Add R4 code to CLI

hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/BaseCommand.java

@@ -57,6 +57,8 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 				version = FhirVersionEnum.DSTU2;
 			} else if ("dstu3".equals(specVersion)) {
 				version = FhirVersionEnum.DSTU3;
+			} else if ("r4".equals(specVersion)) {
+				version = FhirVersionEnum.R4;
 			} else {
 				throw new ParseException("Unknown spec version: " + specVersion);
 			}

hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/ExampleDataUploader.java

@@ -114,6 +114,9 @@ public class ExampleDataUploader extends BaseCommand {
 				specUrl = "http://hl7.org/fhir/dstu2/examples-json.zip";
 				break;
 			case DSTU3:
+				specUrl = "http://hl7.org/fhir/STU3/examples-json.zip";
+				break;
+			case R4:
 				specUrl = "http://build.fhir.org/examples-json.zip";
 				break;
 			default:
@@ -197,18 +200,20 @@ public class ExampleDataUploader extends BaseCommand {
 
 	}
 
-	private IBaseBundle getBundleFromFile(Integer theLimit, File theSuppliedFile, FhirContext theCtx) throws ParseException, UnsupportedEncodingException, IOException {
+	private IBaseBundle getBundleFromFile(Integer theLimit, File theSuppliedFile, FhirContext theCtx) throws ParseException, IOException {
 		switch (theCtx.getVersion().getVersion()) {
 			case DSTU2:
 				return getBundleFromFileDstu2(theLimit, theSuppliedFile, theCtx);
 			case DSTU3:
 				return getBundleFromFileDstu3(theLimit, theSuppliedFile, theCtx);
+			case R4:
+				return getBundleFromFileDstu3(theLimit, theSuppliedFile, theCtx);
 			default:
 				throw new ParseException("Invalid spec version for this command: " + theCtx.getVersion().getVersion());
 		}
 	}
 
-	private void sendBundleToTarget(String targetServer, FhirContext ctx, IBaseBundle bundle) throws Exception, IOException {
+	private void sendBundleToTarget(String targetServer, FhirContext ctx, IBaseBundle bundle) throws Exception {
 		List<IBaseResource> resources = BundleUtil.toListOfResources(ctx, bundle);
 
 		for (Iterator<IBaseResource> iter = resources.iterator(); iter.hasNext(); ) {
@@ -223,13 +228,13 @@ public class ExampleDataUploader extends BaseCommand {
 			}
 		}
 
-		List<IBaseResource> subResourceList = new ArrayList<IBaseResource>();
+		List<IBaseResource> subResourceList = new ArrayList<>();
 		while (resources.size() > 0) {
 
 			IBaseResource nextAddedResource = resources.remove(0);
 			subResourceList.add(nextAddedResource);
 
-			Set<String> checkedTargets = new HashSet<String>();
+			Set<String> checkedTargets = new HashSet<>();
 
 			for (int i = 0; i < subResourceList.size(); i++) {
 				IBaseResource nextCandidateSource = subResourceList.get(i);
@@ -319,6 +324,9 @@ public class ExampleDataUploader extends BaseCommand {
 			case DSTU3:
 				processBundleDstu3(ctx, (org.hl7.fhir.dstu3.model.Bundle) bundle);
 				break;
+			case R4:
+				processBundleR4(ctx, (org.hl7.fhir.r4.model.Bundle) bundle);
+				break;
 			default:
 				throw new IllegalStateException();
 		}
@@ -484,6 +492,72 @@ public class ExampleDataUploader extends BaseCommand {
 
 	}
 
+	private void processBundleR4(FhirContext ctx, org.hl7.fhir.r4.model.Bundle bundle) {
+
+		Map<String, Integer> ids = new HashMap<String, Integer>();
+		Set<String> fullIds = new HashSet<String>();
+
+		for (Iterator<org.hl7.fhir.r4.model.Bundle.BundleEntryComponent> iterator = bundle.getEntry().iterator(); iterator.hasNext(); ) {
+			org.hl7.fhir.r4.model.Bundle.BundleEntryComponent next = iterator.next();
+
+			// DataElement have giant IDs that seem invalid, need to investigate this..
+			if ("Subscription".equals(next.getResource().getResourceType()) || "DataElement".equals(next.getResource().getResourceType())
+				|| "OperationOutcome".equals(next.getResource().getResourceType()) || "OperationDefinition".equals(next.getResource().getResourceType())) {
+				ourLog.info("Skipping " + next.getResource().getResourceType() + " example");
+				iterator.remove();
+			} else {
+				IdDt resourceId = new IdDt(next.getResource().getResourceType() + "/EX" + next.getResource().getIdElement().getIdPart());
+				if (!fullIds.add(resourceId.toUnqualifiedVersionless().getValue())) {
+					ourLog.info("Discarding duplicate resource: " + resourceId.getValue());
+					iterator.remove();
+					continue;
+				}
+
+				String idPart = resourceId.getIdPart();
+				if (idPart != null) {
+					next.getResource().setId(resourceId);
+				} else {
+					ourLog.info("Discarding resource with not explicit ID");
+					iterator.remove();
+				}
+			}
+		}
+		Set<String> qualIds = new TreeSet<String>();
+		for (Iterator<org.hl7.fhir.r4.model.Bundle.BundleEntryComponent> iterator = bundle.getEntry().iterator(); iterator.hasNext(); ) {
+			org.hl7.fhir.r4.model.Bundle.BundleEntryComponent next = iterator.next();
+			if (next.getResource().getIdElement().getIdPart() != null) {
+				String nextId = next.getResource().getIdElement().getValue();
+				next.getRequest().setMethod(org.hl7.fhir.r4.model.Bundle.HTTPVerb.PUT);
+				next.getRequest().setUrl(nextId);
+			}
+		}
+
+		int goodRefs = 0;
+		for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent next : bundle.getEntry()) {
+			List<ResourceReferenceInfo> refs = ctx.newTerser().getAllResourceReferences(next.getResource());
+			for (ResourceReferenceInfo nextRef : refs) {
+				nextRef.getResourceReference().setResource(null);
+				String value = nextRef.getResourceReference().getReferenceElement().toUnqualifiedVersionless().getValue();
+
+				if (isNotBlank(value)) {
+					if (!qualIds.contains(value) && !nextRef.getResourceReference().getReferenceElement().isLocal()) {
+						ourLog.info("Discarding unknown reference: {}", value);
+						nextRef.getResourceReference().getReferenceElement().setValue(null);
+					} else {
+						goodRefs++;
+					}
+				}
+				ourLog.info("Found ref: {}", value);
+			}
+		}
+
+		ourLog.info("{} good references", goodRefs);
+		System.gc();
+
+		ourLog.info("Final bundle: {} entries", bundle.getEntry().size());
+
+	}
+
 	private Bundle getBundleFromFileDstu2(Integer limit, File inputFile, FhirContext ctx) throws IOException, UnsupportedEncodingException {
 
 		Bundle bundle = new Bundle();

hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java

@@ -20,11 +20,9 @@ public class UploadTerminologyCommand extends BaseCommand {
 
 	@Override
 	public String getCommandDescription() {
-		//@formatter:off
 		return "Uploads a terminology package (e.g. a SNOMED CT ZIP file) to a HAPI JPA server. "
 				+ "Note that this command uses a custom operation that is only implemented on HAPI "
 				+ "JPA servers that have been configured to accept it.";
-		//@formatter:on
 	}
 
 	@Override

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

@@ -65,6 +65,8 @@ public class ValidationDataUploader extends BaseCommand {
 			uploadDefinitionsDstu2(targetServer, ctx);
 		} else if (ctx.getVersion().getVersion() == FhirVersionEnum.DSTU3){
 			uploadDefinitionsDstu3(targetServer, ctx);
+		} else if (ctx.getVersion().getVersion() == FhirVersionEnum.R4){
+			uploadDefinitionsR4(targetServer, ctx);
 		}
 	}
 
@@ -256,6 +258,95 @@ public class ValidationDataUploader extends BaseCommand {
 		ourLog.info("Finished uploading definitions to server (took {} ms)", delay);
 	}
 
+	private void uploadDefinitionsR4(String theTargetServer, FhirContext theCtx) throws CommandFailureException {
+		IGenericClient client = newClient(theCtx, theTargetServer);
+		ourLog.info("Uploading definitions to server: " + theTargetServer);
+
+		long start = System.currentTimeMillis();
+		int total = 0;
+		int count = 0;
+		org.hl7.fhir.r4.model.Bundle bundle;
+		String vsContents;
+
+		try {
+			theCtx.getVersion().getPathToSchemaDefinitions();
+			vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/r4/model/valueset/"+"valuesets.xml"), "UTF-8");
+		} catch (IOException e) {
+			throw new CommandFailureException(e.toString());
+		}
+		bundle = theCtx.newXmlParser().parseResource(org.hl7.fhir.r4.model.Bundle.class, vsContents);
+
+		total = bundle.getEntry().size();
+		count = 1;
+		for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent i : bundle.getEntry()) {
+			org.hl7.fhir.r4.model.Resource next = i.getResource();
+			next.setId(next.getIdElement().toUnqualifiedVersionless());
+
+			int bytes = theCtx.newXmlParser().encodeResourceToString(next).length();
+
+			ourLog.info("Uploading ValueSet {}/{} : {} ({} bytes}", new Object[] { count, total, next.getIdElement().getValue(), bytes });
+			try {
+				IIdType id = client.update().resource(next).execute().getId();
+				ourLog.info("  - Got ID: {}", id.getValue());
+			} catch (UnprocessableEntityException e) {
+				ourLog.warn("UnprocessableEntityException: " + e.toString());
+			}
+			count++;
+		}
+
+		try {
+			vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/r4/model/valueset/"+"v3-codesystems.xml"), "UTF-8");
+		} catch (IOException e) {
+			throw new CommandFailureException(e.toString());
+		}
+
+		bundle = theCtx.newXmlParser().parseResource(org.hl7.fhir.r4.model.Bundle.class, vsContents);
+		total = bundle.getEntry().size();
+		count = 1;
+		for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent i : bundle.getEntry()) {
+			org.hl7.fhir.r4.model.Resource next = 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/r4/model/valueset/"+"v2-tables.xml"), "UTF-8");
+		} catch (IOException e) {
+			throw new CommandFailureException(e.toString());
+		}
+		bundle = theCtx.newXmlParser().parseResource(org.hl7.fhir.r4.model.Bundle.class, vsContents);
+		total = bundle.getEntry().size();
+		count = 1;
+		for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent i : bundle.getEntry()) {
+			org.hl7.fhir.r4.model.Resource next = i.getResource();
+			if (next.getIdElement().isIdPartValidLong()) {
+				next.setIdElement(new org.hl7.fhir.r4.model.IdType("v2-"+ next.getIdElement().getIdPart()));
+			}
+			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");
+
+
+		uploadDstu3Profiles(theCtx, client, "profiles-resources");
+		uploadDstu3Profiles(theCtx, client, "profiles-types");
+		uploadDstu3Profiles(theCtx, client, "profiles-others");
+
+		ourLog.info("Finished uploading ValueSets");
+
+		long delay = System.currentTimeMillis() - start;
+
+		ourLog.info("Finished uploading definitions to server (took {} ms)", delay);
+	}
+
 	private void uploadDstu3Profiles(FhirContext ctx, IGenericClient client, String name) throws CommandFailureException {
 		int total;
 		int count;

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -20,6 +20,10 @@
 			<artifactId>postgresql</artifactId>
 			<version>9.4.1212.jre7</version>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.derby</groupId>
+			<artifactId>derby</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-jpaserver-base</artifactId>

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

@@ -6,6 +6,8 @@ import javax.servlet.ServletContext;
 import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 
+import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
+import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.web.context.ContextLoaderListener;
 import org.springframework.web.context.WebApplicationContext;
@@ -125,10 +127,10 @@ public class TestRestfulServer extends RestfulServer {
 			myAppCtx.refresh();
 			setFhirContext(FhirContext.forR4());
 			beans = myAppCtx.getBean("myResourceProvidersR4", List.class);
-			plainProviders.add(myAppCtx.getBean("mySystemProviderR4", JpaSystemProviderDstu3.class));
+			plainProviders.add(myAppCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class));
 			systemDao = myAppCtx.getBean("mySystemDaoR4", IFhirSystemDao.class);
 			etagSupport = ETagSupportEnum.ENABLED;
-			JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, myAppCtx.getBean(DaoConfig.class));
+			JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao, myAppCtx.getBean(DaoConfig.class));
 			confProvider.setImplementationDescription(implDesc);
 			setServerConformanceProvider(confProvider);
 			plainProviders.add(myAppCtx.getBean(TerminologyUploaderProviderR4.class));

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

@@ -57,4 +57,8 @@ public class CommonConfig {
 		return new HolyFooCowInterceptor();
 	}
 
+	public static boolean isLocalTestMode(){
+		return "true".equalsIgnoreCase(System.getProperty("testmode.local"));
+	}
+
 }

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

@@ -8,6 +8,7 @@ import ca.uhn.fhir.validation.ResultSeverityEnum;
 import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
+import org.hibernate.dialect.DerbyTenSevenDialect;
 import org.hibernate.dialect.PostgreSQL94Dialect;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Value;
@@ -70,8 +71,12 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 	@Bean(name = "myPersistenceDataSourceDstu1", destroyMethod = "close")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
+		if (CommonConfig.isLocalTestMode()) {
+			retVal.setUrl("jdbc:derby:memory:fhirtest_dstu2;create=true");
+		} else {
 			retVal.setDriver(new org.postgresql.Driver());
 			retVal.setUrl("jdbc:postgresql://localhost/fhirtest_dstu2");
+		}
 		retVal.setUsername(myDbUsername);
 		retVal.setPassword(myDbPassword);
 		return retVal;
@@ -97,7 +102,11 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
+		if (CommonConfig.isLocalTestMode()) {
+			extraProperties.put("hibernate.dialect", DerbyTenSevenDialect.class.getName());
+		} else {
 			extraProperties.put("hibernate.dialect", PostgreSQL94Dialect.class.getName());
+		}
 		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");

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

@@ -7,6 +7,7 @@ import javax.sql.DataSource;
 
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
+import org.hibernate.dialect.DerbyTenSevenDialect;
 import org.hibernate.dialect.PostgreSQL94Dialect;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Autowire;
@@ -74,8 +75,12 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 	@Bean(name = "myPersistenceDataSourceDstu3", destroyMethod = "close")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
+		if (CommonConfig.isLocalTestMode()) {
+			retVal.setUrl("jdbc:derby:memory:fhirtest_dstu3;create=true");
+		} else {
 			retVal.setDriver(new org.postgresql.Driver());
 			retVal.setUrl("jdbc:postgresql://localhost/fhirtest_dstu3");
+		}
 		retVal.setUsername(myDbUsername);
 		retVal.setPassword(myDbPassword);
 		return retVal;
@@ -94,7 +99,11 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
+		if (CommonConfig.isLocalTestMode()) {
+			extraProperties.put("hibernate.dialect", DerbyTenSevenDialect.class.getName());
+		} else {
 			extraProperties.put("hibernate.dialect", PostgreSQL94Dialect.class.getName());
+		}
 		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");

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

@@ -7,6 +7,8 @@ import javax.sql.DataSource;
 
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
+import org.hibernate.dialect.DerbyTenSevenDialect;
+import org.hibernate.dialect.PostgreSQL94Dialect;
 import org.hibernate.dialect.PostgreSQL95Dialect;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Autowire;
@@ -74,8 +76,12 @@ public class TestR4Config extends BaseJavaConfigR4 {
 	@Bean(name = "myPersistenceDataSourceR4", destroyMethod = "close")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
+		if (CommonConfig.isLocalTestMode()) {
+			retVal.setUrl("jdbc:derby:memory:fhirtest_r4;create=true");
+		} else {
 			retVal.setDriver(new org.postgresql.Driver());
 			retVal.setUrl("jdbc:postgresql://localhost/fhirtest_r4");
+		}
 		retVal.setUsername(myDbUsername);
 		retVal.setPassword(myDbPassword);
 		return retVal;
@@ -94,7 +100,11 @@ public class TestR4Config extends BaseJavaConfigR4 {
 
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
-		extraProperties.put("hibernate.dialect", PostgreSQL95Dialect.class.getName());
+		if (CommonConfig.isLocalTestMode()) {
+			extraProperties.put("hibernate.dialect", DerbyTenSevenDialect.class.getName());
+		} else {
+			extraProperties.put("hibernate.dialect", PostgreSQL94Dialect.class.getName());
+		}
 		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");

hapi-fhir-jpaserver-uhnfhirtest/src/test/java/ca/uhn/fhirtest/UhnFhirTestApp.java

@@ -26,6 +26,8 @@ public class UhnFhirTestApp {
 		System.setProperty("fhir.lucene.location.dstu2", "./target/testlucene_dstu2");
 		System.setProperty("fhir.db.location.dstu3", "./target/fhirtest_dstu3");
 		System.setProperty("fhir.lucene.location.dstu3", "./target/testlucene_dstu3");
+		System.setProperty("fhir.db.location.r4", "./target/fhirtest_r4");
+		System.setProperty("fhir.lucene.location.r4", "./target/testlucene_r4");
 		System.setProperty("fhir.db.location.tdl2", "./target/testdb_tdl2");
 		System.setProperty("fhir.lucene.location.tdl2", "./target/testlucene_tdl2");
 		System.setProperty("fhir.db.location.tdl3", "./target/testdb_tdl3");
@@ -33,9 +35,13 @@ public class UhnFhirTestApp {
 		System.setProperty("fhir.baseurl.dstu2", base);
 		System.setProperty("fhir.baseurl.dstu1", base.replace("Dstu2", "Dstu1"));
 		System.setProperty("fhir.baseurl.dstu3", base.replace("Dstu2", "Dstu3"));
+		System.setProperty("fhir.baseurl.r4", base.replace("Dstu2", "R4"));
 		System.setProperty("fhir.baseurl.tdl2", base.replace("baseDstu2", "testDataLibraryDstu2"));
 		System.setProperty("fhir.baseurl.tdl3", base.replace("baseDstu2", "testDataLibraryStu3"));
 		System.setProperty("fhir.tdlpass", "aa,bb");
+		System.setProperty("fhir.db.username", "SA");
+		System.setProperty("fhir.db.password", "SA");
+		System.setProperty("testmode.local", "true");
 
 		Server server = new Server(myPort);