Merge branch 'master' into ja_2022_date_ordinal_postgres_fail

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
     <parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>6.0.0-PRE1-SNAPSHOT</version>
+		 <version>6.0.0-PRE3-SNAPSHOT</version>
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>
 

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE1-SNAPSHOT</version>
+		<version>6.0.0-PRE3-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE1-SNAPSHOT</version>
+		<version>6.0.0-PRE3-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

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

@@ -246,7 +246,7 @@ default IBaseResource fetchValueSet(String theValueSetUrl) {
 	 * @return Returns a validation result object
 	 */
 	@Nullable
-	default CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
+	default CodeValidationResult validateCode(@Nonnull ValidationSupportContext theValidationSupportContext, @Nonnull ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
 		return null;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/i18n/Msg.java

@@ -25,7 +25,7 @@ public final class Msg {
 
 	/**
 	 * IMPORTANT: Please update the following comment after you add a new code
-	 * Last code value: 2023
+	 * Last code value: 2034
 	 */
 
 	private Msg() {}

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

@@ -199,8 +199,6 @@ protected Iterable<CompositeChildElement> compositeChildIterator(IBase theCompos
 				} else if (myNext.getDef() instanceof RuntimeChildNarrativeDefinition) {
 					if (isSuppressNarratives() || isSummaryMode()) {
 						continue;
-					} else if (theContainedResource) {
-						continue;
 					}
 				} else if (myNext.getDef() instanceof RuntimeChildContainedResources) {
 					if (theContainedResource) {

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

@@ -534,8 +534,6 @@ private void encodeCompositeElementChildrenToStreamWriter(RuntimeResourceDefinit
 						beginArray(theEventWriter, nextChildSpecificName);
 						inArray = true;
 						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, nextChildElem, force, theEncodeContext);
-					} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theContainedResource) {
-						// suppress narratives from contained resources
 					} else {
 						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, nextChildSpecificName, theContainedResource, nextChildElem, false, theEncodeContext);
 					}

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

@@ -446,8 +446,6 @@ private void encodeCompositeElementToStreamWriter(IBaseResource theResource, IBa
 							}
 						}
 						encodeChildElementToStreamWriter(theResource, theEventWriter, nextChild, nextValue, childName, childDef, getExtensionUrl(extension.getUrl()), theContainedResource, nextChildElem, theEncodeContext);
-					} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theContainedResource) {
-						// suppress narratives from contained resources
 					} else {
 						encodeChildElementToStreamWriter(theResource, theEventWriter, nextChild, nextValue, childName, childDef, extensionUrl, theContainedResource, nextChildElem, theEncodeContext);
 					}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java

@@ -218,6 +218,7 @@ public class Constants {
 	public static final String PARAMQUALIFIER_TOKEN_TEXT = ":text";
 	public static final String PARAMQUALIFIER_MDM = ":mdm";
 	public static final String PARAMQUALIFIER_TOKEN_OF_TYPE = ":of-type";
+	public static final String PARAMQUALIFIER_TOKEN_NOT = ":not";
 	public static final int STATUS_HTTP_200_OK = 200;
 	public static final int STATUS_HTTP_201_CREATED = 201;
 	public static final int STATUS_HTTP_204_NO_CONTENT = 204;
@@ -291,6 +292,10 @@ public class Constants {
 	public static final String SUBSCRIPTION_MULTITYPE_STAR = "*";
 	public static final String SUBSCRIPTION_STAR_CRITERIA = SUBSCRIPTION_MULTITYPE_PREFIX + SUBSCRIPTION_MULTITYPE_STAR + SUBSCRIPTION_MULTITYPE_SUFFIX;
 	public static final String INCLUDE_STAR = "*";
+	public static final String PARAMQUALIFIER_TOKEN_IN = ":in";
+	public static final String PARAMQUALIFIER_TOKEN_NOT_IN = ":not-in";
+	public static final String PARAMQUALIFIER_TOKEN_ABOVE = ":above";
+	public static final String PARAMQUALIFIER_TOKEN_BELOW = ":below";
 
 	static {
 		CHARSET_UTF8 = StandardCharsets.UTF_8;

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/IResourceSupportedSvc.java

@@ -0,0 +1,5 @@
+package ca.uhn.fhir.rest.api;
+
+public interface IResourceSupportedSvc {
+	boolean isSupported(String theResourceName);
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/UrlUtil.java

@@ -346,10 +346,6 @@ public static UrlParts parseUrl(String theUrl) {
 		String url = theUrl;
 		UrlParts retVal = new UrlParts();
 		if (url.startsWith("http")) {
-			if (url.startsWith("/")) {
-				url = url.substring(1);
-			}
-
 			int qmIdx = url.indexOf('?');
 			if (qmIdx != -1) {
 				retVal.setParams(defaultIfBlank(url.substring(qmIdx + 1), null));
@@ -372,10 +368,7 @@ public static UrlParts parseUrl(String theUrl) {
 			}
 		}
 
-		if (url.length() > 1 && url.charAt(0) == '/' && Character.isLetter(url.charAt(1)) && url.contains("?")) {
-			url = url.substring(1);
-		}
-		int nextStart = 0;
+		int nextStart = parsingStart;
 		boolean nextIsHistory = false;
 
 		for (int idx = parsingStart; idx < url.length(); idx++) {

hapi-fhir-batch/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE1-SNAPSHOT</version>
+		<version>6.0.0-PRE3-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-batch/src/test/java/ca/uhn/fhir/jpa/batch/config/BatchJobConfig.java

@@ -44,7 +44,7 @@ public Tasklet sampleTasklet() {
 
 	@Bean
 	@StepScope
-	public ItemReader<String> reader() {
+	public SampleItemReader reader() {
 		return new SampleItemReader();
 	}
 

hapi-fhir-bom/pom.xml

@@ -3,14 +3,14 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>ca.uhn.hapi.fhir</groupId>
     <artifactId>hapi-fhir-bom</artifactId>
-    <version>6.0.0-PRE1-SNAPSHOT</version>
+    <version>6.0.0-PRE3-SNAPSHOT</version>
     <packaging>pom</packaging>
 	 <name>HAPI FHIR BOM</name>
 
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE1-SNAPSHOT</version>
+		<version>6.0.0-PRE3-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-checkstyle/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.0.0-PRE1-SNAPSHOT</version>
+		<version>6.0.0-PRE3-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-checkstyle/src/main/java/ca/uhn/fhir/checks/HapiErrorCodeCheck.java

@@ -7,8 +7,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.HashSet;
-import java.util.Set;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * mvn -P CI,ALLMODULES checkstyle:check
@@ -17,7 +17,7 @@
 public final class HapiErrorCodeCheck extends AbstractCheck {
 	private static final Logger ourLog = LoggerFactory.getLogger(HapiErrorCodeCheck.class);
 
-	private static final Set<Integer> ourCodesUsed = new HashSet<>();
+	private static final Map<Integer, String> ourCodesUsed = new HashMap<>();
 
 	@Override
 	public int[] getDefaultTokens() {
@@ -68,10 +68,14 @@ private void validateMessageCode(DetailAST theAst) {
 			DetailAST numberNode = msgNode.getParent().getNextSibling().getFirstChild().getFirstChild();
 			if (TokenTypes.NUM_INT == numberNode.getType()) {
 				Integer code = Integer.valueOf(numberNode.getText());
-				if (!ourCodesUsed.add(code)) {
+				if (ourCodesUsed.containsKey(code)) {
 					log(theAst.getLineNo(), "Two different exception messages call Msg.code(" +
 						code +
-						").  Each thrown exception throw call Msg.code() with a different code.");
+						").  Each thrown exception throw call Msg.code() with a different code. " +
+						"Previously found at: " + ourCodesUsed.get(code));
+				} else {
+					String location = getFileContents().getFileName() + ":" + instantiation.getLineNo() + ":" + instantiation.getColumnNo() + "(" + code + ")";
+					ourCodesUsed.put(code, location);
 				}
 			} else {
 				log(theAst.getLineNo(), "Called Msg.code() with a non-integer argument");

hapi-fhir-checkstyle/src/test/java/ca/uhn/fhir/checks/HapiErrorCodeCheckTest.java

@@ -18,6 +18,7 @@
 import java.util.List;
 
 import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.endsWith;
 import static org.hamcrest.Matchers.startsWith;
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -47,7 +48,8 @@ public void testExpectedErrors() throws CheckstyleException {
 		assertThat(errorLines[0], startsWith("[ERROR] "));
 		assertThat(errorLines[0], endsWith("BadClass.java:7: Exception thrown that does not call Msg.code() [HapiErrorCode]"));
 		assertThat(errorLines[1], startsWith("[ERROR] "));
-		assertThat(errorLines[1], endsWith("BadClass.java:11: Two different exception messages call Msg.code(2).  Each thrown exception throw call Msg.code() with a different code. [HapiErrorCode]"));
+		assertThat(errorLines[1], containsString("BadClass.java:11: Two different exception messages call Msg.code(2).  Each thrown exception throw call Msg.code() with a different code."));
+		assertThat(errorLines[1], containsString("BadClass.java:9:9"));
 	}
 
 	private Checker buildChecker() throws CheckstyleException {

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE1-SNAPSHOT</version>
+		<version>6.0.0-PRE3-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>6.0.0-PRE1-SNAPSHOT</version>
+		<version>6.0.0-PRE3-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.0.0-PRE1-SNAPSHOT</version>
+		<version>6.0.0-PRE3-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java

@@ -20,14 +20,15 @@
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
+import ca.uhn.fhir.jpa.config.HapiJpaConfig;
+import ca.uhn.fhir.jpa.config.JpaDstu2Config;
+import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
 import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
-import org.apache.commons.lang3.time.DateUtils;
-import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
@@ -45,8 +46,8 @@
 
 @Configuration
 @EnableTransactionManagement()
-@Import(CommonConfig.class)
-public class FhirServerConfig extends BaseJavaConfigDstu2 {
+@Import({CommonConfig.class, 	JpaDstu2Config.class, HapiJpaConfig.class})
+public class FhirServerConfig {
 
 	@Autowired
 	private DataSource myDataSource;
@@ -64,10 +65,9 @@ public DaoConfig daoConfig() {
 		return retVal;
 	}
 
-	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
+		LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(myDataSource);
 		retVal.setJpaProperties(myJpaProperties);
@@ -92,13 +92,13 @@ public LoggingInterceptor loggingInterceptor() {
 	 * This interceptor adds some pretty syntax highlighting in responses when a browser is detected
 	 * @return
 	 */
-	@Bean(autowire = Autowire.BY_TYPE)
+	@Bean
 	public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
 		ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
 		return retVal;
 	}
 
-	@Bean(autowire = Autowire.BY_TYPE)
+	@Bean
 	public IServerInterceptor subscriptionSecurityInterceptor() {
 		SubscriptionsRequireManualActivationInterceptorDstu2 retVal = new SubscriptionsRequireManualActivationInterceptorDstu2();
 		return retVal;

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu3.java

@@ -20,14 +20,14 @@
  * #L%
  */
 
-import ca.uhn.fhir.jpa.binstore.DatabaseBlobBinaryStorageSvcImpl;
-import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
-import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.config.HapiJpaConfig;
+import ca.uhn.fhir.jpa.config.dstu3.JpaDstu3Config;
+import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
 import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
-import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
@@ -52,19 +52,18 @@
  */
 @Configuration
 @EnableTransactionManagement()
-@Import(CommonConfig.class)
-public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
+@Import({CommonConfig.class, JpaDstu3Config.class, HapiJpaConfig.class,})
+public class FhirServerConfigDstu3 {
 
 	@Autowired
 	private DataSource myDataSource;
 	@Autowired()
 	@Qualifier("jpaProperties")
 	private Properties myJpaProperties;
 
-	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
+		LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(myDataSource);
 		retVal.setJpaProperties(myJpaProperties);
@@ -89,13 +88,13 @@ public LoggingInterceptor loggingInterceptor() {
 	 * This interceptor adds some pretty syntax highlighting in responses when a browser is detected
 	 * @return
 	 */
-	@Bean(autowire = Autowire.BY_TYPE)
+	@Bean
 	public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
 		ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
 		return retVal;
 	}
 
-	@Bean(autowire = Autowire.BY_TYPE)
+	@Bean
 	public IServerInterceptor subscriptionSecurityInterceptor() {
 		SubscriptionsRequireManualActivationInterceptorDstu3 retVal = new SubscriptionsRequireManualActivationInterceptorDstu3();
 		return retVal;