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Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
James Agnew 2016-05-27 10:27:27 -04:00
parent de1796d114 cd2af98064
commit b4de3aa5dd
19 changed files with 436 additions and 302 deletions
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2
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/BaseRuntimeElementDefinition.java
View File

@ -195,7 +195,7 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
public abstract ChildTypeEnum getChildType();
public enum ChildTypeEnum {
COMPOSITE_DATATYPE, PRIMITIVE_DATATYPE, RESOURCE, RESOURCE_REF, RESOURCE_BLOCK,
COMPOSITE_DATATYPE, PRIMITIVE_DATATYPE, RESOURCE, RESOURCE_BLOCK,
/**
* HAPI style.
*/

45
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeResourceReferenceDefinition.java
View File

@ -1,45 +0,0 @@
package ca.uhn.fhir.context;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Map;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseReference;
public class RuntimeResourceReferenceDefinition extends BaseRuntimeElementCompositeDefinition<IBaseReference> {
public RuntimeResourceReferenceDefinition(String theName, Class<? extends IBaseReference> theImplementingClass, boolean theStandardType) {
super(theName, theImplementingClass, theStandardType);
}
@Override
void sealAndInitialize(FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
super.sealAndInitialize(theContext, theClassToElementDefinitions);
}
@Override
public ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum getChildType() {
return ChildTypeEnum.RESOURCE_REF;
}
}

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -471,7 +471,6 @@ public class JsonParser extends BaseParser implements IParser {
}
break;
}
case RESOURCE_REF:
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
if (theChildName != null) {

211
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java
View File

@ -91,6 +91,7 @@ import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.IModelVisitor;
import ca.uhn.fhir.util.ReflectionUtil;
class ParserState<T> {
@ -128,16 +129,6 @@ class ParserState<T> {
}
}
private BaseState createResourceReferenceState(ParserState<T>.PreResourceState thePreResourceState, IBase newChildInstance) {
BaseState newState;
if (newChildInstance instanceof IBaseReference) {
newState = new ResourceReferenceStateHl7Org(thePreResourceState, (IBaseReference) newChildInstance);
} else {
newState = new ResourceReferenceStateHapi(thePreResourceState, (BaseResourceReferenceDt) newChildInstance);
}
return newState;
}
public void endingElement() throws DataFormatException {
myState.endingElement();
}
@ -159,31 +150,7 @@ class ParserState<T> {
}
private Object newContainedDt(IResource theTarget) {
Object newChildInstance;
try {
newChildInstance = theTarget.getStructureFhirVersionEnum().getVersionImplementation().getContainedType().newInstance();
} catch (InstantiationException e) {
throw new ConfigurationException("Failed to instantiate " + myContext.getVersion().getResourceReferenceType(), e);
} catch (IllegalAccessException e) {
throw new ConfigurationException("Failed to instantiate " + myContext.getVersion().getResourceReferenceType(), e);
}
return newChildInstance;
}
private IBase newResourceReferenceDt(IBaseResource theTarget) {
IBase newChildInstance;
try {
IFhirVersion version;
version = theTarget.getStructureFhirVersionEnum().getVersionImplementation();
newChildInstance = version.getResourceReferenceType().newInstance();
} catch (InstantiationException e) {
throw new ConfigurationException("Failed to instantiate " + myContext.getVersion().getResourceReferenceType(), e);
} catch (IllegalAccessException e) {
throw new ConfigurationException("Failed to instantiate " + myContext.getVersion().getResourceReferenceType(), e);
}
return newChildInstance;
return ReflectionUtil.newInstance(theTarget.getStructureFhirVersionEnum().getVersionImplementation().getContainedType());
}
@SuppressWarnings("unchecked")
@ -1539,13 +1506,6 @@ class ParserState<T> {
push(newState);
return;
}
case RESOURCE_REF: {
IBase newChildInstance = newResourceReferenceDt(myPreResourceState.myInstance);
myDefinition.getMutator().addValue(myParentInstance, newChildInstance);
BaseState newState = createResourceReferenceState(getPreResourceState(), newChildInstance);
push(newState);
return;
}
case PRIMITIVE_XHTML:
case RESOURCE:
case RESOURCE_BLOCK:
@ -1607,7 +1567,6 @@ class ParserState<T> {
}
}
@SuppressWarnings("unchecked")
@Override
public void endingElement() {
pop();
@ -1666,13 +1625,6 @@ class ParserState<T> {
push(newState);
return;
}
case RESOURCE_REF: {
IBase newChildInstance = newResourceReferenceDt(getPreResourceState().myInstance);
child.getMutator().addValue(myInstance, newChildInstance);
BaseState newState = createResourceReferenceState(getPreResourceState(), newChildInstance);
push(newState);
return;
}
case RESOURCE_BLOCK: {
RuntimeResourceBlockDefinition blockTarget = (RuntimeResourceBlockDefinition) target;
IBase newBlockInstance = blockTarget.newInstance();
@ -1846,18 +1798,6 @@ class ParserState<T> {
push(newState);
return;
}
case RESOURCE_REF: {
ICompositeType newChildInstance = (ICompositeType) newResourceReferenceDt(getPreResourceState().myInstance);
myExtension.setValue(newChildInstance);
if (myContext.getVersion().getVersion().isRi()) {
ParserState<T>.ResourceReferenceStateHl7Org newState = new ResourceReferenceStateHl7Org(getPreResourceState(), (IBaseReference) newChildInstance);
push(newState);
} else {
ResourceReferenceStateHapi newState = new ResourceReferenceStateHapi(getPreResourceState(), (BaseResourceReferenceDt) newChildInstance);
push(newState);
}
return;
}
case PRIMITIVE_XHTML:
case RESOURCE:
case RESOURCE_BLOCK:
@ -2304,7 +2244,6 @@ class ParserState<T> {
}
}
@SuppressWarnings("unchecked")
@Override
public void wereBack() {
super.wereBack();
@ -2347,7 +2286,6 @@ class ParserState<T> {
}
}
@SuppressWarnings("unchecked")
@Override
public void wereBack() {
super.wereBack();
@ -2460,151 +2398,6 @@ class ParserState<T> {
}
private class ResourceReferenceStateHapi extends BaseState {
private BaseResourceReferenceDt myInstance;
private ResourceReferenceSubState mySubState;
public ResourceReferenceStateHapi(PreResourceState thePreResourceState, BaseResourceReferenceDt theInstance) {
super(thePreResourceState);
myInstance = theInstance;
mySubState = ResourceReferenceSubState.INITIAL;
}
@Override
public void attributeValue(String theName, String theValue) throws DataFormatException {
if (!"value".equals(theName)) {
return;
}
switch (mySubState) {
case DISPLAY:
myInstance.getDisplayElement().setValue(theValue);
break;
case INITIAL:
throw new DataFormatException("Unexpected attribute: " + theValue);
case REFERENCE:
myInstance.getReference().setValue(theValue);
break;
}
}
@Override
public void endingElement() {
switch (mySubState) {
case INITIAL:
pop();
break;
case DISPLAY:
case REFERENCE:
mySubState = ResourceReferenceSubState.INITIAL;
}
}
@Override
public void enteringNewElement(String theNamespaceUri, String theLocalPart) throws DataFormatException {
switch (mySubState) {
case INITIAL:
if ("display".equals(theLocalPart)) {
mySubState = ResourceReferenceSubState.DISPLAY;
break;
} else if ("reference".equals(theLocalPart)) {
mySubState = ResourceReferenceSubState.REFERENCE;
break;
} else if ("resource".equals(theLocalPart)) {
mySubState = ResourceReferenceSubState.REFERENCE;
break;
}
//$FALL-THROUGH$
case DISPLAY:
case REFERENCE:
throw new DataFormatException("Unexpected element: " + theLocalPart);
}
}
@Override
protected IElement getCurrentElement() {
return myInstance;
}
}
private class ResourceReferenceStateHl7Org extends BaseState {
private IBaseReference myInstance;
private ResourceReferenceSubState mySubState;
public ResourceReferenceStateHl7Org(PreResourceState thePreResourceState, IBaseReference theInstance) {
super(thePreResourceState);
myInstance = theInstance;
mySubState = ResourceReferenceSubState.INITIAL;
}
@Override
public void attributeValue(String theName, String theValue) throws DataFormatException {
if (!"value".equals(theName)) {
return;
}
switch (mySubState) {
case DISPLAY:
myInstance.setDisplay(theValue);
break;
case INITIAL:
throw new DataFormatException("Unexpected attribute: " + theValue);
case REFERENCE:
myInstance.setReference(theValue);
break;
}
}
@Override
public void endingElement() {
switch (mySubState) {
case INITIAL:
pop();
break;
case DISPLAY:
case REFERENCE:
mySubState = ResourceReferenceSubState.INITIAL;
}
}
@Override
public void enteringNewElement(String theNamespaceUri, String theLocalPart) throws DataFormatException {
switch (mySubState) {
case INITIAL:
if ("display".equals(theLocalPart)) {
mySubState = ResourceReferenceSubState.DISPLAY;
break;
} else if ("reference".equals(theLocalPart)) {
mySubState = ResourceReferenceSubState.REFERENCE;
break;
} else if ("resource".equals(theLocalPart)) {
mySubState = ResourceReferenceSubState.REFERENCE;
break;
} else {
logAndSwallowUnexpectedElement(theLocalPart);
break;
}
case DISPLAY:
case REFERENCE:
logAndSwallowUnexpectedElement(theLocalPart);
break;
}
}
@Override
protected IBaseReference getCurrentElement() {
return myInstance;
}
}
private enum ResourceReferenceSubState {
DISPLAY, INITIAL, REFERENCE
}
private class ResourceStateHapi extends ElementCompositeState {
private IResource myInstance;

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java
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@ -531,7 +531,6 @@ public class XmlParser extends BaseParser implements IParser {
}
break;
}
case RESOURCE_REF:
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
theEventWriter.writeStartElement(childName);

11
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
View File

@ -422,16 +422,6 @@ public class FhirTerser {
case PRIMITIVE_DATATYPE:
// These are primitive types, so we don't need to visit their children
break;
case RESOURCE_REF:
IBaseReference resRefDt = (IBaseReference) theElement;
if (resRefDt.getReferenceElement().getValue() == null && resRefDt.getResource() != null) {
IBaseResource theResource = resRefDt.getResource();
if (theResource.getIdElement() == null || theResource.getIdElement().isEmpty() || theResource.getIdElement().isLocal()) {
BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
visit(theResource, null, def, theCallback, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
}
}
break;
case RESOURCE:
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
@ -575,7 +565,6 @@ public class FhirTerser {
case PRIMITIVE_DATATYPE:
// These are primitive types
break;
case RESOURCE_REF:
case RESOURCE:
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {

28
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/ReflectionUtilTest.java Normal file
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@ -0,0 +1,28 @@
package ca.uhn.fhir.util;
import static org.junit.Assert.*;
import java.util.ArrayList;
import java.util.List;
import org.junit.Test;
import ca.uhn.fhir.context.ConfigurationException;
public class ReflectionUtilTest {
@Test
public void testNewInstance() {
assertEquals(ArrayList.class, ReflectionUtil.newInstance(ArrayList.class).getClass());
}
@Test
public void testNewInstanceFail() {
try {
ReflectionUtil.newInstance(List.class);
fail();
} catch (ConfigurationException e) {
assertEquals("Failed to instantiate java.util.List", e.getMessage());
}
}
}

1
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/App.java
View File

@ -40,6 +40,7 @@ public class App {
ourCommands.add(new ValidateCommand());
ourCommands.add(new ValidationDataUploader());
ourCommands.add(new WebsocketSubscribeCommand());
ourCommands.add(new UploadTerminologyCommand());
Collections.sort(ourCommands);
}

159
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java Normal file
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@ -0,0 +1,159 @@
package ca.uhn.fhir.cli;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.fusesource.jansi.Ansi;
import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.dstu3.model.Attachment;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.omg.Dynamic.Parameter;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
import ca.uhn.fhir.model.dstu2.resource.Bundle.EntryRequest;
import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.valueset.BundleTypeEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.client.apache.GZipContentInterceptor;
import ca.uhn.fhir.rest.server.IVersionSpecificBundleFactory;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.ResourceReferenceInfo;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;
public class UploadTerminologyCommand extends BaseCommand {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(UploadTerminologyCommand.class);
@Override
public String getCommandDescription() {
//@formatter:off
return "Uploads a terminology package (e.g. a SNOMED CT ZIP file) to a HAPI JPA server. "
+ "Note that this command uses a custom operation that is only implemented on HAPI "
+ "JPA servers that have been configured to accept it.";
//@formatter:on
}
@Override
public String getCommandName() {
return "upload-terminology";
}
@Override
public Options getOptions() {
Options options = new Options();
Option opt;
addFhirVersionOption(options);
opt = new Option("t", "target", true, "Base URL for the target server (e.g. \"http://example.com/fhir\")");
opt.setRequired(true);
options.addOption(opt);
opt = new Option("u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URL + ")");
opt.setRequired(false);
options.addOption(opt);
opt = new Option("d", "data", true, "Local *.zip containing file to use to upload");
opt.setRequired(false);
options.addOption(opt);
return options;
}
@Override
public void run(CommandLine theCommandLine) throws Exception {
FhirContext ctx = getSpecVersionContext(theCommandLine);
String targetServer = theCommandLine.getOptionValue("t");
if (isBlank(targetServer)) {
throw new ParseException("No target server (-t) specified");
} else if (targetServer.startsWith("http") == false && targetServer.startsWith("file") == false) {
throw new ParseException("Invalid target server specified, must begin with 'http' or 'file'");
}
String termUrl = theCommandLine.getOptionValue("u");
if (isBlank(termUrl)) {
throw new ParseException("No URL provided");
}
String datafile = theCommandLine.getOptionValue("d");
if (isBlank(datafile)) {
throw new ParseException("No data file provided");
}
IGenericClient client = super.newClient(ctx, targetServer);
IBaseParameters inputParameters;
if (ctx.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
Parameters p = new Parameters();
p.addParameter().setName("url").setValue(new StringType(termUrl));
p.addParameter().setName("localfile").setValue(new StringType(datafile));
inputParameters = p;
} else {
throw new ParseException("This command does not support FHIR version " + ctx.getVersion().getVersion());
}
ourLog.info("Beginning upload - This may take a while...");
IBaseParameters response = client
.operation()
.onServer()
.named("upload-external-code-system")
.withParameters(inputParameters)
.execute();
ourLog.info("Upload complete!");
}
}

4
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -210,6 +210,10 @@
</overlays>
<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
<attachClasses>true</attachClasses>
<excludes>
WEB-INF/lib/Saxon-HE-*,
WEB-INF/lib/hapi-*
</excludes>
</configuration>
</plugin>

11
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.demo;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
@ -19,6 +20,7 @@ import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
@ -74,13 +76,14 @@ public class JpaServerDemo extends RestfulServer {
* The system provider implements non-resource-type methods, such as
* transaction, and global history.
*/
Object systemProvider;
List<Object> systemProvider = new ArrayList<Object>();
if (fhirVersion == FhirVersionEnum.DSTU1) {
systemProvider = myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class);
systemProvider.add(myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class));
} else if (fhirVersion == FhirVersionEnum.DSTU2) {
systemProvider = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
systemProvider.add(myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class));
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
systemProvider = myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
systemProvider.add(myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class));
systemProvider.add(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
} else {
throw new IllegalStateException();
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
View File

@ -38,8 +38,11 @@ import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.dstu3.SearchParamExtractorDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu3;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcDstu3;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvc;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
import ca.uhn.fhir.validation.IValidatorModule;
@ -51,6 +54,11 @@ public class BaseDstu3Config extends BaseConfig {
public IHapiTerminologySvcDstu3 terminologyService() {
return new HapiTerminologySvcDstu3();
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologyLoaderSvc terminologyLoaderService() {
return new TerminologyLoaderSvc();
}
@Bean
public HapiWorkerContext workerContext() {
@ -108,4 +116,12 @@ public class BaseDstu3Config extends BaseConfig {
return new SearchParamExtractorDstu3();
}
@Bean(autowire=Autowire.BY_TYPE)
public TerminologyUploaderProviderDstu3 terminologyUploaderProvider() {
TerminologyUploaderProviderDstu3 retVal = new TerminologyUploaderProviderDstu3();
retVal.setContext(defaultFhirContext());
return retVal;
}
}

39
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3.java
View File

@ -1,21 +1,34 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.output.LockableFileWriter;
import org.hl7.fhir.dstu3.model.Attachment;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.springframework.beans.factory.annotation.Autowired;
import ca.uhn.fhir.jpa.provider.BaseJpaProvider;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc.UploadStatistics;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
public class TerminologyUploaderProviderDstu3 extends BaseJpaProvider {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyUploaderProviderDstu3.class);
@Autowired
private IHapiTerminologyLoaderSvc myTerminologyLoaderSvc;
@ -27,24 +40,40 @@ public class TerminologyUploaderProviderDstu3 extends BaseJpaProvider {
public Parameters lookup(
HttpServletRequest theServletRequest,
@OperationParam(name="url", min=1) UriType theUrl,
@OperationParam(name="package", min=1) Attachment thePackage,
@OperationParam(name="package", min=0) Attachment thePackage,
@OperationParam(name="localfile", min=0) StringType theLocalFile,
RequestDetails theRequestDetails
) {
//@formatter:on
startRequest(theServletRequest);
try {
byte[] data = thePackage.getData();
String url = theUrl.getValueAsString();
byte[] data;
if (theLocalFile != null && isNotBlank(theLocalFile.getValue())) {
ourLog.info("Reading in local file: {}", theLocalFile.getValue());
try {
data = IOUtils.toByteArray(new FileInputStream(theLocalFile.getValue()));
} catch (IOException e) {
throw new InternalErrorException(e);
}
} else if (thePackage == null || thePackage.getData() == null || thePackage.getData().length == 0) {
throw new InvalidRequestException("No 'localfile' or 'package' parameter, or package had no data");
} else {
data = thePackage.getData();
}
String url = theUrl != null ? theUrl.getValueAsString() : null;
url = defaultString(url);
UploadStatistics stats;
if (IHapiTerminologyLoaderSvc.SCT_URL.equals(url)) {
myTerminologyLoaderSvc.loadSnomedCt(data, theRequestDetails);
stats = myTerminologyLoaderSvc.loadSnomedCt(data, theRequestDetails);
} else {
throw new InvalidRequestException("Unknown URL: " + url);
}
Parameters retVal = new Parameters();
retVal.addParameter().setName("conceptCount").setValue(new IntegerType(0));
retVal.addParameter().setName("conceptCount").setValue(new IntegerType(stats.getConceptCount()));
return retVal;
} finally {
endRequest(theServletRequest);

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

@ -5,7 +5,20 @@ import ca.uhn.fhir.rest.method.RequestDetails;
public interface IHapiTerminologyLoaderSvc {
String SCT_URL = "http://snomed.info/sct";
void loadSnomedCt(byte[] theZipBytes, RequestDetails theRequestDetails);
UploadStatistics loadSnomedCt(byte[] theZipBytes, RequestDetails theRequestDetails);
public static class UploadStatistics {
private int myConceptCount;
public int getConceptCount() {
return myConceptCount;
}
public UploadStatistics setConceptCount(int theConceptCount) {
myConceptCount = theConceptCount;
return this;
}
}
}

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

@ -131,7 +131,7 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
}
@Override
public void loadSnomedCt(byte[] theZipBytes, RequestDetails theRequestDetails) {
public UploadStatistics loadSnomedCt(byte[] theZipBytes, RequestDetails theRequestDetails) {
List<String> allFilenames = Arrays.asList(SCT_FILE_DESCRIPTION, SCT_FILE_RELATIONSHIP, SCT_FILE_CONCEPT);
Map<String, File> filenameToFile = new HashMap<String, File>();
@ -174,7 +174,7 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
ourLog.info("Beginning SNOMED CT processing");
try {
processSnomedCtFiles(filenameToFile, theRequestDetails);
return processSnomedCtFiles(filenameToFile, theRequestDetails);
} finally {
ourLog.info("Finished SNOMED CT file import, cleaning up temporary files");
for (File nextFile : filenameToFile.values()) {
@ -183,7 +183,7 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
}
}
void processSnomedCtFiles(Map<String, File> filenameToFile, RequestDetails theRequestDetails) {
UploadStatistics processSnomedCtFiles(Map<String, File> filenameToFile, RequestDetails theRequestDetails) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map<String, TermConcept> id2concept = new HashMap<String, TermConcept>();
final Map<String, TermConcept> code2concept = new HashMap<String, TermConcept>();
@ -211,6 +211,8 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
codeSystemVersion.getConcepts().addAll(rootConcepts.values());
myTermSvc.storeNewCodeSystemVersion(SCT_URL, codeSystemVersion, theRequestDetails);
return new UploadStatistics().setConceptCount(code2concept.size());
}
@VisibleForTesting

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java
View File

@ -15,6 +15,7 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.validation.ResultSeverityEnum;

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/BaseResourceProviderDstu3Test.java
View File

@ -50,6 +50,7 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
private static Server ourServer;
protected static String ourServerBase;
private static GenericWebApplicationContext ourWebApplicationContext;
private TerminologyUploaderProviderDstu3 myTerminologyUploaderProvider;
public BaseResourceProviderDstu3Test() {
super();
@ -78,7 +79,9 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
ourRestServer.getFhirContext().setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
ourRestServer.setPlainProviders(mySystemProvider);
myTerminologyUploaderProvider = myAppCtx.getBean(TerminologyUploaderProviderDstu3.class);
ourRestServer.setPlainProviders(mySystemProvider, myTerminologyUploaderProvider);
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(ourRestServer, mySystemDao, myDaoConfig);
confProvider.setImplementationDescription("THIS IS THE DESC");

157
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyProviderDstu3Test.java Normal file
View File

@ -0,0 +1,157 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static org.hamcrest.Matchers.greaterThan;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.Attachment;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
public class TerminologyProviderDstu3Test extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyProviderDstu3Test.class);
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Test
public void testUploadSct() throws Exception {
byte[] packageBytes = createSctZip();
//@formatter:off
Parameters respParam = ourClient
.operation()
.onServer()
.named("upload-external-code-system")
.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URL))
.andParameter("package", new Attachment().setData(packageBytes))
.execute();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertThat(((IntegerType)respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
}
@Test
public void testUploadSctLocalFile() throws Exception {
byte[] packageBytes = createSctZip();
File tempFile = File.createTempFile("tmp", ".zip");
tempFile.deleteOnExit();
FileOutputStream fos = new FileOutputStream(tempFile);
fos.write(packageBytes);
fos.close();
//@formatter:off
Parameters respParam = ourClient
.operation()
.onServer()
.named("upload-external-code-system")
.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URL))
.andParameter("localfile", new StringType(tempFile.getAbsolutePath()))
.execute();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertThat(((IntegerType)respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
}
@Test
public void testUploadInvalidUrl() throws Exception {
byte[] packageBytes = createSctZip();
//@formatter:off
try {
ourClient
.operation()
.onServer()
.named("upload-external-code-system")
.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URL + "FOO"))
.andParameter("package", new Attachment().setData(packageBytes))
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Unknown URL: http://snomed.info/sctFOO", e.getMessage());
}
//@formatter:on
}
@Test
public void testUploadMissingUrl() throws Exception {
byte[] packageBytes = createSctZip();
//@formatter:off
try {
ourClient
.operation()
.onServer()
.named("upload-external-code-system")
.withParameter(Parameters.class, "package", new Attachment().setData(packageBytes))
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Unknown URL: ", e.getMessage());
}
//@formatter:on
}
@Test
public void testUploadMissingPackage() throws Exception {
//@formatter:off
try {
ourClient
.operation()
.onServer()
.named("upload-external-code-system")
.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URL))
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: No 'localfile' or 'package' parameter, or package had no data", e.getMessage());
}
//@formatter:on
}
private byte[] createSctZip() throws IOException {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos);
List<String> inputNames = Arrays.asList("sct2_Concept_Full_INT_20160131.txt","sct2_Concept_Full-en_INT_20160131.txt","sct2_Description_Full-en_INT_20160131.txt","sct2_Identifier_Full_INT_20160131.txt","sct2_Relationship_Full_INT_20160131.txt","sct2_StatedRelationship_Full_INT_20160131.txt","sct2_TextDefinition_Full-en_INT_20160131.txt");
for (String nextName : inputNames) {
zos.putNextEntry(new ZipEntry("SnomedCT_Release_INT_20160131_Full/Terminology/" + nextName));
zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/sct/" + nextName)));
}
zos.close();
byte[] packageBytes = bos.toByteArray();
return packageBytes;
}
}

21
hapi-fhir-structures-dstu/src/main/java/ca/uhn/fhir/model/dstu/FhirDstu1.java
View File

@ -19,8 +19,8 @@ package ca.uhn.fhir.model.dstu;
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.join;
import java.io.InputStream;
import java.util.Collections;
@ -59,7 +59,6 @@ import ca.uhn.fhir.context.RuntimeCompositeDatatypeDefinition;
import ca.uhn.fhir.context.RuntimePrimitiveDatatypeDefinition;
import ca.uhn.fhir.context.RuntimeResourceBlockDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeResourceReferenceDefinition;
import ca.uhn.fhir.model.api.ICompositeDatatype;
import ca.uhn.fhir.model.api.IFhirVersion;
import ca.uhn.fhir.model.api.IPrimitiveDatatype;
@ -168,22 +167,6 @@ public class FhirDstu1 implements IFhirVersion {
private void fillName(StructureElement elem, BaseRuntimeElementDefinition<?> nextDef, String theServerBase) {
assert nextDef != null;
if (nextDef instanceof RuntimeResourceReferenceDefinition) {
// RuntimeResourceReferenceDefinition rr = (RuntimeResourceReferenceDefinition) nextDef;
// for (Class<? extends IBaseResource> next : rr.getResourceTypes()) {
// StructureElementDefinitionType type = elem.getDefinition().addType();
// type.getCode().setValue("ResourceReference");
//
// if (next != IResource.class) {
// @SuppressWarnings("unchecked")
// RuntimeResourceDefinition resDef = rr.getDefinitionForResourceType((Class<? extends IResource>) next);
// type.getProfile().setValueAsString(resDef.getResourceProfile(theServerBase));
// }
// }
return;
}
StructureElementDefinitionType type = elem.getDefinition().addType();
String name = nextDef.getName();