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

Bump corelib to FHIR R5 Final (#4727) 

* Core bump

* Build build issues

* Bump core

* Cleanup

* Cleanup

* Resolve intermittent

* Work on core

* Add failing test for a check

* Test fixes

* Fixes

* DOn't mangle subscriptions

* Fix

* License headers

* Build fixes

* Version bump

* Compile fixes

* Fix compile issues
This commit is contained in:
James Agnew 2023-04-28 06:28:22 -04:00 committed by GitHub
parent 2171ad04a2
commit e2717bd63a
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
173 changed files with 1567 additions and 1182649 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
azure-pipelines.yml
View File

@ -42,8 +42,6 @@ stages:
module: hapi-fhir-checkstyle
- name: hapi_fhir_cli_api
module: hapi-fhir-cli/hapi-fhir-cli-api
# - name: hapi_fhir_cli_jpaserver
# module: hapi-fhir-cli/hapi-fhir-cli-jpaserver
- name: hapi_fhir_client
module: hapi-fhir-client
- name: hapi_fhir_client_okhttp

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -128,7 +128,7 @@ public class FhirContext {
private volatile Boolean myFormatJsonSupported;
private volatile Boolean myFormatNDJsonSupported;
private volatile Boolean myFormatRdfSupported;
private IFhirValidatorFactory myFhirValidatorFactory = fhirContext -> new FhirValidator(fhirContext);
private IFhirValidatorFactory myFhirValidatorFactory = FhirValidator::new;
/**
* @deprecated It is recommended that you use one of the static initializer methods instead

30
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirVersionEnum.java
View File

@ -128,26 +128,22 @@ public enum FhirVersionEnum {
return myIsRi;
}
/**
* Creates a new FhirContext for this FHIR version
*/
public FhirContext newContext() {
switch (this) {
case DSTU2:
return FhirContext.forDstu2();
case DSTU2_HL7ORG:
return FhirContext.forDstu2Hl7Org();
case DSTU2_1:
return FhirContext.forDstu2_1();
case DSTU3:
return FhirContext.forDstu3();
case R4:
return FhirContext.forR4();
case R4B:
return FhirContext.forR4B();
case R5:
return FhirContext.forR5();
}
throw new IllegalStateException(Msg.code(1711) + "Unknown version: " + this); // should not happen
return new FhirContext(this);
}
/**
* Creates a new FhirContext for this FHIR version, or returns a previously created one if one exists. This
* method uses {@link FhirContext#forCached(FhirVersionEnum)} to return a cached instance.
*/
public FhirContext newContextCached() {
return FhirContext.forCached(this);
}
private interface IVersionProvider {
String provideVersion();
}

379
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/DefaultProfileValidationSupport.java
View File

@ -19,35 +19,20 @@
*/
package ca.uhn.fhir.context.support;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.ClasspathUtil;
import org.apache.commons.lang3.StringUtils;
import ca.uhn.fhir.util.ILockable;
import ca.uhn.fhir.util.ReflectionUtil;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import javax.annotation.Nullable;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Optional;
import java.util.Properties;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
* This class returns the vocabulary that is shipped with the base FHIR
@ -61,16 +46,14 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
*/
public class DefaultProfileValidationSupport implements IValidationSupport {
private static final String URL_PREFIX_STRUCTURE_DEFINITION = "http://hl7.org/fhir/StructureDefinition/";
private static final String URL_PREFIX_STRUCTURE_DEFINITION_BASE = "http://hl7.org/fhir/";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DefaultProfileValidationSupport.class);
private static final Map<FhirVersionEnum, IValidationSupport> ourImplementations = Collections.synchronizedMap(new HashMap<>());
private final FhirContext myCtx;
private Map<String, IBaseResource> myCodeSystems;
private Map<String, IBaseResource> myStructureDefinitions;
private Map<String, IBaseResource> myValueSets;
private List<String> myTerminologyResources;
private List<String> myStructureDefinitionResources;
/**
* This module just delegates all calls to a concrete implementation which will
* be in this field. Which implementation gets used depends on the FHIR version.
*/
private final IValidationSupport myDelegate;
private final Runnable myFlush;
/**
* Constructor
@ -79,202 +62,71 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
*/
public DefaultProfileValidationSupport(FhirContext theFhirContext) {
myCtx = theFhirContext;
}
IValidationSupport strategy;
synchronized (ourImplementations) {
strategy = ourImplementations.get(theFhirContext.getVersion().getVersion());
private void initializeResourceLists() {
if (myTerminologyResources != null && myStructureDefinitionResources != null) {
return;
}
List<String> terminologyResources = new ArrayList<>();
List<String> structureDefinitionResources = new ArrayList<>();
switch (getFhirContext().getVersion().getVersion()) {
case DSTU2:
case DSTU2_HL7ORG:
terminologyResources.add("/org/hl7/fhir/instance/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/instance/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml");
Properties profileNameProperties = new Properties();
try {
profileNameProperties.load(DefaultProfileValidationSupport.class.getResourceAsStream("/org/hl7/fhir/instance/model/profile/profiles.properties"));
for (Object nextKey : profileNameProperties.keySet()) {
structureDefinitionResources.add("/org/hl7/fhir/instance/model/profile/" + nextKey);
}
} catch (IOException e) {
throw new ConfigurationException(Msg.code(1740) + e);
if (strategy == null) {
if (theFhirContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R5)) {
/*
* I don't love that we use reflection here, but this class is in
* hapi-fhir-base, and the class we're creating is in
* hapi-fhir-validation. There are complicated dependency chains that
* make this hard to clean up. At some point it'd be nice to figure out
* a cleaner solution though.
*/
strategy = ReflectionUtil.newInstance("org.hl7.fhir.common.hapi.validation.support.DefaultProfileValidationSupportNpmStrategy", IValidationSupport.class, new Class[]{FhirContext.class}, new Object[]{theFhirContext});
((ILockable)strategy).lock();
} else {
strategy = new DefaultProfileValidationSupportBundleStrategy(theFhirContext);
}
break;
case DSTU2_1:
terminologyResources.add("/org/hl7/fhir/dstu2016may/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/dstu2016may/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/dstu2016may/model/valueset/v3-codesystems.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu2016may/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu2016may/model/profile/profiles-types.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu2016may/model/profile/profiles-others.xml");
break;
case DSTU3:
terminologyResources.add("/org/hl7/fhir/dstu3/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/dstu3/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/dstu3/model/valueset/v3-codesystems.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu3/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu3/model/profile/profiles-types.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu3/model/profile/profiles-others.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu3/model/extension/extension-definitions.xml");
break;
case R4:
terminologyResources.add("/org/hl7/fhir/r4/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/r4/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/r4/model/valueset/v3-codesystems.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4/model/profile/profiles-types.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4/model/profile/profiles-others.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4/model/extension/extension-definitions.xml");
break;
case R4B:
terminologyResources.add("/org/hl7/fhir/r4b/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/r4b/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/r4b/model/valueset/v3-codesystems.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/profile/profiles-types.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/profile/profiles-others.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/extension/extension-definitions.xml");
break;
case R5:
structureDefinitionResources.add("/org/hl7/fhir/r5/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/r5/model/profile/profiles-types.xml");
structureDefinitionResources.add("/org/hl7/fhir/r5/model/profile/profiles-others.xml");
structureDefinitionResources.add("/org/hl7/fhir/r5/model/extension/extension-definitions.xml");
terminologyResources.add("/org/hl7/fhir/r5/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/r5/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/r5/model/valueset/v3-codesystems.xml");
break;
ourImplementations.put(theFhirContext.getVersion().getVersion(), strategy);
}
}
myTerminologyResources = terminologyResources;
myStructureDefinitionResources = structureDefinitionResources;
myDelegate = strategy;
if (myDelegate instanceof DefaultProfileValidationSupportBundleStrategy) {
myFlush = ()->((DefaultProfileValidationSupportBundleStrategy) myDelegate).flush();
} else {
myFlush = ()->{};
}
}
@Override
public List<IBaseResource> fetchAllConformanceResources() {
ArrayList<IBaseResource> retVal = new ArrayList<>();
retVal.addAll(myCodeSystems.values());
retVal.addAll(myStructureDefinitions.values());
retVal.addAll(myValueSets.values());
return retVal;
return myDelegate.fetchAllConformanceResources();
}
@Override
public <T extends IBaseResource> List<T> fetchAllStructureDefinitions() {
return toList(provideStructureDefinitionMap());
return myDelegate.fetchAllStructureDefinitions();
}
@Nullable
@Override
public <T extends IBaseResource> List<T> fetchAllNonBaseStructureDefinitions() {
return null;
return myDelegate.fetchAllNonBaseStructureDefinitions();
}
@Override
public IBaseResource fetchCodeSystem(String theSystem) {
return fetchCodeSystemOrValueSet(theSystem, true);
}
private IBaseResource fetchCodeSystemOrValueSet(String theSystem, boolean codeSystem) {
synchronized (this) {
Map<String, IBaseResource> codeSystems = myCodeSystems;
Map<String, IBaseResource> valueSets = myValueSets;
if (codeSystems == null || valueSets == null) {
codeSystems = new HashMap<>();
valueSets = new HashMap<>();
initializeResourceLists();
for (String next : myTerminologyResources) {
loadCodeSystems(codeSystems, valueSets, next);
}
myCodeSystems = codeSystems;
myValueSets = valueSets;
}
// System can take the form "http://url|version"
String system = theSystem;
String version = null;
int pipeIdx = system.indexOf('|');
if (pipeIdx > 0) {
version = system.substring(pipeIdx + 1);
system = system.substring(0, pipeIdx);
}
IBaseResource candidate;
if (codeSystem) {
candidate = codeSystems.get(system);
} else {
candidate = valueSets.get(system);
}
if (candidate != null && isNotBlank(version) && !system.startsWith("http://hl7.org") && !system.startsWith("http://terminology.hl7.org")) {
if (!StringUtils.equals(version, myCtx.newTerser().getSinglePrimitiveValueOrNull(candidate, "version"))) {
candidate = null;
}
}
return candidate;
}
return myDelegate.fetchCodeSystem(theSystem);
}
@Override
public IBaseResource fetchStructureDefinition(String theUrl) {
String url = theUrl;
if (!url.startsWith(URL_PREFIX_STRUCTURE_DEFINITION)) {
if (url.indexOf('/') == -1) {
url = URL_PREFIX_STRUCTURE_DEFINITION + url;
} else if (StringUtils.countMatches(url, '/') == 1) {
url = URL_PREFIX_STRUCTURE_DEFINITION_BASE + url;
}
}
Map<String, IBaseResource> structureDefinitionMap = provideStructureDefinitionMap();
IBaseResource retVal = structureDefinitionMap.get(url);
if (retVal == null) {
if (url.startsWith(URL_PREFIX_STRUCTURE_DEFINITION)) {
/*
* A few built-in R4 SearchParameters have the wrong casing for primitive
* search parameters eg "value.as(String)" when it should be
* "value.as(string)". This lets us be a bit lenient about this.
*/
if (myCtx.getVersion().getVersion() == FhirVersionEnum.R4 || myCtx.getVersion().getVersion() == FhirVersionEnum.R4B || myCtx.getVersion().getVersion() == FhirVersionEnum.R5) {
String end = url.substring(URL_PREFIX_STRUCTURE_DEFINITION.length());
if (Character.isUpperCase(end.charAt(0))) {
String newEnd = Character.toLowerCase(end.charAt(0)) + end.substring(1);
String alternateUrl = URL_PREFIX_STRUCTURE_DEFINITION + newEnd;
retVal = structureDefinitionMap.get(alternateUrl);
if (retVal != null) {
retVal = myCtx.newTerser().clone(retVal);
myCtx.newTerser().setElement(retVal, "type", end);
}
}
}
}
}
return retVal;
return myDelegate.fetchStructureDefinition(theUrl);
}
@Override
public IBaseResource fetchValueSet(String theUrl) {
IBaseResource retVal = fetchCodeSystemOrValueSet(theUrl, false);
return retVal;
return myDelegate.fetchValueSet(theUrl);
}
public void flush() {
myCodeSystems = null;
myStructureDefinitions = null;
myFlush.run();
}
@Override
@ -282,152 +134,6 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
return myCtx;
}
private Map<String, IBaseResource> provideStructureDefinitionMap() {
Map<String, IBaseResource> structureDefinitions = myStructureDefinitions;
if (structureDefinitions == null) {
structureDefinitions = new HashMap<>();
initializeResourceLists();
for (String next : myStructureDefinitionResources) {
loadStructureDefinitions(structureDefinitions, next);
}
myStructureDefinitions = structureDefinitions;
}
return structureDefinitions;
}
private void loadCodeSystems(Map<String, IBaseResource> theCodeSystems, Map<String, IBaseResource> theValueSets, String theClasspath) {
ourLog.info("Loading CodeSystem/ValueSet from classpath: {}", theClasspath);
InputStream inputStream = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
InputStreamReader reader = null;
if (inputStream != null) {
try {
reader = new InputStreamReader(inputStream, Constants.CHARSET_UTF8);
List<IBaseResource> resources = parseBundle(reader);
for (IBaseResource next : resources) {
RuntimeResourceDefinition nextDef = getFhirContext().getResourceDefinition(next);
Map<String, IBaseResource> map = null;
switch (nextDef.getName()) {
case "CodeSystem":
map = theCodeSystems;
break;
case "ValueSet":
map = theValueSets;
break;
}
if (map != null) {
String urlValueString = getConformanceResourceUrl(next);
if (isNotBlank(urlValueString)) {
map.put(urlValueString, next);
}
switch (myCtx.getVersion().getVersion()) {
case DSTU2:
case DSTU2_HL7ORG:
IPrimitiveType<?> codeSystem = myCtx.newTerser().getSingleValueOrNull(next, "ValueSet.codeSystem.system", IPrimitiveType.class);
if (codeSystem != null && isNotBlank(codeSystem.getValueAsString())) {
theCodeSystems.put(codeSystem.getValueAsString(), next);
}
break;
default:
case DSTU2_1:
case DSTU3:
case R4:
case R5:
break;
}
}
}
} finally {
try {
if (reader != null) {
reader.close();
}
inputStream.close();
} catch (IOException e) {
ourLog.warn("Failure closing stream", e);
}
}
} else {
ourLog.warn("Unable to load resource: {}", theClasspath);
}
// Load built-in system
if (myCtx.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
String storageCodeEnum = ClasspathUtil.loadResource("ca/uhn/fhir/context/support/HapiFhirStorageResponseCode.json");
IBaseResource storageCodeCodeSystem = myCtx.newJsonParser().setParserErrorHandler(new LenientErrorHandler()).parseResource(storageCodeEnum);
String url = myCtx.newTerser().getSinglePrimitiveValueOrNull(storageCodeCodeSystem, "url");
theCodeSystems.put(url, storageCodeCodeSystem);
}
}
private void loadStructureDefinitions(Map<String, IBaseResource> theCodeSystems, String theClasspath) {
ourLog.info("Loading structure definitions from classpath: {}", theClasspath);
String packageUserData = null;
if (myCtx.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
packageUserData = "hl7.fhir." + myCtx.getVersion().getVersion().name().replace("DSTU", "R").toLowerCase(Locale.US);
}
try (InputStream valueSetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath)) {
if (valueSetText != null) {
try (InputStreamReader reader = new InputStreamReader(valueSetText, Constants.CHARSET_UTF8)) {
List<IBaseResource> resources = parseBundle(reader);
for (IBaseResource next : resources) {
String nextType = getFhirContext().getResourceType(next);
if ("StructureDefinition".equals(nextType)) {
String url = getConformanceResourceUrl(next);
if (isNotBlank(url)) {
theCodeSystems.put(url, next);
}
}
// This is used by the validator to determine which package a given SD came from.
// I don't love this use of magic strings but that's what is expected currently
if (packageUserData != null) {
next.setUserData("package", packageUserData);
}
}
}
} else {
ourLog.warn("Unable to load resource: {}", theClasspath);
}
} catch (IOException theE) {
ourLog.warn("Unable to load resource: {}", theClasspath);
}
}
private String getConformanceResourceUrl(IBaseResource theResource) {
return getConformanceResourceUrl(getFhirContext(), theResource);
}
private List<IBaseResource> parseBundle(InputStreamReader theReader) {
IBaseResource parsedObject = getFhirContext().newXmlParser().parseResource(theReader);
if (parsedObject instanceof IBaseBundle) {
IBaseBundle bundle = (IBaseBundle) parsedObject;
return BundleUtil.toListOfResources(getFhirContext(), bundle);
} else {
return Collections.singletonList(parsedObject);
}
}
@Nullable
public static String getConformanceResourceUrl(FhirContext theFhirContext, IBaseResource theResource) {
@ -440,8 +146,5 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
return urlValueString;
}
static <T extends IBaseResource> List<T> toList(Map<String, IBaseResource> theMap) {
ArrayList<IBaseResource> retVal = new ArrayList<>(theMap.values());
return (List<T>) Collections.unmodifiableList(retVal);
}
}

430
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/DefaultProfileValidationSupportBundleStrategy.java Normal file
View File

@ -0,0 +1,430 @@
/*-
* #%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 ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.ClasspathUtil;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import javax.annotation.Nullable;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Optional;
import java.util.Properties;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
class DefaultProfileValidationSupportBundleStrategy implements IValidationSupport {
private static final String URL_PREFIX_STRUCTURE_DEFINITION = "http://hl7.org/fhir/StructureDefinition/";
private static final String URL_PREFIX_STRUCTURE_DEFINITION_BASE = "http://hl7.org/fhir/";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DefaultProfileValidationSupport.class);
private final FhirContext myCtx;
private Map<String, IBaseResource> myCodeSystems;
private Map<String, IBaseResource> myStructureDefinitions;
private Map<String, IBaseResource> myValueSets;
private List<String> myTerminologyResources;
private List<String> myStructureDefinitionResources;
/**
* Constructor
*
* @param theFhirContext The context to use
*/
DefaultProfileValidationSupportBundleStrategy(FhirContext theFhirContext) {
myCtx = theFhirContext;
}
private void initializeResourceLists() {
if (myTerminologyResources != null && myStructureDefinitionResources != null) {
return;
}
List<String> terminologyResources = new ArrayList<>();
List<String> structureDefinitionResources = new ArrayList<>();
switch (getFhirContext().getVersion().getVersion()) {
case DSTU2:
case DSTU2_HL7ORG:
terminologyResources.add("/org/hl7/fhir/instance/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/instance/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml");
Properties profileNameProperties = new Properties();
try {
profileNameProperties.load(DefaultProfileValidationSupport.class.getResourceAsStream("/org/hl7/fhir/instance/model/profile/profiles.properties"));
for (Object nextKey : profileNameProperties.keySet()) {
structureDefinitionResources.add("/org/hl7/fhir/instance/model/profile/" + nextKey);
}
} catch (IOException e) {
throw new ConfigurationException(Msg.code(1740) + e);
}
break;
case DSTU2_1:
terminologyResources.add("/org/hl7/fhir/dstu2016may/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/dstu2016may/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/dstu2016may/model/valueset/v3-codesystems.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu2016may/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu2016may/model/profile/profiles-types.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu2016may/model/profile/profiles-others.xml");
break;
case DSTU3:
terminologyResources.add("/org/hl7/fhir/dstu3/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/dstu3/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/dstu3/model/valueset/v3-codesystems.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu3/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu3/model/profile/profiles-types.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu3/model/profile/profiles-others.xml");
structureDefinitionResources.add("/org/hl7/fhir/dstu3/model/extension/extension-definitions.xml");
break;
case R4:
terminologyResources.add("/org/hl7/fhir/r4/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/r4/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/r4/model/valueset/v3-codesystems.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4/model/profile/profiles-types.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4/model/profile/profiles-others.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4/model/extension/extension-definitions.xml");
break;
case R4B:
terminologyResources.add("/org/hl7/fhir/r4b/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/r4b/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/r4b/model/valueset/v3-codesystems.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/profile/profiles-types.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/profile/profiles-others.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/extension/extension-definitions.xml");
break;
case R5:
structureDefinitionResources.add("/org/hl7/fhir/r5/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/r5/model/profile/profiles-types.xml");
structureDefinitionResources.add("/org/hl7/fhir/r5/model/profile/profiles-others.xml");
structureDefinitionResources.add("/org/hl7/fhir/r5/model/extension/extension-definitions.xml");
terminologyResources.add("/org/hl7/fhir/r5/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/r5/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/r5/model/valueset/v3-codesystems.xml");
break;
}
myTerminologyResources = terminologyResources;
myStructureDefinitionResources = structureDefinitionResources;
}
@Override
public List<IBaseResource> fetchAllConformanceResources() {
ArrayList<IBaseResource> retVal = new ArrayList<>();
retVal.addAll(myCodeSystems.values());
retVal.addAll(myStructureDefinitions.values());
retVal.addAll(myValueSets.values());
return retVal;
}
@Override
public <T extends IBaseResource> List<T> fetchAllStructureDefinitions() {
return toList(provideStructureDefinitionMap());
}
@Nullable
@Override
public <T extends IBaseResource> List<T> fetchAllNonBaseStructureDefinitions() {
return null;
}
@Override
public IBaseResource fetchCodeSystem(String theSystem) {
return fetchCodeSystemOrValueSet(theSystem, true);
}
private IBaseResource fetchCodeSystemOrValueSet(String theSystem, boolean codeSystem) {
synchronized (this) {
Map<String, IBaseResource> codeSystems = myCodeSystems;
Map<String, IBaseResource> valueSets = myValueSets;
if (codeSystems == null || valueSets == null) {
codeSystems = new HashMap<>();
valueSets = new HashMap<>();
initializeResourceLists();
for (String next : myTerminologyResources) {
loadCodeSystems(codeSystems, valueSets, next);
}
myCodeSystems = codeSystems;
myValueSets = valueSets;
}
// System can take the form "http://url|version"
String system = theSystem;
String version = null;
int pipeIdx = system.indexOf('|');
if (pipeIdx > 0) {
version = system.substring(pipeIdx + 1);
system = system.substring(0, pipeIdx);
}
IBaseResource candidate;
if (codeSystem) {
candidate = codeSystems.get(system);
} else {
candidate = valueSets.get(system);
}
if (candidate != null && isNotBlank(version) && !system.startsWith("http://hl7.org") && !system.startsWith("http://terminology.hl7.org")) {
if (!StringUtils.equals(version, myCtx.newTerser().getSinglePrimitiveValueOrNull(candidate, "version"))) {
candidate = null;
}
}
return candidate;
}
}
@Override
public IBaseResource fetchStructureDefinition(String theUrl) {
String url = theUrl;
if (!url.startsWith(URL_PREFIX_STRUCTURE_DEFINITION)) {
if (url.indexOf('/') == -1) {
url = URL_PREFIX_STRUCTURE_DEFINITION + url;
} else if (StringUtils.countMatches(url, '/') == 1) {
url = URL_PREFIX_STRUCTURE_DEFINITION_BASE + url;
}
}
Map<String, IBaseResource> structureDefinitionMap = provideStructureDefinitionMap();
IBaseResource retVal = structureDefinitionMap.get(url);
if (retVal == null) {
if (url.startsWith(URL_PREFIX_STRUCTURE_DEFINITION)) {
/*
* A few built-in R4 SearchParameters have the wrong casing for primitive
* search parameters eg "value.as(String)" when it should be
* "value.as(string)". This lets us be a bit lenient about this.
*/
if (myCtx.getVersion().getVersion() == FhirVersionEnum.R4 || myCtx.getVersion().getVersion() == FhirVersionEnum.R4B || myCtx.getVersion().getVersion() == FhirVersionEnum.R5) {
String end = url.substring(URL_PREFIX_STRUCTURE_DEFINITION.length());
if (Character.isUpperCase(end.charAt(0))) {
String newEnd = Character.toLowerCase(end.charAt(0)) + end.substring(1);
String alternateUrl = URL_PREFIX_STRUCTURE_DEFINITION + newEnd;
retVal = structureDefinitionMap.get(alternateUrl);
if (retVal != null) {
retVal = myCtx.newTerser().clone(retVal);
myCtx.newTerser().setElement(retVal, "type", end);
}
}
}
}
}
return retVal;
}
@Override
public IBaseResource fetchValueSet(String theUrl) {
IBaseResource retVal = fetchCodeSystemOrValueSet(theUrl, false);
return retVal;
}
public void flush() {
myCodeSystems = null;
myStructureDefinitions = null;
}
@Override
public FhirContext getFhirContext() {
return myCtx;
}
private Map<String, IBaseResource> provideStructureDefinitionMap() {
Map<String, IBaseResource> structureDefinitions = myStructureDefinitions;
if (structureDefinitions == null) {
structureDefinitions = new HashMap<>();
initializeResourceLists();
for (String next : myStructureDefinitionResources) {
loadStructureDefinitions(structureDefinitions, next);
}
myStructureDefinitions = structureDefinitions;
}
return structureDefinitions;
}
private void loadCodeSystems(Map<String, IBaseResource> theCodeSystems, Map<String, IBaseResource> theValueSets, String theClasspath) {
ourLog.info("Loading CodeSystem/ValueSet from classpath: {}", theClasspath);
InputStream inputStream = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
InputStreamReader reader = null;
if (inputStream != null) {
try {
reader = new InputStreamReader(inputStream, Constants.CHARSET_UTF8);
List<IBaseResource> resources = parseBundle(reader);
for (IBaseResource next : resources) {
RuntimeResourceDefinition nextDef = getFhirContext().getResourceDefinition(next);
Map<String, IBaseResource> map = null;
switch (nextDef.getName()) {
case "CodeSystem":
map = theCodeSystems;
break;
case "ValueSet":
map = theValueSets;
break;
}
if (map != null) {
String urlValueString = getConformanceResourceUrl(next);
if (isNotBlank(urlValueString)) {
map.put(urlValueString, next);
}
switch (myCtx.getVersion().getVersion()) {
case DSTU2:
case DSTU2_HL7ORG:
IPrimitiveType<?> codeSystem = myCtx.newTerser().getSingleValueOrNull(next, "ValueSet.codeSystem.system", IPrimitiveType.class);
if (codeSystem != null && isNotBlank(codeSystem.getValueAsString())) {
theCodeSystems.put(codeSystem.getValueAsString(), next);
}
break;
default:
case DSTU2_1:
case DSTU3:
case R4:
case R4B:
case R5:
break;
}
}
}
} finally {
try {
if (reader != null) {
reader.close();
}
inputStream.close();
} catch (IOException e) {
ourLog.warn("Failure closing stream", e);
}
}
} else {
ourLog.warn("Unable to load resource: {}", theClasspath);
}
// Load built-in system
if (myCtx.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
String storageCodeEnum = ClasspathUtil.loadResource("ca/uhn/fhir/context/support/HapiFhirStorageResponseCode.json");
IBaseResource storageCodeCodeSystem = myCtx.newJsonParser().setParserErrorHandler(new LenientErrorHandler()).parseResource(storageCodeEnum);
String url = myCtx.newTerser().getSinglePrimitiveValueOrNull(storageCodeCodeSystem, "url");
theCodeSystems.put(url, storageCodeCodeSystem);
}
}
private void loadStructureDefinitions(Map<String, IBaseResource> theCodeSystems, String theClasspath) {
ourLog.info("Loading structure definitions from classpath: {}", theClasspath);
String packageUserData = null;
if (myCtx.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
packageUserData = "hl7.fhir." + myCtx.getVersion().getVersion().name().replace("DSTU", "R").toLowerCase(Locale.US);
}
try (InputStream valueSetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath)) {
if (valueSetText != null) {
try (InputStreamReader reader = new InputStreamReader(valueSetText, Constants.CHARSET_UTF8)) {
List<IBaseResource> resources = parseBundle(reader);
for (IBaseResource next : resources) {
String nextType = getFhirContext().getResourceType(next);
if ("StructureDefinition".equals(nextType)) {
String url = getConformanceResourceUrl(next);
if (isNotBlank(url)) {
theCodeSystems.put(url, next);
}
}
// This is used by the validator to determine which package a given SD came from.
// I don't love this use of magic strings but that's what is expected currently
if (packageUserData != null) {
next.setUserData("package", packageUserData);
}
}
}
} else {
ourLog.warn("Unable to load resource: {}", theClasspath);
}
} catch (IOException theE) {
ourLog.warn("Unable to load resource: {}", theClasspath);
}
}
private String getConformanceResourceUrl(IBaseResource theResource) {
return DefaultProfileValidationSupport.getConformanceResourceUrl(getFhirContext(), theResource);
}
private List<IBaseResource> parseBundle(InputStreamReader theReader) {
IBaseResource parsedObject = getFhirContext().newXmlParser().parseResource(theReader);
if (parsedObject instanceof IBaseBundle) {
IBaseBundle bundle = (IBaseBundle) parsedObject;
return BundleUtil.toListOfResources(getFhirContext(), bundle);
} else {
return Collections.singletonList(parsedObject);
}
}
static <T extends IBaseResource> List<T> toList(Map<String, IBaseResource> theMap) {
ArrayList<IBaseResource> retVal = new ArrayList<>(theMap.values());
return (List<T>) Collections.unmodifiableList(retVal);
}
}

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java
View File

@ -126,6 +126,16 @@ public interface IValidationSupport {
return null;
}
/**
* Load and return all possible search parameters
*
* @since 6.6.0
*/
@Nullable
default <T extends IBaseResource> List<T> fetchAllSearchParameters() {
return null;
}
/**
* Load and return all possible structure definitions
*/

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

@ -22,6 +22,7 @@ package ca.uhn.fhir.util;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
@ -171,6 +172,25 @@ public class ExtensionUtil {
.orElse(null);
}
/**
* Given a resource or other structure that can have direct extensions,
* pulls out any extensions that have the given theExtensionUrl and a primitive value type,
* and returns a list of the string version of the extension values.
*/
public static List<String> getExtensionPrimitiveValues(IBaseHasExtensions theBase, String theExtensionUrl) {
List<String> values = theBase
.getExtension()
.stream()
.filter(t -> theExtensionUrl.equals(t.getUrl()))
.filter(t -> t.getValue() instanceof IPrimitiveType<?>)
.map(t->(IPrimitiveType<?>)t.getValue())
.map(IPrimitiveType::getValueAsString)
.filter(StringUtils::isNotBlank)
.collect(Collectors.toList());
return values;
}
/**
* Gets all extensions that match the specified filter predicate
*

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
View File

@ -19,6 +19,8 @@
*/
package ca.uhn.fhir.util;
import java.util.Set;
public class HapiExtensions {
/**
@ -155,6 +157,9 @@ public class HapiExtensions {
*/
public static final String EXTENSION_SEARCHPARAM_UPLIFT_REFCHAIN_ELEMENT_NAME = "element-name";
public static final String EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE = "http://hl7.org/fhir/tools/CustomBaseResource";
public static final String EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE = "http://hl7.org/fhir/tools/CustomTargetResource";
/**
* Non instantiable
*/

26
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ILockable.java Normal file
View File

@ -0,0 +1,26 @@
/*-
* #%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.util;
public interface ILockable {
void lock();
}

23
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ReflectionUtil.java
View File

@ -21,10 +21,13 @@ package ca.uhn.fhir.util;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.apache.commons.lang3.Validate;
import javax.annotation.Nonnull;
import java.lang.reflect.Constructor;
import java.lang.reflect.Field;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.lang.reflect.Modifier;
import java.lang.reflect.ParameterizedType;
@ -244,11 +247,7 @@ public class ReflectionUtil {
@SuppressWarnings("unchecked")
public static <T> T newInstanceOrReturnNull(String theClassName, Class<T> theType, Class<?>[] theArgTypes, Object[] theArgs) {
try {
Class<?> clazz = Class.forName(theClassName);
if (!theType.isAssignableFrom(clazz)) {
throw new ConfigurationException(Msg.code(1787) + theClassName + " is not assignable to " + theType);
}
return (T) clazz.getConstructor(theArgTypes).newInstance(theArgs);
return newInstance(theClassName, theType, theArgTypes, theArgs);
} catch (ConfigurationException e) {
throw e;
} catch (Exception e) {
@ -257,6 +256,20 @@ public class ReflectionUtil {
}
}
@Nonnull
public static <T> T newInstance(String theClassName, Class<T> theType, Class<?>[] theArgTypes, Object[] theArgs) {
try {
Class<?> clazz = Class.forName(theClassName);
if (!theType.isAssignableFrom(clazz)) {
throw new ConfigurationException(Msg.code(1787) + theClassName + " is not assignable to " + theType);
}
return (T) clazz.getConstructor(theArgTypes).newInstance(theArgs);
} catch (ClassNotFoundException | NoSuchMethodException | InstantiationException | IllegalAccessException |
InvocationTargetException e) {
throw new InternalErrorException(Msg.code(2330) + e.getMessage(), e);
}
}
public static boolean typeExists(String theName) {
try {
Class.forName(theName);

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>6.5.16-SNAPSHOT</version>
<version>6.5.17-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>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

9
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>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -27,13 +27,6 @@
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli-jpaserver</artifactId>
<version>${project.version}</version>
<type>jar</type>
<classifier>classes</classifier>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-sql-migrate</artifactId>

1
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java
View File

@ -176,7 +176,6 @@ public abstract class BaseApp {
protected List<BaseCommand> provideCommands() {
ArrayList<BaseCommand> commands = new ArrayList<>();
commands.add(new RunServerCommand());
commands.add(new ExampleDataUploader());
commands.add(new ValidateCommand());
commands.add(new ValidationDataUploader());

221
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java
View File

@ -19,223 +19,12 @@
*/
package ca.uhn.fhir.cli;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.demo.ContextHolder;
import ca.uhn.fhir.jpa.demo.FhirServerConfig;
import ca.uhn.fhir.jpa.demo.FhirServerConfigDstu3;
import ca.uhn.fhir.jpa.demo.FhirServerConfigR4;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.webapp.WebAppContext;
import org.springframework.web.context.ContextLoader;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
/**
* @deprecated Will be removed after 6.6.0
*/
@Deprecated
public class RunServerCommand {
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.net.SocketException;
public class RunServerCommand extends BaseCommand {
private static final String OPTION_DISABLE_REFERENTIAL_INTEGRITY = "disable-referential-integrity";
private static final String OPTION_ALLOW_EXTERNAL_REFS = "allow-external-refs";
private static final String OPTION_REUSE_SEARCH_RESULTS_MILLIS = "reuse-search-results-milliseconds";
private static final int DEFAULT_PORT = 8080;
private static final String OPTION_P = "p";
// TODO: Don't use qualified names for loggers in HAPI CLI.
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RunServerCommand.class);
public static final String RUN_SERVER_COMMAND = "run-server";
private int myPort;
private Server myServer;
@Override
public String getCommandName() {
return RUN_SERVER_COMMAND;
}
@Override
public Options getOptions() {
Options options = new Options();
addFhirVersionOption(options);
options.addOption(OPTION_P, "port", true, "The port to listen on (default is " + DEFAULT_PORT + ")");
options.addOption(null, OPTION_ALLOW_EXTERNAL_REFS, false, "If this flag is set, the server will allow resources to be persisted contaning external resource references");
options.addOption(null, OPTION_DISABLE_REFERENTIAL_INTEGRITY, false, "If this flag is set, the server will not enforce referential integrity");
addOptionalOption(options, "u", "url", "Url", "If this option is set, specifies the JDBC URL to use for the database connection");
Long defaultReuseSearchResults = JpaStorageSettings.DEFAULT_REUSE_CACHED_SEARCH_RESULTS_FOR_MILLIS;
String defaultReuseSearchResultsStr = defaultReuseSearchResults == null ? "off" : String.valueOf(defaultReuseSearchResults);
options.addOption(null, OPTION_REUSE_SEARCH_RESULTS_MILLIS, true, "The time in milliseconds within which the same results will be returned for multiple identical searches, or \"off\" (default is " + defaultReuseSearchResultsStr + ")");
return options;
}
private int parseOptionInteger(CommandLine theCommandLine, String opt, int defaultPort) throws ParseException {
try {
return Integer.parseInt(theCommandLine.getOptionValue(opt, Integer.toString(defaultPort)));
} catch (NumberFormatException e) {
throw new ParseException(Msg.code(1558) + "Invalid value '" + theCommandLine.getOptionValue(opt) + "' (must be numeric)");
}
}
@Override
public void run(CommandLine theCommandLine) throws ParseException {
parseFhirContext(theCommandLine);
myPort = parseOptionInteger(theCommandLine, OPTION_P, DEFAULT_PORT);
if (theCommandLine.hasOption(OPTION_ALLOW_EXTERNAL_REFS)) {
ourLog.info("Server is configured to allow external references");
ContextHolder.setAllowExternalRefs(true);
}
if (theCommandLine.hasOption(OPTION_DISABLE_REFERENTIAL_INTEGRITY)) {
ourLog.info("Server is configured to not enforce referential integrity");
ContextHolder.setDisableReferentialIntegrity(true);
}
ContextHolder.setDatabaseUrl(theCommandLine.getOptionValue("u"));
String reuseSearchResults = theCommandLine.getOptionValue(OPTION_REUSE_SEARCH_RESULTS_MILLIS);
if (reuseSearchResults != null) {
if (reuseSearchResults.equals("off")) {
ourLog.info("Server is configured to not reuse search results");
ContextHolder.setReuseCachedSearchResultsForMillis(null);
} else {
try {
long reuseSearchResultsMillis = Long.parseLong(reuseSearchResults);
if (reuseSearchResultsMillis < 0) {
throw new NumberFormatException(Msg.code(1559) + "expected a positive integer");
}
ourLog.info("Server is configured to reuse search results for " + String.valueOf(reuseSearchResultsMillis) + " milliseconds");
ContextHolder.setReuseCachedSearchResultsForMillis(reuseSearchResultsMillis);
} catch (NumberFormatException e) {
throw new ParseException(Msg.code(1560) + "Invalid value '" + reuseSearchResults + "' (must be a positive integer)");
}
}
}
ContextHolder.setCtx(getFhirContext());
ourLog.info("Preparing HAPI FHIR JPA server on port {}", myPort);
File tempWarFile;
try {
tempWarFile = File.createTempFile("hapi-fhir", ".war");
tempWarFile.deleteOnExit();
InputStream inStream = RunServerCommand.class.getResourceAsStream("/hapi-fhir-cli-jpaserver.war");
OutputStream outStream = new BufferedOutputStream(new FileOutputStream(tempWarFile, false));
IOUtils.copy(inStream, outStream);
} catch (IOException e) {
ourLog.error("Failed to create temporary file", e);
return;
}
final ContextLoaderListener cll = new ContextLoaderListener();
ourLog.info("Starting HAPI FHIR JPA server in {} mode", ContextHolder.getCtx().getVersion().getVersion());
WebAppContext root = new WebAppContext();
root.setAllowDuplicateFragmentNames(true);
root.setWar(tempWarFile.getAbsolutePath());
root.setParentLoaderPriority(true);
root.setContextPath("/");
root.addEventListener(new ServletContextListener() {
@Override
public void contextInitialized(ServletContextEvent theSce) {
theSce.getServletContext().setInitParameter(ContextLoader.CONTEXT_CLASS_PARAM, AnnotationConfigWebApplicationContext.class.getName());
switch (ContextHolder.getCtx().getVersion().getVersion()) {
case DSTU2:
theSce.getServletContext().setInitParameter(ContextLoader.CONFIG_LOCATION_PARAM, FhirServerConfig.class.getName());
break;
case DSTU3:
theSce.getServletContext().setInitParameter(ContextLoader.CONFIG_LOCATION_PARAM, FhirServerConfigDstu3.class.getName());
break;
case R4:
theSce.getServletContext().setInitParameter(ContextLoader.CONFIG_LOCATION_PARAM, FhirServerConfigR4.class.getName());
break;
case DSTU2_1:
case DSTU2_HL7ORG:
break;
}
cll.contextInitialized(theSce);
}
@Override
public void contextDestroyed(ServletContextEvent theSce) {
cll.contextDestroyed(theSce);
}
});
String path = ContextHolder.getPath();
root.addServlet("ca.uhn.fhir.jpa.demo.JpaServerDemo", path + "*");
myServer = new Server(myPort);
myServer.setHandler(root);
try {
myServer.start();
} catch (SocketException e) {
throw new CommandFailureException(Msg.code(1561) + "Server failed to start on port " + myPort + " because of the following error \"" + e.toString() + "\". Note that you can use the '-p' option to specify an alternate port.");
} catch (Exception e) {
ourLog.error("Server failed to start", e);
throw new CommandFailureException(Msg.code(1562) + "Server failed to start", e);
}
ourLog.info("Server started on port {}", myPort);
ourLog.info("Web Testing UI : http://localhost:{}/", myPort);
ourLog.info("Server Base URL: http://localhost:{}{}", myPort, path);
// Never quit.. We'll let the user ctrl-C their way out.
loopForever();
}
@SuppressWarnings("InfiniteLoopStatement")
private void loopForever() {
while (true) {
try {
Thread.sleep(DateUtils.MILLIS_PER_MINUTE);
} catch (InterruptedException theE) {
// ignore
}
}
}
public static void main(String[] theArgs) {
Server server = new Server(22);
String path = "../hapi-fhir-cli-jpaserver";
WebAppContext webAppContext = new WebAppContext();
webAppContext.setContextPath("/");
webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-example");
webAppContext.setParentLoaderPriority(true);
server.setHandler(webAppContext);
try {
server.start();
} catch (Exception e) {
e.printStackTrace();
}
ourLog.info("Started");
}
@Override
public String getCommandDescription() {
return "Start a FHIR server which can be used for testing";
}
}

41
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>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -24,19 +24,6 @@
<version>${project.version}</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli-jpaserver</artifactId>
<version>${project.version}</version>
<type>war</type>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli-jpaserver</artifactId>
<version>${project.version}</version>
<type>jar</type>
<classifier>classes</classifier>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
@ -56,32 +43,6 @@
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy</id>
<phase>process-resources</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli-jpaserver</artifactId>
<type>war</type>
<overWrite>true</overWrite>
<outputDirectory>target/classes</outputDirectory>
<destFileName>hapi-fhir-cli-jpaserver.war</destFileName>
</artifactItem>
</artifactItems>
<!-- other configurations here -->
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>

129
hapi-fhir-cli/hapi-fhir-cli-jpaserver/.gitignore vendored
View File

@ -1,129 +0,0 @@
/target
/jpaserver_derby_files
*.log
ca.uhn.fhir.jpa.entity.ResourceTable/
# Created by https://www.gitignore.io
### Java ###
*.class
# Mobile Tools for Java (J2ME)
.mtj.tmp/
# Package Files #
*.jar
*.war
*.ear
# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid*
### Maven ###
target/
pom.xml.tag
pom.xml.releaseBackup
pom.xml.versionsBackup
pom.xml.next
release.properties
dependency-reduced-pom.xml
buildNumber.properties
### Vim ###
[._]*.s[a-w][a-z]
[._]s[a-w][a-z]
*.un~
Session.vim
.netrwhist
*~
### Intellij ###
# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm
*.iml
## Directory-based project format:
.idea/
# if you remove the above rule, at least ignore the following:
# User-specific stuff:
# .idea/workspace.xml
# .idea/tasks.xml
# .idea/dictionaries
# Sensitive or high-churn files:
# .idea/dataSources.ids
# .idea/dataSources.xml
# .idea/sqlDataSources.xml
# .idea/dynamic.xml
# .idea/uiDesigner.xml
# Gradle:
# .idea/gradle.xml
# .idea/libraries
# Mongo Explorer plugin:
# .idea/mongoSettings.xml
## File-based project format:
*.ipr
*.iws
## Plugin-specific files:
# IntelliJ
/out/
# mpeltonen/sbt-idea plugin
.idea_modules/
# JIRA plugin
atlassian-ide-plugin.xml
# Crashlytics plugin (for Android Studio and IntelliJ)
com_crashlytics_export_strings.xml
crashlytics.properties
crashlytics-build.properties
### Eclipse ###
*.pydevproject
.metadata
.gradle
bin/
tmp/
*.tmp
*.bak
*.swp
*~.nib
local.properties
.settings/
.loadpath
# Eclipse Core
# External tool builders
.externalToolBuilders/
# Locally stored "Eclipse launch configurations"
*.launch
# CDT-specific
.cproject
# JDT-specific (Eclipse Java Development Tools)
.classpath
# PDT-specific
.buildpath
# sbteclipse plugin
.target
# TeXlipse plugin
.texlipse

225
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -1,225 +0,0 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<!-- Note: HAPI projects use the "hapi-fhir" POM as their base to provide easy management. You do not need to use this in your own projects, so the "parent" tag and it's contents below may be removed
if you are using this file as a basis for your own project. -->
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>
<artifactId>hapi-fhir-cli-jpaserver</artifactId>
<packaging>war</packaging>
<name>HAPI FHIR - Command Line Client - Server WAR</name>
<dependencies>
<!-- This dependency includes the core HAPI-FHIR classes -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
<scope>provided</scope>
</dependency>
<!-- This dependency includes the JPA server itself, which is packaged separately from the rest of HAPI FHIR -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
</dependency>
<!-- This dependency is used for the "FHIR Tester" web app overlay -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<type>war</type>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<classifier>classes</classifier>
</dependency>
<!-- HAPI-FHIR uses Logback for logging support. The logback library is included automatically by Maven as a part of the hapi-fhir-base dependency, but you also need to include a logging library. Logback
is used here, but log4j would also be fine. -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<scope>provided</scope>
</dependency>
<!-- Needed for JEE/Servlet support -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
<!-- If you are using HAPI narrative generation, you will need to include Thymeleaf as well. Otherwise the following can be omitted. -->
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
<scope>provided</scope>
</dependency>
<!-- Used for CORS support -->
<!-- Spring Web is used to deploy the server to a web container. -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<scope>provided</scope>
</dependency>
<!-- You may not need this if you are deploying to an application server which provides database connection pools itself. -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
</dependency>
<!-- This example uses H2 embedded database. If you are using another database such as Mysql or Oracle, you may omit the following dependencies and replace them with an appropriate database client
dependency for your database platform. -->
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
</dependency>
<!-- Hibernate search Lucene backend -->
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-lucene</artifactId>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-analyzers-phonetic</artifactId>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-backward-codecs</artifactId>
</dependency>
<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
<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>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
<exclusions>
<exclusion>
<artifactId>Saxon-HE</artifactId>
<groupId>net.sf.saxon</groupId>
</exclusion>
<exclusion>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-core</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<build>
<!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver-example.war -->
<finalName>hapi-fhir-cli-jpaserver</finalName>
<!-- The following is not required for the application to build, but allows you to test it by issuing "mvn jetty:run" from the command line. -->
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<configuration>
<webApp>
<contextPath>/hapi-fhir-jpaserver-example</contextPath>
<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
</webApp>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<!-- The configuration here tells the WAR plugin to include the FHIR Tester overlay. You can omit it if you are not using that feature. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<archive>
<manifestEntries>
<Build-Time>${maven.build.timestamp}</Build-Time>
</manifestEntries>
</archive>
<overlays>
<overlay>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
</overlay>
</overlays>
<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
<attachClasses>true</attachClasses>
<packagingExcludes>
WEB-INF/lib/Saxon-HE-*,
WEB-INF/lib/hapi-*
</packagingExcludes>
</configuration>
</plugin>
<!-- This is to run the integration tests -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
</configuration>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>

31
hapi-fhir-cli/hapi-fhir-cli-jpaserver/readme.intellij.txt
View File

@ -1,31 +0,0 @@
Running hapi-fhir-jpaserver-example in Tomcat from IntelliJ
Install Tomcat.
Make sure you have Tomcat set up in IntelliJ.
File->Settings->Build, Execution, Deployment->Application Servers
Click +
Select "Tomcat Server"
Enter the path to your tomcat deployment for both Tomcat Home (IntelliJ will fill in base directory for you)
Add a Run Configuration for running hapi-fhir-jpaserver-example under Tomcat
Run->Edit Configurations
Click the green +
Select Tomcat Server, Local
Change the name to whatever you wish
Uncheck the "After launch" checkbox
On the "Deployment" tab, click the green +
Select "Artifact"
Select "hapi-fhir-jpaserver-example:war"
In "Application context" type /hapi
Run the configuration
You should now have an "Application Servers" in the list of windows at the bottom.
Click it.
Select your server, and click the green triangle (or the bug if you want to debug)
Wait for the console output to stop
Point your browser (or fiddler, or what have you) to
http://localhost:8080/hapi/base/Patient
You should get an empty bundle back.

97
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
View File

@ -1,97 +0,0 @@
/*-
* #%L
* HAPI FHIR - Command Line Client - Server WAR
* %%
* 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.jpa.demo;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import ca.uhn.fhir.rest.api.Constants;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import javax.sql.DataSource;
import java.util.Properties;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@SuppressWarnings("Duplicates")
@Configuration
public class CommonConfig {
/**
* Configure FHIR properties around the JPA server via this bean
*/
@Bean
public JpaStorageSettings storageSettings() {
JpaStorageSettings retVal = new JpaStorageSettings();
retVal.setAllowMultipleDelete(true);
return retVal;
}
/**
* The following bean configures the database connection. The 'url' property value of "jdbc:h2:file:target./jpaserver_h2_files" indicates that the server should save resources in a
* directory called "jpaserver_h2_files".
* <p>
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
*/
@Bean(destroyMethod = "close")
public DataSource dataSource() {
String url = "jdbc:h2:file:./target/jpaserver_h2_files";
if (isNotBlank(ContextHolder.getDatabaseUrl())) {
url = ContextHolder.getDatabaseUrl();
}
BasicDataSource retVal = new BasicDataSource();
retVal.setDriver(new org.h2.Driver());
retVal.setUrl(url);
retVal.setUsername("");
retVal.setPassword("");
return retVal;
}
@Bean
public Properties jpaProperties() {
Properties extraProperties = new Properties();
//Regular Hibernate Settings
extraProperties.put("hibernate.dialect", HapiFhirH2Dialect.class.getName());
extraProperties.put("hibernate.format_sql", "true");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.jdbc.batch_size", "20");
extraProperties.put("hibernate.cache.use_query_cache", "false");
extraProperties.put("hibernate.cache.use_second_level_cache", "false");
extraProperties.put("hibernate.cache.use_structured_entries", "false");
extraProperties.put("hibernate.cache.use_minimal_puts", "false");
extraProperties.put("hibernate.search.backend.type", "lucene");
extraProperties.put(HibernateOrmMapperSettings.ENABLED, "false");
extraProperties.put(Constants.HIBERNATE_INTEGRATION_ENVERS_ENABLED, storageSettings().isNonResourceDbHistoryEnabled());
return extraProperties;
}
@Bean
public PartitionSettings partitionSettings() {
return new PartitionSettings();
}
}

103
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/ContextHolder.java
View File

@ -1,103 +0,0 @@
/*-
* #%L
* HAPI FHIR - Command Line Client - Server WAR
* %%
* 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.jpa.demo;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import org.apache.commons.cli.ParseException;
import org.apache.commons.lang3.Validate;
public class ContextHolder {
private static boolean ourAllowExternalRefs;
private static FhirContext ourCtx;
private static boolean ourDisableReferentialIntegrity;
private static String ourPath;
private static Long ourReuseSearchResultsMillis;
private static String ourDatabaseUrl;
static {
ourReuseSearchResultsMillis = JpaStorageSettings.DEFAULT_REUSE_CACHED_SEARCH_RESULTS_FOR_MILLIS;
}
public static FhirContext getCtx() {
Validate.notNull(ourPath, "Context not set");
return ourCtx;
}
public static void setCtx(FhirContext theCtx) throws ParseException {
switch (theCtx.getVersion().getVersion()) {
case DSTU2:
ourPath = "/baseDstu2/";
break;
case DSTU2_1:
break;
case DSTU3:
ourPath = "/baseDstu3/";
break;
case R4:
ourPath = "/baseR4/";
break;
case DSTU2_HL7ORG:
default:
throw new ParseException(Msg.code(1531) + "FHIR version not supported by this command: " + theCtx.getVersion().getVersion());
}
ourCtx = theCtx;
}
public static String getPath() {
Validate.notNull(ourPath, "Context not set");
return ourPath;
}
public static Long getReuseCachedSearchResultsForMillis() {
return ourReuseSearchResultsMillis;
}
public static void setReuseCachedSearchResultsForMillis(Long reuseSearchResultsMillis) {
ourReuseSearchResultsMillis = reuseSearchResultsMillis;
}
public static boolean isAllowExternalRefs() {
return ourAllowExternalRefs;
}
public static void setAllowExternalRefs(boolean theAllowExternalRefs) {
ourAllowExternalRefs = theAllowExternalRefs;
}
public static boolean isDisableReferentialIntegrity() {
return ourDisableReferentialIntegrity;
}
public static void setDisableReferentialIntegrity(boolean theDisableReferentialIntegrity) {
ourDisableReferentialIntegrity = theDisableReferentialIntegrity;
}
public static String getDatabaseUrl() {
return ourDatabaseUrl;
}
public static void setDatabaseUrl(String theDatabaseUrl) {
ourDatabaseUrl = theDatabaseUrl;
}
}

114
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java
View File

@ -1,114 +0,0 @@
/*-
* #%L
* HAPI FHIR - Command Line Client - Server WAR
* %%
* 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.jpa.demo;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.config.HapiJpaConfig;
import ca.uhn.fhir.jpa.config.JpaDstu2Config;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Primary;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import java.util.Properties;
@Configuration
@EnableTransactionManagement()
@Import({CommonConfig.class, JpaDstu2Config.class, HapiJpaConfig.class})
public class FhirServerConfig {
@Autowired
private DataSource myDataSource;
@Autowired()
@Qualifier("jpaProperties")
private Properties myJpaProperties;
/**
* Configure FHIR properties around the JPA server via this bean
*/
@Bean
public JpaStorageSettings storageSettings() {
JpaStorageSettings retVal = new JpaStorageSettings();
retVal.setAllowMultipleDelete(true);
return retVal;
}
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(myDataSource);
retVal.setJpaProperties(myJpaProperties);
return retVal;
}
/**
* Do some fancy logging to create a nice access log that has details about each incoming request.
*/
public LoggingInterceptor loggingInterceptor() {
LoggingInterceptor retVal = new LoggingInterceptor();
retVal.setLoggerName("fhirtest.access");
retVal.setMessageFormat(
"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
retVal.setLogExceptions(true);
retVal.setErrorMessageFormat("ERROR - ${requestVerb} ${requestUrl}");
return retVal;
}
/**
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
* @return
*/
@Bean
public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
return retVal;
}
@Bean
public IServerInterceptor subscriptionSecurityInterceptor() {
SubscriptionsRequireManualActivationInterceptorDstu2 retVal = new SubscriptionsRequireManualActivationInterceptorDstu2();
return retVal;
}
@Primary
@Bean
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
}
}

110
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu3.java
View File

@ -1,110 +0,0 @@
/*-
* #%L
* HAPI FHIR - Command Line Client - Server WAR
* %%
* 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.jpa.demo;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.HapiJpaConfig;
import ca.uhn.fhir.jpa.config.dstu3.JpaDstu3Config;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Primary;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import java.util.Properties;
/**
* This class isn't used by default by the example, but
* you can use it as a config if you want to support DSTU3
* instead of DSTU2 in your server.
* <p>
* See https://github.com/hapifhir/hapi-fhir/issues/278
*/
@Configuration
@EnableTransactionManagement()
@Import({CommonConfig.class, JpaDstu3Config.class, HapiJpaConfig.class,})
public class FhirServerConfigDstu3 {
@Autowired
private DataSource myDataSource;
@Autowired()
@Qualifier("jpaProperties")
private Properties myJpaProperties;
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(myDataSource);
retVal.setJpaProperties(myJpaProperties);
return retVal;
}
/**
* Do some fancy logging to create a nice access log that has details about each incoming request.
* @return
*/
public LoggingInterceptor loggingInterceptor() {
LoggingInterceptor retVal = new LoggingInterceptor();
retVal.setLoggerName("fhirtest.access");
retVal.setMessageFormat(
"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
retVal.setLogExceptions(true);
retVal.setErrorMessageFormat("ERROR - ${requestVerb} ${requestUrl}");
return retVal;
}
/**
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
* @return
*/
@Bean
public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
return retVal;
}
@Bean
public IServerInterceptor subscriptionSecurityInterceptor() {
SubscriptionsRequireManualActivationInterceptorDstu3 retVal = new SubscriptionsRequireManualActivationInterceptorDstu3();
return retVal;
}
@Primary
@Bean
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
}
}

110
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigR4.java
View File

@ -1,110 +0,0 @@
/*-
* #%L
* HAPI FHIR - Command Line Client - Server WAR
* %%
* 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.jpa.demo;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.HapiJpaConfig;
import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorR4;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Primary;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import java.util.Properties;
/**
* This class isn't used by default by the example, but
* you can use it as a config if you want to support DSTU3
* instead of DSTU2 in your server.
* <p>
* See https://github.com/hapifhir/hapi-fhir/issues/278
*/
@Configuration
@EnableTransactionManagement()
@Import({CommonConfig.class, JpaR4Config.class, HapiJpaConfig.class})
public class FhirServerConfigR4 {
@Autowired
private DataSource myDataSource;
@Autowired()
@Qualifier("jpaProperties")
private Properties myJpaProperties;
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(myDataSource);
retVal.setJpaProperties(myJpaProperties);
return retVal;
}
/**
* Do some fancy logging to create a nice access log that has details about each incoming request.
* @return
*/
public LoggingInterceptor loggingInterceptor() {
LoggingInterceptor retVal = new LoggingInterceptor();
retVal.setLoggerName("fhirtest.access");
retVal.setMessageFormat(
"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
retVal.setLogExceptions(true);
retVal.setErrorMessageFormat("ERROR - ${requestVerb} ${requestUrl}");
return retVal;
}
/**
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
* @return
*/
@Bean
public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
return retVal;
}
@Bean
public IServerInterceptor subscriptionSecurityInterceptor() {
SubscriptionsRequireManualActivationInterceptorR4 retVal = new SubscriptionsRequireManualActivationInterceptorR4();
return retVal;
}
@Primary
@Bean
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
}
}

77
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirTesterConfig.java
View File

@ -1,77 +0,0 @@
/*-
* #%L
* HAPI FHIR - Command Line Client - Server WAR
* %%
* 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.jpa.demo;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.to.FhirTesterMvcConfig;
import ca.uhn.fhir.to.TesterConfig;
//@formatter:off
/**
* This spring config file configures the web testing module. It serves two
* purposes:
* 1. It imports FhirTesterMvcConfig, which is the spring config for the
* tester itself
* 2. It tells the tester which server(s) to talk to, via the testerConfig()
* method below
*/
@Configuration
@Import(FhirTesterMvcConfig.class)
public class FhirTesterConfig {
/**
* This bean tells the testing webpage which servers it should configure itself
* to communicate with. In this example we configure it to talk to the local
* server, as well as one public server. If you are creating a project to
* deploy somewhere else, you might choose to only put your own server's
* address here.
*
* Note the use of the ${serverBase} variable below. This will be replaced with
* the base URL as reported by the server itself. Often for a simple Tomcat
* (or other container) installation, this will end up being something
* like "http://localhost:8080/hapi-fhir-jpaserver-example". If you are
* deploying your server to a place with a fully qualified domain name,
* you might want to use that instead of using the variable.
*/
@Bean
public TesterConfig testerConfig() {
TesterConfig retVal = new TesterConfig();
retVal
.addServer()
.withId("home")
.withFhirVersion(ContextHolder.getCtx().getVersion().getVersion())
.withBaseUrl("${serverBase}" + ContextHolder.getPath())
.withName("Local Tester");
retVal
.addServer()
.withId("hapi")
.withFhirVersion(FhirVersionEnum.DSTU2)
.withBaseUrl("http://fhirtest.uhn.ca/baseDstu2")
.withName("Public HAPI Test Server");
return retVal;
}
}
//@formatter:on

187
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java
View File

@ -1,187 +0,0 @@
/*-
* #%L
* HAPI FHIR - Command Line Client - Server WAR
* %%
* 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.jpa.demo;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.provider.JpaCapabilityStatementProvider;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProvider;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
import javax.servlet.ServletException;
import java.util.ArrayList;
import java.util.List;
public class JpaServerDemo extends RestfulServer {
private static final long serialVersionUID = 1L;
private WebApplicationContext myAppCtx;
@SuppressWarnings("unchecked")
@Override
protected void initialize() throws ServletException {
super.initialize();
setFhirContext(ContextHolder.getCtx());
// Get the spring context from the web container (it's declared in web.xml)
myAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
/*
* The hapi-fhir-server-resourceproviders-dev.xml file is a spring configuration
* file which is automatically generated as a part of hapi-fhir-jpaserver-base and
* contains bean definitions for a resource provider for each resource type
*/
String resourceProviderBeanName;
FhirVersionEnum fhirVersion = ContextHolder.getCtx().getVersion().getVersion();
switch (fhirVersion) {
case DSTU2:
resourceProviderBeanName = "myResourceProvidersDstu2";
break;
case DSTU3:
resourceProviderBeanName = "myResourceProvidersDstu3";
break;
case R4:
resourceProviderBeanName = "myResourceProvidersR4";
break;
default:
throw new IllegalStateException(Msg.code(1532));
}
ResourceProviderFactory beans = myAppCtx.getBean(resourceProviderBeanName, ResourceProviderFactory.class);
registerProviders(beans.createProviders());
/*
* The system provider implements non-resource-type methods, such as
* transaction, and global history.
*/
List<Object> systemProvider = new ArrayList<Object>();
if (fhirVersion == FhirVersionEnum.DSTU2) {
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
systemProvider.add(myAppCtx.getBean(TerminologyUploaderProvider.class));
} else if (fhirVersion == FhirVersionEnum.R4) {
systemProvider.add(myAppCtx.getBean(TerminologyUploaderProvider.class));
systemProvider.add(myAppCtx.getBean(JpaConfig.GRAPHQL_PROVIDER_NAME));
} else {
throw new IllegalStateException(Msg.code(1533));
}
systemProvider.add(myAppCtx.getBean(JpaSystemProvider.class));
registerProviders(systemProvider);
/*
* The conformance provider exports the supported resources, search parameters, etc for
* this server. The JPA version adds resource counts to the exported statement, so it
* is a nice addition.
*/
if (fhirVersion == FhirVersionEnum.DSTU2) {
IFhirSystemDao<Bundle, MetaDt> systemDao = myAppCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao,
myAppCtx.getBean(JpaStorageSettings.class));
confProvider.setImplementationDescription("Example Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
IFhirSystemDao<org.hl7.fhir.dstu3.model.Bundle, org.hl7.fhir.dstu3.model.Meta> systemDao = myAppCtx
.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao,
myAppCtx.getBean(JpaStorageSettings.class), myAppCtx.getBean(ISearchParamRegistry.class));
confProvider.setImplementationDescription("Example Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.R4) {
IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = myAppCtx
.getBean("mySystemDaoR4", IFhirSystemDao.class);
IValidationSupport validationSupport = myAppCtx.getBean(IValidationSupport.class);
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(this, systemDao,
myAppCtx.getBean(JpaStorageSettings.class), myAppCtx.getBean(ISearchParamRegistry.class), validationSupport);
confProvider.setImplementationDescription("Example Server");
setServerConformanceProvider(confProvider);
} else {
throw new IllegalStateException(Msg.code(1534));
}
/*
* Enable ETag Support (this is already the default)
*/
setETagSupport(ETagSupportEnum.ENABLED);
/*
* This server tries to dynamically generate narratives
*/
FhirContext ctx = getFhirContext();
ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
/*
* Default to XML and pretty printing
*/
setDefaultPrettyPrint(true);
setDefaultResponseEncoding(EncodingEnum.JSON);
/*
* This is a simple paging strategy that keeps the last 10 searches in memory
*/
setPagingProvider(new FifoMemoryPagingProvider(10));
// Register a CORS filter
CorsInterceptor corsInterceptor = new CorsInterceptor();
registerInterceptor(corsInterceptor);
JpaStorageSettings storageSettings = myAppCtx.getBean(JpaStorageSettings.class);
storageSettings.setAllowExternalReferences(ContextHolder.isAllowExternalRefs());
storageSettings.setEnforceReferentialIntegrityOnDelete(!ContextHolder.isDisableReferentialIntegrity());
storageSettings.setEnforceReferentialIntegrityOnWrite(!ContextHolder.isDisableReferentialIntegrity());
storageSettings.setReuseCachedSearchResultsForMillis(ContextHolder.getReuseCachedSearchResultsForMillis());
DaoRegistry daoRegistry = myAppCtx.getBean(DaoRegistry.class);
IInterceptorBroadcaster interceptorBroadcaster = myAppCtx.getBean(IInterceptorBroadcaster.class);
ThreadSafeResourceDeleterSvc threadSafeResourceDeleterSvc = myAppCtx.getBean(ThreadSafeResourceDeleterSvc.class);
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster, threadSafeResourceDeleterSvc);
getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
getInterceptorService().registerInterceptor(new ResponseHighlighterInterceptor());
registerProvider(myAppCtx.getBean(BinaryAccessProvider.class));
}
}

16
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/resources/logback.xml_
View File

@ -1,16 +0,0 @@
<configuration scan="true" scanPeriod="30 seconds">
<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
<level>INFO</level>
</filter>
<encoder>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] %msg%n</pattern>
</encoder>
</appender>
<root level="INFO">
<appender-ref ref="STDOUT" />
</root>
</configuration>

67
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/webapp/WEB-INF/templates/about.html
View File

@ -1,67 +0,0 @@
<!DOCTYPE html>
<html lang="en">
<head th:include="tmpl-head :: head">
<title>About This Server</title>
</head>
<body>
<form action="" method="get" id="outerForm">
<div th:replace="tmpl-navbar-top :: top" ></div>
<div class="container-fluid">
<div class="row">
<div th:replace="tmpl-navbar-left :: left" ></div>
<div class="col-sm-9 col-sm-offset-3 col-md-9 col-md-offset-3 main">
<div th:replace="tmpl-banner :: banner"></div>
<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">About This Server</h3>
</div>
<div class="panel-body">
<div class="pull-right">
<object data="img/fhirtest-architecture.svg" width="383" height="369" type="image/svg+xml"></object>
</div>
<p>
This server provides a nearly complete implementation of the FHIR Specification
using a 100% open source software stack. It is hosted by University Health Network.
</p>
<p>
The architecture in use here is shown in the image on the right. This server is built
from a number of modules of the
<a href="https://github.com/hapifhir/hapi-fhir/">HAPI FHIR</a>
project, which is a 100% open-source (Apache 2.0 Licensed) Java based
implementation of the FHIR specification.
</p>
<p>
</p>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">Data On This Server</h3>
</div>
<div class="panel-body">
<p>
This server is regularly loaded with a standard set of test data sourced
from UHN's own testing environment. Do not use this server to store any data
that you will need later, as we will be regularly resetting it.
</p>
<p>
This is not a production server and it provides no privacy. Do not store any
confidential data here.
</p>
</div>
</div>
</div>
</div>
</div>
<div th:replace="tmpl-footer :: footer" ></div>
</form>
</body>
</html>

16
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/webapp/WEB-INF/templates/tmpl-footer.html
View File

@ -1,16 +0,0 @@
<!DOCTYPE html>
<html lang="en">
<div th:fragment="footer">
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-1395874-6', 'auto');
ga('require', 'displayfeatures');
ga('require', 'linkid', 'linkid.js');
ga('send', 'pageview');
</script>
</div>
</html>

8
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/webapp/WEB-INF/templates/tmpl-home-welcome.html
View File

@ -1,8 +0,0 @@
<!DOCTYPE html>
<html lang="en">
<div th:fragment="banner" class="well">
<p>
This server is deployed using HAPI-FHIR CLI (Command Line Interface).
</p>
</div>
</html>

64
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/webapp/WEB-INF/web.xml
View File

@ -1,64 +0,0 @@
<web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="3.0"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee ./xsd/web-app_3_0.xsd">
<!--
<listener>
<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
</listener>
<context-param>
<param-name>contextClass</param-name>
<param-value>
org.springframework.web.context.support.AnnotationConfigWebApplicationContext
</param-value>
</context-param>
<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>
ca.uhn.fhir.jpa.demo.FhirServerConfig
</param-value>
</context-param>
-->
<!-- Servlets -->
<servlet>
<servlet-name>spring</servlet-name>
<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
<init-param>
<param-name>contextClass</param-name>
<param-value>org.springframework.web.context.support.AnnotationConfigWebApplicationContext</param-value>
</init-param>
<init-param>
<param-name>contextConfigLocation</param-name>
<param-value>ca.uhn.fhir.jpa.demo.FhirTesterConfig</param-value>
</init-param>
<load-on-startup>2</load-on-startup>
</servlet>
<!--
<servlet>
<servlet-name>fhirServlet</servlet-name>
<servlet-class>ca.uhn.fhir.jpa.demo.JpaServerDemo</servlet-class>
<init-param>
<param-name>ImplementationDescription</param-name>
<param-value>FHIR JPA Server</param-value>
</init-param>
<init-param>
<param-name>FhirVersion</param-name>
<param-value>DSTU2</param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>fhirServlet</servlet-name>
<url-pattern>/baseDstu2/*</url-pattern>
</servlet-mapping>
-->
<servlet-mapping>
<servlet-name>spring</servlet-name>
<url-pattern>/</url-pattern>
</servlet-mapping>
</web-app>

2419
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/webapp/WEB-INF/xsd/javaee_6.xsd
View File

File diff suppressed because it is too large Load Diff

389
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/webapp/WEB-INF/xsd/jsp_2_2.xsd
View File

@ -1,389 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema xmlns="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://java.sun.com/xml/ns/javaee"
xmlns:javaee="http://java.sun.com/xml/ns/javaee"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
elementFormDefault="qualified"
attributeFormDefault="unqualified"
version="2.2">
<xsd:annotation>
<xsd:documentation>
DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
Copyright 2003-2009 Sun Microsystems, Inc. All rights reserved.
The contents of this file are subject to the terms of either the
GNU General Public License Version 2 only ("GPL") or the Common
Development and Distribution License("CDDL") (collectively, the
"License"). You may not use this file except in compliance with
the License. You can obtain a copy of the License at
https://glassfish.dev.java.net/public/CDDL+GPL.html or
glassfish/bootstrap/legal/LICENSE.txt. See the License for the
specific language governing permissions and limitations under the
License.
When distributing the software, include this License Header
Notice in each file and include the License file at
glassfish/bootstrap/legal/LICENSE.txt. Sun designates this
particular file as subject to the "Classpath" exception as
provided by Sun in the GPL Version 2 section of the License file
that accompanied this code. If applicable, add the following
below the License Header, with the fields enclosed by brackets []
replaced by your own identifying information:
"Portions Copyrighted [year] [name of copyright owner]"
Contributor(s):
If you wish your version of this file to be governed by only the
CDDL or only the GPL Version 2, indicate your decision by adding
"[Contributor] elects to include this software in this
distribution under the [CDDL or GPL Version 2] license." If you
don't indicate a single choice of license, a recipient has the
option to distribute your version of this file under either the
CDDL, the GPL Version 2 or to extend the choice of license to its
licensees as provided above. However, if you add GPL Version 2
code and therefore, elected the GPL Version 2 license, then the
option applies only if the new code is made subject to such
option by the copyright holder.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
This is the XML Schema for the JSP 2.2 deployment descriptor
types. The JSP 2.2 schema contains all the special
structures and datatypes that are necessary to use JSP files
from a web application.
The contents of this schema is used by the web-common_3_0.xsd
file to define JSP specific content.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
The following conventions apply to all Java EE
deployment descriptor elements unless indicated otherwise.
- In elements that specify a pathname to a file within the
same JAR file, relative filenames (i.e., those not
starting with "/") are considered relative to the root of
the JAR file's namespace. Absolute filenames (i.e., those
starting with "/") also specify names in the root of the
JAR file's namespace. In general, relative names are
preferred. The exception is .war files where absolute
names are preferred for consistency with the Servlet API.
</xsd:documentation>
</xsd:annotation>
<xsd:include schemaLocation="javaee_6.xsd"/>
<!-- **************************************************** -->
<xsd:complexType name="jsp-configType">
<xsd:annotation>
<xsd:documentation>
The jsp-configType is used to provide global configuration
information for the JSP files in a web application. It has
two subelements, taglib and jsp-property-group.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="taglib"
type="javaee:taglibType"
minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element name="jsp-property-group"
type="javaee:jsp-property-groupType"
minOccurs="0"
maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="jsp-fileType">
<xsd:annotation>
<xsd:documentation>
The jsp-file element contains the full path to a JSP file
within the web application beginning with a `/'.
</xsd:documentation>
</xsd:annotation>
<xsd:simpleContent>
<xsd:restriction base="javaee:pathType"/>
</xsd:simpleContent>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="jsp-property-groupType">
<xsd:annotation>
<xsd:documentation>
The jsp-property-groupType is used to group a number of
files so they can be given global property information.
All files so described are deemed to be JSP files. The
following additional properties can be described:
- Control whether EL is ignored.
- Control whether scripting elements are invalid.
- Indicate pageEncoding information.
- Indicate that a resource is a JSP document (XML).
- Prelude and Coda automatic includes.
- Control whether the character sequence #{ is allowed
when used as a String literal.
- Control whether template text containing only
whitespaces must be removed from the response output.
- Indicate the default contentType information.
- Indicate the default buffering model for JspWriter
- Control whether error should be raised for the use of
undeclared namespaces in a JSP page.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:group ref="javaee:descriptionGroup"/>
<xsd:element name="url-pattern"
type="javaee:url-patternType"
maxOccurs="unbounded"/>
<xsd:element name="el-ignored"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Can be used to easily set the isELIgnored
property of a group of JSP pages. By default, the
EL evaluation is enabled for Web Applications using
a Servlet 2.4 or greater web.xml, and disabled
otherwise.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="page-encoding"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of page-encoding are those of the
pageEncoding page directive. It is a
translation-time error to name different encodings
in the pageEncoding attribute of the page directive
of a JSP page and in a JSP configuration element
matching the page. It is also a translation-time
error to name different encodings in the prolog
or text declaration of a document in XML syntax and
in a JSP configuration element matching the document.
It is legal to name the same encoding through
mulitple mechanisms.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="scripting-invalid"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Can be used to easily disable scripting in a
group of JSP pages. By default, scripting is
enabled.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="is-xml"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
If true, denotes that the group of resources
that match the URL pattern are JSP documents,
and thus must be interpreted as XML documents.
If false, the resources are assumed to not
be JSP documents, unless there is another
property group that indicates otherwise.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="include-prelude"
type="javaee:pathType"
minOccurs="0"
maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>
The include-prelude element is a context-relative
path that must correspond to an element in the
Web Application. When the element is present,
the given path will be automatically included (as
in an include directive) at the beginning of each
JSP page in this jsp-property-group.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="include-coda"
type="javaee:pathType"
minOccurs="0"
maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>
The include-coda element is a context-relative
path that must correspond to an element in the
Web Application. When the element is present,
the given path will be automatically included (as
in an include directive) at the end of each
JSP page in this jsp-property-group.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="deferred-syntax-allowed-as-literal"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The character sequence #{ is reserved for EL expressions.
Consequently, a translation error occurs if the #{
character sequence is used as a String literal, unless
this element is enabled (true). Disabled (false) by
default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="trim-directive-whitespaces"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Indicates that template text containing only whitespaces
must be removed from the response output. It has no
effect on JSP documents (XML syntax). Disabled (false)
by default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="default-content-type"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of default-content-type are those of the
contentType page directive. It specifies the default
response contentType if the page directive does not include
a contentType attribute.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="buffer"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of buffer are those of the
buffer page directive. It specifies if buffering should be
used for the output to response, and if so, the size of the
buffer to use.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="error-on-undeclared-namespace"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The default behavior when a tag with unknown namespace is used
in a JSP page (regular syntax) is to silently ignore it. If
set to true, then an error must be raised during the translation
time when an undeclared tag is used in a JSP page. Disabled
(false) by default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="taglibType">
<xsd:annotation>
<xsd:documentation>
The taglibType defines the syntax for declaring in
the deployment descriptor that a tag library is
available to the application. This can be done
to override implicit map entries from TLD files and
from the container.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="taglib-uri"
type="javaee:string">
<xsd:annotation>
<xsd:documentation>
A taglib-uri element describes a URI identifying a
tag library used in the web application. The body
of the taglib-uri element may be either an
absolute URI specification, or a relative URI.
There should be no entries in web.xml with the
same taglib-uri value.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="taglib-location"
type="javaee:pathType">
<xsd:annotation>
<xsd:documentation>
the taglib-location element contains the location
(as a resource relative to the root of the web
application) where to find the Tag Library
Description file for the tag library.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
</xsd:schema>

272
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/webapp/WEB-INF/xsd/web-app_3_0.xsd
View File

@ -1,272 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema xmlns="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://java.sun.com/xml/ns/javaee"
xmlns:javaee="http://java.sun.com/xml/ns/javaee"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
elementFormDefault="qualified"
attributeFormDefault="unqualified"
version="3.0">
<xsd:annotation>
<xsd:documentation>
DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
Copyright 2003-2009 Sun Microsystems, Inc. All rights reserved.
The contents of this file are subject to the terms of either the
GNU General Public License Version 2 only ("GPL") or the Common
Development and Distribution License("CDDL") (collectively, the
"License"). You may not use this file except in compliance with
the License. You can obtain a copy of the License at
https://glassfish.dev.java.net/public/CDDL+GPL.html or
glassfish/bootstrap/legal/LICENSE.txt. See the License for the
specific language governing permissions and limitations under the
License.
When distributing the software, include this License Header
Notice in each file and include the License file at
glassfish/bootstrap/legal/LICENSE.txt. Sun designates this
particular file as subject to the "Classpath" exception as
provided by Sun in the GPL Version 2 section of the License file
that accompanied this code. If applicable, add the following
below the License Header, with the fields enclosed by brackets []
replaced by your own identifying information:
"Portions Copyrighted [year] [name of copyright owner]"
Contributor(s):
If you wish your version of this file to be governed by only the
CDDL or only the GPL Version 2, indicate your decision by adding
"[Contributor] elects to include this software in this
distribution under the [CDDL or GPL Version 2] license." If you
don't indicate a single choice of license, a recipient has the
option to distribute your version of this file under either the
CDDL, the GPL Version 2 or to extend the choice of license to its
licensees as provided above. However, if you add GPL Version 2
code and therefore, elected the GPL Version 2 license, then the
option applies only if the new code is made subject to such
option by the copyright holder.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
<![CDATA[[
This is the XML Schema for the Servlet 3.0 deployment descriptor.
The deployment descriptor must be named "WEB-INF/web.xml" in the
web application's war file. All Servlet deployment descriptors
must indicate the web application schema by using the Java EE
namespace:
http://java.sun.com/xml/ns/javaee
and by indicating the version of the schema by
using the version element as shown below:
<web-app xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="..."
version="3.0">
...
</web-app>
The instance documents may indicate the published version of
the schema using the xsi:schemaLocation attribute for Java EE
namespace with the following location:
http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd
]]>
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
The following conventions apply to all Java EE
deployment descriptor elements unless indicated otherwise.
- In elements that specify a pathname to a file within the
same JAR file, relative filenames (i.e., those not
starting with "/") are considered relative to the root of
the JAR file's namespace. Absolute filenames (i.e., those
starting with "/") also specify names in the root of the
JAR file's namespace. In general, relative names are
preferred. The exception is .war files where absolute
names are preferred for consistency with the Servlet API.
</xsd:documentation>
</xsd:annotation>
<xsd:include schemaLocation="web-common_3_0.xsd"/>
<!-- **************************************************** -->
<xsd:element name="web-app"
type="javaee:web-appType">
<xsd:annotation>
<xsd:documentation>
The web-app element is the root of the deployment
descriptor for a web application. Note that the sub-elements
of this element can be in the arbitrary order. Because of
that, the multiplicity of the elements of distributable,
session-config, welcome-file-list, jsp-config, login-config,
and locale-encoding-mapping-list was changed from "?" to "*"
in this schema. However, the deployment descriptor instance
file must not contain multiple elements of session-config,
jsp-config, and login-config. When there are multiple elements of
welcome-file-list or locale-encoding-mapping-list, the container
must concatenate the element contents. The multiple occurence
of the element distributable is redundant and the container
treats that case exactly in the same way when there is only
one distributable.
</xsd:documentation>
</xsd:annotation>
<xsd:unique name="web-common-servlet-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The servlet element contains the name of a servlet.
The name must be unique within the web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:servlet"/>
<xsd:field xpath="javaee:servlet-name"/>
</xsd:unique>
<xsd:unique name="web-common-filter-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The filter element contains the name of a filter.
The name must be unique within the web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:filter"/>
<xsd:field xpath="javaee:filter-name"/>
</xsd:unique>
<xsd:unique name="web-common-ejb-local-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The ejb-local-ref-name element contains the name of an EJB
reference. The EJB reference is an entry in the web
application's environment and is relative to the
java:comp/env context. The name must be unique within
the web application.
It is recommended that name is prefixed with "ejb/".
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:ejb-local-ref"/>
<xsd:field xpath="javaee:ejb-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-ejb-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The ejb-ref-name element contains the name of an EJB
reference. The EJB reference is an entry in the web
application's environment and is relative to the
java:comp/env context. The name must be unique within
the web application.
It is recommended that name is prefixed with "ejb/".
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:ejb-ref"/>
<xsd:field xpath="javaee:ejb-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-resource-env-ref-uniqueness">
<xsd:annotation>
<xsd:documentation>
The resource-env-ref-name element specifies the name of
a resource environment reference; its value is the
environment entry name used in the web application code.
The name is a JNDI name relative to the java:comp/env
context and must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:resource-env-ref"/>
<xsd:field xpath="javaee:resource-env-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-message-destination-ref-uniqueness">
<xsd:annotation>
<xsd:documentation>
The message-destination-ref-name element specifies the name of
a message destination reference; its value is the
environment entry name used in the web application code.
The name is a JNDI name relative to the java:comp/env
context and must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:message-destination-ref"/>
<xsd:field xpath="javaee:message-destination-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-res-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The res-ref-name element specifies the name of a
resource manager connection factory reference. The name
is a JNDI name relative to the java:comp/env context.
The name must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:resource-ref"/>
<xsd:field xpath="javaee:res-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-env-entry-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The env-entry-name element contains the name of a web
application's environment entry. The name is a JNDI
name relative to the java:comp/env context. The name
must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:env-entry"/>
<xsd:field xpath="javaee:env-entry-name"/>
</xsd:unique>
<xsd:key name="web-common-role-name-key">
<xsd:annotation>
<xsd:documentation>
A role-name-key is specified to allow the references
from the security-role-refs.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:security-role"/>
<xsd:field xpath="javaee:role-name"/>
</xsd:key>
<xsd:keyref name="web-common-role-name-references"
refer="javaee:web-common-role-name-key">
<xsd:annotation>
<xsd:documentation>
The keyref indicates the references from
security-role-ref to a specified role-name.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:servlet/javaee:security-role-ref"/>
<xsd:field xpath="javaee:role-link"/>
</xsd:keyref>
</xsd:element>
</xsd:schema>

1575
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/webapp/WEB-INF/xsd/web-common_3_0.xsd
View File

File diff suppressed because it is too large Load Diff

287
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/webapp/WEB-INF/xsd/xml.xsd
View File

@ -1,287 +0,0 @@
<?xml version='1.0'?>
<?xml-stylesheet href="../2008/09/xsd.xsl" type="text/xsl"?>
<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns ="http://www.w3.org/1999/xhtml"
xml:lang="en">
<xs:annotation>
<xs:documentation>
<div>
<h1>About the XML namespace</h1>
<div class="bodytext">
<p>
This schema document describes the XML namespace, in a form
suitable for import by other schema documents.
</p>
<p>
See <a href="http://www.w3.org/XML/1998/namespace.html">
http://www.w3.org/XML/1998/namespace.html</a> and
<a href="http://www.w3.org/TR/REC-xml">
http://www.w3.org/TR/REC-xml</a> for information
about this namespace.
</p>
<p>
Note that local names in this namespace are intended to be
defined only by the World Wide Web Consortium or its subgroups.
The names currently defined in this namespace are listed below.
They should not be used with conflicting semantics by any Working
Group, specification, or document instance.
</p>
<p>
See further below in this document for more information about <a
href="#usage">how to refer to this schema document from your own
XSD schema documents</a> and about <a href="#nsversioning">the
namespace-versioning policy governing this schema document</a>.
</p>
</div>
</div>
</xs:documentation>
</xs:annotation>
<xs:attribute name="lang">
<xs:annotation>
<xs:documentation>
<div>
<h3>lang (as an attribute name)</h3>
<p>
denotes an attribute whose value
is a language code for the natural language of the content of
any element; its value is inherited. This name is reserved
by virtue of its definition in the XML specification.</p>
</div>
<div>
<h4>Notes</h4>
<p>
Attempting to install the relevant ISO 2- and 3-letter
codes as the enumerated possible values is probably never
going to be a realistic possibility.
</p>
<p>
See BCP 47 at <a href="http://www.rfc-editor.org/rfc/bcp/bcp47.txt">
http://www.rfc-editor.org/rfc/bcp/bcp47.txt</a>
and the IANA language subtag registry at
<a href="http://www.iana.org/assignments/language-subtag-registry">
http://www.iana.org/assignments/language-subtag-registry</a>
for further information.
</p>
<p>
The union allows for the 'un-declaration' of xml:lang with
the empty string.
</p>
</div>
</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:union memberTypes="xs:language">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value=""/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="space">
<xs:annotation>
<xs:documentation>
<div>
<h3>space (as an attribute name)</h3>
<p>
denotes an attribute whose
value is a keyword indicating what whitespace processing
discipline is intended for the content of the element; its
value is inherited. This name is reserved by virtue of its
definition in the XML specification.</p>
</div>
</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:NCName">
<xs:enumeration value="default"/>
<xs:enumeration value="preserve"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="base" type="xs:anyURI"> <xs:annotation>
<xs:documentation>
<div>
<h3>base (as an attribute name)</h3>
<p>
denotes an attribute whose value
provides a URI to be used as the base for interpreting any
relative URIs in the scope of the element on which it
appears; its value is inherited. This name is reserved
by virtue of its definition in the XML Base specification.</p>
<p>
See <a
href="http://www.w3.org/TR/xmlbase/">http://www.w3.org/TR/xmlbase/</a>
for information about this attribute.
</p>
</div>
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="id" type="xs:ID">
<xs:annotation>
<xs:documentation>
<div>
<h3>id (as an attribute name)</h3>
<p>
denotes an attribute whose value
should be interpreted as if declared to be of type ID.
This name is reserved by virtue of its definition in the
xml:id specification.</p>
<p>
See <a
href="http://www.w3.org/TR/xml-id/">http://www.w3.org/TR/xml-id/</a>
for information about this attribute.
</p>
</div>
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attributeGroup name="specialAttrs">
<xs:attribute ref="xml:base"/>
<xs:attribute ref="xml:lang"/>
<xs:attribute ref="xml:space"/>
<xs:attribute ref="xml:id"/>
</xs:attributeGroup>
<xs:annotation>
<xs:documentation>
<div>
<h3>Father (in any context at all)</h3>
<div class="bodytext">
<p>
denotes Jon Bosak, the chair of
the original XML Working Group. This name is reserved by
the following decision of the W3C XML Plenary and
XML Coordination groups:
</p>
<blockquote>
<p>
In appreciation for his vision, leadership and
dedication the W3C XML Plenary on this 10th day of
February, 2000, reserves for Jon Bosak in perpetuity
the XML name "xml:Father".
</p>
</blockquote>
</div>
</div>
</xs:documentation>
</xs:annotation>
<xs:annotation>
<xs:documentation>
<div xml:id="usage" id="usage">
<h2><a name="usage">About this schema document</a></h2>
<div class="bodytext">
<p>
This schema defines attributes and an attribute group suitable
for use by schemas wishing to allow <code>xml:base</code>,
<code>xml:lang</code>, <code>xml:space</code> or
<code>xml:id</code> attributes on elements they define.
</p>
<p>
To enable this, such a schema must import this schema for
the XML namespace, e.g. as follows:
</p>
<pre>
&lt;schema . . .>
. . .
&lt;import namespace="http://www.w3.org/XML/1998/namespace"
schemaLocation="http://www.w3.org/2001/xml.xsd"/>
</pre>
<p>
or
</p>
<pre>
&lt;import namespace="http://www.w3.org/XML/1998/namespace"
schemaLocation="http://www.w3.org/2009/01/xml.xsd"/>
</pre>
<p>
Subsequently, qualified reference to any of the attributes or the
group defined below will have the desired effect, e.g.
</p>
<pre>
&lt;type . . .>
. . .
&lt;attributeGroup ref="xml:specialAttrs"/>
</pre>
<p>
will define a type which will schema-validate an instance element
with any of those attributes.
</p>
</div>
</div>
</xs:documentation>
</xs:annotation>
<xs:annotation>
<xs:documentation>
<div id="nsversioning" xml:id="nsversioning">
<h2><a name="nsversioning">Versioning policy for this schema document</a></h2>
<div class="bodytext">
<p>
In keeping with the XML Schema WG's standard versioning
policy, this schema document will persist at
<a href="http://www.w3.org/2009/01/xml.xsd">
http://www.w3.org/2009/01/xml.xsd</a>.
</p>
<p>
At the date of issue it can also be found at
<a href="http://www.w3.org/2001/xml.xsd">
http://www.w3.org/2001/xml.xsd</a>.
</p>
<p>
The schema document at that URI may however change in the future,
in order to remain compatible with the latest version of XML
Schema itself, or with the XML namespace itself. In other words,
if the XML Schema or XML namespaces change, the version of this
document at <a href="http://www.w3.org/2001/xml.xsd">
http://www.w3.org/2001/xml.xsd
</a>
will change accordingly; the version at
<a href="http://www.w3.org/2009/01/xml.xsd">
http://www.w3.org/2009/01/xml.xsd
</a>
will not change.
</p>
<p>
Previous dated (and unchanging) versions of this schema
document are at:
</p>
<ul>
<li><a href="http://www.w3.org/2009/01/xml.xsd">
http://www.w3.org/2009/01/xml.xsd</a></li>
<li><a href="http://www.w3.org/2007/08/xml.xsd">
http://www.w3.org/2007/08/xml.xsd</a></li>
<li><a href="http://www.w3.org/2004/10/xml.xsd">
http://www.w3.org/2004/10/xml.xsd</a></li>
<li><a href="http://www.w3.org/2001/03/xml.xsd">
http://www.w3.org/2001/03/xml.xsd</a></li>
</ul>
</div>
</div>
</xs:documentation>
</xs:annotation>
</xs:schema>

0
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/test/resources/.keep_hapi-fhir-jpaserver-example
View File

3
hapi-fhir-cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -16,7 +16,6 @@
<name>HAPI FHIR - Command Line Client - Base Project</name>
<modules>
<module>hapi-fhir-cli-jpaserver</module>
<module>hapi-fhir-cli-api</module>
<module>hapi-fhir-cli-app</module>
</modules>

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

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

125
hapi-fhir-converter/src/main/java/ca/uhn/hapi/converters/canonical/VersionCanonicalizer.java
View File

@ -19,11 +19,14 @@
*/
package ca.uhn.hapi.converters.canonical;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.util.HapiExtensions;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_40;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_14_40;
@ -41,10 +44,13 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_43_50;
import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseConformance;
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.IPrimitiveType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
@ -52,12 +58,17 @@ import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.PackageInformation;
import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.StructureDefinition;
import javax.annotation.Nonnull;
import java.util.Date;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -83,14 +94,16 @@ public class VersionCanonicalizer {
private static final BaseAdvisor_14_50 ADVISOR_14_50 = new BaseAdvisor_14_50(false);
private final IStrategy myStrategy;
private final FhirContext myContext;
public VersionCanonicalizer(FhirContext theTargetContext) {
this(theTargetContext.getVersion().getVersion());
public VersionCanonicalizer(FhirVersionEnum theTargetVersion) {
this(theTargetVersion.newContextCached());
}
@SuppressWarnings({"EnhancedSwitchMigration"})
public VersionCanonicalizer(FhirVersionEnum theTargetVersion) {
switch (theTargetVersion) {
public VersionCanonicalizer(FhirContext theTargetContext) {
myContext = theTargetContext;
FhirVersionEnum targetVersion = theTargetContext.getVersion().getVersion();
switch (targetVersion) {
case DSTU2:
myStrategy = new Dstu2Strategy(false);
break;
@ -113,10 +126,12 @@ public class VersionCanonicalizer {
myStrategy = new R5Strategy();
break;
default:
throw new IllegalStateException(Msg.code(193) + "Can't handle version: " + theTargetVersion);
throw new IllegalStateException(Msg.code(193) + "Can't handle version: " + targetVersion);
}
}
@SuppressWarnings({"EnhancedSwitchMigration"})
/**
* Canonical version: R5
@ -125,6 +140,13 @@ public class VersionCanonicalizer {
return myStrategy.capabilityStatementToCanonical(theCapabilityStatement);
}
/**
* Canonical version: R5
*/
public IBaseConformance capabilityStatementFromCanonical(CapabilityStatement theCapabilityStatement) {
return myStrategy.capabilityStatementFromCanonical(theCapabilityStatement);
}
/**
* Canonical version: R4
*/
@ -176,8 +198,39 @@ public class VersionCanonicalizer {
return myStrategy.conceptMapToCanonical(theConceptMap);
}
/**
* Canonical version: R5
* <p>
* Note that this method will look for any nonstandard resource types specified in
* {@literal SearchParameter.base} or {@literal SearchParameter.target} and move them into
* extensions with the URLs {@link HapiExtensions#EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE}
* and {@link HapiExtensions#EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE} respectively. If any
* nonstandard resource types are found, all resource types in the respective list are moved into
* the extension (including standard types) and the source list is cleared.
*/
public <T extends IBaseResource> SearchParameter searchParameterToCanonical(T theSearchParameter) {
return myStrategy.searchParameterToCanonical(theSearchParameter);
/*
* The R4 model allows custom types to be put into SearchParameter.base and
* SearchParameter.target because those fields use a simple CodeType. But
* in R5 it uses an Enumeration, so it's not actually possible to put custom
* resource types into those fields. This means that the version converter fails
* with an exception unless we remove those values from those fields before
* conversion. However, we don't want to affect the state of the originally
* passed in resource since that may affect other things. So, we clone
* it first. This is a pain in the butt, but there doesn't seem to be any
* better option.
*/
T input = myContext.newTerser().clone(theSearchParameter);
List<String> baseExtensionValues = extractNonStandardSearchParameterListAndClearSourceIfAnyArePresent(input, "base");
List<String> targetExtensionValues = extractNonStandardSearchParameterListAndClearSourceIfAnyArePresent(input, "target");
SearchParameter retVal = myStrategy.searchParameterToCanonical(input);
baseExtensionValues.forEach(t -> retVal.addExtension(HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE, new CodeType(t)));
targetExtensionValues.forEach(t -> retVal.addExtension(HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE, new CodeType(t)));
return retVal;
}
public IBaseResource searchParameterFromCanonical(SearchParameter theSearchParameter) {
@ -218,6 +271,28 @@ public class VersionCanonicalizer {
return myStrategy.codeSystemToValidatorCanonical(theResource);
}
@Nonnull
private List<String> extractNonStandardSearchParameterListAndClearSourceIfAnyArePresent(IBaseResource theSearchParameter, String theChildName) {
BaseRuntimeChildDefinition child = myContext.getResourceDefinition(theSearchParameter).getChildByName(theChildName);
List<IBase> baseList = child.getAccessor().getValues(theSearchParameter);
List<String> baseExtensionValues = baseList
.stream()
.filter(Objects::nonNull)
.filter(t -> t instanceof IPrimitiveType)
.map(t -> (IPrimitiveType<?>) t)
.map(IPrimitiveType::getValueAsString)
.filter(StringUtils::isNotBlank)
.collect(Collectors.toList());
if (baseExtensionValues.stream().allMatch(Enumerations.VersionIndependentResourceTypesAll::isValidCode)) {
baseExtensionValues.clear();
} else {
baseList.clear();
}
return baseExtensionValues;
}
private interface IStrategy {
CapabilityStatement capabilityStatementToCanonical(IBaseResource theCapabilityStatement);
@ -251,6 +326,8 @@ public class VersionCanonicalizer {
org.hl7.fhir.r5.model.CodeSystem codeSystemToValidatorCanonical(IBaseResource theResource);
IBaseResource searchParameterFromCanonical(SearchParameter theResource);
IBaseConformance capabilityStatementFromCanonical(CapabilityStatement theResource);
}
private static class Dstu2Strategy implements IStrategy {
@ -278,7 +355,7 @@ public class VersionCanonicalizer {
retVal.setSystem(coding.getSystem());
retVal.setDisplay(coding.getDisplay());
retVal.setVersion(coding.getVersion());
retVal.setUserSelected( ! coding.getUserSelectedElement().isEmpty() && coding.getUserSelected() );
retVal.setUserSelected(!coding.getUserSelectedElement().isEmpty() && coding.getUserSelected());
return retVal;
}
@ -407,6 +484,12 @@ public class VersionCanonicalizer {
return reencodeFromHl7Org(resource);
}
@Override
public IBaseConformance capabilityStatementFromCanonical(CapabilityStatement theResource) {
Resource converted = VersionConvertorFactory_10_50.convertResource(theResource, ADVISOR_10_50);
return (IBaseConformance) reencodeToHl7Org(converted);
}
private Resource reencodeToHl7Org(IBaseResource theInput) {
if (myHl7OrgStructures) {
return (Resource) theInput;
@ -504,6 +587,11 @@ public class VersionCanonicalizer {
public IBaseResource searchParameterFromCanonical(SearchParameter theResource) {
return VersionConvertorFactory_14_50.convertResource(theResource, ADVISOR_14_50);
}
@Override
public IBaseConformance capabilityStatementFromCanonical(CapabilityStatement theResource) {
return (IBaseConformance) VersionConvertorFactory_14_50.convertResource(theResource, ADVISOR_14_50);
}
}
private static class Dstu3Strategy implements IStrategy {
@ -587,6 +675,11 @@ public class VersionCanonicalizer {
public IBaseResource searchParameterFromCanonical(SearchParameter theResource) {
return VersionConvertorFactory_30_50.convertResource(theResource, ADVISOR_30_50);
}
@Override
public IBaseConformance capabilityStatementFromCanonical(CapabilityStatement theResource) {
return (IBaseConformance) VersionConvertorFactory_30_50.convertResource(theResource, ADVISOR_30_50);
}
}
private static class R4Strategy implements IStrategy {
@ -670,6 +763,11 @@ public class VersionCanonicalizer {
return VersionConvertorFactory_40_50.convertResource(theResource, ADVISOR_40_50);
}
@Override
public IBaseConformance capabilityStatementFromCanonical(CapabilityStatement theResource) {
return (IBaseConformance) VersionConvertorFactory_40_50.convertResource(theResource, ADVISOR_40_50);
}
}
private static class R4BStrategy implements IStrategy {
@ -761,8 +859,12 @@ public class VersionCanonicalizer {
return VersionConvertorFactory_43_50.convertResource(theResource, ADVISOR_43_50);
}
}
@Override
public IBaseConformance capabilityStatementFromCanonical(CapabilityStatement theResource) {
return (IBaseConformance) VersionConvertorFactory_43_50.convertResource(theResource, ADVISOR_43_50);
}
}
private static class R5Strategy implements IStrategy {
@ -846,6 +948,11 @@ public class VersionCanonicalizer {
return theResource;
}
@Override
public IBaseConformance capabilityStatementFromCanonical(CapabilityStatement theResource) {
return theResource;
}
}

63
hapi-fhir-converter/src/test/java/ca/uhn/hapi/converters/canonical/VersionCanonicalizerTest.java
View File

@ -2,12 +2,28 @@ package ca.uhn.hapi.converters.canonical;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.util.HapiExtensions;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Enumeration;
import org.hl7.fhir.r5.model.SearchParameter;
import org.junit.jupiter.api.Test;
import javax.annotation.Nonnull;
import java.util.List;
import java.util.stream.Collectors;
import static ca.uhn.fhir.util.ExtensionUtil.getExtensionPrimitiveValues;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.empty;
import static org.junit.jupiter.api.Assertions.assertEquals;
class VersionCanonicalizerTest {
@ -31,4 +47,51 @@ class VersionCanonicalizerTest {
assertEquals("http://foo", outputDstu2.getUrl());
}
@Test
public void testToCanonicalSearchParameter_NoCustomResourceType() {
// Setup
VersionCanonicalizer canonicalizer = new VersionCanonicalizer(FhirVersionEnum.R4);
org.hl7.fhir.r4.model.SearchParameter input = new org.hl7.fhir.r4.model.SearchParameter();
input.addBase("Patient");
input.addBase("Observation");
input.addTarget("Organization");
// Test
org.hl7.fhir.r5.model.SearchParameter actual = canonicalizer.searchParameterToCanonical(input);
// Verify
assertThat(actual.getBase().stream().map(Enumeration::getCode).collect(Collectors.toList()), contains("Patient", "Observation"));
assertThat(actual.getTarget().stream().map(Enumeration::getCode).collect(Collectors.toList()), contains("Organization"));
assertThat(getExtensionPrimitiveValues(actual, HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE), empty());
assertThat(getExtensionPrimitiveValues(actual, HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE), empty());
}
@Test
public void testToCanonicalSearchParameter_WithCustomResourceType() {
// Setup
VersionCanonicalizer canonicalizer = new VersionCanonicalizer(FhirVersionEnum.R4);
org.hl7.fhir.r4.model.SearchParameter input = new org.hl7.fhir.r4.model.SearchParameter();
input.addBase("Base1");
input.addBase("Base2");
input.addTarget("Target1");
input.addTarget("Target2");
// Test
org.hl7.fhir.r5.model.SearchParameter actual = canonicalizer.searchParameterToCanonical(input);
// Verify
assertThat(actual.getBase().stream().map(Enumeration::getCode).collect(Collectors.toList()), empty());
assertThat(actual.getTarget().stream().map(Enumeration::getCode).collect(Collectors.toList()), empty());
assertThat(getExtensionPrimitiveValues(actual, HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE), contains("Base1", "Base2"));
assertThat(getExtensionPrimitiveValues(actual, HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE), contains("Target1", "Target2"));
// Original shouldn't be modified
assertThat(input.getBase().stream().map(CodeType::getCode).toList(), contains("Base1", "Base2"));
assertThat(input.getTarget().stream().map(CodeType::getCode).toList(), contains("Target1", "Target2"));
}
}

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4727-final-r5.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 4727
title: "The FHIR R5 definitions have been upgraded to the final FHIR R5
release version."

9
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4727-remove-jpa-cli.yaml Normal file
View File

@ -0,0 +1,9 @@
---
type: remove
issue: 4727
title: "The HAPI FHIR CLI `run-server` command has been removed. This command
was used to launch a HAPI FHIR JPA Server instance. The
[hapi-fhir-jpaserver-starter](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/)
project has long since duplicated and improved on the CLI version of the
launcher, and maintaining both was been a maintenance burden. Users of the
CLI command are recommended to migrate to the starter project."

22
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/getting_started/versions.md
View File

@ -26,6 +26,28 @@ Note also that after the release of the FHIR DSTU2 specification, the FHIR
</tr>
</thead>
<tbody>
<tr>
<td>HAPI FHIR 6.6.0</td>
<td>JDK11</td>
<td class="versions-table-cell-empty"></td>
<td class="versions-table-cell-draft">1.0.2</td>
<td class="versions-table-cell-release">1.4.0</td>
<td class="versions-table-cell-draft">3.0.2</td>
<td class="versions-table-cell-draft">4.0.1</td>
<td class="versions-table-cell-draft">4.3.0</td>
<td class="versions-table-cell-draft">5.0.0</td>
</tr>
<tr>
<td>HAPI FHIR 6.4.0</td>
<td>JDK11</td>
<td class="versions-table-cell-empty"></td>
<td class="versions-table-cell-draft">1.0.2</td>
<td class="versions-table-cell-release">1.4.0</td>
<td class="versions-table-cell-draft">3.0.2</td>
<td class="versions-table-cell-draft">4.0.1</td>
<td class="versions-table-cell-draft">4.3.0</td>
<td class="versions-table-cell-release">5.0.0-ballot<span class="download-version-hash"><br/>9a044604c1</span></td>
</tr>
<tr>
<td>HAPI FHIR 6.2.0</td>
<td>JDK11</td>

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>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

7
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -426,6 +426,11 @@
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
</dependency>
<dependency>
<groupId>org.exparity</groupId>
<artifactId>hamcrest-date</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

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

@ -27,6 +27,7 @@ import ca.uhn.hapi.converters.canonical.VersionCanonicalizer;
import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.Enumeration;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.support.TransactionSynchronization;
import org.springframework.transaction.support.TransactionSynchronizationManager;
@ -70,7 +71,7 @@ public class JpaResourceDaoSearchParameter<T extends IBaseResource> extends Base
Boolean reindex = theResource != null ? CURRENTLY_REINDEXING.get(theResource) : null;
org.hl7.fhir.r5.model.SearchParameter searchParameter = myVersionCanonicalizer.searchParameterToCanonical(theResource);
List<String> base = theResource != null ? searchParameter.getBase().stream().map(CodeType::getCode).collect(Collectors.toList()) : null;
List<String> base = theResource != null ? searchParameter.getBase().stream().map(Enumeration::getCode).collect(Collectors.toList()) : null;
requestReindexForRelatedResources(reindex, base, theRequestDetails);
}

27
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportJobSchedulingHelperImplTest.java
View File

@ -32,6 +32,7 @@ import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import java.time.LocalDateTime;
import java.time.ZoneId;
import java.time.temporal.ChronoUnit;
import java.util.Calendar;
import java.util.Date;
import java.util.List;
@ -39,6 +40,8 @@ import java.util.Map;
import java.util.Optional;
import java.util.stream.IntStream;
import static org.exparity.hamcrest.date.DateMatchers.within;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyString;
@ -105,7 +108,7 @@ public class BulkDataExportJobSchedulingHelperImplTest {
jobInstances.get(0).setReport(null);
setupTestEnabledNoBinaries(expectedRetentionHours, jobInstances);
setupTestEnabledNoBinaries(jobInstances);
myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
@ -117,7 +120,7 @@ public class BulkDataExportJobSchedulingHelperImplTest {
}
final Date cutoffDate = myCutoffCaptor.getValue();
assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
assertThat(cutoffDate, within(1, ChronoUnit.MINUTES, computeDateFromConfig(expectedRetentionHours)));
}
@Test
@ -128,7 +131,7 @@ public class BulkDataExportJobSchedulingHelperImplTest {
jobInstances.get(0).setReport("{garbage}");
setupTestEnabledNoBinaries(expectedRetentionHours, jobInstances);
setupTestEnabledNoBinaries(jobInstances);
myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
@ -140,7 +143,7 @@ public class BulkDataExportJobSchedulingHelperImplTest {
}
final Date cutoffDate = myCutoffCaptor.getValue();
assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
assertThat(cutoffDate, within(1, ChronoUnit.MINUTES, computeDateFromConfig(expectedRetentionHours)));
}
@Test
@ -163,7 +166,7 @@ public class BulkDataExportJobSchedulingHelperImplTest {
}
final Date cutoffDate = myCutoffCaptor.getValue();
assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
assertThat(cutoffDate, within(1, ChronoUnit.MINUTES, computeDateFromConfig(expectedRetentionHours)));
}
@Test
@ -186,7 +189,7 @@ public class BulkDataExportJobSchedulingHelperImplTest {
}
final Date cutoffDate = myCutoffCaptor.getValue();
assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
assertThat(cutoffDate, within(1, ChronoUnit.MINUTES, computeDateFromConfig(expectedRetentionHours)));
}
@Test
@ -210,7 +213,7 @@ public class BulkDataExportJobSchedulingHelperImplTest {
final Date cutoffDate = myCutoffCaptor.getValue();
assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
assertThat(cutoffDate, within(1, ChronoUnit.MINUTES, computeDateFromConfig(expectedRetentionHours)));
}
@Test
@ -234,7 +237,7 @@ public class BulkDataExportJobSchedulingHelperImplTest {
final Date cutoffDate = myCutoffCaptor.getValue();
assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
assertThat(cutoffDate, within(1, ChronoUnit.MINUTES, computeDateFromConfig(expectedRetentionHours)));
}
@Test
@ -261,7 +264,7 @@ public class BulkDataExportJobSchedulingHelperImplTest {
final Date cutoffDate = myCutoffCaptor.getValue();
assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
assertThat(cutoffDate, within(1, ChronoUnit.MINUTES, computeDateFromConfig(expectedRetentionHours)));
}
@Nonnull
@ -280,8 +283,8 @@ public class BulkDataExportJobSchedulingHelperImplTest {
setupTest(true, theRetentionHours, theJobInstances, true);
}
private void setupTestEnabledNoBinaries(int theRetentionHours, List<JobInstance> theJobInstances) {
setupTest(true, theRetentionHours, theJobInstances, false);
private void setupTestEnabledNoBinaries(List<JobInstance> theJobInstances) {
setupTest(true, 1, theJobInstances, false);
}
private void setupTest(boolean theIsEnabled, int theRetentionHours, List<JobInstance> theJobInstances, boolean theIsEnableBinaryMocks) {
@ -296,11 +299,13 @@ public class BulkDataExportJobSchedulingHelperImplTest {
final Answer<List<JobInstance>> fetchInstancesAnswer = theInvocationOnMock -> {
final TransactionCallback<List<JobInstance>> transactionCallback = theInvocationOnMock.getArgument(0);
//noinspection DataFlowIssue
return transactionCallback.doInTransaction(null);
};
final Answer<Void> purgeExpiredJobsAnswer = theInvocationOnMock -> {
final TransactionCallback<Optional<JobInstance>> transactionCallback = theInvocationOnMock.getArgument(0);
//noinspection DataFlowIssue
transactionCallback.doInTransaction(null);
return null;
};

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -3,7 +3,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

83
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/registry/ReadOnlySearchParamCache.java
View File

@ -33,11 +33,15 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Stream;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
public class ReadOnlySearchParamCache {
// resourceName -> searchParamName -> searchparam
@ -91,51 +95,58 @@ public class ReadOnlySearchParamCache {
Set<String> resourceNames = theFhirContext.getResourceTypes();
IBaseBundle allSearchParameterBundle = null;
/*
* For R4/R4B we include a Bundle of SearchParameters from the core spec in
* hapi-fhir-validation-resources-r4/r4b
*
* For R5 we include the NPM core R5 packages in
* hapi-fhir-validation-resources-r5, so we get them from it
*/
List<IBaseResource> searchParams = null;
if (theFhirContext.getVersion().getVersion() == FhirVersionEnum.R4) {
allSearchParameterBundle = (IBaseBundle) theFhirContext.newJsonParser().parseResource(ClasspathUtil.loadResourceAsStream("org/hl7/fhir/r4/model/sp/search-parameters.json"));
IBaseBundle allSearchParameterBundle = (IBaseBundle) theFhirContext.newJsonParser().parseResource(ClasspathUtil.loadResourceAsStream("org/hl7/fhir/r4/model/sp/search-parameters.json"));
searchParams = BundleUtil.toListOfResources(theFhirContext, allSearchParameterBundle);
} else if (theFhirContext.getVersion().getVersion() == FhirVersionEnum.R4B) {
allSearchParameterBundle = (IBaseBundle) theFhirContext.newXmlParser().parseResource(ClasspathUtil.loadResourceAsStream("org/hl7/fhir/r4b/model/sp/search-parameters.xml"));
IBaseBundle allSearchParameterBundle = (IBaseBundle) theFhirContext.newXmlParser().parseResource(ClasspathUtil.loadResourceAsStream("org/hl7/fhir/r4b/model/sp/search-parameters.xml"));
searchParams = BundleUtil.toListOfResources(theFhirContext, allSearchParameterBundle);
} else if (theFhirContext.getVersion().getVersion() == FhirVersionEnum.R5) {
allSearchParameterBundle = (IBaseBundle) theFhirContext.newXmlParser().parseResource(ClasspathUtil.loadResourceAsStream("org/hl7/fhir/r5/model/sp/search-parameters.xml"));
searchParams = FhirContext.forR5Cached().getValidationSupport().fetchAllSearchParameters();
}
if (allSearchParameterBundle != null) {
// For each SearchParameter resource in the bundle of all search parameters defined in this version of FHIR
for (IBaseResource next : BundleUtil.toListOfResources(theFhirContext, allSearchParameterBundle)) {
RuntimeSearchParam nextCanonical = theCanonicalizer.canonicalizeSearchParameter(next);
searchParams = defaultIfNull(searchParams, Collections.emptyList());
for (IBaseResource next : searchParams) {
RuntimeSearchParam nextCanonical = theCanonicalizer.canonicalizeSearchParameter(next);
if (nextCanonical != null) {
if (nextCanonical != null) {
// Force status to ACTIVE - For whatever reason the R5 draft SPs ship with
// a status of DRAFT which means the server doesn't actually apply them.
// At least this was the case as of 2021-12-24 - JA
nextCanonical = new RuntimeSearchParam(
nextCanonical.getId(),
nextCanonical.getUri(),
nextCanonical.getName(),
nextCanonical.getDescription(),
nextCanonical.getPath(),
nextCanonical.getParamType(),
nextCanonical.getProvidesMembershipInCompartments(),
nextCanonical.getTargets(),
RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE,
nextCanonical.getComboSearchParamType(),
nextCanonical.getComponents(),
nextCanonical.getBase());
// Force status to ACTIVE - For whatever reason the R5 draft SPs ship with
// a status of DRAFT which means the server doesn't actually apply them.
// At least this was the case as of 2021-12-24 - JA
nextCanonical = new RuntimeSearchParam(
nextCanonical.getId(),
nextCanonical.getUri(),
nextCanonical.getName(),
nextCanonical.getDescription(),
nextCanonical.getPath(),
nextCanonical.getParamType(),
nextCanonical.getProvidesMembershipInCompartments(),
nextCanonical.getTargets(),
RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE,
nextCanonical.getComboSearchParamType(),
nextCanonical.getComponents(),
nextCanonical.getBase());
Collection<String> base = nextCanonical.getBase();
if (base.contains("Resource") || base.contains("DomainResource")) {
base = resourceNames;
}
Collection<String> base = nextCanonical.getBase();
if (base.contains("Resource") || base.contains("DomainResource")) {
base = resourceNames;
}
// Add it to our return value if permitted by the pattern parameters
for (String nextResourceName : base) {
ResourceSearchParams resourceSearchParams = retVal.myResourceNameToSpNameToSp.computeIfAbsent(nextResourceName, t -> new ResourceSearchParams(nextResourceName));
String nextParamName = nextCanonical.getName();
if (theSearchParamPatternsToInclude == null || searchParamMatchesAtLeastOnePattern(theSearchParamPatternsToInclude, nextResourceName, nextParamName)) {
resourceSearchParams.addSearchParamIfAbsent(nextParamName, nextCanonical);
}
// Add it to our return value if permitted by the pattern parameters
for (String nextResourceName : base) {
ResourceSearchParams resourceSearchParams = retVal.myResourceNameToSpNameToSp.computeIfAbsent(nextResourceName, t -> new ResourceSearchParams(nextResourceName));
String nextParamName = nextCanonical.getName();
if (theSearchParamPatternsToInclude == null || searchParamMatchesAtLeastOnePattern(theSearchParamPatternsToInclude, nextResourceName, nextParamName)) {
resourceSearchParams.addSearchParamIfAbsent(nextParamName, nextCanonical);
}
}
}

86
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/registry/SearchParameterCanonicalizer.java
View File

@ -27,36 +27,20 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.DatatypeUtil;
import ca.uhn.fhir.util.ExtensionUtil;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.PhoneticEncoderUtil;
import ca.uhn.fhir.util.*;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.SearchParameter;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.instance.model.api.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.*;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.startsWith;
import static org.apache.commons.lang3.StringUtils.*;
@Service
public class SearchParameterCanonicalizer {
@ -69,6 +53,16 @@ public class SearchParameterCanonicalizer {
myFhirContext = theFhirContext;
}
private static Collection<String> toStrings(Collection<? extends IPrimitiveType<String>> theBase) {
HashSet<String> retVal = new HashSet<>();
for (IPrimitiveType<String> next : theBase) {
if (isNotBlank(next.getValueAsString())) {
retVal.add(next.getValueAsString());
}
}
return retVal;
}
public RuntimeSearchParam canonicalizeSearchParameter(IBaseResource theSearchParameter) {
RuntimeSearchParam retVal;
switch (myFhirContext.getVersion().getVersion()) {
@ -266,7 +260,23 @@ public class SearchParameterCanonicalizer {
String name = terser.getSinglePrimitiveValueOrNull(theNextSp, "code");
String description = terser.getSinglePrimitiveValueOrNull(theNextSp, "description");
String path = terser.getSinglePrimitiveValueOrNull(theNextSp, "expression");
List<String> base = terser.getValues(theNextSp, "base", IPrimitiveType.class).stream().map(t -> t.getValueAsString()).collect(Collectors.toList());
List<String> base = terser
.getValues(theNextSp, "base", IPrimitiveType.class)
.stream()
.map(IPrimitiveType::getValueAsString)
.collect(Collectors.toList());
if (theNextSp instanceof IBaseHasExtensions) {
((IBaseHasExtensions) theNextSp)
.getExtension()
.stream()
.filter(t -> HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE.equals(t.getUrl()))
.filter(t -> t.getValue() instanceof IPrimitiveType)
.map(t -> ((IPrimitiveType<?>) t.getValue()))
.map(IPrimitiveType::getValueAsString)
.filter(StringUtils::isNotBlank)
.forEach(base::add);
}
RestSearchParameterTypeEnum paramType = null;
RuntimeSearchParam.RuntimeSearchParamStatusEnum status = null;
@ -314,7 +324,23 @@ public class SearchParameterCanonicalizer {
break;
}
Set<String> providesMembershipInCompartments = Collections.emptySet();
Set<String> targets = terser.getValues(theNextSp, "target", IPrimitiveType.class).stream().map(t -> t.getValueAsString()).collect(Collectors.toSet());
Set<String> targets = terser
.getValues(theNextSp, "target", IPrimitiveType.class)
.stream()
.map(IPrimitiveType::getValueAsString)
.collect(Collectors.toSet());
if (theNextSp instanceof IBaseHasExtensions) {
((IBaseHasExtensions) theNextSp)
.getExtension()
.stream()
.filter(t -> HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE.equals(t.getUrl()))
.filter(t -> t.getValue() instanceof IPrimitiveType)
.map(t -> ((IPrimitiveType<?>) t.getValue()))
.map(IPrimitiveType::getValueAsString)
.filter(StringUtils::isNotBlank)
.forEach(targets::add);
}
if (isBlank(name) || isBlank(path) || paramType == null) {
if ("_text".equals(name) || "_content".equals(name)) {
@ -356,7 +382,6 @@ public class SearchParameterCanonicalizer {
return new RuntimeSearchParam(id, uri, name, description, path, paramType, providesMembershipInCompartments, targets, status, unique, components, base);
}
/**
* Extracts any extensions from the resource and populates an extension field in the
*/
@ -396,22 +421,11 @@ public class SearchParameterCanonicalizer {
IPhoneticEncoder encoder = PhoneticEncoderUtil.getEncoder(stringValue);
if (encoder != null) {
theRuntimeSearchParam.setPhoneticEncoder(encoder);
}
else {
} else {
ourLog.error("Invalid PhoneticEncoderEnum value '" + stringValue + "'");
}
}
}
private static Collection<String> toStrings(Collection<? extends IPrimitiveType<String>> theBase) {
HashSet<String> retVal = new HashSet<>();
for (IPrimitiveType<String> next : theBase) {
if (isNotBlank(next.getValueAsString())) {
retVal.add(next.getValueAsString());
}
}
return retVal;
}
}

63
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/registry/SearchParameterCanonicalizerTest.java Normal file
View File

@ -0,0 +1,63 @@
package ca.uhn.fhir.jpa.searchparam.registry;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.hapi.converters.canonical.VersionCanonicalizer;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.SearchParameter;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.mockito.junit.jupiter.MockitoExtension;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ExtendWith(MockitoExtension.class)
public class SearchParameterCanonicalizerTest {
private static final Logger ourLog = LoggerFactory.getLogger(SearchParameterCanonicalizerTest.class);
@ParameterizedTest
@ValueSource(booleans = {false, true})
public void testCanonicalizeSearchParameterWithCustomType(boolean theConvertToR5) {
SearchParameter sp = new SearchParameter();
sp.setId("SearchParameter/meal-chef");
sp.setUrl("http://example.org/SearchParameter/meal-chef");
sp.addBase("Meal");
sp.addBase("Patient");
sp.setCode("chef");
sp.setType(Enumerations.SearchParamType.REFERENCE);
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setExpression("Meal.chef | Observation.subject");
sp.addTarget("Chef");
sp.addTarget("Observation");
IBaseResource searchParamToCanonicalize = sp;
SearchParameterCanonicalizer svc;
if (theConvertToR5) {
VersionCanonicalizer versionCanonicalizer = new VersionCanonicalizer(FhirContext.forR4Cached());
searchParamToCanonicalize = versionCanonicalizer.searchParameterToCanonical(sp);
FhirContext fhirContextR5 = FhirContext.forR5Cached();
ourLog.info("R5 Subscription: {}", fhirContextR5.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParamToCanonicalize));
svc = new SearchParameterCanonicalizer(fhirContextR5);
} else {
svc = new SearchParameterCanonicalizer(FhirContext.forR4Cached());
}
RuntimeSearchParam output = svc.canonicalizeSearchParameter(searchParamToCanonicalize);
assertEquals("chef", output.getName());
assertEquals(RestSearchParameterTypeEnum.REFERENCE, output.getParamType());
assertEquals(RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE, output.getStatus());
assertThat(output.getPathsSplit(), containsInAnyOrder("Meal.chef", "Observation.subject"));
assertThat(output.getBase(), containsInAnyOrder("Meal", "Patient"));
assertThat(output.getTargets(), contains("Chef", "Observation"));
}
}

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-dstu2/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-dstu3/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

3
hapi-fhir-jpaserver-test-r4/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -37,7 +37,6 @@
<dependency>
<groupId>org.exparity</groupId>
<artifactId>hamcrest-date</artifactId>
<version>2.0.7</version>
<exclusions>
<exclusion>
<artifactId>*</artifactId>

4
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCustomTypeR4Test.java
View File

@ -16,8 +16,10 @@ public class FhirResourceDaoCustomTypeR4Test extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCustomTypeR4Test.class);
@Override
@BeforeEach
public void before() {
public void before() throws Exception {
super.before();
myFhirContext.setDefaultTypeForProfile(CustomObservationR4.PROFILE, CustomObservationR4.class);
}

5
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ComboUniqueParamIT.java
View File

@ -854,6 +854,11 @@ public class FhirResourceDaoR4ComboUniqueParamIT extends BaseComboParamsR4Test {
createUniqueIndexCoverageBeneficiary();
runInTransaction(() -> {
List<ResourceIndexedComboStringUnique> uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
assertEquals(0, uniques.size(), uniques.toString());
});
executeReindex("Coverage?");
runInTransaction(() -> {

2
hapi-fhir-jpaserver-test-r4b/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-r5/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

3
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5CodeSystemTest.java
View File

@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import ca.uhn.fhir.jpa.test.Batch2JobHelper;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.Enumerations;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
@ -158,7 +159,7 @@ public class FhirResourceDaoR5CodeSystemTest extends BaseJpaR5Test {
private IIdType createLargeCodeSystem(String theVersion) {
CodeSystem cs = new CodeSystem();
cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
cs.setContent(Enumerations.CodeSystemContentMode.COMPLETE);
cs.setUrl("http://foo");
if (theVersion != null) {
cs.setVersion(theVersion);

2
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5SearchNoFtTest.java
View File

@ -259,7 +259,7 @@ public class FhirResourceDaoR5SearchNoFtTest extends BaseJpaR5Test {
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setType(Enumerations.SearchParamType.TOKEN);
sp.setExpression("Bundle.entry[0].resource.as(Composition).subject.resolve().as(Patient).identifier");
sp.addBase("Bundle");
sp.addBase(Enumerations.VersionIndependentResourceTypesAll.BUNDLE);
ourLog.info("SP: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(sp));
mySearchParameterDao.update(sp, mySrd);

3
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5ValueSetMultiVersionTest.java
View File

@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.ValueSet;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
@ -35,7 +36,7 @@ public class FhirResourceDaoR5ValueSetMultiVersionTest extends BaseJpaR5Test {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setVersion(theVersion);
codeSystem.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
codeSystem.setContent(Enumerations.CodeSystemContentMode.COMPLETE);
for (String codeSystemCode : theCodeSystemCodes) {
codeSystem.addConcept().setCode(codeSystemCode);
}

2
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/SearchParamExtractorR5Test.java
View File

@ -38,7 +38,7 @@ public class SearchParamExtractorR5Test {
appointment.setStart(new Date());
appointment.setEnd(new Date());
Appointment.AppointmentParticipantComponent participant = new Appointment.AppointmentParticipantComponent();
participant.setStatus(Enumerations.ParticipationStatus.ACCEPTED);
participant.setStatus(Appointment.ParticipationStatus.ACCEPTED);
appointment.setParticipant(Collections.singletonList(participant));

12
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/UpliftedRefchainsAndChainedSortingR5Test.java
View File

@ -154,10 +154,10 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setType(Enumerations.SearchParamType.REFERENCE);
sp.setExpression("Bundle.entry[0].resource.as(Composition)");
subjectSp.getBase().forEach(sp::addBase);
subjectSp.getTargets().forEach(sp::addTarget);
subjectSp.getBase().forEach(t->sp.addBase(Enumerations.VersionIndependentResourceTypesAll.fromCode(t)));
subjectSp.getTargets().forEach(t->sp.addTarget(Enumerations.VersionIndependentResourceTypesAll.fromCode(t)));
ourLog.info("SP: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(sp));
mySearchParameterDao.update(sp, mySrd);
mySearchParameterDao.create(sp, mySrd);
mySearchParamRegistry.forceRefresh();
@ -1063,9 +1063,9 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setType(Enumerations.SearchParamType.REFERENCE);
sp.setExpression(subjectSp.getPath());
subjectSp.getBase().forEach(sp::addBase);
subjectSp.getTargets().forEach(sp::addTarget);
mySearchParameterDao.update(sp, mySrd);
subjectSp.getBase().forEach(t->sp.addBase(Enumerations.VersionIndependentResourceTypesAll.fromCode(t)));
subjectSp.getTargets().forEach(t->sp.addTarget(Enumerations.VersionIndependentResourceTypesAll.fromCode(t)));
mySearchParameterDao.create(sp, mySrd);
mySearchParamRegistry.forceRefresh();
}

84
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5CodeSystemTest.java
View File

@ -42,7 +42,7 @@ public class ResourceProviderR5CodeSystemTest extends BaseResourceProviderR5Test
parentChildCs.setUrl(SYSTEM_PARENTCHILD);
parentChildCs.setName("Parent Child CodeSystem");
parentChildCs.setStatus(Enumerations.PublicationStatus.ACTIVE);
parentChildCs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
parentChildCs.setContent(Enumerations.CodeSystemContentMode.COMPLETE);
parentChildCs.setHierarchyMeaning(CodeSystem.CodeSystemHierarchyMeaning.ISA);
CodeSystem.ConceptDefinitionComponent parentA = parentChildCs.addConcept().setCode("ParentA").setDisplay("Parent A");
@ -193,47 +193,59 @@ public class ResourceProviderR5CodeSystemTest extends BaseResourceProviderR5Test
@Test
public void testLookupOperationByCodeAndSystemBuiltInCode() {
// First test with no version specified (should return the one and only version defined).
Parameters respParam = myClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("ACSN"))
.andParameter("system", new UriType("http://terminology.hl7.org/CodeSystem/v2-0203"))
.execute();
{
Parameters respParam = myClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("ACSN"))
.andParameter("system", new UriType("http://terminology.hl7.org/CodeSystem/v2-0203"))
.execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals("name", respParam.getParameter().get(0).getName());
assertEquals("v2.0203", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("version", respParam.getParameter().get(1).getName());
assertEquals("2.9", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(2).getName());
assertEquals("Accession ID", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
assertEquals("abstract", respParam.getParameter().get(3).getName());
assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
Parameters.ParametersParameterComponent param0 = respParam.getParameter().get(0);
assertEquals("name", param0.getName());
assertEquals("IdentifierType", ((StringType) param0.getValue()).getValue());
Parameters.ParametersParameterComponent param1 = respParam.getParameter().get(1);
assertEquals("version", param1.getName());
assertEquals("2.9.0", ((StringType) param1.getValue()).getValue());
Parameters.ParametersParameterComponent param2 = respParam.getParameter().get(2);
assertEquals("display", param2.getName());
assertEquals("Accession ID", ((StringType) param2.getValue()).getValue());
Parameters.ParametersParameterComponent param3 = respParam.getParameter().get(3);
assertEquals("abstract", param3.getName());
assertEquals(false, ((BooleanType) param3.getValue()).getValue());
}
// Repeat with version specified.
respParam = myClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("ACSN"))
.andParameter("system", new UriType("http://terminology.hl7.org/CodeSystem/v2-0203"))
.andParameter("version", new StringType("2.9"))
.execute();
{
Parameters respParam = myClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("ACSN"))
.andParameter("system", new UriType("http://terminology.hl7.org/CodeSystem/v2-0203"))
.andParameter("version", new StringType("2.9.0"))
.execute();
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals("name", respParam.getParameter().get(0).getName());
assertEquals("v2.0203", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("version", respParam.getParameter().get(1).getName());
assertEquals("2.9", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(2).getName());
assertEquals("Accession ID", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
assertEquals("abstract", respParam.getParameter().get(3).getName());
assertEquals(false, ((BooleanType) respParam.getParameter().get(3).getValue()).getValue());
Parameters.ParametersParameterComponent param0 = respParam.getParameter().get(0);
assertEquals("name", param0.getName());
assertEquals("IdentifierType", ((StringType) param0.getValue()).getValue());
Parameters.ParametersParameterComponent param1 = respParam.getParameter().get(1);
assertEquals("version", param1.getName());
assertEquals("2.9.0", ((StringType) param1.getValue()).getValue());
Parameters.ParametersParameterComponent param2 = respParam.getParameter().get(2);
assertEquals("display", param2.getName());
assertEquals("Accession ID", ((StringType) param2.getValue()).getValue());
Parameters.ParametersParameterComponent param3 = respParam.getParameter().get(3);
assertEquals("abstract", param3.getName());
assertEquals(false, ((BooleanType) param3.getValue()).getValue());
}
}

4
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5CodeSystemVersionedTest.java
View File

@ -52,7 +52,7 @@ public class ResourceProviderR5CodeSystemVersionedTest extends BaseResourceProvi
parentChildCs.setVersion("1");
parentChildCs.setName("Parent Child CodeSystem 1");
parentChildCs.setStatus(Enumerations.PublicationStatus.ACTIVE);
parentChildCs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
parentChildCs.setContent(Enumerations.CodeSystemContentMode.COMPLETE);
parentChildCs.setHierarchyMeaning(CodeSystem.CodeSystemHierarchyMeaning.ISA);
CodeSystem.ConceptDefinitionComponent parentA = parentChildCs.addConcept().setCode("ParentA").setDisplay("Parent A");
@ -68,7 +68,7 @@ public class ResourceProviderR5CodeSystemVersionedTest extends BaseResourceProvi
parentChildCs.setName("Parent Child CodeSystem 2");
parentChildCs.setUrl(SYSTEM_PARENTCHILD);
parentChildCs.setStatus(Enumerations.PublicationStatus.ACTIVE);
parentChildCs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
parentChildCs.setContent(Enumerations.CodeSystemContentMode.COMPLETE);
parentChildCs.setHierarchyMeaning(CodeSystem.CodeSystemHierarchyMeaning.ISA);
parentA = parentChildCs.addConcept().setCode("ParentA").setDisplay("Parent A v2");

2
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ValueSetTest.java
View File

@ -30,7 +30,7 @@ import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Bundle.HTTPVerb;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.Enumerations;

2
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ValueSetVersionedTest.java
View File

@ -20,7 +20,7 @@ import org.hl7.fhir.r4.model.codesystems.HttpVerb;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.CodeableConcept;

14
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/search/reindex/InstanceReindexServiceImplR5Test.java
View File

@ -72,7 +72,6 @@ public class InstanceReindexServiceImplR5Test extends BaseJpaR5Test {
.sorted()
.toList();
assertThat(indexInstances.toString(), indexInstances, contains(
"_profile NO_CHANGE Reference true",
"active NO_CHANGE Token true",
"address NO_CHANGE String true",
"address-city NO_CHANGE String true",
@ -80,8 +79,6 @@ public class InstanceReindexServiceImplR5Test extends BaseJpaR5Test {
"address-postalcode NO_CHANGE String true",
"address-state NO_CHANGE String true",
"address-use NO_CHANGE Token true",
"age NO_CHANGE Number true",
"birthOrderBoolean NO_CHANGE Token true",
"birthdate NO_CHANGE Date true",
"death-date NO_CHANGE Date true",
"email NO_CHANGE Token true",
@ -90,7 +87,6 @@ public class InstanceReindexServiceImplR5Test extends BaseJpaR5Test {
"identifier NO_CHANGE Token true",
"language NO_CHANGE Token true",
"link NO_CHANGE Reference true",
"mothersMaidenName NO_CHANGE String true",
"organization NO_CHANGE Reference true",
"part-agree NO_CHANGE Reference true",
"phone NO_CHANGE Token true",
@ -136,7 +132,7 @@ public class InstanceReindexServiceImplR5Test extends BaseJpaR5Test {
Parameters outcome = (Parameters) mySvc.reindexDryRun(new SystemRequestDetails(), id, null);
ourLog.info("Output:{}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
Parameters.ParametersParameterComponent index = findSingleIndex(outcome, ResearchStudy.SP_RECRUITMENTTARGET, "NumberIndexes");
Parameters.ParametersParameterComponent index = findSingleIndex(outcome, ResearchStudy.SP_RECRUITMENT_TARGET, "NumberIndexes");
assertEquals("NO_CHANGE", getPartValue("Action", index));
assertEquals("Number", getPartValue("Type", index));
assertEquals("3", getPartValue("Value", index));
@ -294,7 +290,7 @@ public class InstanceReindexServiceImplR5Test extends BaseJpaR5Test {
IIdType p1id = myPatientDao.create(p1, mySrd).getId().toUnqualifiedVersionless();
SearchParameter eyeColourSp = new SearchParameter();
eyeColourSp.addBase("Patient");
eyeColourSp.addBase(Enumerations.VersionIndependentResourceTypesAll.PATIENT);
eyeColourSp.setCode("eyecolour");
eyeColourSp.setType(Enumerations.SearchParamType.STRING);
eyeColourSp.setTitle("Eye Colour");
@ -326,7 +322,7 @@ public class InstanceReindexServiceImplR5Test extends BaseJpaR5Test {
sp.setCode("family");
sp.setExpression("Patient.name.family + '|'");
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.addBase("Patient");
sp.addBase(Enumerations.VersionIndependentResourceTypesAll.PATIENT);
mySearchParameterDao.update(sp, mySrd);
sp = new SearchParameter();
@ -335,14 +331,14 @@ public class InstanceReindexServiceImplR5Test extends BaseJpaR5Test {
sp.setCode("given");
sp.setExpression("Patient.name.given");
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.addBase("Patient");
sp.addBase(Enumerations.VersionIndependentResourceTypesAll.PATIENT);
mySearchParameterDao.update(sp, mySrd);
sp = new SearchParameter();
sp.setId("SearchParameter/patient-names-and-gender");
sp.setType(Enumerations.SearchParamType.COMPOSITE);
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.addBase("Patient");
sp.addBase(Enumerations.VersionIndependentResourceTypesAll.PATIENT);
sp.addComponent()
.setExpression("Patient")
.setDefinition("SearchParameter/patient-family");

10
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/subscription/SubscriptionTopicR5Test.java
View File

@ -31,14 +31,14 @@ public class SubscriptionTopicR5Test extends BaseSubscriptionsR5Test {
@Test
public void testRestHookSubscriptionTopicApplicationFhirJson() throws Exception {
// WIP SR4B test update, delete, etc
createEncounterSubscriptionTopic(Encounter.EncounterStatus.PLANNED, Encounter.EncounterStatus.COMPLETED, SubscriptionTopic.InteractionTrigger.CREATE);
createEncounterSubscriptionTopic(Enumerations.EncounterStatus.PLANNED, Enumerations.EncounterStatus.COMPLETED, SubscriptionTopic.InteractionTrigger.CREATE);
waitForRegisteredSubscriptionTopicCount(1);
Subscription subscription = createTopicSubscription(SUBSCRIPTION_TOPIC_TEST_URL);
waitForActivatedSubscriptionCount(1);
assertEquals(0, getSystemProviderCount());
Encounter sentEncounter = sendEncounterWithStatus(Encounter.EncounterStatus.COMPLETED, false);
Encounter sentEncounter = sendEncounterWithStatus(Enumerations.EncounterStatus.COMPLETED, false);
await().until(() -> getSystemProviderCount() > 0);
@ -50,7 +50,7 @@ public class SubscriptionTopicR5Test extends BaseSubscriptionsR5Test {
validateSubscriptionStatus(subscription, sentEncounter, ss);
Encounter encounter = (Encounter) resources.get(1);
assertEquals(Encounter.EncounterStatus.COMPLETED, encounter.getStatus());
assertEquals(Enumerations.EncounterStatus.COMPLETED, encounter.getStatus());
assertEquals(sentEncounter.getIdElement(), encounter.getIdElement());
}
@ -61,7 +61,7 @@ public class SubscriptionTopicR5Test extends BaseSubscriptionsR5Test {
return postSubscription(subscription);
}
private SubscriptionTopic createEncounterSubscriptionTopic(Encounter.EncounterStatus theFrom, Encounter.EncounterStatus theCurrent, SubscriptionTopic.InteractionTrigger... theInteractionTriggers) throws InterruptedException {
private SubscriptionTopic createEncounterSubscriptionTopic(Enumerations.EncounterStatus theFrom, Enumerations.EncounterStatus theCurrent, SubscriptionTopic.InteractionTrigger... theInteractionTriggers) throws InterruptedException {
SubscriptionTopic retval = new SubscriptionTopic();
retval.setUrl(SUBSCRIPTION_TOPIC_TEST_URL);
retval.setStatus(Enumerations.PublicationStatus.ACTIVE);
@ -78,7 +78,7 @@ public class SubscriptionTopicR5Test extends BaseSubscriptionsR5Test {
return retval;
}
private Encounter sendEncounterWithStatus(Encounter.EncounterStatus theStatus, boolean theExpectDelivery) throws InterruptedException {
private Encounter sendEncounterWithStatus(Enumerations.EncounterStatus theStatus, boolean theExpectDelivery) throws InterruptedException {
Encounter encounter = new Encounter();
encounter.setStatus(theStatus);

25
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestR5IT.java
View File

@ -675,29 +675,6 @@ public class RestHookTestR5IT extends BaseSubscriptionsR5Test {
return createSubscriptionTopic(subscriptionTopic);
}
@Test
public void testSubscriptionWithHeaders() throws Exception {
createSubscriptionTopic();
// Add some headers, and we'll also turn back to requested status for fun
Subscription subscription = createTopicSubscription();
waitForActivatedSubscriptionCount(1);
subscription.addHeader("X-Foo: FOO");
subscription.addHeader("X-Bar: BAR");
updateResource(subscription, false);
Observation sentObservation = sendObservationExpectDelivery();
// Should see 1 subscription notification
assertReceivedTransactionCount(1);
Observation receivedObservation = assertBundleAndGetObservation(subscription, sentObservation);
Assertions.assertEquals(Constants.CT_FHIR_JSON_NEW, getLastSystemProviderContentType());
assertThat(getLastSystemProviderHeaders(), hasItem("X-Foo: FOO"));
assertThat(getLastSystemProviderHeaders(), hasItem("X-Bar: BAR"));
}
@Test
public void testDisableSubscription() throws Exception {
createSubscriptionTopic();
@ -792,7 +769,7 @@ public class RestHookTestR5IT extends BaseSubscriptionsR5Test {
String criteria = "Observation?accessType=Catheter,PD%20Catheter";
SearchParameter sp = new SearchParameter();
sp.addBase("Observation");
sp.addBase(Enumerations.VersionIndependentResourceTypesAll.OBSERVATION);
sp.setCode("accessType");
sp.setType(Enumerations.SearchParamType.TOKEN);
sp.setExpression("Observation.extension('Observation#accessType')");

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

107
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/validation/Meal.java Normal file
View File

@ -0,0 +1,107 @@
/*-
* #%L
* Smile CDR - CDR
* %%
* Copyright (C) 2016 - 2023 Smile CDR, Inc.
* %%
* All rights reserved.
* #L%
*/
package ca.uhn.fhir.jpa.dao.validation;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.*;
import java.util.ArrayList;
import java.util.List;
/**
* This class is a custom resource class structure representing a Meal that was
* prepared by a chef (Patient).
*/
@ResourceDef(name = "Meal", profile = "http://example.org/StructureDefinition/Meal")
public class Meal extends DomainResource {
public static final Base[] EMPTY_BASE_ARRAY = new Base[0];
@Child(name = "identifier", min = 0, max = Child.MAX_UNLIMITED)
private List<Identifier> myIdentifier;
@Child(name = "name")
private StringType myName;
@Child(name = "chef", type = {Patient.class})
private Reference myChef;
/**
* By convention in HAPI FHIR, the getter for a repeating (List) field should create
* the list if it isn't already initialized.
*/
public List<Identifier> getIdentifier() {
if (myIdentifier == null) {
myIdentifier = new ArrayList<>();
}
return myIdentifier;
}
/**
* Every field annotated with {@link Child @Child} needs a getter
*/
public StringType getName() {
return myName;
}
/**
* Every non-List field annotated with {@link Child @Child} needs a setter too
*/
public void setName(StringType theName) {
myName = theName;
}
public Reference getChef() {
return myChef;
}
public void setChef(Reference theChef) {
myChef = theChef;
}
/**
* All resource classes must implement the {@literal copy()} method.
*/
@Override
public DomainResource copy() {
Meal retVal = new Meal();
super.copyValues(retVal);
for (Identifier next : getIdentifier()) {
retVal.getIdentifier().add(next.copy());
}
retVal.myName = myName != null ? myName.copy() : null;
retVal.myChef = myChef != null ? myChef.copy() : null;
return retVal;
}
@Override
public String fhirType() {
return "Meal";
}
@Override
public Base[] getProperty(int theHash, String theName, boolean theCheckValid) throws FHIRException {
switch (theName) {
case "identifier":
return myIdentifier != null ? myIdentifier.toArray(EMPTY_BASE_ARRAY) : EMPTY_BASE_ARRAY;
case "chef":
return myChef != null ? new Base[]{myChef} : EMPTY_BASE_ARRAY;
case "name":
return myName != null ? new Base[]{myName} : EMPTY_BASE_ARRAY;
default:
return super.getProperty(theHash, theName, theCheckValid);
}
}
@Override
public ResourceType getResourceType() {
return null;
}
}

64
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/validation/SearchParameterDaoValidatorTest.java Normal file
View File

@ -0,0 +1,64 @@
package ca.uhn.fhir.jpa.dao.validation;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.hapi.converters.canonical.VersionCanonicalizer;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.SearchParameter;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.Spy;
import org.mockito.junit.jupiter.MockitoExtension;
import static org.mockito.Mockito.mock;
@ExtendWith(MockitoExtension.class)
public class SearchParameterDaoValidatorTest {
@Spy
private FhirContext ourCtx = FhirContext.forR4Cached();
@Mock
private ISearchParamRegistry mySearchParamRegistry;
@Spy
private JpaStorageSettings myStorageSettings = new JpaStorageSettings();
@InjectMocks
private SearchParameterDaoValidator mySvc;
private VersionCanonicalizer myVersionCanonicalizer = new VersionCanonicalizer(ourCtx);
@Test
public void testValidateSubscription() {
SearchParameter sp = new SearchParameter();
sp.setId("SearchParameter/patient-eyecolour");
sp.setUrl("http://example.org/SearchParameter/patient-eyecolour");
sp.addBase("Patient");
sp.setCode("eyecolour");
sp.setType(Enumerations.SearchParamType.TOKEN);
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setExpression("Patient.extension('http://foo')");
sp.addTarget("Patient");
org.hl7.fhir.r5.model.SearchParameter canonicalSp = myVersionCanonicalizer.searchParameterToCanonical(sp);
mySvc.validate(canonicalSp);
}
@Test
public void testValidateSubscriptionWithCustomType() {
SearchParameter sp = new SearchParameter();
sp.setId("SearchParameter/meal-chef");
sp.setUrl("http://example.org/SearchParameter/meal-chef");
sp.addBase("Meal");
sp.setCode("chef");
sp.setType(Enumerations.SearchParamType.REFERENCE);
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setExpression("Meal.chef");
sp.addTarget("Chef");
org.hl7.fhir.r5.model.SearchParameter canonicalSp = myVersionCanonicalizer.searchParameterToCanonical(sp);
mySvc.validate(canonicalSp);
}
}

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-serviceloaders/hapi-fhir-caching-api/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

4
hapi-fhir-serviceloaders/hapi-fhir-caching-caffeine/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -21,7 +21,7 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-api</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
</dependency>
<dependency>

2
hapi-fhir-serviceloaders/hapi-fhir-caching-guava/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-serviceloaders/hapi-fhir-caching-testing/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<artifactId>hapi-deployable-pom</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.5.16-SNAPSHOT</version>
<version>6.5.17-SNAPSHOT</version>
</parent>

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