Merge remote-tracking branch 'origin/master' into hl7org_structs

hapi-fhir-base/pom.xml

@@ -223,6 +223,13 @@
 		</profile>
 		<profile>
 			<id>ANDROID</id>
+			<dependencies>
+				<dependency>
+					<groupId>ca.uhn.hapi.fhir</groupId>
+					<artifactId>hapi-fhir-structures-dstu</artifactId>
+					<version>0.8-SNAPSHOT</version>
+				</dependency>
+			</dependencies>
 			<build>
 				<plugins>
 					<plugin>
@@ -238,6 +245,18 @@
 								<configuration>
 									<shadedArtifactAttached>false</shadedArtifactAttached>
 									<createDependencyReducedPom>true</createDependencyReducedPom>
+									<artifactSet>
+										<includes>
+											<!-- 
+											<include>javax.json:javax.json-api</include>
+											-->
+											<include>ca.uhn.hapi.fhir:hapi-fhir-structures-dstu</include>
+											<include>org.glassfish:javax.json</include>
+											<include>org.codehaus.woodstox:woodstox-core-asl</include>
+											<include>javax.xml.stream:stax-api</include>
+											<include>org.codehaus.woodstox:stax2-api</include>
+										</includes>
+									</artifactSet>
 									<relocations>
 										<relocation>
 											<pattern>javax.xml.stream</pattern>

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

@@ -137,7 +137,7 @@ public abstract class BaseRuntimeElementDefinition<T extends IElement> {
 		for (RuntimeChildDeclaredExtensionDefinition next : myExtensions) {
 			String extUrl = next.getExtensionUrl();
 			if (myUrlToExtension.containsKey(extUrl)) {
-				throw new ConfigurationException("Duplicate extension URL: " + extUrl);
+				throw new ConfigurationException("Duplicate extension URL[" + extUrl + "] in Element[" + getName() + "]");
 			} else {
 				myUrlToExtension.put(extUrl, next);
 			}

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

@@ -294,7 +294,7 @@ class ModelScanner {
 		}
 
 		if (blockDefinition == null && datatypeDefinition == null && resourceDefinition == null) {
-			throw new ConfigurationException("Resource type does not contain any valid HAPI-FHIR annotations: " + theClass.getCanonicalName());
+			throw new ConfigurationException("Resource class[" + theClass.getName() + "] does not contain any valid HAPI-FHIR annotations");
 		}
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/base/composite/BaseHumanNameDt.java

@@ -102,28 +102,24 @@ public abstract class BaseHumanNameDt extends BaseIdentifiableElement {
 	public String getSuffixAsSingleString() {
 		return ca.uhn.fhir.util.DatatypeUtil.joinStringsSpaceSeparated(getSuffix());
 	}
-	
+
 	/**
-	 * Gets the value(s) for <b>text</b> (Text representation of the full name).
-	 * creating it if it does
-	 * not exist. Will not return <code>null</code>.
+	 * Gets the value(s) for <b>text</b> (Text representation of the full name). creating it if it does not exist. Will not return <code>null</code>.
 	 *
-     * <p>
-     * <b>Definition:</b>
-     * A full text representation of the name
-     * </p> 
+	 * <p>
+	 * <b>Definition:</b> A full text representation of the name
+	 * </p>
 	 */
-	public abstract StringDt getText() ;
+	public abstract StringDt getTextElement();
 
 	/**
 	 * Sets the value(s) for <b>text</b> (Text representation of the full name)
 	 *
-     * <p>
-     * <b>Definition:</b>
-     * A full text representation of the name
-     * </p> 
+	 * <p>
+	 * <b>Definition:</b> A full text representation of the name
+	 * </p>
 	 */
-	public abstract BaseHumanNameDt setText(StringDt theValue);	
+	public abstract BaseHumanNameDt setText(StringDt theValue);
 
 	@Override
 	public String toString() {
@@ -132,15 +128,26 @@ public abstract class BaseHumanNameDt extends BaseIdentifiableElement {
 		b.append("given", getGivenAsSingleString());
 		return b.toString();
 	}
-	
-	public String getNameAsSingleString(){
+
+	/**
+	 * Returns all of the components of the name (prefix, given, family, suffix) as a 
+	 * single string with a single spaced string separating each part. 
+	 * <p>
+	 * If none of the parts are populated, returns the {@link #getTextElement() text}
+	 * element value instead.
+	 * </p>
+	 */
+	public String getNameAsSingleString() {
 		List<StringDt> nameParts = new ArrayList<StringDt>();
 		nameParts.addAll(getPrefix());
 		nameParts.addAll(getGiven());
 		nameParts.addAll(getFamily());
 		nameParts.addAll(getSuffix());
-		if(nameParts.size() > 0) return ca.uhn.fhir.util.DatatypeUtil.joinStringsSpaceSeparated(nameParts);
-		else return getText().getValue();
+		if (nameParts.size() > 0) {
+			return ca.uhn.fhir.util.DatatypeUtil.joinStringsSpaceSeparated(nameParts);
+		} else {
+			return getTextElement().getValue();
+		}
 	}
-	
+
 }

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

@@ -41,6 +41,7 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.util.VersionUtil;
+
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.exception.ExceptionUtils;
@@ -50,6 +51,7 @@ import javax.servlet.ServletOutputStream;
 import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
+
 import java.io.IOException;
 import java.io.OutputStreamWriter;
 import java.io.UnsupportedEncodingException;
@@ -723,16 +725,19 @@ public class RestfulServer extends HttpServlet {
 
 			Collection<IResourceProvider> resourceProvider = getResourceProviders();
 			if (resourceProvider != null) {
-				Map<Class<? extends IResource>, IResourceProvider> typeToProvider = new HashMap<Class<? extends IResource>, IResourceProvider>();
+				Map<String, IResourceProvider> typeToProvider = new HashMap<String, IResourceProvider>();
 				for (IResourceProvider nextProvider : resourceProvider) {
+					
 					Class<? extends IResource> resourceType = nextProvider.getResourceType();
 					if (resourceType == null) {
 						throw new NullPointerException("getResourceType() on class '" + nextProvider.getClass().getCanonicalName() + "' returned null");
 					}
-					if (typeToProvider.containsKey(resourceType)) {
-						throw new ServletException("Multiple providers for type: " + resourceType.getCanonicalName());
+					
+					String resourceName = myFhirContext.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() + "]");
 					}
-					typeToProvider.put(resourceType, nextProvider);
+					typeToProvider.put(resourceName, nextProvider);
 					providedResourceScanner.scanForProvidedResources(nextProvider);
 				}
 				ourLog.info("Got {} resource providers", typeToProvider.size());

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

@@ -33,6 +33,7 @@ import java.util.Map;
 
 import ca.uhn.fhir.context.*;
 import ca.uhn.fhir.model.api.ICompositeDatatype;
+
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.text.WordUtils;
 
@@ -57,7 +58,7 @@ import ca.uhn.fhir.rest.server.provider.ServerProfileProvider;
 public class FhirDstu1 implements IFhirVersion {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirDstu1.class);
-	private Map<RuntimeChildDeclaredExtensionDefinition, String> myExtensionDefToCode = new HashMap<RuntimeChildDeclaredExtensionDefinition, String>();
+//	private Map<RuntimeChildDeclaredExtensionDefinition, String> myExtensionDefToCode = new HashMap<RuntimeChildDeclaredExtensionDefinition, String>();
 	private String myId;
 
 	@Override
@@ -158,7 +159,7 @@ public class FhirDstu1 implements IFhirVersion {
 
 		String expectedPath = StringUtils.join(path, '.');
 
-		ourLog.info("Filling profile for: {} - Path: {}", expectedPath);
+		ourLog.debug("Filling profile for: {} - Path: {}", expectedPath);
 		String name = def.getName();
 		if (!expectedPath.equals(name)) {
 			path.pollLast();
@@ -267,11 +268,12 @@ public class FhirDstu1 implements IFhirVersion {
 		return retVal;
 	}
 
-	private void scanForExtensions(Profile theProfile, BaseRuntimeElementDefinition<?> def) {
+	private Map<RuntimeChildDeclaredExtensionDefinition, String> scanForExtensions(Profile theProfile, BaseRuntimeElementDefinition<?> def) {
 		BaseRuntimeElementCompositeDefinition<?> cdef = ((BaseRuntimeElementCompositeDefinition<?>) def);
 
+		Map<RuntimeChildDeclaredExtensionDefinition, String> extensionDefToCode = new HashMap<RuntimeChildDeclaredExtensionDefinition, String>();
 		for (RuntimeChildDeclaredExtensionDefinition nextChild : cdef.getExtensions()) {
-			if (myExtensionDefToCode.containsKey(nextChild)) {
+			if (extensionDefToCode.containsKey(nextChild)) {
 				continue;
 			}
 
@@ -288,10 +290,10 @@ public class FhirDstu1 implements IFhirVersion {
 			}
 
 			defn.setCode(code);
-			if (myExtensionDefToCode.values().contains(code)) {
+			if (extensionDefToCode.values().contains(code)) {
 				throw new IllegalStateException("Duplicate extension code: " + code);
 			}
-			myExtensionDefToCode.put(nextChild, code);
+			extensionDefToCode.put(nextChild, code);
 
 			if (nextChild.getChildType() != null && IPrimitiveDatatype.class.isAssignableFrom(nextChild.getChildType())) {
 				RuntimePrimitiveDatatypeDefinition pdef = (RuntimePrimitiveDatatypeDefinition) nextChild.getSingleChildOrThrow();
@@ -306,11 +308,13 @@ public class FhirDstu1 implements IFhirVersion {
 				for (RuntimeChildDeclaredExtensionDefinition nextChildExt : pdef.getExtensions()) {
 					StructureElementDefinitionType type = defn.getDefinition().addType();
 					type.setCode(DataTypeEnum.EXTENSION);
-					type.setProfile("#" + myExtensionDefToCode.get(nextChildExt));
+					type.setProfile("#" + extensionDefToCode.get(nextChildExt));
 				}
 
 			}
 		}
+		
+		return extensionDefToCode;
 	}
 
 	@Override

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/context/DuplicateExtensionTest.java

@@ -0,0 +1,82 @@
+package ca.uhn.fhir.context;
+
+import junit.framework.TestCase;
+
+import org.junit.Test;
+
+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.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ProvidesResources;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.model.dstu.resource.Observation;
+import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.dstu.resource.Profile;
+import ca.uhn.fhir.model.primitive.StringDt;
+
+/**
+ * Created by Bill de Beaubien on 12/10/2014.
+ */
+public class DuplicateExtensionTest extends TestCase {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DuplicateExtensionTest.class);
+	
+	@Test
+	public void testScannerShouldAddProvidedResources() {
+		FhirContext ctx = new FhirContext();
+		RuntimeResourceDefinition patientDef = ctx.getResourceDefinition(CustomPatient.class);
+		Profile profile = (Profile) patientDef.toProfile();
+
+		String res = ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(profile);
+		ourLog.info(res);
+		
+		RuntimeResourceDefinition observationDef = ctx.getResourceDefinition(CustomObservation.class);
+		profile = (Profile) observationDef.toProfile();
+	}
+
+	@ResourceDef(name = "Observation", id = "CustomObservation")
+	class CustomObservation extends Observation {
+		@Child(name = "idExt", order = 0)
+		@Extension(url = "http://foo.org#id", definedLocally = true, isModifier = false)
+		@Description(shortDefinition = "Contains the id of the resource")
+		private StringDt myIdExt;
+
+		public StringDt getIdExt() {
+			if (myIdExt == null) {
+				myIdExt = new StringDt();
+			}
+			return myIdExt;
+		}
+
+		public void setIdExt(StringDt theIdExt) {
+			myIdExt = theIdExt;
+		}
+	}
+
+	@ProvidesResources(resources = CustomObservation.class)
+	class CustomObservationProvider {
+	}
+
+	@ResourceDef(name = "Patient", id = "CustomPatient")
+	class CustomPatient extends Patient {
+		@Child(name = "idExt", order = 0)
+		@Extension(url = "http://foo.org#id", definedLocally = true, isModifier = false)
+		@Description(shortDefinition = "Contains the id of the resource")
+		private StringDt myIdExt;
+
+		public StringDt getIdExt() {
+			if (myIdExt == null) {
+				myIdExt = new StringDt();
+			}
+			return myIdExt;
+		}
+
+		public void setIdExt(StringDt theIdExt) {
+			myIdExt = theIdExt;
+		}
+	}
+
+	@ProvidesResources(resources = CustomPatient.class)
+	class CustomPatientProvider {
+	}
+}

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/ServerInvalidDefinitionTest.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.rest.server;
 import static org.junit.Assert.*;
 
 import java.util.List;
+import java.util.Map;
 
 import javax.servlet.ServletException;
 
@@ -10,8 +11,13 @@ import org.hamcrest.core.StringContains;
 import org.junit.Test;
 
 import ca.uhn.fhir.model.api.BaseResource;
+import ca.uhn.fhir.model.api.IElement;
 import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.dstu.composite.ContainedDt;
+import ca.uhn.fhir.model.dstu.composite.NarrativeDt;
 import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Read;
@@ -62,6 +68,21 @@ public class ServerInvalidDefinitionTest {
 		}
 	}
 
+	@Test
+	public void testMultipleResourceProviderForSameType() {
+		RestfulServer srv = new RestfulServer();
+		srv.setResourceProviders(new PatientResourceProvider1(), new PatientResourceProvider2());
+
+		try {
+			srv.init();
+			fail();
+		} catch (ServletException e) {
+			assertThat(e.getCause().toString(), StringContains.containsString("[Patient]"));
+			assertThat(e.getCause().toString(), StringContains.containsString("PatientResourceProvider1]"));
+			assertThat(e.getCause().toString(), StringContains.containsString("PatientResourceProvider2]"));
+		}
+	}
+
 	@Test
 	public void testSearchWithId() {
 		RestfulServer srv = new RestfulServer();
@@ -76,6 +97,19 @@ public class ServerInvalidDefinitionTest {
 		}
 	}
 
+	@Test
+	public void testProviderWithNonResourceType() {
+		RestfulServer srv = new RestfulServer();
+		srv.setResourceProviders(new ProviderWithNonResourceType());
+
+		try {
+			srv.init();
+			fail();
+		} catch (ServletException e) {
+			assertThat(e.getCause().toString(), StringContains.containsString("ConfigurationException"));
+			assertThat(e.getCause().toString(), StringContains.containsString("does not contain any valid HAPI-FHIR annotations"));
+		}
+	}
 	/**
 	 * Normal, should initialize properly
 	 */
@@ -127,6 +161,74 @@ public class ServerInvalidDefinitionTest {
 		}
 
 	}
+	
+	
+	public static class ProviderWithNonResourceType implements IResourceProvider {
+
+		@Override
+		public Class<? extends IResource> getResourceType() {
+			return new IResource() {
+				
+				@Override
+				public boolean isEmpty() {
+					return false;
+				}
+				
+				@Override
+				public <T extends IElement> List<T> getAllPopulatedChildElementsOfType(Class<T> theType) {
+					return null;
+				}
+				
+				@Override
+				public void setResourceMetadata(Map<ResourceMetadataKeyEnum<?>, Object> theMap) {
+				}
+				
+				@Override
+				public void setLanguage(CodeDt theLanguage) {
+				}
+				
+				@Override
+				public void setId(IdDt theId) {
+				}
+				
+				@Override
+				public NarrativeDt getText() {
+					return null;
+				}
+				
+				@Override
+				public String getResourceName() {
+					return null;
+				}
+				
+				@Override
+				public Map<ResourceMetadataKeyEnum<?>, Object> getResourceMetadata() {
+					return null;
+				}
+				
+				@Override
+				public CodeDt getLanguage() {
+					return null;
+				}
+				
+				@Override
+				public IdDt getId() {
+					return null;
+				}
+				
+				@Override
+				public ContainedDt getContained() {
+					return null;
+				}
+			}.getClass();
+		}
+
+		@Search
+		public List<Patient> read(@IdParam IdDt theId, @RequiredParam(name = "aaa") StringParam theParam) {
+			return null;
+		}
+
+	}
 
 	public static class InvalidSpecialParameterNameResourceProvider implements IResourceProvider {
 
@@ -156,4 +258,32 @@ public class ServerInvalidDefinitionTest {
 
 	}
 
+	public static class PatientResourceProvider1 implements IResourceProvider {
+
+		@Override
+		public Class<Patient> getResourceType() {
+			return Patient.class;
+		}
+
+		@Read
+		public Patient read(@IdParam IdDt theId) {
+			return null;
+		}
+
+	}
+
+	public static class PatientResourceProvider2 implements IResourceProvider {
+
+		@Override
+		public Class<Patient> getResourceType() {
+			return Patient.class;
+		}
+
+		@Read
+		public Patient read(@IdParam IdDt theId) {
+			return null;
+		}
+
+	}
+
 }

hapi-fhir-structures-hl7org-dev/bin/.gitignore

@@ -0,0 +1 @@
+/bin/

hapi-fhir-structures-hl7org-dev/bin/.project

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>hapi-fhir-structures-hl7org-dev</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/model/dstu/composite/HumanNameDt.java

@@ -566,6 +566,11 @@ public class HumanNameDt
 		return this;
 	}
 
+	@Override
+	public StringDt getTextElement() {
+		return getText();
+	}
+
   
 
 

pom.xml

@@ -114,6 +114,11 @@
 			<name>Tahura Chaudhry</name>
 			<organization>University Health Network</organization>
 		</developer>
+		<developer>
+			<id>b.debeaubien</id>
+			<name>Bill de Beaubien</name>
+			<organization>Systems Made Simple</organization>
+		</developer>
 	</developers>
 
 	<licenses>

restful-server-example/.settings/org.eclipse.wst.common.component

@@ -9,7 +9,7 @@
         <dependent-module archiveName="hapi-fhir-structures-dstu-0.8-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/hapi-fhir-structures-dstu/hapi-fhir-structures-dstu">
             <dependency-type>uses</dependency-type>
         </dependent-module>
-        <dependent-module deploy-path="/" handle="module:/overlay/prj/hapi-fhir-testpage-overlay?includes=**/**&amp;excludes=META-INF/MANIFEST.MF">
+        <dependent-module deploy-path="/" handle="module:/overlay/var/M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-testpage-overlay/0.8-SNAPSHOT/hapi-fhir-testpage-overlay-0.8-SNAPSHOT.war?unpackFolder=target/m2e-wtp/overlays&amp;includes=**/**&amp;excludes=META-INF/MANIFEST.MF">
             <dependency-type>consumes</dependency-type>
         </dependent-module>
         <dependent-module deploy-path="/" handle="module:/overlay/slf/?includes=**/**&amp;excludes=META-INF/MANIFEST.MF">

restful-server-example/src/main/java/ca/uhn/example/model/MyOrganization.java

@@ -43,7 +43,7 @@ public class MyOrganization extends Organization {
 	 * of this file.
 	 */
 	@Description(shortDefinition="Contains emergency contact details")
-	@Extension(url = "http://foo#billingCode", isModifier = false, definedLocally = true)
+	@Extension(url = "http://foo#emergencyContact", isModifier = false, definedLocally = true)
 	@Child(name = "emergencyContact", min=0, max=Child.MAX_UNLIMITED)
 	private List<EmergencyContact> myEmergencyContact;
 	

src/changes/changes.xml

@@ -169,7 +169,11 @@
 				Encoding a Binary resource without a content type set should not result in a NullPointerException. Thanks
 				to Alexander Kley for reporting!
 			</action>
-		</release>			
+			<action type="add">
+				Server gives a more helpful error message if multiple IResourceProvider implementations
+				are provided for the same resource type. Thanks to wanghaisheng for the idea!
+			</action>
+		</release>
 		<release version="0.7" date="2014-Oct-23">
 			<action type="add" issue="30">
 				<![CDATA[<b>API CHANGE:</b>]]> The TagList class previously implemented ArrayList semantics,