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

This commit is contained in:
James Agnew 2015-06-22 10:52:13 -04:00
parent 4b0e390366 f2f4b2a6ee
commit 9c89eb2dee
246 changed files with 2032 additions and 1451 deletions
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20
.travis.yml Normal file
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@ -0,0 +1,20 @@
# Use docker-based build environment (instead of openvz)
sudo: false
language: java
jdk:
- oraclejdk7
env:
global:
- MAVEN_OPTS="-XX:MaxPermSize=512m -Xmx4g"
cache:
directories:
- '$HOME/.m2/repository'
install: /bin/true
script:
- mvn -B clean install && cd hapi-fhir-cobertura && mvn -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID -P COBERTURA clean cobertura:cobertura coveralls:report
# - mvn -B clean install -Dcobertura.skip=true && mvn -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID -P COBERTURA clean cobertura:cobertura coveralls:report

4
README.md
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@ -3,6 +3,10 @@ hapi-fhir
HAPI FHIR - Java API for HL7 FHIR Clients and Servers
[![Build Status](https://travis-ci.org/jamesagnew/hapi-fhir.svg?branch=master)](https://travis-ci.org/jamesagnew/hapi-fhir)
[![Coverage Status](https://coveralls.io/repos/jamesagnew/hapi-fhir/badge.svg?branch=master)](https://coveralls.io/r/jamesagnew/hapi-fhir?branch=master)
[![Maven Central](https://maven-badges.herokuapp.com/maven-central/ca.uhn.hapi.fhir/hapi-fhir-base/badge.svg)](http://search.maven.org/#search|ga|1|ca.uhn.hapi.fhir)
Complete project documentation is available here:
http://jamesagnew.github.io/hapi-fhir/

16
examples/pom.xml
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@ -1,4 +1,5 @@
<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">
<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>
<parent>
@ -42,6 +43,19 @@
</dependency>
</dependencies>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>${maven_project_info_plugin_version}</version>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
</reporting>
<build>
<plugins>
<plugin>

14
examples/src/main/java/example/ClientExamples.java
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@ -19,7 +19,7 @@ public class ClientExamples {
@SuppressWarnings("unused")
public void createProxy() {
// START SNIPPET: proxy
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
// Set connections to access the network via the HTTP proxy at
// example.com : 8888
@ -36,7 +36,7 @@ public class ClientExamples {
@SuppressWarnings("unused")
public void createTimeouts() {
// START SNIPPET: timeouts
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
// Set how long to try and establish the initial TCP connection (in ms)
ctx.getRestfulClientFactory().setConnectTimeout(20 * 1000);
@ -53,7 +53,7 @@ public class ClientExamples {
public void createSecurity() {
// START SNIPPET: security
// Create a context and get the client factory so it can be configured
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
IRestfulClientFactory clientFactory = ctx.getRestfulClientFactory();
// Create an HTTP basic auth interceptor
@ -74,7 +74,7 @@ public class ClientExamples {
public void createCookie() {
// START SNIPPET: cookie
// Create a context and get the client factory so it can be configured
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
IRestfulClientFactory clientFactory = ctx.getRestfulClientFactory();
// Create a cookie interceptor. This cookie will have the name "mycookie" and
@ -95,7 +95,7 @@ public class ClientExamples {
public void createSecurityBearer() {
// START SNIPPET: securityBearer
// Create a context and get the client factory so it can be configured
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
IRestfulClientFactory clientFactory = ctx.getRestfulClientFactory();
// In reality the token would have come from an authorization server
@ -117,7 +117,7 @@ public class ClientExamples {
{
// START SNIPPET: logging
// Create a context and get the client factory so it can be configured
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
IRestfulClientFactory clientFactory = ctx.getRestfulClientFactory();
// Create a logging interceptor
@ -141,7 +141,7 @@ public class ClientExamples {
{
// START SNIPPET: clientConfig
// Create a client
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
IPatientClient client = ctx.newRestfulClient(IPatientClient.class, "http://localhost:9999/");
// Request JSON encoding from the server (_format=json)

2
examples/src/main/java/example/CompleteExampleClient.java
View File

@ -37,7 +37,7 @@ public class CompleteExampleClient {
public static void main(String[] args) throws IOException {
// Create a client factory
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
// Create the client
String serverBase = "http://fhir.healthintersections.com.au/open";

2
examples/src/main/java/example/ExampleRestfulClient.java
View File

@ -11,7 +11,7 @@ public class ExampleRestfulClient {
//START SNIPPET: client
public static void main(String[] args) {
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
String serverBase = "http://foo.com/fhirServerBase";
// Create the client

3
examples/src/main/java/example/Extensions.java
View File

@ -49,7 +49,8 @@ ExtensionDt givenExt = new ExtensionDt(false, "http://examples.com#moreext", new
given.addUndeclaredExtension(givenExt);
//END SNIPPET: resourceStringExtension
String output = new FhirContext().newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
FhirContext ctx = FhirContext.forDstu2();
String output = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
System.out.println(output);

2
examples/src/main/java/example/HttpProxy.java
View File

@ -39,7 +39,7 @@ public class HttpProxy {
.disableCookieManagement();
CloseableHttpClient httpClient = clientBuilder.build();
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
String serverBase = "http://spark.furore.com/fhir/";
ctx.getRestfulClientFactory().setHttpClient(httpClient);
IGenericClient client = ctx.newRestfulGenericClient(serverBase);

6
examples/src/main/java/example/MyPatientUse.java
View File

@ -65,19 +65,19 @@ patient.getImportantDates().add(new DateTimeDt("2014-01-26T11:11:11"));
patient.addName().addFamily("Smith").addGiven("John").addGiven("Quincy").addSuffix("Jr");
IParser p = new FhirContext().newXmlParser().setPrettyPrint(true);
IParser p = FhirContext.forDstu2().newXmlParser().setPrettyPrint(true);
String messageString = p.encodeResourceToString(patient);
System.out.println(messageString);
//END SNIPPET: patientUse
//START SNIPPET: patientParse
IParser parser = new FhirContext().newXmlParser();
IParser parser = FhirContext.forDstu2().newXmlParser();
MyPatient newPatient = parser.parseResource(MyPatient.class, messageString);
//END SNIPPET: patientParse
{
FhirContext ctx2 = new FhirContext();
FhirContext ctx2 = FhirContext.forDstu2();
RuntimeResourceDefinition def = ctx2.getResourceDefinition(patient);
System.out.println(ctx2.newXmlParser().setPrettyPrint(true).encodeResourceToString(def.toProfile()));
}

2
examples/src/main/java/example/Narrative.java
View File

@ -18,7 +18,7 @@ patient.addIdentifier().setSystem("urn:foo").setValue("7000135");
patient.addName().addFamily("Smith").addGiven("John").addGiven("Edward");
patient.addAddress().addLine("742 Evergreen Terrace").setCity("Springfield").setState("ZZ");
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
// Use the narrative generator
ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());

2
examples/src/main/java/example/NarrativeGenerator.java
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@ -16,7 +16,7 @@ public class NarrativeGenerator {
String propFile = "classpath:/com/foo/customnarrative.properties";
CustomThymeleafNarrativeGenerator gen = new CustomThymeleafNarrativeGenerator(propFile);
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
ctx.setNarrativeGenerator(gen);
//END SNIPPET: gen

2
examples/src/main/java/example/QuickUsage.java
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@ -30,7 +30,7 @@ patient.addName().addFamily("Smith").addGiven("John").addGiven("Q").addSuffix("J
patient.setGender(AdministrativeGenderEnum.MALE);
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
String xmlEncoded = ctx.newXmlParser().encodeResourceToString(patient);
String jsonEncoded = ctx.newJsonParser().encodeResourceToString(patient);

2
examples/src/main/java/example/ResourceRefs.java
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@ -6,7 +6,7 @@ import ca.uhn.fhir.model.dstu2.resource.Patient;
public class ResourceRefs {
private static FhirContext ourCtx = new FhirContext();
private static FhirContext ourCtx = FhirContext.forDstu2();
public static void main(String[] args) {
manualContained();

4
examples/src/main/java/example/RestfulPatientResourceProviderMore.java
View File

@ -933,7 +933,7 @@ public interface HistoryClient extends IBasicClient {
public void bbbbb() throws DataFormatException, IOException {
//START SNIPPET: metadataClientUsage
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
MetadataClient client = ctx.newRestfulClient(MetadataClient.class, "http://spark.furore.com/fhir");
Conformance metadata = client.getServerMetadata();
System.out.println(ctx.newXmlParser().encodeResourceToString(metadata));
@ -973,7 +973,7 @@ private interface IPatientClient extends IBasicClient
public void clientRead() {
//START SNIPPET: clientReadTags
IPatientClient client = new FhirContext().newRestfulClient(IPatientClient.class, "http://foo/fhir");
IPatientClient client = FhirContext.forDstu2().newRestfulClient(IPatientClient.class, "http://foo/fhir");
Patient patient = client.readPatient(new IdDt("1234"));
// Access the tag list

2
examples/src/main/java/example/ServerInterceptors.java
View File

@ -43,7 +43,7 @@ ExtensionDt ext2 = new ExtensionDt(false, "http://examples.com#moreext", new Str
given.addUndeclaredExtension(ext2);
//END SNIPPET: resourceStringExtension
String output = new FhirContext().newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
String output = FhirContext.forDstu2().newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
System.out.println(output);

2
examples/src/main/java/example/TagsExamples.java
View File

@ -20,7 +20,7 @@ public class TagsExamples {
@SuppressWarnings("unused")
public void getResourceTags() {
// START SNIPPET: getResourceTags
IGenericClient client = new FhirContext().newRestfulGenericClient("http://fhir.healthintersections.com.au/open");
IGenericClient client = FhirContext.forDstu2().newRestfulGenericClient("http://fhir.healthintersections.com.au/open");
Patient p = client.read(Patient.class, "1");
// Retrieve the list of tags from the resource metadata

4
examples/src/main/java/example/ValidatorExamples.java
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@ -37,7 +37,7 @@ public class ValidatorExamples {
public void validateResource() {
// START SNIPPET: basicValidation
// As always, you need a context
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
// Create and populate a new patient object
Patient p = new Patient();
@ -73,7 +73,7 @@ public class ValidatorExamples {
private static void validateFiles() throws Exception {
// START SNIPPET: validateFiles
FhirContext ctx = new FhirContext();
FhirContext ctx = FhirContext.forDstu2();
// Create a validator and configure it
FhirValidator validator = ctx.newValidator();

12
hapi-deployable-pom/pom.xml
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@ -18,14 +18,10 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>2.7</version>
<reportSets>
<reportSet>
<reports>
<report>scm</report>
</reports>
</reportSet>
</reportSets>
<version>${maven_project_info_plugin_version}</version>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>

38
hapi-fhir-base/pom.xml
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@ -160,7 +160,7 @@
<version>${junit_version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
@ -180,7 +180,7 @@
<id>SITE</id>
<reporting>
<plugins>
<!--
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
@ -192,16 +192,15 @@
</reportSet>
</reportSets>
<configuration>
<linkXRef>false</linkXRef>
<sourceDirectories>
<sourceDirectory>hapi-fhir-base/src/main/java</sourceDirectory>
</sourceDirectories>
</configuration>
</plugin>
<!--<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>findbugs-maven-plugin</artifactId>
<version>3.0.0</version>
<configuration>
</configuration>
</plugin>-->
-->
<!--<plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>findbugs-maven-plugin</artifactId>
<version>3.0.0</version> <configuration> </configuration> </plugin> -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jxr-plugin</artifactId>
@ -213,20 +212,11 @@
<report>jxr</report>
</reports>
</reportSet>
<!--
<reportSet>
<id>restful-server-example</id>
<reports>
<report>jxr</report>
</reports>
<configuration>
<sourcePath>../restful-server-example/src/main/java</sourcePath>
<destDir>${project.reporting.outputDirectory}/rse-xref</destDir>
<outputDirectory>tmp</outputDirectory>
<reportOutputDirectory>rse-xref</reportOutputDirectory>
</configuration>
</reportSet>
-->
<!-- <reportSet> <id>restful-server-example</id> <reports> <report>jxr</report>
</reports> <configuration> <sourcePath>../restful-server-example/src/main/java</sourcePath>
<destDir>${project.reporting.outputDirectory}/rse-xref</destDir> <outputDirectory>tmp</outputDirectory>
<reportOutputDirectory>rse-xref</reportOutputDirectory> </configuration>
</reportSet> -->
</reportSets>
</plugin>
<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-linkcheck-plugin</artifactId>

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/BaseRuntimeChildDatatypeDefinition.java
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@ -41,14 +41,15 @@ public abstract class BaseRuntimeChildDatatypeDefinition extends BaseRuntimeDecl
public BaseRuntimeChildDatatypeDefinition(Field theField, String theElementName, Child theChildAnnotation, Description theDescriptionAnnotation, Class<? extends IBase> theDatatype) {
super(theField, theChildAnnotation, theDescriptionAnnotation, theElementName);
assert Modifier.isInterface(theDatatype.getModifiers()) == false : "Type of " + theDatatype + " shouldn't be here"; // should use RuntimeChildAny
// should use RuntimeChildAny
assert Modifier.isInterface(theDatatype.getModifiers()) == false : "Type of " + theDatatype + " shouldn't be here";
myDatatype = theDatatype;
}
@Override
public String getChildNameByDatatype(Class<? extends IBase> theDatatype) {
Class<?> nextType = theDatatype;
while(nextType.equals(Object.class)==false) {
while (nextType.equals(Object.class) == false) {
if (myDatatype.equals(nextType)) {
return getElementName();
}
@ -60,7 +61,7 @@ public abstract class BaseRuntimeChildDatatypeDefinition extends BaseRuntimeDecl
@Override
public BaseRuntimeElementDefinition<?> getChildElementDefinitionByDatatype(Class<? extends IBase> theDatatype) {
Class<?> nextType = theDatatype;
while(nextType.equals(Object.class)==false) {
while (nextType.equals(Object.class) == false) {
if (myDatatype.equals(nextType)) {
return myElementDefinition;
}
@ -102,11 +103,10 @@ public abstract class BaseRuntimeChildDatatypeDefinition extends BaseRuntimeDecl
}
myCodeType = theType;
}
@Override
public String toString() {
return getClass().getSimpleName() + "[" + getElementName() + "]";
}
}

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

@ -32,7 +32,7 @@ public abstract class BaseRuntimeChildDefinition {
@Override
public String toString() {
return getClass().getSimpleName()+"[" + getElementName() + "]";
return getClass().getSimpleName() + "[" + getElementName() + "]";
}
public abstract BaseRuntimeElementDefinition<?> getChildByName(String theName);
@ -52,11 +52,11 @@ public abstract class BaseRuntimeChildDefinition {
}
public abstract String getElementName();
public abstract int getMax();
public abstract int getMin();
public interface IMutator {
void setValue(Object theTarget, IBase theValue);
@ -71,7 +71,7 @@ public abstract class BaseRuntimeChildDefinition {
return null;
}
// public String getExtensionUrl() {
// return null;
// }
// public String getExtensionUrl() {
// return null;
// }
}

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

@ -41,7 +41,7 @@ public abstract class BaseRuntimeElementCompositeDefinition<T extends IBase> ext
super(theName, theImplementingClass, theStandardType);
}
public void addChild(BaseRuntimeChildDefinition theNext) {
void addChild(BaseRuntimeChildDefinition theNext) {
if (theNext == null) {
throw new NullPointerException();
}

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

@ -30,9 +30,6 @@ import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseEnumFactory;
import ca.uhn.fhir.model.api.IValueSetEnumBinder;
public abstract class BaseRuntimeElementDefinition<T extends IBase> {

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

@ -40,8 +40,8 @@ import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.view.ViewGenerator;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParserErrorHandler;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.IParserErrorHandler;
import ca.uhn.fhir.parser.JsonParser;
import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.parser.XmlParser;

12
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ModelScanner.java
View File

@ -48,21 +48,21 @@ import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.ICompositeType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseDatatypeElement;
import org.hl7.fhir.instance.model.api.IBaseEnumFactory;
import org.hl7.fhir.instance.model.api.IBaseEnumeration;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IBaseXhtml;
import org.hl7.fhir.instance.model.api.IBaseDatatypeElement;
import org.hl7.fhir.instance.model.api.ICompositeType;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.INarrative;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import ca.uhn.fhir.model.api.CodeableConceptElement;
import ca.uhn.fhir.model.api.ExtensionDt;

81
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ProvidedResourceScanner.java
View File

@ -20,7 +20,8 @@ package ca.uhn.fhir.context;
* #L%
*/
import ca.uhn.fhir.model.api.IResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.model.api.annotation.ProvidesResources;
/**
@ -30,42 +31,48 @@ import ca.uhn.fhir.model.api.annotation.ProvidesResources;
* @see ca.uhn.fhir.model.api.annotation.ProvidesResources
*/
public class ProvidedResourceScanner {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ModelScanner.class);
private FhirContext myContext;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ProvidedResourceScanner.class);
private FhirContext myContext;
/**
* Constructor
* @param theContext - context whose resource definition list is to be updated by the scanner
*/
public ProvidedResourceScanner(FhirContext theContext) {
myContext = theContext;
}
/**
* Constructor
*
* @param theContext
* - context whose resource definition list is to be updated by the scanner
*/
public ProvidedResourceScanner(FhirContext theContext) {
myContext = theContext;
}
/**
* If {@code theProvider} is tagged with the {@code ProvidesResources} annotation, this method will add every resource listed
* by the {@code resources} method.
* <p>
* Notes:
* </p>
* <ul>
* <li>if {@code theProvider} isn't annotated with {@code resources} nothing is done; it's expected that most RestfulServers and
* ResourceProviders won't be annotated.</li>
* <li>any object listed in {@code resources} that doesn't implement {@code IResource} will generate a warning in the log.</li>
* </ul>
*
* @param theProvider - Normally, either a {@link ca.uhn.fhir.rest.server.RestfulServer} or a {@link ca.uhn.fhir.rest.server.IResourceProvider}
* that might be annotated with {@link ca.uhn.fhir.model.api.annotation.ProvidesResources}
*/
public void scanForProvidedResources(Object theProvider) {
ProvidesResources annotation = theProvider.getClass().getAnnotation(ProvidesResources.class);
if (annotation == null)
return;
for (Class clazz : annotation.resources()) {
if (IResource.class.isAssignableFrom(clazz)) {
myContext.getResourceDefinition(clazz);
} else {
ourLog.warn(clazz.getSimpleName() + "is not assignable from IResource");
}
}
}
/**
* If {@code theProvider} is tagged with the {@code ProvidesResources} annotation, this method will add every
* resource listed by the {@code resources} method.
* <p>
* Notes:
* </p>
* <ul>
* <li>if {@code theProvider} isn't annotated with {@code resources} nothing is done; it's expected that most
* RestfulServers and ResourceProviders won't be annotated.</li>
* <li>any object listed in {@code resources} that doesn't implement {@code IResource} will generate a warning in the
* log.</li>
* </ul>
*
* @param theProvider
* - Normally, either a {@link ca.uhn.fhir.rest.server.RestfulServer} or a
* {@link ca.uhn.fhir.rest.server.IResourceProvider} that might be annotated with
* {@link ca.uhn.fhir.model.api.annotation.ProvidesResources}
*/
@SuppressWarnings("unchecked")
public void scanForProvidedResources(Object theProvider) {
ProvidesResources annotation = theProvider.getClass().getAnnotation(ProvidesResources.class);
if (annotation == null)
return;
for (Class<?> clazz : annotation.resources()) {
if (IBaseResource.class.isAssignableFrom(clazz)) {
myContext.getResourceDefinition((Class<? extends IBaseResource>) clazz);
} else {
ourLog.warn(clazz.getSimpleName() + "is not assignable from IResource");
}
}
}
}

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

@ -31,7 +31,6 @@ import java.util.Map;
import java.util.Set;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseEnumeration;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.model.api.IResource;

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

@ -30,7 +30,6 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.base.composite.BaseContainedDt;
public class RuntimeChildDirectResource extends BaseRuntimeDeclaredChildDefinition {

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

@ -26,17 +26,14 @@ import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
public class RuntimeChildResourceDefinition extends BaseRuntimeDeclaredChildDefinition {

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

@ -20,7 +20,7 @@ package ca.uhn.fhir.context;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.*;
import org.hl7.fhir.instance.model.api.ICompositeType;

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

@ -20,7 +20,7 @@ package ca.uhn.fhir.context;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.util.Map;

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

@ -27,9 +27,9 @@ import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IAnyResource;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.annotation.ResourceDef;

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

@ -24,9 +24,9 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IAnyResource;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/IResource.java
View File

@ -20,6 +20,10 @@ package ca.uhn.fhir.model.api;
* #L%
*/
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import ca.uhn.fhir.model.base.composite.BaseContainedDt;
import ca.uhn.fhir.model.base.composite.BaseNarrativeDt;
@ -27,12 +31,6 @@ import ca.uhn.fhir.model.base.resource.ResourceMetadataMap;
import ca.uhn.fhir.model.primitive.CodeDt;
import ca.uhn.fhir.model.primitive.IdDt;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;
import org.hl7.fhir.instance.model.api.IIdType;
/**
* This interface is the parent interface for all FHIR Resource definition
* classes. Classes implementing this interface should be annotated

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

@ -26,6 +26,8 @@ import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
import java.util.Enumeration;
import net.sourceforge.cobertura.CoverageIgnore;
import org.hl7.fhir.instance.model.api.IBaseEnumFactory;
import ca.uhn.fhir.model.api.IElement;
@ -106,17 +108,21 @@ public @interface Child {
*/
Class<? extends IBaseEnumFactory<?>> enumFactory() default NoEnumFactory.class;
@CoverageIgnore
public static class NoEnumFactory implements IBaseEnumFactory<Enum<?>> {
@CoverageIgnore
private NoEnumFactory() {
// non instantiable
}
@CoverageIgnore
@Override
public Enum<?> fromCode(String theCodeString) throws IllegalArgumentException {
return null;
}
@CoverageIgnore
@Override
public String toCode(Enum<?> theCode) {
return null;

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/base/composite/BaseQuantityDt.java
View File

@ -34,7 +34,6 @@ import ca.uhn.fhir.model.primitive.DecimalDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.StringParam;
public abstract class BaseQuantityDt extends BaseIdentifiableElement implements ICompositeDatatype, IQueryParameterType {

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/valueset/QuantityCompararatorEnum.java
View File

@ -24,8 +24,10 @@ package ca.uhn.fhir.model.dstu.valueset;
import java.util.HashMap;
import java.util.Map;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.api.IValueSetEnumBinder;
@CoverageIgnore
public enum QuantityCompararatorEnum {
/**

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/valueset/RestfulOperationSystemEnum.java
View File

@ -24,8 +24,10 @@ package ca.uhn.fhir.model.dstu.valueset;
import java.util.HashMap;
import java.util.Map;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.api.IValueSetEnumBinder;
@CoverageIgnore
public enum RestfulOperationSystemEnum {
/**

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/valueset/RestfulOperationTypeEnum.java
View File

@ -24,8 +24,10 @@ package ca.uhn.fhir.model.dstu.valueset;
import java.util.HashMap;
import java.util.Map;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.api.IValueSetEnumBinder;
@CoverageIgnore
public enum RestfulOperationTypeEnum {
/**

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/valueset/SecurityEventObjectSensitivityEnum.java
View File

@ -24,8 +24,10 @@ package ca.uhn.fhir.model.dstu.valueset;
import java.util.HashMap;
import java.util.Map;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.api.IValueSetEnumBinder;
@CoverageIgnore
public enum SecurityEventObjectSensitivityEnum {
;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/valueset/SecurityEventObjectTypeEnum.java
View File

@ -24,8 +24,10 @@ package ca.uhn.fhir.model.dstu.valueset;
import java.util.HashMap;
import java.util.Map;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.api.IValueSetEnumBinder;
@CoverageIgnore
public enum SecurityEventObjectTypeEnum {
/**

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/BaseDateTimeDt.java
View File

@ -20,11 +20,7 @@ package ca.uhn.fhir.model.primitive;
* #L%
*/
import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.DAY;
import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.MILLI;
import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.MONTH;
import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.SECOND;
import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.YEAR;
import static ca.uhn.fhir.model.api.TemporalPrecisionEnum.*;
import java.text.ParseException;
import java.util.ArrayList;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/IdDt.java
View File

@ -29,8 +29,8 @@ import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import ca.uhn.fhir.model.api.IPrimitiveDatatype;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/PositiveIntDt.java
View File

@ -20,11 +20,13 @@ package ca.uhn.fhir.model.primitive;
* #L%
*/
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.api.annotation.DatatypeDef;
import ca.uhn.fhir.model.api.annotation.SimpleSetter;
import ca.uhn.fhir.parser.DataFormatException;
@DatatypeDef(name = "positiveInt")
@CoverageIgnore
public class PositiveIntDt extends IntegerDt {
/**

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/UnsignedIntDt.java
View File

@ -20,11 +20,13 @@ package ca.uhn.fhir.model.primitive;
* #L%
*/
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.api.annotation.DatatypeDef;
import ca.uhn.fhir.model.api.annotation.SimpleSetter;
import ca.uhn.fhir.parser.DataFormatException;
@DatatypeDef(name = "unsignedInt")
@CoverageIgnore
public class UnsignedIntDt extends IntegerDt {
/**

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/valueset/BundleEntrySearchModeEnum.java
View File

@ -24,8 +24,10 @@ package ca.uhn.fhir.model.valueset;
import java.util.HashMap;
import java.util.Map;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.api.IValueSetEnumBinder;
@CoverageIgnore
public enum BundleEntrySearchModeEnum {
MATCH("match", "http://hl7.org/fhir/search-entry-mode"),

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/valueset/BundleEntryTransactionMethodEnum.java
View File

@ -24,6 +24,7 @@ package ca.uhn.fhir.model.valueset;
import java.util.HashMap;
import java.util.Map;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.api.IValueSetEnumBinder;
/**
@ -31,6 +32,7 @@ import ca.uhn.fhir.model.api.IValueSetEnumBinder;
* on a DSTU2 server. It is preferably to use the new DSTU2 Bundle (<code>ca.uhn.fhir.model.dstu2.resource.Bundle</code>)
* for this purpose.
*/
@CoverageIgnore
public enum BundleEntryTransactionMethodEnum {
GET("GET", "http://hl7.org/fhir/http-verb"),

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/valueset/BundleTypeEnum.java
View File

@ -24,8 +24,10 @@ package ca.uhn.fhir.model.valueset;
import java.util.HashMap;
import java.util.Map;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.api.IValueSetEnumBinder;
@CoverageIgnore
public enum BundleTypeEnum {
TRANSACTION("transaction", "http://hl7.org/fhir/bundle-type"),

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/view/ViewGenerator.java
View File

@ -32,7 +32,6 @@ import ca.uhn.fhir.context.RuntimeChildDeclaredExtensionDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.api.BaseElement;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IElement;
import ca.uhn.fhir.model.api.IResource;
public class ViewGenerator {

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative/BaseThymeleafNarrativeGenerator.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.narrative;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.io.File;
import java.io.FileInputStream;
@ -292,6 +292,7 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
loadProperties(next);
}
} catch (IOException e) {
ourLog.info("Failed to load property file " + propFileName, e);
throw new ConfigurationException("Can not load property file " + propFileName, e);
}

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
View File

@ -38,14 +38,14 @@ import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IDomainResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;

19
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -20,9 +20,7 @@ package ca.uhn.fhir.parser;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.io.IOException;
import java.io.Reader;
@ -50,11 +48,8 @@ import javax.json.stream.JsonGeneratorFactory;
import javax.json.stream.JsonParsingException;
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.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseBooleanDatatype;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
@ -63,8 +58,10 @@ import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions;
import org.hl7.fhir.instance.model.api.IBaseIntegerDatatype;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IBaseReference;
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 ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
@ -82,7 +79,6 @@ import ca.uhn.fhir.model.api.BaseBundle;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.BundleEntry;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IElement;
import ca.uhn.fhir.model.api.IIdentifiableElement;
import ca.uhn.fhir.model.api.IPrimitiveDatatype;
import ca.uhn.fhir.model.api.IResource;
@ -94,18 +90,13 @@ import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.base.composite.BaseContainedDt;
import ca.uhn.fhir.model.base.composite.BaseNarrativeDt;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
import ca.uhn.fhir.model.primitive.CodeDt;
import ca.uhn.fhir.model.primitive.DecimalDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.IntegerDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.model.primitive.XhtmlDt;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.util.ElementUtil;
import ca.uhn.fhir.util.UrlUtil;
/**
* This class is the FHIR JSON parser/encoder. Users should not interact with this class directly, but should use {@link FhirContext#newJsonParser()} to get an instance.

51
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java
View File

@ -91,7 +91,8 @@ import ca.uhn.fhir.util.PrettyPrintWriterWrapper;
import ca.uhn.fhir.util.XmlUtil;
/**
* This class is the FHIR XML parser/encoder. Users should not interact with this class directly, but should use {@link FhirContext#newXmlParser()} to get an instance.
* This class is the FHIR XML parser/encoder. Users should not interact with this class directly, but should use
* {@link FhirContext#newXmlParser()} to get an instance.
*/
public class XmlParser extends BaseParser implements IParser {
@ -110,7 +111,8 @@ public class XmlParser extends BaseParser implements IParser {
private boolean myPrettyPrint;
/**
* Do not use this constructor, the recommended way to obtain a new instance of the XML parser is to invoke {@link FhirContext#newXmlParser()}.
* Do not use this constructor, the recommended way to obtain a new instance of the XML parser is to invoke
* {@link FhirContext#newXmlParser()}.
*
* @param theParserErrorHandler
*/
@ -187,13 +189,11 @@ public class XmlParser extends BaseParser implements IParser {
}
for (@SuppressWarnings("unchecked")
Iterator<Attribute> iter = elem.getAttributes(); iter.hasNext();) {
@SuppressWarnings("unchecked")
Iterator<Attribute> attributes = elem.getAttributes();
for (Iterator<Attribute> iter = attributes; iter.hasNext();) {
Attribute next = iter.next();
// if
// (next.getName().getLocalPart().equals("value")) {
parserState.attributeValue(next.getName().getLocalPart(), next.getValue());
// }
}
} else if (nextEvent.isAttribute()) {
@ -446,8 +446,7 @@ public class XmlParser extends BaseParser implements IParser {
theEventWriter.close();
}
private void encodeChildElementToStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, IBase nextValue, String childName, BaseRuntimeElementDefinition<?> childDef,
String theExtensionUrl, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
private void encodeChildElementToStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, IBase nextValue, String childName, BaseRuntimeElementDefinition<?> childDef, String theExtensionUrl, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
if (nextValue == null || nextValue.isEmpty()) {
if (isChildContained(childDef, theIncludedResource)) {
// We still want to go in..
@ -502,9 +501,10 @@ public class XmlParser extends BaseParser implements IParser {
case CONTAINED_RESOURCE_LIST:
case CONTAINED_RESOURCES: {
/*
* Disable per #103 for (IResource next : value.getContainedResources()) { if (getContainedResources().getResourceId(next) != null) { continue; }
* theEventWriter.writeStartElement("contained"); encodeResourceToXmlStreamWriter(next, theEventWriter, true, fixContainedResourceId(next.getId().getValue()));
* theEventWriter.writeEndElement(); }
* Disable per #103 for (IResource next : value.getContainedResources()) { if
* (getContainedResources().getResourceId(next) != null) { continue; }
* theEventWriter.writeStartElement("contained"); encodeResourceToXmlStreamWriter(next, theEventWriter, true,
* fixContainedResourceId(next.getId().getValue())); theEventWriter.writeEndElement(); }
*/
for (IBaseResource next : getContainedResources().getContainedResources()) {
IIdType resourceId = getContainedResources().getResourceId(next);
@ -548,8 +548,7 @@ public class XmlParser extends BaseParser implements IParser {
}
private void encodeCompositeElementChildrenToStreamWriter(IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter, List<? extends BaseRuntimeChildDefinition> children,
boolean theIncludedResource) throws XMLStreamException, DataFormatException {
private void encodeCompositeElementChildrenToStreamWriter(IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter, List<? extends BaseRuntimeChildDefinition> children, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
for (BaseRuntimeChildDefinition nextChild : children) {
if (nextChild.getElementName().equals("extension") || nextChild.getElementName().equals("modifierExtension")) {
continue;
@ -586,7 +585,8 @@ public class XmlParser extends BaseParser implements IParser {
// RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
// String childName = nextChild.getChildNameByDatatype(child.getDatatype());
// BaseRuntimeElementDefinition<?> type = child.getChildByName(childName);
// encodeChildElementToStreamWriter(theResource, theEventWriter, narr2, childName, type, null, theIncludedResource);
// encodeChildElementToStreamWriter(theResource, theEventWriter, narr2, childName, type, null,
// theIncludedResource);
// continue;
// }
}
@ -594,8 +594,7 @@ public class XmlParser extends BaseParser implements IParser {
if (nextChild instanceof RuntimeChildContainedResources) {
if (!theIncludedResource) {
encodeChildElementToStreamWriter(theResource, theEventWriter, null, nextChild.getChildNameByDatatype(null), nextChild.getChildElementDefinitionByDatatype(null), null,
theIncludedResource);
encodeChildElementToStreamWriter(theResource, theEventWriter, null, nextChild.getChildNameByDatatype(null), nextChild.getChildElementDefinitionByDatatype(null), null, theIncludedResource);
}
} else {
@ -641,8 +640,7 @@ public class XmlParser extends BaseParser implements IParser {
}
}
private void encodeCompositeElementToStreamWriter(IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter, BaseRuntimeElementCompositeDefinition<?> theElementDefinition,
boolean theIncludedResource) throws XMLStreamException, DataFormatException {
private void encodeCompositeElementToStreamWriter(IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter, BaseRuntimeElementCompositeDefinition<?> theElementDefinition, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource);
encodeCompositeElementChildrenToStreamWriter(theResource, theElement, theEventWriter, theElementDefinition.getExtensions(), theIncludedResource);
encodeCompositeElementChildrenToStreamWriter(theResource, theElement, theEventWriter, theElementDefinition.getChildren(), theIncludedResource);
@ -665,8 +663,9 @@ public class XmlParser extends BaseParser implements IParser {
}
/**
* This is just to work around the fact that casting java.util.List<ca.uhn.fhir.model.api.ExtensionDt> to java.util.List<? extends org.hl7.fhir.instance.model.api.IBaseExtension<?, ?>> seems to be
* rejected by the compiler some of the time.
* This is just to work around the fact that casting java.util.List<ca.uhn.fhir.model.api.ExtensionDt> to
* java.util.List<? extends org.hl7.fhir.instance.model.api.IBaseExtension<?, ?>> seems to be rejected by the
* compiler some of the time.
*/
private <Q extends IBaseExtension<?, ?>> List<IBaseExtension<?, ?>> toBaseExtensionList(final List<Q> theList) {
List<IBaseExtension<?, ?>> retVal = new ArrayList<IBaseExtension<?, ?>>(theList.size());
@ -691,11 +690,10 @@ public class XmlParser extends BaseParser implements IParser {
}
}
private void encodeResourceToStreamWriterInDstu2Format(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter,
BaseRuntimeElementCompositeDefinition<?> resDef, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
private void encodeResourceToStreamWriterInDstu2Format(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter, BaseRuntimeElementCompositeDefinition<?> resDef, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
/*
* DSTU2 requires extensions to come in a specific spot within the encoded content - This is a bit of a messy way to make that happen, but hopefully this won't matter as much once we use the
* HL7 structures
* DSTU2 requires extensions to come in a specific spot within the encoded content - This is a bit of a messy way
* to make that happen, but hopefully this won't matter as much once we use the HL7 structures
*/
List<BaseRuntimeChildDefinition> preExtensionChildren = new ArrayList<BaseRuntimeChildDefinition>();
@ -885,8 +883,7 @@ public class XmlParser extends BaseParser implements IParser {
}
}
private void encodeUndeclaredExtensions(IBaseResource theResource, XMLStreamWriter theWriter, List<? extends IBaseExtension<?, ?>> theExtensions, String tagName, boolean theIncludedResource)
throws XMLStreamException, DataFormatException {
private void encodeUndeclaredExtensions(IBaseResource theResource, XMLStreamWriter theWriter, List<? extends IBaseExtension<?, ?>> theExtensions, String tagName, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
for (IBaseExtension<?, ?> next : theExtensions) {
if (next == null || (ElementUtil.isEmpty(next.getValue()) && next.getExtension().isEmpty())) {
continue;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/exceptions/FhirClientConnectionException.java
View File

@ -20,12 +20,14 @@ package ca.uhn.fhir.rest.client.exceptions;
* #L%
*/
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
/**
* Represents a failure by the HAPI FHIR Client to successfully communicate
* with a FHIR server, because of IO failures, incomprehensible response, etc.
*/
@CoverageIgnore
public class FhirClientConnectionException extends BaseServerResponseException {
private static final long serialVersionUID = 1L;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/exceptions/FhirClientInappropriateForServerException.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.rest.client.exceptions;
* #L%
*/
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
/**
@ -27,6 +28,7 @@ import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
* communicate with a server which is a valid FHIR server but is incompatible
* with this client for some reason.
*/
@CoverageIgnore
public class FhirClientInappropriateForServerException extends BaseServerResponseException {
private static final long serialVersionUID = 1L;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/exceptions/InvalidResponseException.java
View File

@ -20,8 +20,10 @@ package ca.uhn.fhir.rest.client.exceptions;
* #L%
*/
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
@CoverageIgnore
public class InvalidResponseException extends BaseServerResponseException {
private static final long serialVersionUID = 1L;

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

@ -25,10 +25,13 @@ import static org.apache.commons.lang3.StringUtils.*;
import java.io.IOException;
import java.io.Reader;
import net.sourceforge.cobertura.CoverageIgnore;
import org.apache.commons.io.IOUtils;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
@CoverageIgnore
public class NonFhirResponseException extends BaseServerResponseException {
private static final long serialVersionUID = 1L;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/TokenClientParam.java
View File

@ -1,6 +1,6 @@
package ca.uhn.fhir.rest.gclient;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.*;
import java.util.Arrays;
import java.util.List;

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseHttpClientInvocationWithContents.java
View File

@ -48,7 +48,6 @@ import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.IVersionSpecificBundleFactory;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.validation.FhirValidator;
/**
* @author James Agnew

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseMethodBinding.java
View File

@ -34,8 +34,6 @@ import java.util.List;
import java.util.Set;
import java.util.TreeSet;
import javax.servlet.ServletInputStream;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseResourceReturningMethodBinding.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.rest.method;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.io.IOException;
import java.io.Reader;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/ConditionalParamBinder.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.rest.method;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.lang.reflect.Method;
import java.util.Collection;

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/HistoryMethodBinding.java
View File

@ -20,8 +20,7 @@ package ca.uhn.fhir.rest.method;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.lang.reflect.Method;
import java.lang.reflect.Modifier;

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/HttpGetClientInvocation.java
View File

@ -29,7 +29,6 @@ import java.util.Map.Entry;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpRequestBase;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.rest.client.BaseHttpClientInvocation;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/UpdateMethodBinding.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.rest.method;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.lang.reflect.Method;
import java.util.Collections;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/NumberParam.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.rest.param;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.math.BigDecimal;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ParameterUtil.java
View File

@ -20,8 +20,6 @@ package ca.uhn.fhir.rest.param;
* #L%
*/
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collections;

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

@ -20,8 +20,8 @@ package ca.uhn.fhir.rest.param;
* #L%
*/
import static ca.uhn.fhir.rest.param.ParameterUtil.escape;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static ca.uhn.fhir.rest.param.ParameterUtil.*;
import static org.apache.commons.lang3.StringUtils.*;
import java.math.BigDecimal;
import java.util.List;

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ReferenceParam.java
View File

@ -20,8 +20,7 @@ package ca.uhn.fhir.rest.param;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import org.hl7.fhir.instance.model.api.IBaseResource;

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ResourceParameter.java
View File

@ -20,8 +20,7 @@ package ca.uhn.fhir.rest.param;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.io.ByteArrayInputStream;
import java.io.IOException;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/UriParam.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.rest.param;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.*;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.ToStringBuilder;

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/BundleInclusionRule.java
View File

@ -20,11 +20,11 @@ package ca.uhn.fhir.rest.server;
* #L%
*/
import java.util.Set;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.util.ResourceReferenceInfo;
import java.util.Set;
/**
* Created by Bill de Beaubien on 3/4/2015.
*

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/BundleProviders.java
View File

@ -25,7 +25,6 @@ import java.util.List;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.primitive.InstantDt;
/**

118
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/ResponseResourceList.java
View File

@ -1,118 +0,0 @@
package ca.uhn.fhir.rest.server;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2015 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.ArrayList;
import java.util.List;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseResource;
/**
* Used by {@link IBundleProvider} to provide a single page worth of results.
*
* If the server chooses to, it may return a different number of matching results to the number that the user requested.
* For example, if the client requested 100 results but the server decided to return only 10 (perhaps because they were
* very large), this value should be set to 10. Note that this count refers only to resources which are included in the
* indexes provided to {@link IBundleProvider#getResources(int, int)}, so it should not reflect any additional results
* added to the response as a result of _include parameters, OperationOutcome's etc.
*/
public class ResponseResourceList {
/**
* Singleton unmodifiable empty list
*/
public static final ResponseResourceList EMPTY = new EmptyResponseResourceList();
private List<IBaseResource> myIncludeResults;
private List<IBaseResource> myMatchResults;
/**
* Adds an "include" results. Include results are results which are added as a result of <code>_include</code>
* directives in search requests.
*/
public void addIncludeResults(IBaseResource theIncludeResult) {
if (myIncludeResults == null) {
myIncludeResults = new ArrayList<IBaseResource>();
}
myIncludeResults.add(theIncludeResult);
}
/**
* Adds a "match" result. A match result is a result added as a direct result of the operation in question. E.g. for
* a search invocation a match result would be a result which directly matched the search criteria. For a history
* invocation it would be a historical version of a resource or the current version.
*/
public void addMatchResult(IBaseResource theResource) {
Validate.notNull(theResource, "theResource must not be null");
if (myMatchResults == null) {
myMatchResults = new ArrayList<IBaseResource>();
}
myMatchResults.add(theResource);
}
public List<IBaseResource> getIncludeResults() {
return myIncludeResults;
}
public List<IBaseResource> getMatchResults() {
return myMatchResults;
}
/**
* Sets the "include" results. Include results are results which are added as a result of <code>_include</code>
* directives in search requests.
*/
public void setIncludeResults(List<IBaseResource> theIncludeResults) {
myIncludeResults = theIncludeResults;
}
/**
* Sets the "match" results. A match result is a result added as a direct result of the operation in question. E.g.
* for a search invocation a match result would be a result which directly matched the search criteria. For a
* history invocation it would be a historical version of a resource or the current version.
*/
public void setMatchResults(List<IBaseResource> theMatchResults) {
myMatchResults = theMatchResults;
}
private static final class EmptyResponseResourceList extends ResponseResourceList {
@Override
public void addIncludeResults(IBaseResource theIncludeResult) {
throw new UnsupportedOperationException();
}
@Override
public void addMatchResult(IBaseResource theResource) {
throw new UnsupportedOperationException();
}
@Override
public void setIncludeResults(List<IBaseResource> theIncludeResults) {
throw new UnsupportedOperationException();
}
@Override
public void setMatchResults(List<IBaseResource> theMatchResults) {
throw new UnsupportedOperationException();
}
}
}

29
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.rest.server;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.io.IOException;
import java.lang.annotation.Annotation;
@ -103,12 +103,18 @@ public class RestfulServer extends HttpServlet {
private boolean myUseBrowserFriendlyContentTypes;
/**
* Constructor
* Constructor. Note that if no {@link FhirContext} is passed in to the server (either through the constructor, or
* through {@link #setFhirContext(FhirContext)}) the server will determine which version of FHIR to support
* through classpath scanning. This is brittle, and it is highly recommended to explicitly specify
* a FHIR version.
*/
public RestfulServer() {
this(new FhirContext());
this(null);
}
/**
* Constructor
*/
public RestfulServer(FhirContext theCtx) {
myFhirContext = theCtx;
}
@ -200,7 +206,7 @@ public class RestfulServer extends HttpServlet {
int count = 0;
for (Method m : ReflectionUtil.getDeclaredMethods(clazz)) {
BaseMethodBinding<?> foundMethodBinding = BaseMethodBinding.bindMethod(m, myFhirContext, theProvider);
BaseMethodBinding<?> foundMethodBinding = BaseMethodBinding.bindMethod(m, getFhirContext(), theProvider);
if (foundMethodBinding == null) {
continue;
}
@ -220,7 +226,7 @@ public class RestfulServer extends HttpServlet {
if (resourceName == null) {
resourceBinding = myServerBinding;
} else {
RuntimeResourceDefinition definition = myFhirContext.getResourceDefinition(resourceName);
RuntimeResourceDefinition definition = getFhirContext().getResourceDefinition(resourceName);
if (myResourceNameToProvider.containsKey(definition.getName())) {
resourceBinding = myResourceNameToProvider.get(definition.getName());
} else {
@ -270,7 +276,7 @@ public class RestfulServer extends HttpServlet {
if (Modifier.isPublic(m.getModifiers())) {
ourLog.debug("Scanning public method: {}#{}", theSystemProvider.getClass(), m.getName());
BaseMethodBinding<?> foundMethodBinding = BaseMethodBinding.bindMethod(m, myFhirContext, theSystemProvider);
BaseMethodBinding<?> foundMethodBinding = BaseMethodBinding.bindMethod(m, getFhirContext(), theSystemProvider);
if (foundMethodBinding != null) {
if (foundMethodBinding instanceof ConformanceMethodBinding) {
myServerConformanceMethod = foundMethodBinding;
@ -318,6 +324,9 @@ public class RestfulServer extends HttpServlet {
* creating their own.
*/
public FhirContext getFhirContext() {
if (myFhirContext == null) {
myFhirContext = new FhirContext();
}
return myFhirContext;
}
@ -419,7 +428,7 @@ public class RestfulServer extends HttpServlet {
}
public IResourceProvider getServerProfilesProvider() {
return myFhirContext.getVersion().createServerProfilesProvider(this);
return getFhirContext().getVersion().createServerProfilesProvider(this);
}
/**
@ -462,7 +471,7 @@ public class RestfulServer extends HttpServlet {
NarrativeModeEnum narrativeMode = RestfulServerUtils.determineNarrativeMode(theRequest);
boolean respondGzip = theRequest.isRespondGzip();
IVersionSpecificBundleFactory bundleFactory = myFhirContext.newBundleFactory();
IVersionSpecificBundleFactory bundleFactory = getFhirContext().newBundleFactory();
Set<Include> includes = new HashSet<Include>();
String[] reqIncludes = theRequest.getServletRequest().getParameterValues(Constants.PARAM_INCLUDE);
@ -765,7 +774,7 @@ public class RestfulServer extends HttpServlet {
throw new NullPointerException("getResourceType() on class '" + nextProvider.getClass().getCanonicalName() + "' returned null");
}
String resourceName = myFhirContext.getResourceDefinition(resourceType).getName();
String resourceName = getFhirContext().getResourceDefinition(resourceType).getName();
if (typeToProvider.containsKey(resourceName)) {
throw new ServletException("Multiple resource providers return resource type[" + resourceName + "]: First[" + typeToProvider.get(resourceName).getClass().getCanonicalName()
+ "] and Second[" + nextProvider.getClass().getCanonicalName() + "]");
@ -792,7 +801,7 @@ public class RestfulServer extends HttpServlet {
Object confProvider = getServerConformanceProvider();
if (confProvider == null) {
confProvider = myFhirContext.getVersion().createServerConformanceProvider(this);
confProvider = getFhirContext().getVersion().createServerConformanceProvider(this);
}
findSystemMethods(confProvider);

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServerUtils.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.rest.server;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.io.IOException;
import java.io.OutputStreamWriter;

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

@ -1,5 +1,6 @@
package ca.uhn.fhir.rest.server.exceptions;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.rest.server.Constants;
/*
@ -25,6 +26,7 @@ import ca.uhn.fhir.rest.server.Constants;
/**
* Represents an <b>HTTP 401 Client Unauthorized</b> response, which means that the client needs to provide credentials, or has provided invalid credentials.
*/
@CoverageIgnore
public class AuthenticationException extends BaseServerResponseException {
public static final int STATUS_CODE = Constants.STATUS_HTTP_401_CLIENT_UNAUTHORIZED;

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

@ -1,5 +1,6 @@
package ca.uhn.fhir.rest.server.exceptions;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
import ca.uhn.fhir.rest.server.Constants;
@ -35,6 +36,7 @@ import ca.uhn.fhir.rest.server.Constants;
* Summary</a>.
* </p>
*/
@CoverageIgnore
public class ForbiddenOperationException extends BaseServerResponseException {
public static final int STATUS_CODE = Constants.STATUS_HTTP_403_FORBIDDEN;

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

@ -1,5 +1,6 @@
package ca.uhn.fhir.rest.server.exceptions;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
import ca.uhn.fhir.rest.server.Constants;
@ -39,6 +40,7 @@ import ca.uhn.fhir.rest.server.Constants;
*
* @see UnprocessableEntityException Which should be used for business level validation failures
*/
@CoverageIgnore
public class InternalErrorException extends BaseServerResponseException {
public static final int STATUS_CODE = Constants.STATUS_HTTP_500_INTERNAL_ERROR;

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

@ -1,5 +1,6 @@
package ca.uhn.fhir.rest.server.exceptions;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
import ca.uhn.fhir.rest.server.Constants;
@ -36,6 +37,7 @@ import ca.uhn.fhir.rest.server.Constants;
*
* @see UnprocessableEntityException Which should be used for business level validation failures
*/
@CoverageIgnore
public class InvalidRequestException extends BaseServerResponseException {
public static final int STATUS_CODE = Constants.STATUS_HTTP_400_BAD_REQUEST;

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

@ -1,5 +1,6 @@
package ca.uhn.fhir.rest.server.exceptions;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
import ca.uhn.fhir.rest.server.Constants;
@ -32,6 +33,7 @@ import ca.uhn.fhir.rest.server.Constants;
* Summary</a>.
* </p>
*/
@CoverageIgnore
public class NotImplementedOperationException extends BaseServerResponseException {
public static final int STATUS_CODE = Constants.STATUS_HTTP_501_NOT_IMPLEMENTED;

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

@ -1,5 +1,6 @@
package ca.uhn.fhir.rest.server.exceptions;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
import ca.uhn.fhir.rest.server.Constants;
@ -33,6 +34,7 @@ import ca.uhn.fhir.rest.server.Constants;
* Summary</a>.
* </p>
*/
@CoverageIgnore
public class NotModifiedException extends BaseServerResponseException {
public static final int STATUS_CODE = Constants.STATUS_HTTP_304_NOT_MODIFIED;

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

@ -20,6 +20,7 @@ package ca.uhn.fhir.rest.server.exceptions;
* #L%
*/
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.server.Constants;
@ -30,6 +31,7 @@ import ca.uhn.fhir.rest.server.Constants;
* be specified in an HTTP header, and none was.
*/
@SuppressWarnings("deprecation")
@CoverageIgnore
public class PreconditionFailedException extends ResourceVersionNotSpecifiedException {
@SuppressWarnings("hiding")
public static final int STATUS_CODE = Constants.STATUS_HTTP_412_PRECONDITION_FAILED;

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

@ -20,6 +20,7 @@ package ca.uhn.fhir.rest.server.exceptions;
* #L%
*/
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
@ -30,6 +31,7 @@ import ca.uhn.fhir.rest.server.Constants;
* Represents an <b>HTTP 410 Resource Gone</b> response, which geenerally
* indicates that the resource has been deleted
*/
@CoverageIgnore
public class ResourceGoneException extends BaseServerResponseException {
public static final int STATUS_CODE = Constants.STATUS_HTTP_410_GONE;

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

@ -20,6 +20,8 @@ package ca.uhn.fhir.rest.server.exceptions;
* #L%
*/
import net.sourceforge.cobertura.CoverageIgnore;
import org.hl7.fhir.instance.model.api.IIdType;
import ca.uhn.fhir.model.api.IResource;
@ -31,6 +33,7 @@ import ca.uhn.fhir.rest.server.Constants;
/**
* Represents an <b>HTTP 404 Resource Not Found</b> response, which means that the request is pointing to a resource that does not exist.
*/
@CoverageIgnore
public class ResourceNotFoundException extends BaseServerResponseException {
private static final long serialVersionUID = 1L;

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

@ -20,6 +20,7 @@ package ca.uhn.fhir.rest.server.exceptions;
* #L%
*/
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
import ca.uhn.fhir.rest.annotation.Delete;
import ca.uhn.fhir.rest.annotation.Update;
@ -30,6 +31,7 @@ import ca.uhn.fhir.rest.server.Constants;
* thrown in methods which accept a version (e.g. {@link Update}, {@link Delete})
* when the operation fails because of a version conflict as specified in the FHIR specification.
*/
@CoverageIgnore
public class ResourceVersionConflictException extends BaseServerResponseException {
public static final int STATUS_CODE = Constants.STATUS_HTTP_409_CONFLICT;
private static final long serialVersionUID = 1L;

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

@ -20,6 +20,7 @@ package ca.uhn.fhir.rest.server.exceptions;
* #L%
*/
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
import ca.uhn.fhir.rest.server.Constants;
@ -28,6 +29,7 @@ import ca.uhn.fhir.rest.server.Constants;
* strangely named and will be removed at some point.
*/
@Deprecated
@CoverageIgnore
public class ResourceVersionNotSpecifiedException extends BaseServerResponseException {
public static final int STATUS_CODE = Constants.STATUS_HTTP_412_PRECONDITION_FAILED;
private static final long serialVersionUID = 1L;

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

@ -1,5 +1,6 @@
package ca.uhn.fhir.rest.server.exceptions;
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
/*
@ -26,6 +27,7 @@ import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
* Exception for use when a response is received or being sent that does not correspond to any other exception type. An HTTP status code must be provided, and will be provided to the caller in the
* case of a server implementation.
*/
@CoverageIgnore
public class UnclassifiedServerFailureException extends BaseServerResponseException {
/**

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

@ -20,6 +20,7 @@ package ca.uhn.fhir.rest.server.exceptions;
* #L%
*/
import net.sourceforge.cobertura.CoverageIgnore;
import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
import ca.uhn.fhir.rest.server.Constants;
@ -32,6 +33,7 @@ import ca.uhn.fhir.rest.server.Constants;
*
* @see InvalidRequestException Which corresponds to an <b>HTTP 400 Bad Request</b> failure
*/
@CoverageIgnore
public class UnprocessableEntityException extends BaseServerResponseException {
private static final String DEFAULT_MESSAGE = "Unprocessable Entity";

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/ExceptionHandlingInterceptor.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.rest.server.interceptor;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.io.IOException;
import java.util.Map;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/InterceptorAdapter.java
View File

@ -26,8 +26,6 @@ import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import ca.uhn.fhir.rest.server.RestfulServer;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.model.api.Bundle;

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/IModelVisitor.java
View File

@ -20,6 +20,8 @@ package ca.uhn.fhir.util;
* #L%
*/
import java.util.List;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -28,8 +30,6 @@ import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
import java.util.List;
/**
* @see FhirTerser#visit(IBaseResource, IModelVisitor)
*/

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ResourceReferenceInfo.java
View File

@ -31,7 +31,6 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
/**
* Created by Bill de Beaubien on 2/26/2015.

411
hapi-fhir-cobertura/pom.xml Normal file
View File

@ -0,0 +1,411 @@
<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>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>1.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-cobertura</artifactId>
<packaging>jar</packaging>
<name>HAPI FHIR - Consolidated Test Project</name>
<dependencies>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>1.1-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu</artifactId>
<version>1.1-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>1.1-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>1.1-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>1.1-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>com.phloc</groupId>
<artifactId>phloc-schematron</artifactId>
<version>${phloc_schematron_version}</version>
</dependency>
<dependency>
<groupId>com.phloc</groupId>
<artifactId>phloc-commons</artifactId>
<version>${phloc_commons_version}</version>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
<version>${thymeleaf-version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>${slf4j_version}</version>
</dependency>
<!-- <dependency> <groupId>org.slf4j</groupId> <artifactId>slf4j-nop</artifactId>
<version>${slf4j_version}</version> </dependency> -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>${logback_version}</version>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>java-hamcrest</artifactId>
<version>${hamcrest_version}</version>
<scope>test</scope>
</dependency>
<!-- Test Database -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
<version>${derby_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>commons-dbcp</groupId>
<artifactId>commons-dbcp</artifactId>
<version>1.4</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.1.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
<version>${jetty_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<version>${jetty_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
<version>${jetty_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<version>${jetty_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
<version>${jetty_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.9.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.sf.json-lib</groupId>
<artifactId>json-lib</artifactId>
<version>2.4</version>
<classifier>jdk15</classifier>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.sf.json-lib</groupId>
<artifactId>json-lib</artifactId>
<version>2.4</version>
<classifier>jdk15-sources</classifier>
<scope>test</scope>
</dependency>
<dependency>
<groupId>directory-naming</groupId>
<artifactId>naming-java</artifactId>
<version>0.8</version>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>java-hamcrest</artifactId>
<version>${hamcrest_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${guava_version}</version>
</dependency>
<dependency>
<groupId>org.ebaysf.web</groupId>
<artifactId>cors-filter</artifactId>
<version>${ebay_cors_filter_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>xmlunit</groupId>
<artifactId>xmlunit</artifactId>
<version>${xmlunit_version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<properties>
</properties>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<configuration>
<skipDeploy>true</skipDeploy>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
<version>${maven_cobertura_plugin_version}</version>
<configuration>
<skip>false</skip>
<formats>
<format>html</format>
<format>xml</format>
</formats>
<maxmem>256m</maxmem>
<instrumentation>
<ignores>
<ignore>ca.uhn.fhir.model.dstu.valueset.*</ignore>
</ignores>
<excludes>
<ignore>**/valueset/*.class</ignore>
<ignore>**/exceptions/*.class</ignore>
</excludes>
<!-- <ignoreMethodAnnotations> <ignoreMethodAnnotation>net.sourceforge.cobertura.CoverageIgnore</ignoreMethodAnnotation>
</ignoreMethodAnnotations> -->
</instrumentation>
</configuration>
<executions>
<execution>
<phase>verify</phase>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.eluder.coveralls</groupId>
<artifactId>coveralls-maven-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<coberturaReports>
<coberturaReport>
${basedir}/target/coverage.xml
</coberturaReport>
</coberturaReports>
<sourceEncoding>UTF-8</sourceEncoding>
<serviceName>travis-ci</serviceName>
<serviceJobId>${env.TRAVIS_JOB_ID}</serviceJobId>
<sourceDirectories>
<sourceDirectory>../hapi-fhir-structures-dstu/src/test/java</sourceDirectory>
<sourceDirectory>../hapi-fhir-structures-dstu2/src/test/java</sourceDirectory>
<sourceDirectory>../hapi-fhir-structures-hl7org-dstu2/src/test/java</sourceDirectory>
<sourceDirectory>../hapi-fhir-jpaserver-base/src/test/java</sourceDirectory>
<sourceDirectory>../hapi-fhir-base/src/main/java</sourceDirectory>
<sourceDirectory>../hapi-fhir-jpaserver-base/src/main/java</sourceDirectory>
</sourceDirectories>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>${maven_build_helper_plugin_version}</version>
<executions>
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>../hapi-fhir-base/src/main/java</source>
<source>../hapi-fhir-jpaserver-base/src/main/java</source>
</sources>
</configuration>
</execution>
<execution>
<id>add-test-source</id>
<phase>generate-test-sources</phase>
<goals>
<goal>add-test-source</goal>
</goals>
<configuration>
<sources>
<source>../hapi-fhir-structures-dstu/src/test/java</source>
<source>../hapi-fhir-structures-dstu2/src/test/java</source>
<source>../hapi-fhir-structures-hl7org-dstu2/src/test/java</source>
<source>../hapi-fhir-jpaserver-base/src/test/java</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<runOrder>alphabetical</runOrder>
<reuseForks>false</reuseForks>
<argLine>-Xms512m -Xmx1024m</argLine>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
<version>${maven_cobertura_plugin_version}</version>
<configuration>
</configuration>
<executions>
<execution>
<phase>verify</phase>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- <plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>cobertura-maven-plugin</artifactId>
<version>${maven_cobertura_plugin_version}</version> <configuration> <check>
<branchRate>85</branchRate> <lineRate>85</lineRate> <haltOnFailure>true</haltOnFailure>
<totalBranchRate>85</totalBranchRate> <totalLineRate>85</totalLineRate> <packageLineRate>85</packageLineRate>
<packageBranchRate>85</packageBranchRate> <regexes> <regex> <pattern>com.example.reallyimportant.*</pattern>
<branchRate>90</branchRate> <lineRate>80</lineRate> </regex> <regex> <pattern>com.example.boringcode.*</pattern>
<branchRate>40</branchRate> <lineRate>30</lineRate> </regex> </regexes> </check>
</configuration> <executions> <execution> <goals> <goal>clean</goal> <goal>check</goal>
</goals> </execution> </executions> </plugin> -->
</plugins>
<resources>
</resources>
<testResources>
<testResource>
<directory>../hapi-fhir-jpaserver-base/src/test/resources</directory>
</testResource>
<testResource>
<directory>../hapi-fhir-structures-dstu/src/test/resources</directory>
</testResource>
<testResource>
<directory>../hapi-fhir-structures-dstu2/src/test/resources</directory>
</testResource>
<testResource>
<directory>../hapi-fhir-structures-hl7org-dstu2/src/test/resources</directory>
</testResource>
</testResources>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
<version>${maven_cobertura_plugin_version}</version>
<reportSets>
<reportSet>
<reports>
<report>cobertura</report>
</reports>
</reportSet>
</reportSets>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>${maven_project_info_plugin_version}</version>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<reportSets>
<reportSet>
<reports>
<report>checkstyle</report>
</reports>
</reportSet>
</reportSets>
<configuration>
<linkXRef>false</linkXRef>
</configuration>
</plugin>
</plugins>
</reporting>
</project>

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseFhirResourceDao.java
View File

@ -1002,7 +1002,7 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
return singleCode;
}
private void createSort(CriteriaBuilder theBuilder, Root<ResourceTable> theFrom, SortSpec theSort, List<Order> theOrders, List<Predicate> thePredicates) {
private void createSort(CriteriaBuilder theBuilder, Root<ResourceTable> theFrom, SortSpec theSort, List<Order> theOrders) {
if (theSort == null || isBlank(theSort.getParamName())) {
return;
}
@ -1017,7 +1017,7 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
theOrders.add(theBuilder.desc(theFrom.get("myId")));
}
createSort(theBuilder, theFrom, theSort.getChain(), theOrders, null);
createSort(theBuilder, theFrom, theSort.getChain(), theOrders);
return;
}
@ -1039,6 +1039,10 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
joinAttrName = "myParamsDate";
sortAttrName = "myValueLow";
break;
case REFERENCE:
joinAttrName = "myResourceLinks";
sortAttrName = "myTargetResourcePid";
break;
default:
throw new NotImplementedException("This server does not support _sort specifications of type " + param.getParamType() + " - Can't serve _sort=" + theSort.getParamName());
}
@ -1054,7 +1058,7 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
theOrders.add(theBuilder.desc(stringJoin.get(sortAttrName)));
}
createSort(theBuilder, theFrom, theSort.getChain(), theOrders, null);
createSort(theBuilder, theFrom, theSort.getChain(), theOrders);
}
@Override
@ -1142,6 +1146,10 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
return outcome;
}
/**
* May
* @param theResource The resource that is about to be stored
*/
protected void preProcessResourceForStorage(T theResource) {
// nothing by default
}
@ -1655,7 +1663,7 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
CriteriaQuery<Tuple> cq = builder.createTupleQuery();
Root<ResourceTable> from = cq.from(ResourceTable.class);
predicates.add(from.get("myId").in(loadPids));
createSort(builder, from, theParams.getSort(), orders, predicates);
createSort(builder, from, theParams.getSort(), orders);
if (orders.size() > 0) {
Set<Long> originalPids = loadPids;
loadPids = new LinkedHashSet<Long>();

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

@ -7,7 +7,7 @@ import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu2.resource.Condition;
public class BaseFhirDaoTest {
public class BaseFhirDaoTest extends BaseJpaTest {
private static FhirContext ourCtx = FhirContext.forDstu2();

20
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java Normal file
View File

@ -0,0 +1,20 @@
package ca.uhn.fhir.jpa.dao;
import java.sql.DriverManager;
import java.sql.SQLException;
import java.sql.SQLNonTransientConnectionException;
import org.junit.AfterClass;
public class BaseJpaTest {
@AfterClass
public static void afterClassShutdownDerby() throws SQLException {
// try {
// DriverManager.getConnection("jdbc:derby:memory:myUnitTestDB;drop=true");
// } catch (SQLNonTransientConnectionException e) {
// // expected.. for some reason....
// }
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu1Test.java
View File

@ -25,7 +25,7 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
public class FhirResourceDaoDstu1Test {
public class FhirResourceDaoDstu1Test extends BaseJpaTest {
private static ClassPathXmlApplicationContext ourCtx;
private static IFhirResourceDao<Device> ourDeviceDao;

63
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2Test.java
View File

@ -93,7 +93,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@SuppressWarnings("unchecked")
public class FhirResourceDaoDstu2Test {
public class FhirResourceDaoDstu2Test extends BaseJpaTest {
private static ClassPathXmlApplicationContext ourCtx;
private static IFhirResourceDao<Device> ourDeviceDao;
@ -2210,6 +2210,67 @@ public class FhirResourceDaoDstu2Test {
assertThat(actual, contains(id3, id2, id1, id4));
}
@Test
public void testSortByReference() {
String methodName = "testSortByReference";
Organization o1 = new Organization();
IdDt oid1 = ourOrganizationDao.create(o1).getId().toUnqualifiedVersionless();
Organization o2 = new Organization();
IdDt oid2 = ourOrganizationDao.create(o2).getId().toUnqualifiedVersionless();
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.addName().addFamily("testSortF1").addGiven("testSortG1");
p.getManagingOrganization().setReference(oid1);
IdDt id1 = ourPatientDao.create(p).getId().toUnqualifiedVersionless();
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.addName().addFamily("testSortF2").addGiven("testSortG2");
p.getManagingOrganization().setReference(oid2);
IdDt id2 = ourPatientDao.create(p).getId().toUnqualifiedVersionless();
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.addName().addFamily("testSortF3").addGiven("testSortG3");
p.getManagingOrganization().setReference(oid1);
IdDt id3 = ourPatientDao.create(p).getId().toUnqualifiedVersionless();
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.getManagingOrganization().setReference(oid2);
IdDt id4 = ourPatientDao.create(p).getId().toUnqualifiedVersionless();
SearchParameterMap pm;
List<IdDt> actual;
pm = new SearchParameterMap();
pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", methodName));
pm.setSort(new SortSpec(Patient.SP_ORGANIZATION));
actual = toUnqualifiedVersionlessIds(ourPatientDao.search(pm));
assertEquals(4, actual.size());
assertThat(actual.subList(0, 2), containsInAnyOrder(id1, id3));
assertThat(actual.subList(2, 4), containsInAnyOrder(id2, id4));
pm = new SearchParameterMap();
pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", methodName));
pm.setSort(new SortSpec(Patient.SP_ORGANIZATION).setOrder(SortOrderEnum.ASC));
actual = toUnqualifiedVersionlessIds(ourPatientDao.search(pm));
assertEquals(4, actual.size());
assertThat(actual.subList(0, 2), containsInAnyOrder(id1, id3));
assertThat(actual.subList(2, 4), containsInAnyOrder(id2, id4));
pm = new SearchParameterMap();
pm.add(Patient.SP_IDENTIFIER, new TokenParam("urn:system", methodName));
pm.setSort(new SortSpec(Patient.SP_ORGANIZATION).setOrder(SortOrderEnum.DESC));
actual = toUnqualifiedVersionlessIds(ourPatientDao.search(pm));
assertEquals(4, actual.size());
assertThat(actual.subList(0, 2), containsInAnyOrder(id2, id4));
assertThat(actual.subList(2, 4), containsInAnyOrder(id1, id3));
}
@Test
public void testStoreUnversionedResources() {
Organization o1 = new Organization();

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu1Test.java
View File

@ -45,7 +45,7 @@ import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
public class FhirSystemDaoDstu1Test {
public class FhirSystemDaoDstu1Test extends BaseJpaTest {
private static ClassPathXmlApplicationContext ourCtx;
private static FhirContext ourFhirContext;

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