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

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/IClientInterceptor.java

@@ -25,6 +25,14 @@ import java.io.IOException;
 import ca.uhn.fhir.rest.client.api.IHttpRequest;
 import ca.uhn.fhir.rest.client.api.IHttpResponse;
 
+/**
+ * This interface represents an interceptor which can be used to access (and optionally change or take actions upon)
+ * requests that are being sent by the HTTP client, and responses received by it.
+ * <p>
+ * See the <a href="http://jamesagnew.github.io/hapi-fhir/doc_rest_client_interceptor.html">HAPI Documentation Client Interceptor</a>
+ * page for more information on how to use this feature.
+ * </p> 
+ */
 public interface IClientInterceptor {
 
 	/**

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java

@@ -218,6 +218,47 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 				q.setParameter("status", INDEX_STATUS_INDEXING_FAILED);
 				q.setParameter("id", theId);
 				q.executeUpdate();
+				
+				q = myEntityManager.createQuery("DELETE FROM ResourceTag t WHERE t.myResourceId = :id");
+				q.setParameter("id", theId);
+				q.executeUpdate();
+
+				q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamCoords t WHERE t.myResourcePid = :id");
+				q.setParameter("id", theId);
+				q.executeUpdate();
+
+				q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamDate t WHERE t.myResourcePid = :id");
+				q.setParameter("id", theId);
+				q.executeUpdate();
+
+				q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamNumber t WHERE t.myResourcePid = :id");
+				q.setParameter("id", theId);
+				q.executeUpdate();
+
+				q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamQuantity t WHERE t.myResourcePid = :id");
+				q.setParameter("id", theId);
+				q.executeUpdate();
+
+				q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamString t WHERE t.myResourcePid = :id");
+				q.setParameter("id", theId);
+				q.executeUpdate();
+
+				q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamToken t WHERE t.myResourcePid = :id");
+				q.setParameter("id", theId);
+				q.executeUpdate();
+
+				q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamUri t WHERE t.myResourcePid = :id");
+				q.setParameter("id", theId);
+				q.executeUpdate();
+
+				q = myEntityManager.createQuery("DELETE FROM ResourceLink t WHERE t.mySourceResourcePid = :id");
+				q.setParameter("id", theId);
+				q.executeUpdate();
+
+				q = myEntityManager.createQuery("DELETE FROM ResourceLink t WHERE t.myTargetResourcePid = :id");
+				q.setParameter("id", theId);
+				q.executeUpdate();
+
 				return null;
 			}
 		});

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSearchParameterDstu2.java

@@ -47,7 +47,7 @@ public class FhirResourceDaoSearchParameterDstu2 extends FhirResourceDaoDstu2<Se
 		}
 
 		int count = mySystemDao.performReindexingPass(100);
-		for (int i = 0; i < 50 && count > 0; i++) {
+		for (int i = 0; i < 50 && count != 0; i++) {
 			count = mySystemDao.performReindexingPass(100);
 			try {
 				Thread.sleep(DateUtils.MILLIS_PER_SECOND);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSearchParameterDstu3.java

@@ -49,7 +49,7 @@ public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<Se
 		}
 
 		int count = mySystemDao.performReindexingPass(100);
-		for (int i = 0; i < 50 && count > 0; i++) {
+		for (int i = 0; i < 50 && count != 0; i++) {
 			count = mySystemDao.performReindexingPass(100);
 			try {
 				Thread.sleep(DateUtils.MILLIS_PER_SECOND);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaConformanceProviderDstu3.java

@@ -35,6 +35,7 @@ import org.hl7.fhir.dstu3.model.Conformance.ConditionalDeleteStatus;
 import org.hl7.fhir.dstu3.model.Conformance.ConformanceRestComponent;
 import org.hl7.fhir.dstu3.model.Conformance.ConformanceRestResourceComponent;
 import org.hl7.fhir.dstu3.model.Conformance.ConformanceRestResourceSearchParamComponent;
+import org.hl7.fhir.dstu3.model.Conformance.ResourceVersionPolicy;
 import org.hl7.fhir.dstu3.model.Enumerations.SearchParamType;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -42,6 +43,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.ExtensionConstants;
@@ -87,6 +89,8 @@ public class JpaConformanceProviderDstu3 extends org.hl7.fhir.dstu3.hapi.rest.se
 
 			for (ConformanceRestResourceComponent nextResource : nextRest.getResource()) {
 
+				nextResource.setVersioning(ResourceVersionPolicy.VERSIONEDUPDATE);
+				
 				ConditionalDeleteStatus conditionalDelete = nextResource.getConditionalDelete();
 				if (conditionalDelete == ConditionalDeleteStatus.MULTIPLE && myDaoConfig.isAllowMultipleDelete() == false) {
 					nextResource.setConditionalDelete(ConditionalDeleteStatus.SINGLE);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvc.java

@@ -394,6 +394,24 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		// Grab the existing versions so we can delete them later
 		List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystemResourcePid);
 
+		/*
+		 * For now we always delete old versions.. At some point it would be nice to allow configuration to keep old versions
+		 */
+
+		ourLog.info("Deleting old code system versions");
+		for (TermCodeSystemVersion next : existing) {
+			ourLog.info(" * Deleting code system version {}", next.getPid());
+			myConceptParentChildLinkDao.deleteByCodeSystemVersion(next.getPid());
+			myConceptDao.deleteByCodeSystemVersion(next.getPid());
+		}
+
+		ourLog.info("Flushing...");
+		
+		myConceptParentChildLinkDao.flush();
+		myConceptDao.flush();
+
+		ourLog.info("Done flushing");
+
 		/*
 		 * Do the upload
 		 */
@@ -452,17 +470,6 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
 		myConceptDao.flush();
 		myConceptParentChildLinkDao.flush();
 
-		/*
-		 * For now we always delete old versions.. At some point it would be nice to allow configuration to keep old versions
-		 */
-
-		ourLog.info("Deleting old code system versions");
-		for (TermCodeSystemVersion next : existing) {
-			ourLog.info(" * Deleting code system version {}", next.getPid());
-			myConceptParentChildLinkDao.deleteByCodeSystemVersion(next.getPid());
-			myConceptDao.deleteByCodeSystemVersion(next.getPid());
-		}
-
 		ourLog.info("Done deleting old code system versions");
 		
 		if (myConceptsToSaveLater.size() > 0 || myConceptLinksToSaveLater.size() > 0) {

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/TestRestfulServer.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1;
 import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
+import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.server.ETagSupportEnum;
 import ca.uhn.fhir.rest.server.EncodingEnum;
@@ -71,13 +72,12 @@ public class TestRestfulServer extends RestfulServer {
 		// retrieve all the appropriate resource providers and the
 		// conformance provider
 		List<IResourceProvider> beans;
-		JpaSystemProviderDstu1 systemProviderDstu1 = null;
-		JpaSystemProviderDstu2 systemProviderDstu2 = null;
-		JpaSystemProviderDstu3 systemProviderDstu3 = null;
 		@SuppressWarnings("rawtypes")
 		IFhirSystemDao systemDao;
 		ETagSupportEnum etagSupport;
 		String baseUrlProperty;
+		List<Object> plainProviders = new ArrayList<Object>();
+		
 		switch (fhirVersionParam.trim().toUpperCase()) {
 		case "DSTU1": {
 			myAppCtx = new AnnotationConfigWebApplicationContext();
@@ -87,7 +87,7 @@ public class TestRestfulServer extends RestfulServer {
 			myAppCtx.refresh();
 			setFhirContext(FhirContext.forDstu1());
 			beans = myAppCtx.getBean("myResourceProvidersDstu1", List.class);
-			systemProviderDstu1 = myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class);
+			plainProviders.add(myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class));
 			systemDao = myAppCtx.getBean("mySystemDaoDstu1", IFhirSystemDao.class);
 			etagSupport = ETagSupportEnum.DISABLED;
 			JpaConformanceProviderDstu1 confProvider = new JpaConformanceProviderDstu1(this, systemDao);
@@ -111,7 +111,7 @@ public class TestRestfulServer extends RestfulServer {
 			myAppCtx.refresh();
 			setFhirContext(FhirContext.forDstu2());
 			beans = myAppCtx.getBean("myResourceProvidersDstu2", List.class);
-			systemProviderDstu2 = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
+			plainProviders.add(myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class));
 			systemDao = myAppCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
 			etagSupport = ETagSupportEnum.ENABLED;
 			JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao, myAppCtx.getBean(DaoConfig.class));
@@ -134,12 +134,13 @@ public class TestRestfulServer extends RestfulServer {
 			myAppCtx.refresh();
 			setFhirContext(FhirContext.forDstu3());
 			beans = myAppCtx.getBean("myResourceProvidersDstu3", List.class);
-			systemProviderDstu3 = myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
+			plainProviders.add(myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class));
 			systemDao = myAppCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
 			etagSupport = ETagSupportEnum.ENABLED;
 			JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, myAppCtx.getBean(DaoConfig.class));
 			confProvider.setImplementationDescription(implDesc);
 			setServerConformanceProvider(confProvider);
+			plainProviders.add(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
 			break;
 		}
 		default:
@@ -167,17 +168,7 @@ public class TestRestfulServer extends RestfulServer {
 		}
 		setResourceProviders(beans);
 
-		List<Object> provList = new ArrayList<Object>();
+		setPlainProviders(plainProviders);
-		if (systemProviderDstu1 != null) {
-			provList.add(systemProviderDstu1);
-		}
-		if (systemProviderDstu2 != null) {
-			provList.add(systemProviderDstu2);
-		}
-		if (systemProviderDstu3 != null) {
-			provList.add(systemProviderDstu3);
-		}
-		setPlainProviders(provList);
 
 		/*
 		 * We want to format the response using nice HTML if it's a browser, since this

hapi-fhir-osgi-core/pom.xml

@@ -132,10 +132,10 @@
 				<configuration>
 					<instructions>
 						<!--<Export-Package>ca.uhn.fhir</Export-Package> <Export-Package>org.hl7.fhir</Export-Package> -->
-						<Bundle-SymbolicName>${pom.artifactId}</Bundle-SymbolicName>
+						<Bundle-SymbolicName>${project.artifactId}</Bundle-SymbolicName>
 						<!--<Embed-Dependency>*;scope=!provided|test</Embed-Dependency> <Embed-Directory>lib</Embed-Directory> <Embed-Transitive>true</Embed-Transitive> -->
 						<_nouses>true</_nouses>
-						<_removeheaders>Built-By, Include-Resource, Private-Package</_removeheaders>
+						<_removeheaders>Built-By, Include-Resource, Private-Package, Require-Capability</_removeheaders>
 						<!-- <Private-Package>org.foo.myproject.*</Private-Package> <Bundle-Activator>org.foo.myproject.impl1.Activator</Bundle-Activator> -->
 						<!-- <Embed-Dependency>*;scope=compile|runtime;inline=false;artifactId=hapi-fhir-*</Embed-Dependency> -->
 						<Import-Package>
@@ -146,6 +146,7 @@
 							com.google.*;resolution:=optional;-remove-attribute:=version,
 							com.phloc.commons;resolution:=optional;-remove-attribute:=version,
 							com.phloc.*;resolution:=optional;-remove-attribute:=version,
+							javassist;-remove-attribute:=version,
 							javax.*;-remove-attribute:=version,
 							net.sf.saxon;resolution:=optional,
 							org.apache.commons.*;-remove-attribute:=version,

hapi-fhir-osgi-core/src/main/java/ca/uhn/fhir/osgi/FhirServerImpl.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.osgi.impl;
+package ca.uhn.fhir.osgi;
 
 /*
  * #%L
@@ -31,8 +31,6 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.osgi.FhirConfigurationException;
-import ca.uhn.fhir.osgi.FhirServer;
 import ca.uhn.fhir.rest.server.RestfulServer;
 
 /**

src/site/xdoc/hacking_hapi_fhir.xml

@@ -120,6 +120,29 @@
 				import more later.
 			</p>
 			<img src="./images/hacking_import_step2.png"/>
+			
+			<subsection name="Troubleshooting">
+			
+				<p>
+					When importing the HAPI projects into Eclipse, sometimes Eclipse 
+					will fail to correctly import libraries. If you import a module
+					into Eclipse and it fails to compile with many errors relating to
+					packages other than HAPI's, the following steps will fix this:
+				</p>
+				<ul>
+					<li>Delete the project from your Eclipse workspace</li>
+					<li>
+						On the local filesystem, delete the files <code>.project</code>
+						and <code>.classpath</code>, and the directory <code>.settings</code>
+						from each module you want to open.
+					</li>
+					<li>
+						Import each module again using the instructions above
+					</li>
+				</ul>
+				
+			</subsection>
+			
 		</section>
 	</body>