilities.server.HttpServletExtension;
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.DefaultParser;
import org.apache.commons.cli.ParseException;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.eclipse.jetty.ee10.servlet.ServletHandler;
import org.eclipse.jetty.ee10.servlet.ServletHolder;
import org.hl7.fhir.r4.model.IdType;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.api.extension.RegisterExtension;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.slf4j.Logger;
@ -46,33 +49,29 @@ public class HeaderPassthroughOptionTest {
private static final Logger ourLog = LoggerFactory.getLogger(HeaderPassthroughOptionTest.class);
final String FHIR_VERSION = "r4";
private FhirContext myCtx = FhirContext.forR4();
private Server myServer;
private int myPort;
private final FhirContext myCtx = FhirContext.forR4Cached();
private final String headerKey1 = "test-header-key-1";
private final String headerValue1 = "test header value-1";
private static final String ourConceptsFileName = "target/concepts.csv";
private static final String ourHierarchyFileName = "target/hierarchy.csv";
private static final AtomicInteger ourFilenameCounter = new AtomicInteger();
private final CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
private final UploadTerminologyCommand testedCommand =
new RequestCapturingUploadTerminologyCommand(myCapturingInterceptor);
private final TerminologyUploaderProvider myProvider = new TerminologyUploaderProvider();
@Mock
protected ITermLoaderSvc myTermLoaderSvc;
private static final AtomicInteger ourFilenameCounter = new AtomicInteger();
@RegisterExtension
public RestfulServerExtension myServer = new RestfulServerExtension(myCtx)
.registerProvider(myProvider);
@BeforeEach
public void beforeEach() throws Exception {
myServer = new Server(0);
TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTermLoaderSvc);
ServletHandler proxyHandler = new ServletHandler();
RestfulServer servlet = new RestfulServer(myCtx);
servlet.registerProvider(provider);
ServletHolder servletHolder = new ServletHolder(servlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
myServer.setHandler(proxyHandler);
JettyUtil.startServer(myServer);
myPort = JettyUtil.getPortForStartedServer(myServer);
public void beforeEach() {
myProvider.setContext(myCtx);
myProvider.setTerminologyLoaderSvc(myTermLoaderSvc);
when(myTermLoaderSvc.loadCustom(eq("http://foo"), anyList(), any()))
.thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
}
@ -85,7 +84,7 @@ public class HeaderPassthroughOptionTest {
String[] args = new String[]{
"-v", FHIR_VERSION,
"-m", "SNAPSHOT",
"-t", "http://localhost:" + myPort,
"-t", myServer.getBaseUrl(),
"-u", "http://foo",
"-d", getConceptFilename(filenameCounter),
"-d", getHierarchyFilename(filenameCounter),
@ -115,7 +114,7 @@ public class HeaderPassthroughOptionTest {
String[] args = new String[]{
"-v", FHIR_VERSION,
"-m", "SNAPSHOT",
"-t", "http://localhost:" + myPort,
"-t", myServer.getBaseUrl(),
"-u", "http://foo",
"-d", getConceptFilename(filenameCounter),
"-d", getHierarchyFilename(filenameCounter),
@ -149,7 +148,7 @@ public class HeaderPassthroughOptionTest {
String[] args = new String[]{
"-v", FHIR_VERSION,
"-m", "SNAPSHOT",
"-t", "http://localhost:" + myPort,
"-t", myServer.getBaseUrl(),
"-u", "http://foo",
"-d", getConceptFilename(filenameCounter),
"-d", getHierarchyFilename(filenameCounter),

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

7
hapi-fhir-client-okhttp/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -81,11 +81,6 @@
<artifactId>jetty-server</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.jboss.resteasy</groupId>
<artifactId>resteasy-client</artifactId>

869
hapi-fhir-client-okhttp/src/test/java/ca/uhn/fhir/okhttp/GenericOkHttpClientDstu2Test.java
View File

File diff suppressed because it is too large Load Diff

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

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

16
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/apache/ApacheHttpClient.java
View File

@ -22,19 +22,29 @@ package ca.uhn.fhir.rest.client.apache;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.client.api.*;
import ca.uhn.fhir.rest.client.api.Header;
import ca.uhn.fhir.rest.client.api.IHttpClient;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.apache.http.HttpEntity;
import org.apache.http.NameValuePair;
import org.apache.http.client.HttpClient;
import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.client.methods.*;
import org.apache.http.client.methods.HttpDelete;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpOptions;
import org.apache.http.client.methods.HttpPatch;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.client.methods.HttpRequestBase;
import org.apache.http.entity.ByteArrayEntity;
import org.apache.http.message.BasicNameValuePair;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.*;
/**
* A Http Client based on Apache. This is an adapter around the class

16
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/apache/ApacheHttpResponse.java
View File

@ -26,14 +26,24 @@ import ca.uhn.fhir.rest.client.impl.BaseHttpResponse;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.StopWatch;
import org.apache.commons.io.IOUtils;
import org.apache.http.Header;
import org.apache.http.HttpEntity;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.entity.ContentType;
import org.apache.http.*;
import java.io.*;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.util.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* A Http Response based on Apache. This is an adapter around the class

4
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/apache/BaseHttpClient.java
View File

@ -20,7 +20,9 @@
package ca.uhn.fhir.rest.client.apache;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.client.api.Header;
import ca.uhn.fhir.rest.client.api.HttpClientUtil;
import ca.uhn.fhir.rest.client.api.IHttpClient;

4
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/apache/GZipContentInterceptor.java
View File

@ -20,7 +20,9 @@
package ca.uhn.fhir.rest.client.apache;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.client.api.*;
import ca.uhn.fhir.rest.client.api.IClientInterceptor;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.api.IHttpResponse;
import org.apache.http.Header;
import org.apache.http.HttpEntityEnclosingRequest;
import org.apache.http.client.methods.HttpRequestBase;

4
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/interceptor/BasicAuthInterceptor.java
View File

@ -20,7 +20,9 @@
package ca.uhn.fhir.rest.client.interceptor;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.client.api.*;
import ca.uhn.fhir.rest.client.api.IClientInterceptor;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.api.IHttpResponse;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;

4
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/interceptor/CookieInterceptor.java
View File

@ -20,7 +20,9 @@
package ca.uhn.fhir.rest.client.interceptor;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.client.api.*;
import ca.uhn.fhir.rest.client.api.IClientInterceptor;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.api.IHttpResponse;
/**
* HTTP interceptor to be used for adding Cookie to requests.

40
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/BaseMethodBinding.java
View File

@ -19,16 +19,41 @@
*/
package ca.uhn.fhir.rest.client.method;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.annotation.AddTags;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.Delete;
import ca.uhn.fhir.rest.annotation.DeleteTags;
import ca.uhn.fhir.rest.annotation.GetPage;
import ca.uhn.fhir.rest.annotation.History;
import ca.uhn.fhir.rest.annotation.Metadata;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.Patch;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.annotation.Transaction;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.annotation.Validate;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.client.exceptions.NonFhirResponseException;
import ca.uhn.fhir.rest.client.impl.BaseHttpClientInvocation;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnclassifiedServerFailureException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.ReflectionUtil;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.instance.model.api.IAnyResource;
@ -37,7 +62,10 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import java.io.IOException;
import java.io.InputStream;
import java.lang.reflect.Method;
import java.util.*;
import java.util.Collection;
import java.util.List;
import java.util.Set;
import java.util.TreeSet;
public abstract class BaseMethodBinding<T> implements IClientResponseHandler<T> {

4
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/BaseOutcomeReturningMethodBinding.java
View File

@ -32,7 +32,9 @@ import org.hl7.fhir.instance.model.api.IIdType;
import java.io.InputStream;
import java.lang.reflect.Method;
import java.util.*;
import java.util.List;
import java.util.Map;
import java.util.Set;
abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<MethodOutcome> {
static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseOutcomeReturningMethodBinding.class);

7
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/BaseOutcomeReturningMethodBindingWithResourceIdButNoResourceBody.java
View File

@ -19,9 +19,12 @@
*/
package ca.uhn.fhir.rest.client.method;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.annotation.Delete;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.param.ParameterUtil;
import org.hl7.fhir.instance.model.api.IBaseResource;

4
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/ConditionalParamBinder.java
View File

@ -29,7 +29,9 @@ import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.lang.reflect.Method;
import java.util.*;
import java.util.Collection;
import java.util.List;
import java.util.Map;
class ConditionalParamBinder implements IParameter {

5
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/DeleteMethodBinding.java
View File

@ -31,7 +31,10 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import java.lang.reflect.Method;
import java.util.*;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.Set;
public class DeleteMethodBinding extends BaseOutcomeReturningMethodBindingWithResourceIdButNoResourceBody {

4
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/HistoryMethodBinding.java
View File

@ -31,7 +31,9 @@ import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.instance.model.api.*;
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 java.lang.reflect.Method;
import java.lang.reflect.Modifier;

4
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/NullParameter.java
View File

@ -24,7 +24,9 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.lang.reflect.Method;
import java.util.*;
import java.util.Collection;
import java.util.List;
import java.util.Map;
class NullParameter implements IParameter {

8
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/OperationMethodBinding.java
View File

@ -31,7 +31,13 @@ import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ParametersUtil;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.lang.reflect.Method;
import java.lang.reflect.Modifier;

11
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/PatchMethodBinding.java
View File

@ -24,7 +24,9 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.annotation.Patch;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.client.impl.BaseHttpClientInvocation;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -33,7 +35,12 @@ import org.hl7.fhir.instance.model.api.IIdType;
import java.lang.annotation.Annotation;
import java.lang.reflect.Method;
import java.util.*;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.ListIterator;
import java.util.Map;
import java.util.Set;
/**
* Base class for an operation that has a resource type but not a resource body in the

4
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/RawParamsParmeter.java
View File

@ -26,7 +26,9 @@ import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.lang.reflect.Method;
import java.util.*;
import java.util.Collection;
import java.util.List;
import java.util.Map;
public class RawParamsParmeter implements IParameter {

13
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/ReadMethodBinding.java
View File

@ -24,18 +24,25 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.valueset.BundleTypeEnum;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.annotation.Elements;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import java.io.IOException;
import java.io.InputStream;
import java.lang.reflect.Method;
import java.util.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Map;
public class ReadMethodBinding extends BaseResourceReturningMethodBinding
implements IClientResponseHandlerHandlesBinary<Object> {

61
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/SearchParameter.java
View File

@ -19,16 +19,56 @@
*/
package ca.uhn.fhir.rest.client.method;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimePrimitiveDatatypeDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
import ca.uhn.fhir.model.base.composite.BaseQuantityDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.annotation.OptionalParam;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.param.binder.*;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.param.CompositeAndListParam;
import ca.uhn.fhir.rest.param.CompositeOrListParam;
import ca.uhn.fhir.rest.param.CompositeParam;
import ca.uhn.fhir.rest.param.DateAndListParam;
import ca.uhn.fhir.rest.param.DateOrListParam;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasAndListParam;
import ca.uhn.fhir.rest.param.HasOrListParam;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.NumberAndListParam;
import ca.uhn.fhir.rest.param.NumberOrListParam;
import ca.uhn.fhir.rest.param.NumberParam;
import ca.uhn.fhir.rest.param.QuantityAndListParam;
import ca.uhn.fhir.rest.param.QuantityOrListParam;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
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.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriAndListParam;
import ca.uhn.fhir.rest.param.UriOrListParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.param.binder.CalendarBinder;
import ca.uhn.fhir.rest.param.binder.DateBinder;
import ca.uhn.fhir.rest.param.binder.FhirPrimitiveBinder;
import ca.uhn.fhir.rest.param.binder.IParamBinder;
import ca.uhn.fhir.rest.param.binder.QueryParameterAndBinder;
import ca.uhn.fhir.rest.param.binder.QueryParameterOrBinder;
import ca.uhn.fhir.rest.param.binder.QueryParameterTypeBinder;
import ca.uhn.fhir.rest.param.binder.StringBinder;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.CollectionUtil;
import ca.uhn.fhir.util.ReflectionUtil;
@ -36,7 +76,16 @@ import org.apache.commons.lang3.builder.ToStringBuilder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
public class SearchParameter extends BaseQueryParameter {

8
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/TransactionParameter.java
View File

@ -19,7 +19,9 @@
*/
package ca.uhn.fhir.rest.client.method;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.rest.annotation.TransactionParam;
@ -28,7 +30,9 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import java.lang.reflect.Method;
import java.lang.reflect.Modifier;
import java.util.*;
import java.util.Collection;
import java.util.List;
import java.util.Map;
public class TransactionParameter implements IParameter {

38
hapi-fhir-converter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -33,8 +33,8 @@
<optional>true</optional>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<groupId>jakarta.servlet</groupId>
<artifactId>jakarta.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
@ -126,36 +126,6 @@
<artifactId>xmlunit-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-http</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
@ -183,7 +153,7 @@
<instructions>
<Import-Package>
ca.uhn.fhir.rest.server*;resolution:=optional,
javax.servlet.http;resolution:=optional,
jakarta.servlet.http;resolution:=optional,
*
</Import-Package>
</instructions>

4
hapi-fhir-converter/src/main/java/ca/uhn/hapi/converters/server/VersionedApiConverterInterceptor.java
View File

@ -31,6 +31,8 @@ import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;
import ca.uhn.fhir.rest.server.interceptor.auth.AuthorizationConstants;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import org.hl7.fhir.converter.NullVersionConverterAdvisor10_30;
import org.hl7.fhir.converter.NullVersionConverterAdvisor10_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_30;
@ -41,8 +43,6 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.util.StringTokenizer;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;

53
hapi-fhir-converter/src/test/java/ca/uhn/hapi/converters/server/VersionedApiConverterInterceptorR4Test.java
View File

@ -5,7 +5,9 @@ import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.test.utilities.HttpClientExtension;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.io.IOUtils;
@ -15,14 +17,15 @@ import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.eclipse.jetty.ee10.servlet.ServletHandler;
import org.eclipse.jetty.ee10.servlet.ServletHolder;
import org.hl7.fhir.dstu3.model.HumanName;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
@ -35,16 +38,21 @@ import static org.hamcrest.MatcherAssert.assertThat;
public class VersionedApiConverterInterceptorR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(VersionedApiConverterInterceptorR4Test.class);
private static CloseableHttpClient ourClient;
private static FhirContext ourCtx = FhirContext.forDstu3();
private static int ourPort;
private static final FhirContext ourCtx = FhirContext.forDstu3Cached();
private static Server ourServer;
@RegisterExtension
public static final RestfulServerExtension ourServer = new RestfulServerExtension(ourCtx)
.registerProvider(new DummyPatientResourceProvider())
.registerInterceptor(new VersionedApiConverterInterceptor())
.setDefaultResponseEncoding(EncodingEnum.JSON);
@RegisterExtension
public static final HttpClientExtension ourClient = new HttpClientExtension();
@Test
public void testSearchNormal() throws Exception {
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient");
HttpGet httpGet = new HttpGet(ourServer.getBaseUrl() + "/Patient");
try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(responseContent);
@ -54,7 +62,7 @@ public class VersionedApiConverterInterceptorR4Test {
@Test
public void testSearchConvertToR2() throws Exception {
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient");
HttpGet httpGet = new HttpGet(ourServer.getBaseUrl() + "/Patient");
httpGet.addHeader("Accept", "application/fhir+json; fhirVersion=1.0");
try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
@ -65,7 +73,7 @@ public class VersionedApiConverterInterceptorR4Test {
@Test
public void testSearchConvertToR2ByFormatParam() throws Exception {
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_format=" + UrlUtil.escapeUrlParam("application/fhir+json; fhirVersion=1.0"));
HttpGet httpGet = new HttpGet(ourServer.getBaseUrl() + "/Patient?_format=" + UrlUtil.escapeUrlParam("application/fhir+json; fhirVersion=1.0"));
try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(responseContent);
@ -75,36 +83,9 @@ public class VersionedApiConverterInterceptorR4Test {
@AfterAll
public static void afterClassClearContext() throws Exception {
JettyUtil.closeServer(ourServer);
TestUtil.randomizeLocaleAndTimezone();
}
@BeforeAll
public static void beforeClass() throws Exception {
ourServer = new Server(0);
DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
ServletHandler proxyHandler = new ServletHandler();
RestfulServer servlet = new RestfulServer(ourCtx);
servlet.setDefaultResponseEncoding(EncodingEnum.JSON);
servlet.setDefaultPrettyPrint(true);
servlet.registerInterceptor(new VersionedApiConverterInterceptor());
servlet.setResourceProviders(patientProvider);
ServletHolder servletHolder = new ServletHolder(servlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
ourServer.setHandler(proxyHandler);
JettyUtil.startServer(ourServer);
ourPort = JettyUtil.getPortForStartedServer(ourServer);
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
ourClient = builder.build();
}
public static class DummyPatientResourceProvider implements IResourceProvider {
@Override

16
hapi-fhir-dist/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -249,18 +249,12 @@
<artifactId>thymeleaf</artifactId>
</dependency>
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
<exclusions>
<exclusion>
<artifactId>Saxon-HE</artifactId>
<groupId>net.sf.saxon</groupId>
</exclusion>
</exclusions>
<groupId>com.helger.schematron</groupId>
<artifactId>ph-schematron-api</artifactId>
</dependency>
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-commons</artifactId>
<groupId>com.helger.schematron</groupId>
<artifactId>ph-schematron-xslt</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>

10
hapi-fhir-docs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -72,10 +72,6 @@
<artifactId>jackson-dataformat-yaml</artifactId>
</dependency>
<dependency>
<groupId>javax.ejb</groupId>
<artifactId>ejb-api</artifactId>
</dependency>
<dependency>
<groupId>javax.ws.rs</groupId>
<artifactId>jsr311-api</artifactId>
@ -104,8 +100,8 @@
</dependency>
<!-- Needed for JEE/Servlet support -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<groupId>jakarta.servlet</groupId>
<artifactId>jakarta.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
<dependency>

9
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/AuthorizationInterceptors.java
View File

@ -35,7 +35,14 @@ import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
import ca.uhn.fhir.rest.server.interceptor.auth.*;
import ca.uhn.fhir.rest.server.interceptor.auth.AdditionalCompartmentSearchParameters;
import ca.uhn.fhir.rest.server.interceptor.auth.AuthorizationInterceptor;
import ca.uhn.fhir.rest.server.interceptor.auth.AuthorizedList;
import ca.uhn.fhir.rest.server.interceptor.auth.IAuthRule;
import ca.uhn.fhir.rest.server.interceptor.auth.PolicyEnum;
import ca.uhn.fhir.rest.server.interceptor.auth.RuleBuilder;
import ca.uhn.fhir.rest.server.interceptor.auth.SearchNarrowingConsentService;
import ca.uhn.fhir.rest.server.interceptor.auth.SearchNarrowingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.consent.ConsentInterceptor;
import ca.uhn.fhir.rest.server.interceptor.consent.RuleFilteringConsentService;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;

3
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/AuthorizingTesterUiClientFactory.java
View File

@ -23,8 +23,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.BasicAuthInterceptor;
import ca.uhn.fhir.rest.server.util.ITestingUiClientFactory;
import javax.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletRequest;
public class AuthorizingTesterUiClientFactory implements ITestingUiClientFactory {

2
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/BalpExample.java
View File

@ -26,11 +26,11 @@ import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.storage.interceptor.balp.AsyncMemoryQueueBackedFhirClientBalpSink;
import ca.uhn.fhir.storage.interceptor.balp.IBalpAuditContextServices;
import ca.uhn.fhir.storage.interceptor.balp.IBalpAuditEventSink;
import jakarta.servlet.ServletException;
import org.hl7.fhir.r4.model.Reference;
import java.util.List;
import javax.annotation.Nonnull;
import javax.servlet.ServletException;
public class BalpExample {

8
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ClientTransactionExamples.java
View File

@ -21,7 +21,13 @@ package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Reference;
public class ClientTransactionExamples {

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

@ -29,7 +29,11 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

2
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/Dstu2Examples.java
View File

@ -24,9 +24,9 @@ import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import jakarta.servlet.ServletException;
import java.util.Collection;
import javax.servlet.ServletException;
@SuppressWarnings("serial")
public class Dstu2Examples {

3
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ExampleRestfulClient.java
View File

@ -20,7 +20,8 @@
package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.context.FhirContext;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import java.util.List;

4
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ExampleRestfulServlet.java
View File

@ -21,11 +21,11 @@ package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import jakarta.servlet.ServletException;
import jakarta.servlet.annotation.WebServlet;
import java.util.ArrayList;
import java.util.List;
import javax.servlet.ServletException;
import javax.servlet.annotation.WebServlet;
// START SNIPPET: servlet

9
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ExtensionsDstu3.java
View File

@ -22,7 +22,14 @@ package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import java.io.IOException;
import java.util.List;

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

@ -22,7 +22,11 @@ package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
public class FhirContextIntro {

12
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/FhirDataModel.java
View File

@ -22,7 +22,17 @@ package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.SimpleQuantity;
import org.hl7.fhir.r4.model.StringType;
import java.util.Date;
import java.util.List;

10
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/JaxRsConformanceProvider.java
View File

@ -22,13 +22,13 @@ package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.jaxrs.server.AbstractJaxRsConformanceProvider;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.IResourceProvider;
import jakarta.ejb.EJB;
import jakarta.ejb.Stateless;
import jakarta.ws.rs.Path;
import jakarta.ws.rs.Produces;
import jakarta.ws.rs.core.MediaType;
import java.util.concurrent.ConcurrentHashMap;
import javax.ejb.EJB;
import javax.ejb.Stateless;
import javax.ws.rs.Path;
import javax.ws.rs.Produces;
import javax.ws.rs.core.MediaType;
/**
* Conformance Rest Service

22
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/JaxRsPatientRestProvider.java
View File

@ -21,22 +21,30 @@ package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.jaxrs.server.AbstractJaxRsResourceProvider;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import jakarta.ejb.Local;
import jakarta.ejb.Stateless;
import jakarta.ws.rs.GET;
import jakarta.ws.rs.POST;
import jakarta.ws.rs.Path;
import jakarta.ws.rs.PathParam;
import jakarta.ws.rs.Produces;
import jakarta.ws.rs.core.MediaType;
import jakarta.ws.rs.core.Response;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import javax.ejb.Local;
import javax.ejb.Stateless;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import javax.ws.rs.*;
/**
* A demo JaxRs Patient Rest Provider
*/

2
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/PartitionExamples.java
View File

@ -28,13 +28,13 @@ import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
import jakarta.servlet.http.HttpServletRequest;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Set;
import javax.servlet.http.HttpServletRequest;
@SuppressWarnings("InnerClassMayBeStatic")
public class PartitionExamples {

5
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/RequestCounterInterceptor.java
View File

@ -22,9 +22,8 @@ package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Interceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
// START SNIPPET: interceptor
@Interceptor

4
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/RequestExceptionInterceptor.java
View File

@ -23,10 +23,10 @@ import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import java.io.IOException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
// START SNIPPET: interceptor
public class RequestExceptionInterceptor {

63
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/RestfulPatientResourceProviderMore.java
View File

@ -27,19 +27,70 @@ import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.annotation.At;
import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
import ca.uhn.fhir.rest.annotation.Count;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.Delete;
import ca.uhn.fhir.rest.annotation.Elements;
import ca.uhn.fhir.rest.annotation.History;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.IncludeParam;
import ca.uhn.fhir.rest.annotation.Metadata;
import ca.uhn.fhir.rest.annotation.Offset;
import ca.uhn.fhir.rest.annotation.OptionalParam;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.annotation.Since;
import ca.uhn.fhir.rest.annotation.Sort;
import ca.uhn.fhir.rest.annotation.Transaction;
import ca.uhn.fhir.rest.annotation.TransactionParam;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.annotation.Validate;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.client.api.IBasicClient;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.param.CompositeParam;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
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.IResourceProvider;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.CapabilityStatement;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.DiagnosticReport;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Identifier.IdentifierUse;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import java.io.IOException;
import java.math.BigDecimal;
@ -47,8 +98,6 @@ import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Set;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
@SuppressWarnings("unused")
public abstract class RestfulPatientResourceProviderMore implements IResourceProvider {

5
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/SecurityInterceptors.java
View File

@ -25,11 +25,10 @@ import ca.uhn.fhir.interceptor.api.Interceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import org.apache.commons.codec.binary.Base64;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
public class SecurityInterceptors {
public void basicAuthInterceptorRealm() {

5
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ServerETagExamples.java
View File

@ -21,9 +21,8 @@ package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.RestfulServer;
import javax.servlet.ServletException;
import javax.servlet.annotation.WebServlet;
import jakarta.servlet.ServletException;
import jakarta.servlet.annotation.WebServlet;
@SuppressWarnings("serial")
public class ServerETagExamples {

10
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ServerOperations.java
View File

@ -24,7 +24,13 @@ import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.r4.model.Bundle;
@ -36,8 +42,6 @@ import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
public class ServerOperations {
private static final Logger ourLog = LoggerFactory.getLogger(ServerOperations.class);

4
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ServletExamples.java
View File

@ -37,14 +37,14 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.SearchPreferHandlingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.StaticCapabilityStatementInterceptor;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import jakarta.servlet.ServletException;
import jakarta.servlet.annotation.WebServlet;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.r4.model.CapabilityStatement;
import org.hl7.fhir.r4.model.Enumerations;
import org.springframework.web.cors.CorsConfiguration;
import java.util.Arrays;
import javax.servlet.ServletException;
import javax.servlet.annotation.WebServlet;
@SuppressWarnings({"serial", "RedundantThrows", "InnerClassMayBeStatic"})
public class ServletExamples {

2
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ValidatorExamples.java
View File

@ -36,6 +36,7 @@ import ca.uhn.fhir.validation.SchemaBaseValidator;
import ca.uhn.fhir.validation.SingleValidationMessage;
import ca.uhn.fhir.validation.ValidationResult;
import ca.uhn.fhir.validation.schematron.SchematronBaseValidator;
import jakarta.servlet.ServletException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.filefilter.WildcardFileFilter;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
@ -60,7 +61,6 @@ import java.io.File;
import java.io.FileReader;
import java.util.List;
import javax.annotation.Nonnull;
import javax.servlet.ServletException;
@SuppressWarnings({"serial", "unused"})
public class ValidatorExamples {

25
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/changes.yaml
View File

@ -0,0 +1,25 @@
---
- item:
type: "add"
title: "The version of a few dependencies have been bumped to the latest versions
(dependent HAPI modules listed in brackets):
<ul>
<li>Spring Framework (JPA): 5.3.27 -&gt; 6.0.12</li>
<li>Spring Data BOM (JPA): 2021.2.2 -&gt; 2023.0.0</li>
<li>Hibernate (JPA): 5.6.15.Final -&gt; 6.2.8.Final</li>
<li>Hibernate Validator (JPA): 6.1.5.Final -&gt; 8.0.0.Final</li>
<li>Hibernate Search (JPA): 6.1.6.Final -&gt; 6.2.1.Final</li>
<li>Spring Boot (Boot+Starter): 2.7.12 -&gt; 3.1.4</li>
<li>Jetty (CLI): 10.0.14 -&gt; 12.0.2</li>
<li>Phloc Schematron (Schematron Validator): 5.6.5 -&gt; 7.1.2</li>
<li>RestEasy (JAX-RS Server): 5.0.2.Final -&gt; 6.2.5.Final</li>
</ul>"
- item:
type: "change"
title: "HAPI FHIR JPA now requires PostgreSQL 10+. Previously Postgres 9.4
was supported but this version has been dropped."
- item:
type: "remove"
title: "The legacy `$lastn` support has been removed, and only the redesigned 'advanced' version is now
supported. The advanced version requires Elasticsearch."

25
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/database_support.md
View File

@ -1,19 +1,20 @@
# Database Support
HAPI FHIR JPA Server maintains active support for several databases:
HAPI FHIR JPA Server maintains active support for several databases.
- [MS SQL Server](https://www.microsoft.com/en-us/sql-server/sql-server-2019)
- [PostgreSQL](https://www.postgresql.org/)
- [Oracle](https://www.oracle.com/ca-en/database/12c-database/)
The supported databases are regularly tested for ongoing compliance and performance, and HAPI FHIR has specific performance optimizations for each platform. Make sure to use the HAPI FHIR dialect class as opposed to the default hibernate dialect class.
Use of any of the above databases is fully supported by HAPI-FHIR, and code is actively written to work with them.
| Database | Status | Hibernate Dialect Class | Notes |
|-----------------------------------------------------------------------------|---------------|----------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------|
| [MS SQL Server](https://www.microsoft.com/en-us/sql-server/sql-server-2019) | **Supported** | `ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect` | |
| [PostgreSQL](https://www.postgresql.org/) | **Supported** | `ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect` | |
| [Oracle](https://www.oracle.com/ca-en/database/12c-database/) | **Supported** | `ca.uhn.fhir.jpa.model.dialect.HapiFhirOracleDialect` | |
| [Cockroach DB](https://www.cockroachlabs.com/) | Experimental | `ca.uhn.fhir.jpa.model.dialect.HapiFhirCockroachDialect` | A CockroachDB dialect was contributed by a HAPI FHIR community member. This dialect is not regularly tested, use with caution. |
| MySQL | Deprecated | `ca.uhn.fhir.jpa.model.dialect.HapiFhirMySQLDialect` | MySQL and MariaDB exhibit poor performance with HAPI FHIR and have therefore been deprecated. These databases should not be used. |
| MariaDB | Deprecated | `ca.uhn.fhir.jpa.model.dialect.HapiFhirMariaDBDialect` | MySQL and MariaDB exhibit poor performance with HAPI FHIR and have therefore been deprecated. These databases should not be used. |
# Experimental Support
HAPI FHIR currently provides experimental for the following databases, but does not actively support them, or write code specifically to work with them:
- [Cockroach DB](https://www.cockroachlabs.com/)
HAPI FHIR uses the Hibernate ORM to provide database abstraction. This means that HAPI FHIR could theoretically also work on other databases supported by Hibernate.
For example, although we do not regularly test or validate on other platforms, community members have reported successfully running HAPI FHIR on:
@ -21,9 +22,3 @@ For example, although we do not regularly test or validate on other platforms, c
- Cache
- Firebird
# Deprecated Support
These databases were previously supported by HAPI FHIR JPA Server, but have since been deprecated, and should not be used.
- [MySQL](https://www.mysql.com/)

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

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

27
hapi-fhir-jaxrsserver-base/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.11.4-SNAPSHOT</version>
<version>6.11.5-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -74,20 +74,22 @@
</dependency>
<dependency>
<groupId>javax.ejb</groupId>
<artifactId>ejb-api</artifactId>
<scope>provided</scope>
<groupId>jakarta.ejb</groupId>
<artifactId>jakarta.ejb-api</artifactId>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>provided</scope>
<groupId>jakarta.servlet</groupId>
<artifactId>jakarta.servlet-api</artifactId>
</dependency>
<dependency>
<groupId>org.jboss.spec.javax.ws.rs</groupId>
<artifactId>jboss-jaxrs-api_2.1_spec</artifactId>
<scope>provided</scope>
<groupId>jakarta.ws.rs</groupId>
<artifactId>jakarta.ws.rs-api</artifactId>
</dependency>
<dependency>
<groupId>jakarta.interceptor</groupId>
<artifactId>jakarta.interceptor-api</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
@ -109,11 +111,6 @@
<artifactId>jetty-server</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>

14
hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/client/JaxRsHttpClient.java
View File

@ -29,20 +29,20 @@ import ca.uhn.fhir.rest.client.api.IHttpClient;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.impl.BaseHttpClientInvocation;
import ca.uhn.fhir.rest.client.method.MethodUtil;
import jakarta.ws.rs.client.Client;
import jakarta.ws.rs.client.Entity;
import jakarta.ws.rs.client.Invocation.Builder;
import jakarta.ws.rs.core.Form;
import jakarta.ws.rs.core.MultivaluedHashMap;
import jakarta.ws.rs.core.MultivaluedMap;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import java.util.List;
import java.util.Map;
import javax.ws.rs.client.Client;
import javax.ws.rs.client.Entity;
import javax.ws.rs.client.Invocation.Builder;
import javax.ws.rs.core.Form;
import javax.ws.rs.core.MultivaluedHashMap;
import javax.ws.rs.core.MultivaluedMap;
/**
* A Http Request based on JaxRs. This is an adapter around the class
* {@link javax.ws.rs.client.Client Client}
* {@link jakarta.ws.rs.client.Client Client}
*
* @author Peter Van Houte | peter.vanhoute@agfa.com | Agfa Healthcare
*/

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