Merge pull request #987 from jamesagnew/983-ci-failures

983 ci failures

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

@@ -959,6 +959,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 
 	@Override
 	public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
+		/*
+		 * We do a null check here because Smile's module system tries to
+		 * initialize the application context twice if two modules depend on
+		 * the persistence module. The second time sets the dependency's appctx.
+		 */
 		if (myApplicationContext == null) {
 			myApplicationContext = theApplicationContext;
 		}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInterceptorR4Test.java

@@ -16,6 +16,7 @@ import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
+import org.hamcrest.Matchers;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
@@ -35,6 +36,7 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
+import java.util.stream.Collectors;
 
 import static org.hamcrest.Matchers.startsWith;
 import static org.junit.Assert.*;
@@ -174,12 +176,6 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 		ResourceProviderInterceptorR4Test.verifyDaoInterceptor(myDaoInterceptor);
 	}
 
-	/*
-	 * This is a weird way of verifying, but because this class
-	 * is a child of a superclass that has other test children
-	 * it's possible that other tests are hitting the server
-	 * at the same time
-	 */
 	@Test
 	public void testCreateResourceInTransaction() throws IOException {
 		String methodName = "testCreateResourceInTransaction";
@@ -220,15 +216,17 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
 		 * DAO Interceptor
 		 */
 
+		/*
+		 * Sometimes we get more than 2 hits of the  incomingRequestPreHandled
+		 * method. My working theory is that it's a scheduled background job,
+		 * such as the subscription interceptor or the search parameter cache
+		 * updating.
+		 */
 		ardCaptor = ArgumentCaptor.forClass(ActionRequestDetails.class);
 		opTypeCaptor = ArgumentCaptor.forClass(RestOperationTypeEnum.class);
-		verify(myDaoInterceptor, times(2)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
+		verify(myDaoInterceptor, atLeast(2)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
-		assertEquals(RestOperationTypeEnum.TRANSACTION, opTypeCaptor.getAllValues().get(0));
+		assertThat(ardCaptor.getAllValues().stream().map(ActionRequestDetails::getResourceType).collect(Collectors.toList()), Matchers.contains("Bundle", "Patient"));
-		assertEquals("Bundle", ardCaptor.getAllValues().get(0).getResourceType());
+		assertThat(opTypeCaptor.getAllValues(), Matchers.contains(RestOperationTypeEnum.TRANSACTION, RestOperationTypeEnum.CREATE));
-		assertNotNull(ardCaptor.getAllValues().get(0).getResource());
-		assertEquals(RestOperationTypeEnum.CREATE, opTypeCaptor.getAllValues().get(1));
-		assertEquals("Patient", ardCaptor.getAllValues().get(1).getResourceType());
-		assertNotNull(ardCaptor.getAllValues().get(1).getResource());
 
 		rdCaptor = ArgumentCaptor.forClass(RequestDetails.class);
 		srCaptor = ArgumentCaptor.forClass(HttpServletRequest.class);

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

@@ -31,7 +31,7 @@ public interface IServerConformanceProvider<T extends IBaseResource> {
 	 * 
 	 * See the class documentation for an important note if you are extending this class
 	 */
-	public abstract T getServerConformance(HttpServletRequest theRequest);
+	T getServerConformance(HttpServletRequest theRequest);
 
 	/**
 	 * This setter is needed in implementation classes (along with
@@ -40,5 +40,5 @@ public interface IServerConformanceProvider<T extends IBaseResource> {
 	 * 
 	 * @param theRestfulServer
 	 */
-	public void setRestfulServer(RestfulServer theRestfulServer);
+	void setRestfulServer(RestfulServer theRestfulServer);
 }

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.context.ProvidedResourceScanner;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.api.AddProfileTagEnum;
 import ca.uhn.fhir.context.api.BundleInclusionRule;
+import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.annotation.Destroy;
 import ca.uhn.fhir.rest.annotation.IdParam;
@@ -125,6 +126,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	private boolean myUncompressIncomingContents = true;
 	private boolean myUseBrowserFriendlyContentTypes;
 	private ITenantIdentificationStrategy myTenantIdentificationStrategy;
+	private Date myConformanceDate;
 
 	/**
 	 * Constructor. Note that if no {@link FhirContext} is passed in to the server (either through the constructor, or
@@ -194,19 +196,14 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		result.setServerName(getServerName());
 		result.setFhirContext(getFhirContext());
 		result.setServerAddressStrategy(myServerAddressStrategy);
-		InputStream inputStream = null;
+		try (InputStream inputStream = getClass().getResourceAsStream("/META-INF/MANIFEST.MF")) {
-		try {
-			inputStream = getClass().getResourceAsStream("/META-INF/MANIFEST.MF");
 			if (inputStream != null) {
 				Manifest manifest = new Manifest(inputStream);
-				result.setConformanceDate(manifest.getMainAttributes().getValue("Build-Time"));
+				String value = manifest.getMainAttributes().getValue("Build-Time");
+				result.setConformanceDate(new InstantDt(value));
 			}
-		} catch (IOException e) {
+		} catch (Exception e) {
 			// fall through
-		} finally {
-			if (inputStream != null) {
-				IOUtils.closeQuietly(inputStream);
-			}
 		}
 		return result;
 	}
@@ -573,10 +570,10 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	 *
 	 * @param theList The list of interceptors (may be null)
 	 */
-	public void setInterceptors(List<IServerInterceptor> theList) {
+	public void setInterceptors(IServerInterceptor... theList) {
 		myInterceptors.clear();
 		if (theList != null) {
-			myInterceptors.addAll(theList);
+			myInterceptors.addAll(Arrays.asList(theList));
 		}
 	}
 
@@ -606,8 +603,11 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	 *
 	 * @see #setResourceProviders(Collection)
 	 */
-	public void setPlainProviders(Object... theProv) {
+	public void setPlainProviders(Collection<Object> theProviders) {
-		setPlainProviders(Arrays.asList(theProv));
+		myPlainProviders.clear();
+		if (theProviders != null) {
+			myPlainProviders.addAll(theProviders);
+		}
 	}
 
 	/**
@@ -637,10 +637,10 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	/**
 	 * Sets the resource providers for this server
 	 */
-	public void setResourceProviders(IResourceProvider... theResourceProviders) {
+	public void setResourceProviders(Collection<IResourceProvider> theResourceProviders) {
 		myResourceProviders.clear();
 		if (theResourceProviders != null) {
-			myResourceProviders.addAll(Arrays.asList(theResourceProviders));
+			myResourceProviders.addAll(theResourceProviders);
 		}
 	}
 
@@ -1518,10 +1518,10 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	 *
 	 * @param theList The list of interceptors (may be null)
 	 */
-	public void setInterceptors(IServerInterceptor... theList) {
+	public void setInterceptors(List<IServerInterceptor> theList) {
 		myInterceptors.clear();
 		if (theList != null) {
-			myInterceptors.addAll(Arrays.asList(theList));
+			myInterceptors.addAll(theList);
 		}
 	}
 
@@ -1530,11 +1530,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	 *
 	 * @see #setResourceProviders(Collection)
 	 */
-	public void setPlainProviders(Collection<Object> theProviders) {
+	public void setPlainProviders(Object... theProv) {
-		myPlainProviders.clear();
+		setPlainProviders(Arrays.asList(theProv));
-		if (theProviders != null) {
-			myPlainProviders.addAll(theProviders);
-		}
 	}
 
 	/**
@@ -1552,10 +1549,10 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	/**
 	 * Sets the resource providers for this server
 	 */
-	public void setResourceProviders(Collection<IResourceProvider> theResourceProviders) {
+	public void setResourceProviders(IResourceProvider... theResourceProviders) {
 		myResourceProviders.clear();
 		if (theResourceProviders != null) {
-			myResourceProviders.addAll(theResourceProviders);
+			myResourceProviders.addAll(Arrays.asList(theResourceProviders));
 		}
 	}
 

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

@@ -21,11 +21,13 @@ package ca.uhn.fhir.rest.server;
  */
 
 import java.util.Collection;
+import java.util.Date;
 import java.util.List;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
 import ca.uhn.fhir.util.VersionUtil;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
@@ -38,7 +40,7 @@ public class RestulfulServerConfiguration {
     private String serverName = "HAPI FHIR";
     private FhirContext fhirContext;
     private IServerAddressStrategy serverAddressStrategy;
-    private String conformanceDate;
+    private IPrimitiveType<Date> myConformanceDate;
     
     /**
      * Constructor
@@ -73,11 +75,10 @@ public class RestulfulServerConfiguration {
     }
 
     /**
-     * Set the serverBindings
+     * Set the theServerBindings
-     * @param serverBindings the serverBindings to set
      */
-    public RestulfulServerConfiguration setServerBindings(List<BaseMethodBinding<?>> serverBindings) {
+    public RestulfulServerConfiguration setServerBindings(List<BaseMethodBinding<?>> theServerBindings) {
-        this.serverBindings = serverBindings;
+        this.serverBindings = theServerBindings;
         return this;
     }
 
@@ -169,20 +170,22 @@ public class RestulfulServerConfiguration {
     }
 
 
-    /**
+	/**
-     * Get the conformanceDate
+	 * Get the date that will be specified in the conformance profile
-     * @return the conformanceDate
+	 * exported by this server. Typically this would be populated with
-     */
+	 * an InstanceType.
-    public String getConformanceDate() {
+	 */
-        return conformanceDate;
+    public IPrimitiveType<Date> getConformanceDate() {
+        return myConformanceDate;
     }
 
     /**
-     * Set the conformanceDate
+     * Set the date that will be specified in the conformance profile
-     * @param conformanceDate the conformanceDate to set
+	  * exported by this server. Typically this would be populated with
+	  * an InstanceType.
      */
-    public void setConformanceDate(String conformanceDate) {
+    public void setConformanceDate(IPrimitiveType<Date> theConformanceDate) {
-        this.conformanceDate = conformanceDate;
+        myConformanceDate = theConformanceDate;
     }
     
 }

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/hapi/rest/server/ServerConformanceProvider.java

@@ -49,6 +49,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.method.*;
 import ca.uhn.fhir.rest.server.method.OperationMethodBinding.ReturnType;
 import ca.uhn.fhir.rest.server.method.SearchParameter;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 /**
  * Server FHIR Provider which serves the conformance statement for a RESTful server implementation
@@ -132,10 +133,10 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 	}
 
 	private DateTimeType conformanceDate() {
-		String buildDate = getServerConfiguration().getConformanceDate();
+		IPrimitiveType<Date> buildDate = getServerConfiguration().getConformanceDate();
-		if (buildDate != null) {
+		if (buildDate != null && buildDate.getValue() != null) {
 			try {
-				return new DateTimeType(buildDate);
+				return new DateTimeType(buildDate.getValueAsString());
 			} catch (DataFormatException e) {
 				// fall through
 			}

hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2/ServerConformanceProvider.java

@@ -30,6 +30,7 @@ import ca.uhn.fhir.rest.server.method.*;
 import ca.uhn.fhir.rest.server.method.OperationMethodBinding.ReturnType;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import javax.servlet.ServletContext;
 import javax.servlet.http.HttpServletRequest;
@@ -136,10 +137,10 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 	}
 
 	private DateTimeDt conformanceDate() {
-		String buildDate = getServerConfiguration().getConformanceDate();
+		IPrimitiveType<Date> buildDate = getServerConfiguration().getConformanceDate();
-		if (buildDate != null) {
+		if (buildDate != null && buildDate.getValue() != null) {
 			try {
-				return new DateTimeDt(buildDate);
+				return new DateTimeDt(buildDate.getValueAsString());
 			} catch (DataFormatException e) {
 				// fall through
 			}

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/rest/server/ServerCapabilityStatementProvider.java

@@ -27,6 +27,7 @@ import org.hl7.fhir.dstu3.model.OperationDefinition.OperationKind;
 import org.hl7.fhir.dstu3.model.OperationDefinition.OperationParameterUse;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import javax.servlet.ServletContext;
 import javax.servlet.http.HttpServletRequest;
@@ -76,7 +77,7 @@ public class ServerCapabilityStatementProvider implements IServerConformanceProv
   private Callable<RestulfulServerConfiguration> myServerConfiguration;
 
   /**
-   * No-arg constructor and seetter so that the ServerConfirmanceProvider can be Spring-wired with the RestfulService avoiding the potential reference cycle that would happen.
+   * No-arg constructor and setter so that the ServerConformanceProvider can be Spring-wired with the RestfulService avoiding the potential reference cycle that would happen.
    */
   public ServerCapabilityStatementProvider() {
     super();
@@ -139,10 +140,10 @@ public class ServerCapabilityStatementProvider implements IServerConformanceProv
   }
 
   private DateTimeType conformanceDate() {
-    String buildDate = getServerConfiguration().getConformanceDate();
+    IPrimitiveType<Date> buildDate = getServerConfiguration().getConformanceDate();
-    if (buildDate != null) {
+    if (buildDate != null && buildDate.getValue() != null) {
       try {
-        return new DateTimeType(buildDate);
+        return new DateTimeType(buildDate.getValueAsString());
       } catch (DataFormatException e) {
         // fall through
       }

hapi-fhir-structures-dstu3/src/test/java/org/hl7/fhir/dstu3/hapi/rest/server/ServerCapabilityStatementProviderDstu3Test.java

@@ -15,6 +15,7 @@ import java.util.*;
 import javax.servlet.ServletConfig;
 import javax.servlet.http.HttpServletRequest;
 
+import ca.uhn.fhir.model.primitive.InstantDt;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.CapabilityStatement.*;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -527,29 +528,42 @@ public class ServerCapabilityStatementProviderDstu3Test {
 	@Test
 	public void testSearchReferenceParameterWithList() throws Exception {
 
-		RestfulServer rsNoType = new RestfulServer(ourCtx);
+		RestfulServer rsNoType = new RestfulServer(ourCtx){
+			@Override
+			public RestulfulServerConfiguration createConfiguration() {
+				RestulfulServerConfiguration retVal = super.createConfiguration();
+				retVal.setConformanceDate(new InstantDt("2011-02-22T11:22:33Z"));
+				return retVal;
+			}
+		};
 		rsNoType.registerProvider(new SearchProviderWithListNoType());
 		ServerCapabilityStatementProvider scNoType = new ServerCapabilityStatementProvider(rsNoType);
 		rsNoType.setServerConformanceProvider(scNoType);
 		rsNoType.init(createServletConfig());
-		scNoType.getServerConfiguration().setConformanceDate("2011-02-22T11:22:33Z");
 
 		CapabilityStatement conformance = scNoType.getServerConformance(createHttpServletRequest());
 		String confNoType = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance);
 		ourLog.info(confNoType);
 
-		RestfulServer rsWithType = new RestfulServer(ourCtx);
+		RestfulServer rsWithType = new RestfulServer(ourCtx){
+			@Override
+			public RestulfulServerConfiguration createConfiguration() {
+				RestulfulServerConfiguration retVal = super.createConfiguration();
+				retVal.setConformanceDate(new InstantDt("2011-02-22T11:22:33Z"));
+				return retVal;
+			}
+		};
 		rsWithType.registerProvider(new SearchProviderWithListWithType());
 		ServerCapabilityStatementProvider scWithType = new ServerCapabilityStatementProvider(rsWithType);
 		rsWithType.setServerConformanceProvider(scWithType);
 		rsWithType.init(createServletConfig());
-		scWithType.getServerConfiguration().setConformanceDate("2011-02-22T11:22:33Z");
 
 		CapabilityStatement conformanceWithType = scWithType.getServerConformance(createHttpServletRequest());
 		String confWithType = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformanceWithType);
 		ourLog.info(confWithType);
 
 		assertEquals(confNoType, confWithType);
+		assertThat(confNoType, containsString("<date value=\"2011-02-22T11:22:33Z\"/>"));
 	}
 
 	@Test

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/conf/ServerConformanceProvider.java

@@ -50,6 +50,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.method.*;
 import ca.uhn.fhir.rest.server.method.OperationMethodBinding.ReturnType;
 import ca.uhn.fhir.rest.server.method.SearchParameter;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 /**
  * Server FHIR Provider which serves the conformance statement for a RESTful
@@ -314,10 +315,10 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
   }
 
   private DateTimeType conformanceDate() {
-    String buildDate = getServerConfiguration().getConformanceDate();
+    IPrimitiveType<Date> buildDate = getServerConfiguration().getConformanceDate();
-    if (buildDate != null) {
+    if (buildDate != null && buildDate.getValue() != null) {
       try {
-        return new DateTimeType(buildDate);
+        return new DateTimeType(buildDate.getValueAsString());
       } catch (DataFormatException e) {
         // fall through
       }

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/rest/server/ServerCapabilityStatementProvider.java

@@ -21,6 +21,7 @@ import ca.uhn.fhir.rest.server.method.SearchParameter;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.CapabilityStatement.*;
 import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
@@ -139,10 +140,10 @@ public class ServerCapabilityStatementProvider implements IServerConformanceProv
   }
 
   private DateTimeType conformanceDate() {
-    String buildDate = getServerConfiguration().getConformanceDate();
+    IPrimitiveType<Date> buildDate = getServerConfiguration().getConformanceDate();
-    if (buildDate != null) {
+    if (buildDate != null && buildDate.getValue() != null) {
       try {
-        return new DateTimeType(buildDate);
+        return new DateTimeType(buildDate.getValueAsString());
       } catch (DataFormatException e) {
         // fall through
       }