Merge branch 'master' into OWASPprofile

example-projects/hapi-fhir-jpaserver-cds-example/pom.xml

@@ -224,13 +224,17 @@
 		</pluginManagement>
 
 		<plugins>
-			<!-- Tell Maven which Java source version you want to use -->
+
+			<!--
+			The CQF-Ruler project has some OWASP dependency security failures which we don't want
+			to cause the whole build to fail. TODO: investigate these
+			-->
 			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-compiler-plugin</artifactId>
+				<groupId>org.owasp</groupId>
+				<artifactId>dependency-check-maven</artifactId>
 				<configuration>
-					<source>1.7</source>
-					<target>1.7</target>
+					<failBuildOnCVSS>99</failBuildOnCVSS>
+					<failOnError>false</failOnError>
 				</configuration>
 			</plugin>
 

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

@@ -20,29 +20,32 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.Include;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import javax.persistence.EntityManager;
 import java.util.Collection;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
-import javax.persistence.EntityManager;
-
-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.rest.param.DateRangeParam;
-
 public interface ISearchBuilder {
 
 	Iterator<Long> createQuery(SearchParameterMap theParams, String theSearchUuid);
 
-	void setType(Class<? extends IBaseResource> theResourceType, String theResourceName);
-
 	void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids, boolean theForHistoryOperation, EntityManager theEntityManager,
 									FhirContext theContext, IDao theDao);
 
 	Set<Long> loadReverseIncludes(IDao theCallingDao, FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode,
 											DateRangeParam theLastUpdated);
 
+	/**
+	 * How many results may be fetched at once
+	 */
+	void setFetchSize(int theFetchSize);
+
+	void setType(Class<? extends IBaseResource> theResourceType, String theResourceName);
+
 }

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

@@ -59,6 +59,9 @@ import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.tuple.Pair;
 import org.hibernate.ScrollMode;
 import org.hibernate.ScrollableResults;
+import org.hibernate.engine.spi.EntityKey;
+import org.hibernate.engine.spi.PersistenceContext;
+import org.hibernate.internal.SessionImpl;
 import org.hibernate.query.Query;
 import org.hl7.fhir.dstu3.model.BaseResource;
 import org.hl7.fhir.instance.model.api.IAnyResource;
@@ -104,6 +107,7 @@ public class SearchBuilder implements ISearchBuilder {
 	private ISearchParamRegistry mySearchParamRegistry;
 	private String mySearchUuid;
 	private IHapiTerminologySvc myTerminologySvc;
+	private int myFetchSize;
 
 	/**
 	 * Constructor
@@ -1926,6 +1930,11 @@ public class SearchBuilder implements ISearchBuilder {
 		}
 	}
 
+	@Override
+	public void setFetchSize(int theFetchSize) {
+		myFetchSize = theFetchSize;
+	}
+
 	@Override
 	public void setType(Class<? extends IBaseResource> theResourceType, String theResourceName) {
 		myResourceType = theResourceType;
@@ -2181,6 +2190,7 @@ public class SearchBuilder implements ISearchBuilder {
 				final TypedQuery<Long> query = createQuery(mySort, maximumResults);
 
 				Query<Long> hibernateQuery = (Query<Long>) query;
+				hibernateQuery.setFetchSize(myFetchSize);
 				ScrollableResults scroll = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
 				myResultsIterator = new ScrollableResultsIterator(scroll);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java

@@ -206,6 +206,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		Class<? extends IBaseResource> resourceTypeClass = myContext.getResourceDefinition(theResourceType).getImplementingClass();
 		final ISearchBuilder sb = theCallingDao.newSearchBuilder();
 		sb.setType(resourceTypeClass, theResourceType);
+		sb.setFetchSize(mySyncSize);
 
 		final Integer loadSynchronousUpTo;
 		if (theCacheControlDirective != null && theCacheControlDirective.isNoStore()) {
@@ -233,7 +234,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				public SimpleBundleProvider doInTransaction(TransactionStatus theStatus) {
 
 					// Load the results synchronously
-					final List<Long> pids = new ArrayList<Long>();
+					final List<Long> pids = new ArrayList<>();
 
 					Iterator<Long> resultIter = sb.createQuery(theParams, searchUuid);
 					while (resultIter.hasNext()) {
@@ -458,8 +459,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		private final SearchParameterMap myParams;
 		private final String myResourceType;
 		private final Search mySearch;
-		private final ArrayList<Long> mySyncedPids = new ArrayList<Long>();
-		private final ArrayList<Long> myUnsyncedPids = new ArrayList<Long>();
+		private final ArrayList<Long> mySyncedPids = new ArrayList<>();
+		private final ArrayList<Long> myUnsyncedPids = new ArrayList<>();
 		private boolean myAbortRequested;
 		private int myCountSaved = 0;
 		private String mySearchUuid;
@@ -503,7 +504,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		 * It is called automatically by the thread pool.
 		 */
 		@Override
-		public Void call() throws Exception {
+		public Void call() {
 			StopWatch sw = new StopWatch();
 
 			try {
@@ -631,10 +632,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			boolean keepWaiting;
 			do {
 				synchronized (mySyncedPids) {
-					keepWaiting = false;
-					if (mySyncedPids.size() < theToIndex && mySearch.getStatus() == SearchStatusEnum.LOADING) {
-						keepWaiting = true;
-					}
+					keepWaiting = mySyncedPids.size() < theToIndex && mySearch.getStatus() == SearchStatusEnum.LOADING;
 				}
 				if (keepWaiting) {
 					ourLog.info("Waiting, as we only have {} results", mySyncedPids.size());

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/StatelessSessionFactoryBean.java

@@ -0,0 +1,157 @@
+package ca.uhn.fhir.jpa.util;
+
+import org.aopalliance.intercept.MethodInterceptor;
+import org.aopalliance.intercept.MethodInvocation;
+import org.hibernate.SessionFactory;
+import org.hibernate.StatelessSession;
+import org.hibernate.engine.spi.SessionImplementor;
+import org.springframework.aop.framework.ProxyFactory;
+import org.springframework.beans.factory.FactoryBean;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.jdbc.datasource.DataSourceUtils;
+import org.springframework.orm.jpa.EntityManagerFactoryUtils;
+import org.springframework.orm.jpa.LocalEntityManagerFactoryBean;
+import org.springframework.transaction.support.ResourceHolderSynchronization;
+import org.springframework.transaction.support.TransactionSynchronizationAdapter;
+import org.springframework.transaction.support.TransactionSynchronizationManager;
+
+import javax.persistence.EntityManager;
+import javax.persistence.EntityManagerFactory;
+import java.sql.Connection;
+
+import static org.springframework.orm.jpa.EntityManagerFactoryUtils.ENTITY_MANAGER_SYNCHRONIZATION_ORDER;
+import static org.springframework.util.ReflectionUtils.invokeMethod;
+
+/**
+ * Hibernate's {@link StatelessSession} factory which will be bound to the
+ * current transaction. This factory returns a Proxy which delegates method
+ * calls to the underlying {@link StatelessSession} bound to transaction. At the
+ * end of the transaction the session is automatically closed. This class
+ * borrows idea's from {@link DataSourceUtils},
+ * {@link EntityManagerFactoryUtils}, {@link ResourceHolderSynchronization} and
+ * {@link LocalEntityManagerFactoryBean}.
+ */
+public class StatelessSessionFactoryBean implements FactoryBean<StatelessSession> {
+
+	private SessionFactory sessionFactory;
+
+	@Autowired
+	public StatelessSessionFactoryBean(SessionFactory theSessionFactory) {
+		this.sessionFactory = theSessionFactory;
+	}
+
+	@Override
+	public StatelessSession getObject() throws Exception {
+		StatelessSessionInterceptor statelessSessionInterceptor = new StatelessSessionInterceptor(
+			 sessionFactory);
+		return ProxyFactory.getProxy(StatelessSession.class, statelessSessionInterceptor);
+	}
+
+	@Override
+	public Class<?> getObjectType() {
+		return StatelessSession.class;
+	}
+
+	@Override
+	public boolean isSingleton() {
+		return true;
+	}
+
+	/**
+	 * Use this to override the {@link SessionFactory} obtained from the
+	 * {@link EntityManagerFactory}. Please note that the connection will still
+	 * be used from the {@link EntityManager}.
+	 */
+	public void setSessionFactory(SessionFactory sessionFactory) {
+		this.sessionFactory = sessionFactory;
+	}
+
+	private static class StatelessSessionInterceptor implements MethodInterceptor {
+
+		private final SessionFactory sessionFactory;
+
+		public StatelessSessionInterceptor(
+													  SessionFactory sessionFactory) {
+			this.sessionFactory = sessionFactory;
+		}
+
+		private void bindWithTransaction(StatelessSession statelessSession) {
+			TransactionSynchronizationManager
+				.registerSynchronization(new StatelessSessionSynchronization(sessionFactory,
+					statelessSession));
+			TransactionSynchronizationManager.bindResource(sessionFactory, statelessSession);
+		}
+
+		private StatelessSession getCurrentSession() {
+			if (!TransactionSynchronizationManager.isActualTransactionActive()) {
+				throw new IllegalStateException(
+					"There should be an active transaction for the current thread.");
+			}
+			StatelessSession statelessSession = (StatelessSession) TransactionSynchronizationManager
+				.getResource(sessionFactory);
+			if (statelessSession == null) {
+				statelessSession = openNewStatelessSession();
+				bindWithTransaction(statelessSession);
+			}
+			return statelessSession;
+		}
+
+		@Override
+		public Object invoke(MethodInvocation invocation) throws Throwable {
+			StatelessSession statelessSession = getCurrentSession();
+			return invokeMethod(invocation.getMethod(), statelessSession, invocation.getArguments());
+		}
+
+		/**
+		 * It is important we obtain the physical (real) connection otherwise it
+		 * will be double proxied and there will be problems releasing the
+		 * connection.
+		 */
+		private Connection obtainPhysicalConnection() {
+			EntityManager entityManager = EntityManagerFactoryUtils
+				.getTransactionalEntityManager(sessionFactory);
+			SessionImplementor sessionImplementor = (SessionImplementor) entityManager
+				.getDelegate();
+//			return sessionImplementor.getTransactionCoordinator().getJdbcCoordinator()
+//				.getLogicalConnection().getConnection();
+			return null;
+		}
+
+		private StatelessSession openNewStatelessSession() {
+			Connection connection = obtainPhysicalConnection();
+			return sessionFactory.openStatelessSession(connection);
+		}
+	}
+
+	private static class StatelessSessionSynchronization extends TransactionSynchronizationAdapter {
+
+		private final SessionFactory sessionFactory;
+		private final StatelessSession statelessSession;
+
+		public StatelessSessionSynchronization(SessionFactory sessionFactory,
+															StatelessSession statelessSession) {
+			this.sessionFactory = sessionFactory;
+			this.statelessSession = statelessSession;
+		}
+
+		@Override
+		public void beforeCommit(boolean readOnly) {
+			if (!readOnly) {
+//				((TransactionContext) statelessSession).flu
+			}
+		}
+
+		@Override
+		public void beforeCompletion() {
+			TransactionSynchronizationManager.unbindResource(sessionFactory);
+			statelessSession.close();
+		}
+
+		@Override
+		public int getOrder() {
+			return ENTITY_MANAGER_SYNCHRONIZATION_ORDER - 100;
+		}
+
+	}
+
+}

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java

@@ -68,6 +68,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		retVal.getTreatBaseUrlsAsLocal().add("https://fhirtest.uhn.ca/baseDstu2");
 		retVal.setCountSearchResultsUpTo(TestR4Config.COUNT_SEARCH_RESULTS_UP_TO);
 		retVal.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
+		retVal.setFetchSizeDefaultMaximum(10000);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -57,6 +57,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		retVal.getTreatBaseUrlsAsLocal().add("https://fhirtest.uhn.ca/baseDstu3");
 		retVal.setCountSearchResultsUpTo(TestR4Config.COUNT_SEARCH_RESULTS_UP_TO);
 		retVal.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
+		retVal.setFetchSizeDefaultMaximum(10000);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java

@@ -58,6 +58,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 		retVal.getTreatBaseUrlsAsLocal().add("https://fhirtest.uhn.ca/baseR4");
 		retVal.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
 		retVal.setCountSearchResultsUpTo(TestR4Config.COUNT_SEARCH_RESULTS_UP_TO);
+		retVal.setFetchSizeDefaultMaximum(10000);
 		return retVal;
 	}
 

osgi/hapi-fhir-karaf-features/pom.xml

@@ -7,7 +7,7 @@
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
 		<version>3.3.0-SNAPSHOT</version>
-		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
+		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
 	<groupId>ca.uhn.hapi.fhir.karaf</groupId>

osgi/hapi-fhir-karaf-integration-tests/pom.xml

@@ -21,7 +21,7 @@
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
 		<version>3.3.0-SNAPSHOT</version>
-		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
+		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
    <artifactId>hapi-fhir-karaf-integration-tests</artifactId>

pom.xml

@@ -1,5 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
+			xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 
 	<parent>
 		<groupId>org.sonatype.oss</groupId>
@@ -1320,7 +1321,8 @@
 				<plugin>
 					<groupId>org.jacoco</groupId>
 					<artifactId>
-						jacoco-maven-plugin</artifactId>
+						jacoco-maven-plugin
+					</artifactId>
 					<version>0.7.9</version>
 				</plugin>
 				<plugin>
@@ -1568,7 +1570,9 @@
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
-									<replacetoken>http://netdna.bootstrapcdn.com/twitter-bootstrap/2.3.1/css/bootstrap-responsive.min.css</replacetoken>
+									<replacetoken>
+										http://netdna.bootstrapcdn.com/twitter-bootstrap/2.3.1/css/bootstrap-responsive.min.css
+									</replacetoken>
 									<replacevalue>./css/bootstrap-responsive.min.css</replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
@@ -1578,8 +1582,10 @@
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
-									<replacetoken>http://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css</replacetoken>
-									<replacevalue>https://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css</replacevalue>
+									<replacetoken>http://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css
+									</replacetoken>
+									<replacevalue>https://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css
+									</replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
@@ -1623,28 +1629,35 @@
 								<echo>Adding Fontawesome</echo>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
-									<replacetoken><![CDATA[<a href="download.html" title="Download">Download</a>]]></replacetoken>
-									<replacevalue><![CDATA[<a href="download.html"  title="Download"><i class="fa fa-download"></i> Download</a>]]></replacevalue>
+									<replacetoken>
+										<![CDATA[<a href="download.html" title="Download">Download</a>]]></replacetoken>
+									<replacevalue>
+										<![CDATA[<a href="download.html"  title="Download"><i class="fa fa-download"></i> Download</a>]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
-									<replacetoken><![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project" class="externalLink">GitHub Project</a>]]></replacetoken>
-									<replacevalue><![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project"  class="externalLink"><i class="fa fa-github"></i> GitHub Project</a>]]></replacevalue>
+									<replacetoken>
+										<![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project" class="externalLink">GitHub Project</a>]]></replacetoken>
+									<replacevalue>
+										<![CDATA[<a href="https://github.com/jamesagnew/hapi-fhir/" title="GitHub Project"  class="externalLink"><i class="fa fa-github"></i> GitHub Project</a>]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Test Servers <]]></replacetoken>
-									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-fire"></i>&nbsp;Test Servers&nbsp;<]]></replacevalue>
+									<replacevalue>
+										<![CDATA[data-toggle="dropdown"><i class="fa fa-fire"></i>&nbsp;Test Servers&nbsp;<]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Documentation <]]></replacetoken>
-									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-book"></i>&nbsp;Documentation&nbsp;<]]></replacevalue>
+									<replacevalue>
+										<![CDATA[data-toggle="dropdown"><i class="fa fa-book"></i>&nbsp;Documentation&nbsp;<]]></replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
 									<replacetoken><![CDATA[data-toggle="dropdown">Get Help <]]></replacetoken>
-									<replacevalue><![CDATA[data-toggle="dropdown"><i class="fa fa-support"></i>&nbsp;Get Help&nbsp;<]]></replacevalue>
+									<replacevalue>
+										<![CDATA[data-toggle="dropdown"><i class="fa fa-support"></i>&nbsp;Get Help&nbsp;<]]></replacevalue>
 								</replace>
 								<echo>Changing Breadcrumbs</echo>
 								<replace dir="target/site" summary="true">
@@ -1860,9 +1873,12 @@
 				<configuration>
 					<reportsDirectories>
 						<reportDirectory>${project.basedir}/hapi-fhir-base/target/surefire-reports/</reportDirectory>
-						<reportDirectory>${project.basedir}/hapi-fhir-structures-dstu/target/surefire-reports/</reportDirectory>
-						<reportDirectory>${project.basedir}/hapi-fhir-structures-dstu2/target/surefire-reports/</reportDirectory>
-						<reportDirectory>${project.basedir}/hapi-fhir-jpaserver-base/target/surefire-reports/</reportDirectory>
+						<reportDirectory>${project.basedir}/hapi-fhir-structures-dstu/target/surefire-reports/
+						</reportDirectory>
+						<reportDirectory>${project.basedir}/hapi-fhir-structures-dstu2/target/surefire-reports/
+						</reportDirectory>
+						<reportDirectory>${project.basedir}/hapi-fhir-jpaserver-base/target/surefire-reports/
+						</reportDirectory>
 					</reportsDirectories>
 				</configuration>
 			</plugin>
@@ -1977,8 +1993,6 @@
 				<module>hapi-tinder-plugin</module>
 				<module>hapi-tinder-test</module>
 				<module>hapi-fhir-client</module>
-				<module>hapi-fhir-karaf-features</module>
-				<module>hapi-fhir-karaf-integration-tests</module>
 				<module>hapi-fhir-server</module>
 				<module>hapi-fhir-validation</module>
 				<!--<module>hapi-fhir-narrativegenerator</module>-->
@@ -2006,6 +2020,8 @@
 				<module>hapi-fhir-cli</module>
 				<module>hapi-fhir-dist</module>
 				<module>examples</module>
+				<module>osgi/hapi-fhir-karaf-features</module>
+				<module>osgi/hapi-fhir-karaf-integration-tests</module>
 				<module>example-projects/hapi-fhir-base-example-embedded-ws</module>
 				<module>example-projects/hapi-fhir-standalone-overlay-example</module>
 				<module>example-projects/hapi-fhir-jpaserver-cds-example</module>