Add validation

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/App.java

@@ -35,6 +35,7 @@ public class App {
 		ourCommands.add(new RunServerCommand());
 		ourCommands.add(new ExampleDataUploader());
 		ourCommands.add(new ValidateCommand());
+		ourCommands.add(new ValidationDataUploader());
 
 		Collections.sort(ourCommands);
 	}

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java

@@ -48,6 +48,8 @@ public class RunServerCommand extends BaseCommand {
 	public void run(CommandLine theCommandLine) throws ParseException {
 		myPort = parseOptionInteger(theCommandLine, OPTION_P, DEFAULT_PORT);
 
+//		((ch.qos.logback.classic.Logger)LoggerFactory.getLogger("/")).setLevel(Level.ERROR);
+
 		ourLog.info("Preparing HAPI FHIR JPA server");
 		File tempWarFile;
 		try {
@@ -81,6 +83,8 @@ public class RunServerCommand extends BaseCommand {
 		ourLog.info("Server started on port {}", myPort);
 		ourLog.info("Web Testing UI : http://localhost:{}/", myPort);
 		ourLog.info("Server Base URL: http://localhost:{}/baseDstu2/", myPort);
+		
+		
 	}
 
 	public void run(String[] theArgs) {

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/ValidationDataUploader.java

@@ -1,134 +1,157 @@
 package ca.uhn.fhir.cli;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
 import java.io.IOException;
-import java.io.UnsupportedEncodingException;
 
 import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
-import org.apache.http.client.ClientProtocolException;
-import org.hl7.fhir.instance.model.Bundle;
-import org.hl7.fhir.instance.model.Bundle.BundleEntryComponent;
-import org.hl7.fhir.instance.model.StructureDefinition;
-import org.hl7.fhir.instance.model.ValueSet;
 import org.springframework.core.io.Resource;
 import org.springframework.core.io.support.PathMatchingResourcePatternResolver;
 import org.springframework.core.io.support.ResourcePatternResolver;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
+import ca.uhn.fhir.model.dstu2.resource.StructureDefinition;
+import ca.uhn.fhir.model.dstu2.resource.ValueSet;
+import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.client.IGenericClient;
 
 public class ValidationDataUploader extends BaseCommand {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValidationDataUploader.class);
 
-	public static void main(String[] args) throws Exception {
+	@Override
-		new ValidationDataUploader().execute();
+	public String getCommandDescription() {
+		return "Uploads the conformance resources (StructureDefinition and ValueSet) from the official FHIR definitions.";
 	}
 
-	private void execute() throws IOException, ClientProtocolException, UnsupportedEncodingException {
+	@Override
-		ourLog.info("Starting...");
+	public String getCommandName() {
+		return "upload-definitions";
+	}
 
-		FhirContext ctx = FhirContext.forDstu2Hl7Org();
+	@Override
+	public Options getOptions() {
+		Options options = new Options();
+		Option opt;
 
-		IGenericClient client = newClient(ctx,"");
+		opt = new Option("t", "target", true, "Base URL for the target server (e.g. \"http://example.com/fhir\")");
+		opt.setRequired(true);
+		options.addOption(opt);
 
-		int total;
+		return options;
-		int count;
+	}
 
-		// String vsContents =
+	@Override
-		// IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/valuesets.xml"),
+	public void run(CommandLine theCommandLine) throws ParseException {
-		// "UTF-8");
+		String targetServer = theCommandLine.getOptionValue("t");
-		// Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, vsContents);
+		if (isBlank(targetServer)) {
-		//
+			throw new ParseException("No target server (-t) specified");
-		// int total = bundle.getEntry().size();
+		} else if (targetServer.startsWith("http") == false) {
-		// int count = 1;
+			throw new ParseException("Invalid target server specified, must begin with 'http'");
-		// for (BundleEntryComponent i : bundle.getEntry()) {
+		}
-		// ValueSet next = (ValueSet) i.getResource();
-		// next.setId(next.getIdElement().toUnqualifiedVersionless());
-		//
-		// ourLog.info("Uploading ValueSet {}/{} : {}", new Object[] {count,total,next.getIdElement().getValue()});
-		// client.update().resource(next).execute();
-		//
-		// count++;
-		// }
-		//
-		// ourLog.info("Finished uploading ValueSets");
 
-//		String vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml"), "UTF-8");
+		FhirContext ctx = FhirContext.forDstu2();
-//		Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, vsContents);
+		ourLog.info("Uploading definitions to server: " + targetServer);
-//		total = bundle.getEntry().size();
-//		count = 1;
-//		for (BundleEntryComponent i : bundle.getEntry()) {
-//			ValueSet next = (ValueSet) i.getResource();
-//			next.setId(next.getIdElement().toUnqualifiedVersionless());
-//
-//			ourLog.info("Uploading v3-codesystems ValueSet {}/{} : {}", new Object[] { count, total, next.getIdElement().getValue() });
-//			client.update().resource(next).execute();
-//
-//			count++;
-//		}
 
+		IGenericClient client = newClient(ctx, targetServer);
+		long start = System.currentTimeMillis();
 
-		String vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/v2-tables.xml"), "UTF-8");
+		String vsContents;
+		try {
+			vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/valuesets.xml"), "UTF-8");
+		} catch (IOException e) {
+			throw new CommandFailureException(e.toString());
+		}
 		Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, vsContents);
+
+		int total = bundle.getEntry().size();
+		int count = 1;
+		for (Entry i : bundle.getEntry()) {
+			ValueSet next = (ValueSet) i.getResource();
+			next.setId(next.getIdElement().toUnqualifiedVersionless());
+
+			ourLog.info("Uploading ValueSet {}/{} : {}", new Object[] { count, total, next.getIdElement().getValue() });
+			client.update().resource(next).execute();
+
+			count++;
+		}
+
+		try {
+			vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml"), "UTF-8");
+		} catch (IOException e) {
+			throw new CommandFailureException(e.toString());
+		}
+
+		bundle = ctx.newXmlParser().parseResource(Bundle.class, vsContents);
 		total = bundle.getEntry().size();
 		count = 1;
-		for (BundleEntryComponent i : bundle.getEntry()) {
+		for (Entry i : bundle.getEntry()) {
-			if (count > 1900) {
+			ValueSet next = (ValueSet) i.getResource();
+			next.setId(next.getIdElement().toUnqualifiedVersionless());
+
+			ourLog.info("Uploading v3-codesystems ValueSet {}/{} : {}", new Object[] { count, total, next.getIdElement().getValue() });
+			client.update().resource(next).execute();
+
+			count++;
+		}
+
+		try {
+			vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/v2-tables.xml"), "UTF-8");
+		} catch (IOException e) {
+			throw new CommandFailureException(e.toString());
+		}
+		bundle = ctx.newXmlParser().parseResource(Bundle.class, vsContents);
+		total = bundle.getEntry().size();
+		count = 1;
+		for (Entry i : bundle.getEntry()) {
 			ValueSet next = (ValueSet) i.getResource();
 			next.setId(next.getIdElement().toUnqualifiedVersionless());
 
 			ourLog.info("Uploading v2-tables ValueSet {}/{} : {}", new Object[] { count, total, next.getIdElement().getValue() });
 			client.update().resource(next).execute();
-			}
 			count++;
 		}
 
 		ourLog.info("Finished uploading ValueSets");
 
 		ResourcePatternResolver patternResolver = new PathMatchingResourcePatternResolver();
-		Resource[] mappingLocations = patternResolver.getResources("classpath*:org/hl7/fhir/instance/model/profile/*.profile.xml");
+		Resource[] mappingLocations;
+		try {
+			mappingLocations = patternResolver.getResources("classpath*:org/hl7/fhir/instance/model/profile/*.profile.xml");
+		} catch (IOException e) {
+			throw new CommandFailureException(e.toString());
+		}
 		total = mappingLocations.length;
 		count = 1;
 		for (Resource i : mappingLocations) {
-			if (count > 140) {
+			StructureDefinition next;
-			StructureDefinition next = ctx.newXmlParser().parseResource(StructureDefinition.class, IOUtils.toString(i.getInputStream(), "UTF-8"));
+			try {
+				next = ctx.newXmlParser().parseResource(StructureDefinition.class, IOUtils.toString(i.getInputStream(), "UTF-8"));
+			} catch (DataFormatException | IOException e) {
+				throw new CommandFailureException(e.toString());
+			}
 			next.setId(next.getIdElement().toUnqualifiedVersionless());
 
 			ourLog.info("Uploading StructureDefinition {}/{} : {}", new Object[] { count, total, next.getIdElement().getValue() });
+			try {
 				client.update().resource(next).execute();
+			} catch (Exception e) {
+				ourLog.warn("Failed to upload {} - {}", next.getIdElement().getValue(), e.getMessage());
 			}
 			count++;
 		}
 
 		ourLog.info("Finished uploading ValueSets");
 
-	}
+		long delay = System.currentTimeMillis() - start;
-
-	@Override
-	public String getCommandDescription() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public String getCommandName() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public Options getOptions() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void run(CommandLine theCommandLine) throws ParseException {
-		// TODO Auto-generated method stub
 
+		ourLog.info("Finished uploading definitions to server (took {} ms)", delay);
 	}
 
 }

hapi-fhir-cli/src/main/resources/logback-cli-on.xml

@@ -8,38 +8,11 @@
 		</encoder>
 	</appender>
 
-	<logger name="java.sql" additivity="false" level="warn">
+	<logger name="ca.uhn.fhir.cli" additivity="false" level="info">
-		<appender-ref ref="STDOUT" />
-	</logger>
-	<logger name="ca.uhn.fhir.jpa" additivity="false" level="info">
-		<appender-ref ref="STDOUT" />
-	</logger>
-	<logger name="ca.uhn.fhir.rest" additivity="false" level="warn">
-		<appender-ref ref="STDOUT" />
-	</logger>
-	<logger name="org.eclipse" additivity="false" level="warn">
-		<appender-ref ref="STDOUT" />
-	</logger>
-	<logger name="org.springframework" additivity="false" level="warn">
-		<appender-ref ref="STDOUT" />
-	</logger>
-	<logger name="org.apache" additivity="false" level="info">
-		<appender-ref ref="STDOUT" />
-	</logger>
-	<logger name="org.thymeleaf" additivity="false" level="warn">
-		<appender-ref ref="STDOUT" />
-	</logger>
-	<logger name="org.hibernate" additivity="false" level="warn">
 		<appender-ref ref="STDOUT" />
 	</logger>
 
-	<!-- 
+	<root level="warn">
-	<logger name="ca.uhn.fhir.rest.client" additivity="false" level="trace">
-		<appender-ref ref="STDOUT" />
-	</logger>
- 	-->
- 	
-	<root level="info">
 		<appender-ref ref="STDOUT" />
 	</root>
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java

@@ -101,17 +101,15 @@ public class FhirResourceDaoSubscriptionDstu2 extends FhirResourceDaoDstu2<Subsc
 
 		// SubscriptionCandidateResource
 
-		TypedQuery<SubscriptionTable> q = myEntityManager.createNamedQuery("Q_HFJ_SUBSCRIPTION_NEXT_CHECK", SubscriptionTable.class);
+		Collection<Long> subscriptions = mySubscriptionTableDao.finsSubscriptionsWhichNeedToBeChecked(SubscriptionStatusEnum.ACTIVE, new Date());
-		q.setParameter("next_check", new Date());
-		q.setParameter("status", SubscriptionStatusEnum.ACTIVE);
-		List<SubscriptionTable> subscriptions = q.getResultList();
 
 		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
 		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
-		for (final SubscriptionTable nextSubscriptionTable : subscriptions) {
+		for (final Long nextSubscriptionTablePid : subscriptions) {
 			txTemplate.execute(new TransactionCallback<Void>() {
 				@Override
 				public Void doInTransaction(TransactionStatus theStatus) {
+					SubscriptionTable nextSubscriptionTable = mySubscriptionTableDao.findOne(nextSubscriptionTablePid);
 					pollForNewUndeliveredResources(nextSubscriptionTable);
 					return null;
 				}

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

@@ -29,6 +29,7 @@ import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.query.Param;
 
 import ca.uhn.fhir.jpa.entity.SubscriptionTable;
+import ca.uhn.fhir.model.dstu2.valueset.SubscriptionStatusEnum;
 
 public interface ISubscriptionTableDao extends JpaRepository<SubscriptionTable, Long> {
 
@@ -46,4 +47,6 @@ public interface ISubscriptionTableDao extends JpaRepository<SubscriptionTable,
 	@Query("SELECT t FROM SubscriptionTable t WHERE t.myLastClientPoll < :cutoff OR (t.myLastClientPoll IS NULL AND t.myCreated < :cutoff)")
 	public Collection<SubscriptionTable> findInactiveBeforeCutoff(@Param("cutoff") Date theCutoff);
 
+	@Query("SELECT t.myId FROM SubscriptionTable t WHERE t.myStatus = :status AND t.myNextCheck <= :next_check")
+	public Collection<Long> finsSubscriptionsWhichNeedToBeChecked(@Param("status") SubscriptionStatusEnum theStatus, @Param("next_check") Date theNextCheck);
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/SubscriptionTable.java

@@ -52,7 +52,6 @@ import ca.uhn.fhir.model.dstu2.valueset.SubscriptionStatusEnum;
 })
 @NamedQueries({
 	@NamedQuery(name="Q_HFJ_SUBSCRIPTION_SET_STATUS", query="UPDATE SubscriptionTable t SET t.myStatus = :status WHERE t.myResId = :res_id"),
-	@NamedQuery(name="Q_HFJ_SUBSCRIPTION_NEXT_CHECK", query="SELECT t FROM SubscriptionTable t WHERE t.myStatus = :status AND t.myNextCheck <= :next_check"),
 	@NamedQuery(name="Q_HFJ_SUBSCRIPTION_GET_BY_RES", query="SELECT t FROM SubscriptionTable t WHERE t.myResId = :res_id")
 })
 //@formatter:on

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SubscriptionsDstu2Test.java

@@ -6,6 +6,7 @@ import static org.junit.Assert.fail;
 
 import java.net.URI;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 import org.eclipse.jetty.websocket.api.Session;
@@ -19,6 +20,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.Test;
 
 import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptor;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.dstu2.resource.Subscription;
@@ -250,6 +252,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
 			mySubscriptionDao.read(new IdDt("Subscription", socket.mySubsId));
 
 			Observation obs = new Observation();
+			ResourceMetadataKeyEnum.PROFILES.put(obs, Collections.singletonList(new IdDt("http://foo")));
 			obs.getSubject().setReference(pId);
 			obs.setStatus(ObservationStatusEnum.FINAL);
 			IIdType afterId1 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
@@ -301,6 +304,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
 		IIdType pId = myPatientDao.create(p).getId().toUnqualifiedVersionless();
 
 		Subscription subs = new Subscription();
+		ResourceMetadataKeyEnum.PROFILES.put(subs, Collections.singletonList(new IdDt("http://foo")));
 		subs.getChannel().setType(SubscriptionChannelTypeEnum.WEBSOCKET);
 		subs.setCriteria("Observation?subject=Patient/" + pId.getIdPart());
 		subs.setStatus(SubscriptionStatusEnum.ACTIVE);