Merge remote-tracking branch 'remotes/origin/master' into feature_2020_09_02_term_multi_version_support

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

@@ -40,9 +40,8 @@ public class HapiLocalizer {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(HapiLocalizer.class);
 	private static boolean ourFailOnMissingMessage;
 	private final Map<String, MessageFormat> myKeyToMessageFormat = new ConcurrentHashMap<>();
-	private List<ResourceBundle> myBundle = new ArrayList<>();
+	private List<ResourceBundle> myBundle;
 	private final Map<String, String> myHardcodedMessages = new HashMap<>();
-	private String[] myBundleNames;
 	private Locale myLocale = Locale.getDefault();
 
 	public HapiLocalizer() {
@@ -50,8 +49,7 @@ public class HapiLocalizer {
 	}
 
 	public HapiLocalizer(String... theBundleNames) {
-		myBundleNames = theBundleNames;
-		init();
+		init(theBundleNames);
 		addMessage("hapi.version", VersionUtil.getVersion());
 	}
 
@@ -159,8 +157,9 @@ public class HapiLocalizer {
 		return new MessageFormat(pattern.toString());
 	}
 
-	protected void init() {
-		for (String nextName : myBundleNames) {
+	protected void init(String[] theBundleNames) {
+		myBundle = new ArrayList<>();
+		for (String nextName : theBundleNames) {
 			myBundle.add(ResourceBundle.getBundle(nextName));
 		}
 	}

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/atlas/points.json

@@ -243,10 +243,10 @@
 			"description": "With the ACS App, Community Health Agents (CHA) work gets faster and faster, and they can take better care of their community. Best of all, it is 100% free to the Health Agent.",
 			"link": "http://ephealth.com.br/?lang=en",
 			"contactName": "Alan Lescano",
-			"contactEmail": "alan@ephealth.com.br",
+			"contactEmail": "alan.lesc1@gmail.com",
 			"city": "Sao Paulo, Brazil",
-			"lat": -6.6167,
-			"lon": -38.1500,
+			"lat": -23.533773,
+			"lon": -46.625290,
 			"added": "2019-09-29"
 		},
 		{
@@ -259,16 +259,7 @@
 			"added": "2019-11-25"
 		},
 		{
-			"title": "Software Interoperability Lab for Asia",
-			"description": "",
-			"link": "",
-			"city": "Manila, Philippines",
-			"lat": 14.6914,
-			"lon": 120.9686,
-			"added": "2019-11-25"
-		},
-		{
-			"title": "Software Interoperability Lab for Asia",
+			"title": "Standards and Interoperability Lab Asia",
 			"description": "SIL-A maintains a suite of tools used to promote interoperability and medical informatics across Asia.",
 			"link": "http://sil-asia.org/",
 			"city": "Manila, Philippines",

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2078-update-resources-on-package-reinstall.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 2078
+title: "When using package support to install a package with STORE_AND_INSTALL mode, resources that are already
+   present in the database will now be updated to the contents of the version in the package."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/changes.yaml

@@ -4,5 +4,11 @@
     title: "The version of a few dependencies have been bumped to the latest versions
     (dependent HAPI modules listed in brackets):
     <ul>
-        <li>Flyway (JPA): 6.4.1-&gt; 6.5.4</li>
+        <li>Jackson (Base): 2.10.0 -&gt; 2.11.2</li>
+        <li>Flyway (JPA): 6.4.1 -&gt; 6.5.4</li>
+        <li>UCUM (JPA): 1.0.2 -&gt; 1.0.3</li>
+        <li>JQuery (Testpage Overlay): 3.3.1 -&gt; 3.5.1</li>
+        <li>Awesome Bootstrap Checkbos (Testpage Overlay): 1.0.1 -&gt; 1.0.2</li>
+        <li>MomentJS (Testpage Overlay): 2.15.1 -&gt; 2.27.0</li>
+        <li>Select2 (Testpage Overlay): 4.0.3 -&gt; 4.0.13</li>
     </ul>"

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

@@ -45,7 +45,7 @@ public class DaoSearchParamProvider implements ISearchParamProvider {
 	@Override
 	public int refreshCache(SearchParamRegistryImpl theSearchParamRegistry, long theRefreshInterval) {
 		int retVal = 0;
-		if (myDaoRegistry.getResourceDao("SearchParameter") != null) {
+		if (myDaoRegistry.getResourceDaoOrNull("SearchParameter") != null) {
 			retVal = theSearchParamRegistry.doRefresh(theRefreshInterval);
 		}
 		return retVal;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImpl.java

@@ -29,11 +29,13 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
 import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.SearchParameterUtil;
 import com.google.common.annotations.VisibleForTesting;
@@ -94,6 +96,8 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 	private PlatformTransactionManager myTxManager;
 	@Autowired
 	private INpmPackageVersionDao myPackageVersionDao;
+	@Autowired
+	private ISearchParamRegistry mySearchParamRegistry;
 
 	/**
 	 * Constructor
@@ -161,6 +165,9 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 
 				if (theInstallationSpec.getInstallMode() == PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL) {
 					install(npmPackage, theInstallationSpec, retVal);
+
+					// If any SearchParameters were installed, let's load them right away
+					mySearchParamRegistry.refreshCacheIfNecessary();
 				}
 
 			} catch (IOException e) {
@@ -304,11 +311,20 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 		IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());
 		SearchParameterMap map = createSearchParameterMapFor(theResource);
 		IBundleProvider searchResult = dao.search(map);
-		if (searchResult.isEmpty()) {
+		if (validForUpload(theResource)) {
+			if (searchResult.isEmpty()) {
 
-			if (validForUpload(theResource)) {
+				ourLog.info("Creating new resource matching {}", map.toNormalizedQueryString(myFhirContext));
 				theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
 				dao.create(theResource);
+
+			} else {
+
+				ourLog.info("Updating existing resource matching {}", map.toNormalizedQueryString(myFhirContext));
+				theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
+				theResource.setId(searchResult.getResources(0,1).get(0).getIdElement().toUnqualifiedVersionless());
+				dao.update(theResource);
+
 			}
 
 		}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmTestR4.java

@@ -11,8 +11,11 @@ import ca.uhn.fhir.jpa.model.entity.NpmPackageEntity;
 import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
 import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionResourceEntity;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.ReferenceParam;
+import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.test.utilities.JettyUtil;
@@ -22,7 +25,13 @@ import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.ImplementationGuide;
+import org.hl7.fhir.r4.model.Organization;
+import org.hl7.fhir.r4.model.PractitionerRole;
+import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.SearchParameter;
 import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.utilities.cache.NpmPackage;
 import org.junit.jupiter.api.AfterEach;
@@ -230,7 +239,6 @@ public class NpmTestR4 extends BaseJpaR4Test {
 	}
 
 
-
 	@Test
 	public void testInstallR4PackageWithNoDescription() throws Exception {
 		myDaoConfig.setAllowExternalReferences(true);
@@ -433,6 +441,53 @@ public class NpmTestR4 extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testInstallPkgContainingSearchParameter() throws IOException {
+		myDaoConfig.setAllowExternalReferences(true);
+
+		byte[] contents0111 = loadClasspathBytes("/packages/test-exchange-sample.tgz");
+		myFakeNpmServlet.myResponses.put("/test-exchange.fhir.us.com/2.1.1", contents0111);
+
+		contents0111 = loadClasspathBytes("/packages/test-exchange-sample-2.tgz");
+		myFakeNpmServlet.myResponses.put("/test-exchange.fhir.us.com/2.1.2", contents0111);
+
+		// Install older version
+		PackageInstallationSpec spec = new PackageInstallationSpec().setName("test-exchange.fhir.us.com").setVersion("2.1.1").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
+		igInstaller.install(spec);
+
+		IBundleProvider spSearch = mySearchParameterDao.search(SearchParameterMap.newSynchronous("code", new TokenParam("network-id")));
+		assertEquals(1, spSearch.sizeOrThrowNpe());
+		SearchParameter sp = (SearchParameter) spSearch.getResources(0, 1).get(0);
+		assertEquals("network-id", sp.getCode());
+		assertEquals("2.1", sp.getVersion());
+		assertEquals(Enumerations.PublicationStatus.ACTIVE, sp.getStatus());
+
+		Organization org = new Organization();
+		org.setName("Hello");
+		IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
+
+		PractitionerRole pr = new PractitionerRole();
+		pr.addExtension().setUrl("http://test-exchange.com/fhir/us/providerdataexchange/StructureDefinition/networkreference").setValue(new Reference(orgId));
+		myPractitionerRoleDao.create(pr);
+
+		SearchParameterMap map = SearchParameterMap.newSynchronous("network-id", new ReferenceParam(orgId.getValue()));
+		spSearch = myPractitionerRoleDao.search(map);
+		assertEquals(1, spSearch.sizeOrThrowNpe());
+		
+		// Install newer version
+		spec = new PackageInstallationSpec().setName("test-exchange.fhir.us.com").setVersion("2.1.2").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
+		igInstaller.install(spec);
+
+		spSearch = mySearchParameterDao.search(SearchParameterMap.newSynchronous("code", new TokenParam("network-id")));
+		assertEquals(1, spSearch.sizeOrThrowNpe());
+		sp = (SearchParameter) spSearch.getResources(0, 1).get(0);
+		assertEquals("network-id", sp.getCode());
+		assertEquals(Enumerations.PublicationStatus.ACTIVE, sp.getStatus());
+		assertEquals("2.2", sp.getVersion());
+
+	}
+	
+
 	@Test
 	public void testLoadContents() throws IOException {
 		byte[] contents0111 = loadClasspathBytes("/packages/hl7.fhir.uv.shorthand-0.11.1.tgz");

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseColumnCalculatorTask.java

@@ -50,6 +50,7 @@ public abstract class BaseColumnCalculatorTask extends BaseTableColumnTask {
 	protected static final Logger ourLog = LoggerFactory.getLogger(BaseColumnCalculatorTask.class);
 	private int myBatchSize = 10000;
 	private ThreadPoolExecutor myExecutor;
+	private String myPidColumnName;
 
 	/**
 	 * Constructor
@@ -160,6 +161,10 @@ public abstract class BaseColumnCalculatorTask extends BaseTableColumnTask {
 			rejectedExecutionHandler);
 	}
 
+	public void setPidColumnName(String thePidColumnName) {
+		myPidColumnName = thePidColumnName;
+	}
+
 	private Future<?> updateRows(List<Map<String, Object>> theRows) {
 		Runnable task = () -> {
 			StopWatch sw = new StopWatch();
@@ -193,8 +198,8 @@ public abstract class BaseColumnCalculatorTask extends BaseTableColumnTask {
 						sqlBuilder.append(nextNewValueEntry.getKey()).append(" = ?");
 						arguments.add(nextNewValueEntry.getValue());
 					}
-					sqlBuilder.append(" WHERE SP_ID = ?");
-					arguments.add((Number) nextRow.get("SP_ID"));
+					sqlBuilder.append(" WHERE " + myPidColumnName + " = ?");
+					arguments.add((Number) nextRow.get(myPidColumnName));
 
 					// Apply update SQL
 					newJdbcTemplate().update(sqlBuilder.toString(), arguments.toArray());

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTask.java

@@ -60,6 +60,14 @@ public abstract class BaseTask {
 		mySchemaVersion = theSchemaVersion;
 	}
 
+	public String getProductVersion() {
+		return myProductVersion;
+	}
+
+	public String getSchemaVersion() {
+		return mySchemaVersion;
+	}
+
 	public boolean isNoColumnShrink() {
 		return myNoColumnShrink;
 	}
@@ -137,16 +145,18 @@ public abstract class BaseTask {
 		return myConnectionProperties;
 	}
 
-	public void setConnectionProperties(DriverTypeEnum.ConnectionProperties theConnectionProperties) {
+	public BaseTask setConnectionProperties(DriverTypeEnum.ConnectionProperties theConnectionProperties) {
 		myConnectionProperties = theConnectionProperties;
+		return this;
 	}
 
 	public DriverTypeEnum getDriverType() {
 		return myDriverType;
 	}
 
-	public void setDriverType(DriverTypeEnum theDriverType) {
+	public BaseTask setDriverType(DriverTypeEnum theDriverType) {
 		myDriverType = theDriverType;
+		return this;
 	}
 
 	public abstract void validate();

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTask.java

@@ -46,6 +46,7 @@ public class CalculateHashesTask extends BaseColumnCalculatorTask {
 	public CalculateHashesTask(VersionEnum theRelease, String theVersion) {
 		super(theRelease, theVersion);
 		setDescription("Calculate resource search parameter index hashes");
+		setPidColumnName("SP_ID");
 	}
 
 	@Override

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateOrdinalDatesTask.java

@@ -28,6 +28,7 @@ public class CalculateOrdinalDatesTask extends BaseColumnCalculatorTask {
 		super(theRelease, theVersion);
 		setDescription("Calculate SP_LOW_VALUE_DATE_ORDINAL and SP_HIGH_VALUE_DATE_ORDINAL based on existing SP_VALUE_LOW and SP_VALUE_HIGH date values in Date Search Params");
 		setWhereClause("(SP_VALUE_LOW_DATE_ORDINAL IS NULL AND SP_VALUE_LOW IS NOT NULL) OR (SP_VALUE_HIGH_DATE_ORDINAL IS NULL AND SP_VALUE_HIGH IS NOT NULL)");
+		setPidColumnName("SP_ID");
 	}
 
 	@Override

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIndexTask.java

@@ -86,9 +86,13 @@ public class DropIndexTask extends BaseTableTask {
 			@Language("SQL") String findConstraintSql = "SELECT DISTINCT constraint_name FROM user_cons_columns WHERE constraint_name = ? AND table_name = ?";
 			@Language("SQL") String dropConstraintSql = "ALTER TABLE " + getTableName() + " DROP CONSTRAINT ?";
 			findAndDropConstraint(findConstraintSql, dropConstraintSql);
-
 			findConstraintSql = "SELECT DISTINCT constraint_name FROM all_constraints WHERE index_name = ? AND table_name = ?";
 			findAndDropConstraint(findConstraintSql, dropConstraintSql);
+		} else if (getDriverType() == DriverTypeEnum.MSSQL_2012) {
+			// Legacy deletion for SQL Server unique indexes
+			@Language("SQL") String findConstraintSql = "SELECT tc.CONSTRAINT_NAME FROM INFORMATION_SCHEMA.TABLE_CONSTRAINTS AS tc WHERE tc.CONSTRAINT_NAME = ? AND tc.TABLE_NAME = ?";
+			@Language("SQL") String dropConstraintSql = "ALTER TABLE " + getTableName() + " DROP CONSTRAINT ?";
+			findAndDropConstraint(findConstraintSql, dropConstraintSql);
 		}
 
 		Set<String> indexNames = JdbcUtils.getIndexNames(getConnectionProperties(), getTableName());

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropTableTask.java

@@ -63,14 +63,15 @@ public class DropTableTask extends BaseTableTask {
 			}
 		}
 
+		DropIndexTask theIndexTask = new DropIndexTask(getProductVersion(), getSchemaVersion());
+		theIndexTask
+			.setTableName(getTableName())
+			.setConnectionProperties(getConnectionProperties())
+			.setDriverType(getDriverType());
 		for (String nextIndex : indexNames) {
-			List<String> sqls = DropIndexTask.createDropIndexSql(getConnectionProperties(), getTableName(), nextIndex, getDriverType());
-			if (!sqls.isEmpty()) {
-				logInfo(ourLog, "Dropping index {} on table {} in preparation for table delete", nextIndex, getTableName());
-			}
-			for (@Language("SQL") String sql : sqls) {
-				executeSql(getTableName(), sql);
-			}
+			theIndexTask
+				.setIndexName(nextIndex)
+				.execute();
 		}
 
 		logInfo(ourLog, "Dropping table: {}", getTableName());

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

@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
 import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
+import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
@@ -15,6 +16,7 @@ import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.dialect.PostgreSQL94Dialect;
 import org.hl7.fhir.dstu2.model.Subscription;
+import org.hl7.fhir.r5.utils.IResourceValidator;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -81,6 +83,15 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		return daoConfig().getModelConfig();
 	}
 
+	@Override
+	@Bean
+	public ValidationSettings validationSettings() {
+		ValidationSettings retVal = super.validationSettings();
+		retVal.setLocalReferenceValidationDefaultPolicy(IResourceValidator.ReferenceValidationPolicy.CHECK_VALID);
+		return retVal;
+	}
+
+
 	@Bean(name = "myPersistenceDataSourceDstu1", destroyMethod = "close")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();

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

@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
 import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
+import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
@@ -15,6 +16,7 @@ import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.dialect.PostgreSQL94Dialect;
 import org.hl7.fhir.dstu2.model.Subscription;
+import org.hl7.fhir.r5.utils.IResourceValidator;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
@@ -80,6 +82,17 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 	}
 
 
+	@Override
+	@Bean
+	public ValidationSettings validationSettings() {
+		ValidationSettings retVal = super.validationSettings();
+		retVal.setLocalReferenceValidationDefaultPolicy(IResourceValidator.ReferenceValidationPolicy.CHECK_VALID);
+		return retVal;
+	}
+
+
+
+
 	@Override
 	@Bean(autowire = Autowire.BY_TYPE)
 	public DatabaseBackedPagingProvider databaseBackedPagingProvider() {

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

@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
 import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
+import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.rest.client.interceptor.ThreadLocalCapturingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
@@ -16,6 +17,7 @@ import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.dialect.PostgreSQL94Dialect;
 import org.hl7.fhir.dstu2.model.Subscription;
+import org.hl7.fhir.r5.utils.IResourceValidator;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
@@ -81,6 +83,15 @@ public class TestR4Config extends BaseJavaConfigR4 {
 	}
 
 
+	@Override
+	@Bean
+	public ValidationSettings validationSettings() {
+		ValidationSettings retVal = super.validationSettings();
+		retVal.setLocalReferenceValidationDefaultPolicy(IResourceValidator.ReferenceValidationPolicy.CHECK_VALID);
+		return retVal;
+	}
+
+
 	@Bean(name = "myPersistenceDataSourceR4", destroyMethod = "close")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR5Config.java

@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
 import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
+import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
@@ -15,6 +16,7 @@ import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.dialect.PostgreSQL94Dialect;
 import org.hl7.fhir.dstu2.model.Subscription;
+import org.hl7.fhir.r5.utils.IResourceValidator;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
@@ -79,6 +81,16 @@ public class TestR5Config extends BaseJavaConfigR5 {
 		return daoConfig().getModelConfig();
 	}
 
+	@Override
+	@Bean
+	public ValidationSettings validationSettings() {
+		ValidationSettings retVal = super.validationSettings();
+		retVal.setLocalReferenceValidationDefaultPolicy(IResourceValidator.ReferenceValidationPolicy.CHECK_VALID);
+		return retVal;
+	}
+
+
+
 
 	@Bean(name = "myPersistenceDataSourceR5", destroyMethod = "close")
 	public DataSource dataSource() {

hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/ITestDataBuilder.java

@@ -106,6 +106,13 @@ public interface ITestDataBuilder {
 		};
 	}
 
+	/**
+	 * Set Organization.name
+	 */
+	default Consumer<IBaseResource> withName(String theStatus) {
+		return t -> __setPrimitiveChild(getFhirContext(), t, "name", "string", theStatus);
+	}
+
 	default Consumer<IBaseResource> withId(String theId) {
 		return t -> {
 			assertThat(theId, matchesPattern("[a-zA-Z0-9]+"));
@@ -129,6 +136,10 @@ public interface ITestDataBuilder {
 		return createResource("Patient", theModifiers);
 	}
 
+	default IIdType createOrganization(Consumer<IBaseResource>... theModifiers) {
+		return createResource("Organization", theModifiers);
+	}
+
 	default IIdType createResource(String theResourceType, Consumer<IBaseResource>[] theModifiers) {
 		IBaseResource resource = getFhirContext().getResourceDefinition(theResourceType).newInstance();
 		for (Consumer<IBaseResource> next : theModifiers) {
@@ -155,6 +166,30 @@ public interface ITestDataBuilder {
 		};
 	}
 
+	default  Consumer<IBaseResource> withObservationHasMember(@Nullable IIdType theHasMember) {
+		return t -> {
+			if (theHasMember != null) {
+				IBaseReference reference = (IBaseReference) getFhirContext().getElementDefinition("Reference").newInstance();
+				reference.setReference(theHasMember.getValue());
+
+				RuntimeResourceDefinition resourceDef = getFhirContext().getResourceDefinition(t.getClass());
+				resourceDef.getChildByName("hasMember").getMutator().addValue(t, reference);
+			}
+		};
+	}
+
+	default  Consumer<IBaseResource> withOrganization(@Nullable IIdType theHasMember) {
+		return t -> {
+			if (theHasMember != null) {
+				IBaseReference reference = (IBaseReference) getFhirContext().getElementDefinition("Reference").newInstance();
+				reference.setReference(theHasMember.getValue());
+
+				RuntimeResourceDefinition resourceDef = getFhirContext().getResourceDefinition(t.getClass());
+				resourceDef.getChildByName("managingOrganization").getMutator().addValue(t, reference);
+			}
+		};
+	}
+
 	/**
 	 * Users of this API must implement this method
 	 */

hapi-fhir-testpage-overlay/src/main/webapp/WEB-INF/templates/tmpl-head.html

@@ -29,8 +29,8 @@
    <script th:src="@{/resources/moment/min/moment-with-locales.min.js}"></script>
    <link th:href="@{/resources/Eonasdan-bootstrap-datetimepicker/css/bootstrap-datetimepicker.min.css}" rel="stylesheet" />
    <script th:src="@{/resources/Eonasdan-bootstrap-datetimepicker/js/bootstrap-datetimepicker.js}"></script>
-   <link th:href="@{/resources/select2/dist/css/select2.css}" rel="stylesheet"/>
-   <script th:src="@{/resources/select2/dist/js/select2.min.js}"></script>
+   <link th:href="@{/resources/select2/css/select2.css}" rel="stylesheet"/>
+   <script th:src="@{/resources/select2/js/select2.min.js}"></script>
 
 
    <script src="js/RestfulTester.js" type="text/javascript"></script>

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/FhirInstanceValidator.java

@@ -38,8 +38,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
 	private boolean assumeValidRestReferences;
 	private List<String> myExtensionDomains = Collections.emptyList();
 	private IResourceValidator.IValidatorResourceFetcher validatorResourceFetcher;
-	private volatile FhirContext myDstu2Context;
-	private volatile FhirContext myHl7OrgDstu2Context;
 
 	/**
 	 * Constructor
@@ -136,8 +134,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
 	/**
 	 * Returns the {@link IValidationSupport validation support} in use by this validator. Default is an instance of
 	 * DefaultProfileValidationSupport if the no-arguments constructor for this object was used.
-	 *
-	 * @return
 	 */
 	public IValidationSupport getValidationSupport() {
 		return myValidationSupport;
@@ -276,24 +272,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
 		return wrappedWorkerContext;
 	}
 
-	private FhirContext getDstu2Context() {
-		FhirContext dstu2Context = myDstu2Context;
-		if (dstu2Context == null) {
-			dstu2Context = FhirContext.forDstu2();
-			myDstu2Context = dstu2Context;
-		}
-		return dstu2Context;
-	}
-
-	private FhirContext getHl7OrgDstu2Context() {
-		FhirContext hl7OrgDstu2Context = myHl7OrgDstu2Context;
-		if (hl7OrgDstu2Context == null) {
-			hl7OrgDstu2Context = FhirContext.forDstu2Hl7Org();
-			myHl7OrgDstu2Context = hl7OrgDstu2Context;
-		}
-		return hl7OrgDstu2Context;
-	}
-
 	public IResourceValidator.IValidatorResourceFetcher getValidatorResourceFetcher() {
 		return validatorResourceFetcher;
 	}

hapi-tinder-plugin/pom.xml

@@ -210,7 +210,7 @@
 		<dependency>
 			<groupId>org.apache.ant</groupId>
 			<artifactId>ant</artifactId>
-			<version>1.7.0</version>
+			<version>1.10.8</version>
 		</dependency>
 		
 		<!-- This is just used for  -->

pom.xml

@@ -679,7 +679,7 @@
 	<properties>
 
 		<fhir_core_version>5.1.0</fhir_core_version>
-		<ucum_version>1.0.2</ucum_version>
+		<ucum_version>1.0.3</ucum_version>
 
 		<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>
 
@@ -726,8 +726,8 @@
 		<hibernate_validator_version>6.1.3.Final</hibernate_validator_version>
 		<httpcore_version>4.4.13</httpcore_version>
 		<httpclient_version>4.5.12</httpclient_version>
-		<jackson_version>2.10.0</jackson_version>
-		<jackson_databind_version>2.10.0</jackson_databind_version>
+		<jackson_version>2.11.2</jackson_version>
+		<jackson_databind_version>2.11.2</jackson_databind_version>
 		<maven_assembly_plugin_version>3.1.0</maven_assembly_plugin_version>
 		<maven_license_plugin_version>1.8</maven_license_plugin_version>
 		<resteasy_version>4.0.0.Beta3</resteasy_version>
@@ -1018,11 +1018,6 @@
 				<artifactId>javax.ws.rs-api</artifactId>
 				<version>2.0.1</version>
 			</dependency>
-			<dependency>
-				<groupId>io.github.devacfr.maven.skins</groupId>
-				<artifactId>reflow-velocity-tools</artifactId>
-				<version>2.0.0-beta2</version>
-			</dependency>
 			<dependency>
 				<groupId>io.swagger</groupId>
 				<artifactId>swagger-annotations</artifactId>
@@ -1572,6 +1567,12 @@
 				<groupId>org.webjars</groupId>
 				<artifactId>bootstrap</artifactId>
 				<version>3.3.7</version>
+				<exclusions>
+					<exclusion>
+						<groupId>org.webjars</groupId>
+						<artifactId>jquery</artifactId>
+					</exclusion>
+				</exclusions>
 			</dependency>
 			<dependency>
 				<groupId>org.webjars</groupId>
@@ -1586,7 +1587,7 @@
 			<dependency>
 				<groupId>org.webjars.bower</groupId>
 				<artifactId>awesome-bootstrap-checkbox</artifactId>
-				<version>1.0.1</version>
+				<version>1.0.2</version>
 			</dependency>
 			<dependency>
 				<groupId>org.webjars</groupId>
@@ -1596,17 +1597,23 @@
 			<dependency>
 				<groupId>org.webjars</groupId>
 				<artifactId>select2</artifactId>
-				<version>4.0.3</version>
+				<version>4.0.13</version>
+				<exclusions>
+					<exclusion>
+						<groupId>org.webjars</groupId>
+						<artifactId>jquery</artifactId>
+					</exclusion>
+				</exclusions>
 			</dependency>
 			<dependency>
 				<groupId>org.webjars.bower</groupId>
 				<artifactId>jquery</artifactId>
-				<version>3.3.1</version>
+				<version>3.5.1</version>
 			</dependency>
 			<dependency>
 				<groupId>org.webjars.bower</groupId>
 				<artifactId>moment</artifactId>
-				<version>2.15.1</version>
+				<version>2.27.0</version>
 			</dependency>
 			<dependency>
 				<groupId>org.xmlunit</groupId>
@@ -1873,49 +1880,6 @@
 						</excludes>
 					</configuration>
 				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-site-plugin</artifactId>
-					<version>3.7.1</version>
-					<configuration>
-						<skip>false</skip>
-						<skipDeploy>true</skipDeploy>
-						<inputEncoding>UTF-8</inputEncoding>
-						<outputEncoding>UTF-8</outputEncoding>
-						<relativizeDecorationLinks>false</relativizeDecorationLinks>
-					</configuration>
-					<dependencies>
-						<dependency>
-							<groupId>org.apache.maven.wagon</groupId>
-							<artifactId>wagon-scm</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.maven.scm</groupId>
-							<artifactId>maven-scm-manager-plexus</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.maven.scm</groupId>
-							<artifactId>maven-scm-provider-gitexe</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.maven.scm</groupId>
-							<artifactId>maven-scm-api</artifactId>
-						</dependency>
-						<!-- <dependency> <groupId>org.apache.maven.doxia</groupId> <artifactId>doxia-core</artifactId> </dependency> -->
-						<dependency>
-							<groupId>org.apache.maven.doxia</groupId>
-							<artifactId>doxia-module-markdown</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>io.github.devacfr.maven.skins</groupId>
-							<artifactId>reflow-velocity-tools</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.velocity</groupId>
-							<artifactId>velocity</artifactId>
-						</dependency>
-					</dependencies>
-				</plugin>
 				<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself. -->
 				<plugin>
 					<groupId>org.eclipse.m2e</groupId>
@@ -2310,59 +2274,6 @@
 					</execution>
 				</executions>
 			</plugin>
-			<plugin>
-				<artifactId>maven-site-plugin</artifactId>
-				<inherited>false</inherited>
-				<executions>
-					<execution>
-						<id>stage-for-scm-publish</id>
-						<phase>post-site</phase>
-						<goals>
-							<goal>stage</goal>
-						</goals>
-						<configuration>
-							<stagingDirectory>${siteMainDirectory}</stagingDirectory>
-						</configuration>
-					</execution>
-				</executions>
-				<dependencies>
-					<dependency>
-						<groupId>org.apache.maven.wagon</groupId>
-						<artifactId>wagon-scm</artifactId>
-						<version>3.0.0</version>
-					</dependency>
-					<dependency>
-						<groupId>org.apache.maven.scm</groupId>
-						<artifactId>maven-scm-manager-plexus</artifactId>
-						<version>1.9.5</version>
-					</dependency>
-					<dependency>
-						<groupId>org.apache.maven.scm</groupId>
-						<artifactId>maven-scm-provider-gitexe</artifactId>
-						<version>1.9.5</version>
-					</dependency>
-					<dependency>
-						<groupId>org.apache.maven.scm</groupId>
-						<artifactId>maven-scm-api</artifactId>
-						<version>1.9.5</version>
-					</dependency>
-					<dependency>
-						<groupId>org.apache.maven.doxia</groupId>
-						<artifactId>doxia-module-markdown</artifactId>
-						<version>1.8</version>
-					</dependency>
-					<dependency>
-						<groupId>io.github.devacfr.maven.skins</groupId>
-						<artifactId>reflow-velocity-tools</artifactId>
-						<version>2.0.0-beta2</version>
-					</dependency>
-					<dependency>
-						<groupId>org.apache.velocity</groupId>
-						<artifactId>velocity</artifactId>
-						<version>1.7</version>
-					</dependency>
-				</dependencies>
-			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-scm-publish-plugin</artifactId>