Merge remote-tracking branch 'origin/rev_include' also closes #73

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/AbstractResourceDaoJdbc.java

@@ -27,6 +27,7 @@
 import org.highmed.dsf.fhir.search.SearchQuery;
 import org.highmed.dsf.fhir.search.SearchQuery.SearchQueryBuilder;
 import org.highmed.dsf.fhir.search.SearchQueryParameter;
+import org.highmed.dsf.fhir.search.SearchQueryRevIncludeParameterFactory;
 import org.highmed.dsf.fhir.search.parameters.ResourceId;
 import org.highmed.dsf.fhir.search.parameters.ResourceLastUpdated;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -106,33 +107,40 @@ public Resource getResource()
 	private final String resourceColumn;
 	private final String resourceIdColumn;
 
-	private final List<Supplier<SearchQueryParameter<R>>> searchParameterFactories;
+	private final List<Supplier<SearchQueryParameter<R>>> searchParameterFactories = new ArrayList<>();
+	private final List<Supplier<SearchQueryRevIncludeParameterFactory>> searchRevIncludeParameterFactories = new ArrayList<>();
 
 	private final PreparedStatementFactory<R> preparedStatementFactory;
 
+	@SafeVarargs
+	protected static <T> List<T> with(T... t)
+	{
+		return Arrays.asList(t);
+	}
+
 	/*
 	 * Using a suppliers for SearchParameters, implementations are not thread safe and because of that they need to be
 	 * created on a request basis
 	 */
-	@SafeVarargs
 	AbstractResourceDaoJdbc(DataSource dataSource, FhirContext fhirContext, Class<R> resourceType, String resourceTable,
 			String resourceColumn, String resourceIdColumn,
-			Supplier<SearchQueryParameter<R>>... searchParameterFactories)
+			List<Supplier<SearchQueryParameter<R>>> searchParameterFactories,
+			List<Supplier<SearchQueryRevIncludeParameterFactory>> searchRevIncludeParameterFactories)
 	{
 		this(dataSource, fhirContext, resourceType, resourceTable, resourceColumn, resourceIdColumn,
 				new PreparedStatementFactoryDefault<>(fhirContext, resourceType, resourceTable, resourceIdColumn,
 						resourceColumn),
-				searchParameterFactories);
+				searchParameterFactories, searchRevIncludeParameterFactories);
 	}
 
 	/*
 	 * Using a suppliers for SearchParameters, implementations are not thread safe and because of that they need to be
 	 * created on a request basis
 	 */
-	@SafeVarargs
 	AbstractResourceDaoJdbc(DataSource dataSource, FhirContext fhirContext, Class<R> resourceType, String resourceTable,
 			String resourceColumn, String resourceIdColumn, PreparedStatementFactory<R> preparedStatementFactory,
-			Supplier<SearchQueryParameter<R>>... searchParameterFactories)
+			List<Supplier<SearchQueryParameter<R>>> searchParameterFactories,
+			List<Supplier<SearchQueryRevIncludeParameterFactory>> searchRevIncludeParameterFactories)
 	{
 		this.dataSource = dataSource;
 		this.fhirContext = fhirContext;
@@ -145,7 +153,10 @@ public Resource getResource()
 
 		this.preparedStatementFactory = preparedStatementFactory;
 
-		this.searchParameterFactories = Arrays.asList(searchParameterFactories);
+		if (searchParameterFactories != null)
+			this.searchParameterFactories.addAll(searchParameterFactories);
+		if (searchRevIncludeParameterFactories != null)
+			this.searchRevIncludeParameterFactories.addAll(searchRevIncludeParameterFactories);
 	}
 
 	@Override
@@ -789,7 +800,7 @@ public PartialResult<R> searchWithTransaction(Connection connection, DbSearchQue
 
 		List<R> partialResult = new ArrayList<>();
 		List<Resource> includes = new ArrayList<>();
-
+		
 		if (!query.isCountOnly(overallCount)) // TODO ask db if count 0
 		{
 			try (PreparedStatement statement = connection.prepareStatement(query.getSearchSql()))
@@ -868,6 +879,8 @@ public final SearchQuery<R> createSearchQuery(int page, int count)
 		return SearchQueryBuilder.create(resourceType, getResourceTable(), getResourceColumn(), page, count)
 				.with(new ResourceId(getResourceIdColumn()), new ResourceLastUpdated(getResourceColumn()))
 				.with(searchParameterFactories.stream().map(Supplier::get).toArray(SearchQueryParameter[]::new))
+				.withRevInclude(searchRevIncludeParameterFactories.stream().map(Supplier::get)
+						.toArray(SearchQueryRevIncludeParameterFactory[]::new))
 				.build();
 	}
 }

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/AbstractStructureDefinitionDaoJdbc.java

@@ -28,8 +28,10 @@ public AbstractStructureDefinitionDaoJdbc(BasicDataSource dataSource, FhirContex
 			String resourceColumn, String resourceIdColumn)
 	{
 		super(dataSource, fhirContext, StructureDefinition.class, resourceTable, resourceColumn, resourceIdColumn,
-				() -> new StructureDefinitionIdentifier(resourceColumn),
-				() -> new StructureDefinitionUrl(resourceColumn), () -> new StructureDefinitionVersion(resourceColumn));
+				with(() -> new StructureDefinitionIdentifier(resourceColumn),
+						() -> new StructureDefinitionUrl(resourceColumn),
+						() -> new StructureDefinitionVersion(resourceColumn)),
+				with());
 
 		readByUrl = new ReadByUrlDaoJdbc<StructureDefinition>(this::getDataSource, this::getResource, resourceTable,
 				resourceColumn, resourceIdColumn);

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/BinaryDaoJdbc.java

@@ -18,7 +18,7 @@ public class BinaryDaoJdbc extends AbstractResourceDaoJdbc<Binary> implements Bi
 	public BinaryDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
 		super(dataSource, fhirContext, Binary.class, "binaries", "binary_json", "binary_id",
-				new PreparedStatementFactoryBinary(fhirContext), BinaryContentType::new);
+				new PreparedStatementFactoryBinary(fhirContext), with(BinaryContentType::new), with());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/BundleDaoJdbc.java

@@ -15,7 +15,8 @@ public class BundleDaoJdbc extends AbstractResourceDaoJdbc<Bundle> implements Bu
 {
 	public BundleDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
-		super(dataSource, fhirContext, Bundle.class, "bundles", "bundle", "bundle_id", BundleIdentifier::new);
+		super(dataSource, fhirContext, Bundle.class, "bundles", "bundle", "bundle_id", with(BundleIdentifier::new),
+				with());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/CodeSystemDaoJdbc.java

@@ -19,10 +19,10 @@ public class CodeSystemDaoJdbc extends AbstractResourceDaoJdbc<CodeSystem> imple
 	public CodeSystemDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
 		super(dataSource, fhirContext, CodeSystem.class, "code_systems", "code_system", "code_system_id",
-				CodeSystemUrl::new, CodeSystemVersion::new, CodeSystemIdentifier::new);
+				with(CodeSystemUrl::new, CodeSystemVersion::new, CodeSystemIdentifier::new), with());
 
-		readByUrl = new ReadByUrlDaoJdbc<>(this::getDataSource, this::getResource, getResourceTable(), getResourceColumn(),
-				getResourceIdColumn());
+		readByUrl = new ReadByUrlDaoJdbc<>(this::getDataSource, this::getResource, getResourceTable(),
+				getResourceColumn(), getResourceIdColumn());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/EndpointDaoJdbc.java

@@ -11,6 +11,7 @@
 import org.highmed.dsf.fhir.search.parameters.EndpointName;
 import org.highmed.dsf.fhir.search.parameters.EndpointOrganization;
 import org.highmed.dsf.fhir.search.parameters.EndpointStatus;
+import org.highmed.dsf.fhir.search.parameters.rev.include.OrganizationEndpointRevInclude;
 import org.hl7.fhir.r4.model.Endpoint;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -24,7 +25,8 @@ public class EndpointDaoJdbc extends AbstractResourceDaoJdbc<Endpoint> implement
 	public EndpointDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
 		super(dataSource, fhirContext, Endpoint.class, "endpoints", "endpoint", "endpoint_id",
-				EndpointOrganization::new, EndpointIdentifier::new, EndpointName::new, EndpointStatus::new);
+				with(EndpointOrganization::new, EndpointIdentifier::new, EndpointName::new, EndpointStatus::new),
+				with(OrganizationEndpointRevInclude::new));
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/GroupDaoJdbc.java

@@ -2,6 +2,7 @@
 
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.highmed.dsf.fhir.dao.GroupDao;
+import org.highmed.dsf.fhir.search.parameters.rev.include.ResearchStudyEnrollmentRevInclude;
 import org.hl7.fhir.r4.model.Group;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -10,7 +11,8 @@ public class GroupDaoJdbc extends AbstractResourceDaoJdbc<Group> implements Grou
 {
 	public GroupDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
-		super(dataSource, fhirContext, Group.class, "groups", "group_json", "group_id");
+		super(dataSource, fhirContext, Group.class, "groups", "group_json", "group_id", with(),
+				with(ResearchStudyEnrollmentRevInclude::new));
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/HealthcareServiceDaoJdbc.java

@@ -8,13 +8,12 @@
 
 import ca.uhn.fhir.context.FhirContext;
 
-public class HealthcareServiceDaoJdbc extends AbstractResourceDaoJdbc<HealthcareService>
-		implements HealthcareServiceDao
+public class HealthcareServiceDaoJdbc extends AbstractResourceDaoJdbc<HealthcareService> implements HealthcareServiceDao
 {
 	public HealthcareServiceDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
 		super(dataSource, fhirContext, HealthcareService.class, "healthcare_services", "healthcare_service",
-				"healthcare_service_id", HealthcareServiceIdentifier::new, HealthcareServiceActive::new);
+				"healthcare_service_id", with(HealthcareServiceIdentifier::new, HealthcareServiceActive::new), with());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/LocationDaoJdbc.java

@@ -11,7 +11,8 @@ public class LocationDaoJdbc extends AbstractResourceDaoJdbc<Location> implement
 {
 	public LocationDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
-		super(dataSource, fhirContext, Location.class, "locations", "location", "location_id", LocationIdentifier::new);
+		super(dataSource, fhirContext, Location.class, "locations", "location", "location_id",
+				with(LocationIdentifier::new), with());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/NamingSystemDaoJdbc.java

@@ -12,7 +12,7 @@ public class NamingSystemDaoJdbc extends AbstractResourceDaoJdbc<NamingSystem> i
 	public NamingSystemDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
 		super(dataSource, fhirContext, NamingSystem.class, "naming_systems", "naming_system", "naming_system_id",
-				NamingSystemName::new);
+				with(NamingSystemName::new), with());
 
 	}
 

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/OrganizationDaoJdbc.java

@@ -13,6 +13,7 @@
 import org.highmed.dsf.fhir.search.parameters.OrganizationIdentifier;
 import org.highmed.dsf.fhir.search.parameters.OrganizationName;
 import org.highmed.dsf.fhir.search.parameters.OrganizationType;
+import org.highmed.dsf.fhir.search.parameters.rev.include.EndpointOrganizationRevInclude;
 import org.hl7.fhir.r4.model.Organization;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -26,7 +27,9 @@ public class OrganizationDaoJdbc extends AbstractResourceDaoJdbc<Organization> i
 	public OrganizationDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
 		super(dataSource, fhirContext, Organization.class, "organizations", "organization", "organization_id",
-				OrganizationName::new, OrganizationEndpoint::new, OrganizationIdentifier::new, OrganizationActive::new, OrganizationType::new);
+				with(OrganizationName::new, OrganizationEndpoint::new, OrganizationIdentifier::new,
+						OrganizationActive::new, OrganizationType::new),
+				with(EndpointOrganizationRevInclude::new));
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/PatientDaoJdbc.java

@@ -12,8 +12,8 @@ public class PatientDaoJdbc extends AbstractResourceDaoJdbc<Patient> implements
 {
 	public PatientDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
-		super(dataSource, fhirContext, Patient.class, "patients", "patient", "patient_id", PatientIdentifier::new,
-				PatientActive::new);
+		super(dataSource, fhirContext, Patient.class, "patients", "patient", "patient_id",
+				with(PatientIdentifier::new, PatientActive::new), with());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/PractitionerDaoJdbc.java

@@ -13,7 +13,7 @@ public class PractitionerDaoJdbc extends AbstractResourceDaoJdbc<Practitioner> i
 	public PractitionerDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
 		super(dataSource, fhirContext, Practitioner.class, "practitioners", "practitioner", "practitioner_id",
-				PractitionerIdentifier::new, PractitionerActive::new);
+				with(PractitionerIdentifier::new, PractitionerActive::new), with());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/PractitionerRoleDaoJdbc.java

@@ -8,13 +8,12 @@
 
 import ca.uhn.fhir.context.FhirContext;
 
-public class PractitionerRoleDaoJdbc extends AbstractResourceDaoJdbc<PractitionerRole>
-		implements PractitionerRoleDao
+public class PractitionerRoleDaoJdbc extends AbstractResourceDaoJdbc<PractitionerRole> implements PractitionerRoleDao
 {
 	public PractitionerRoleDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
 		super(dataSource, fhirContext, PractitionerRole.class, "practitioner_roles", "practitioner_role",
-				"practitioner_role_id", PractitionerRoleIdentifier::new, PractitionerRoleActive::new);
+				"practitioner_role_id", with(PractitionerRoleIdentifier::new, PractitionerRoleActive::new), with());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/ProvenanceDaoJdbc.java

@@ -10,7 +10,7 @@ public class ProvenanceDaoJdbc extends AbstractResourceDaoJdbc<Provenance> imple
 {
 	public ProvenanceDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
-		super(dataSource, fhirContext, Provenance.class, "provenances", "provenance", "provenance_id");
+		super(dataSource, fhirContext, Provenance.class, "provenances", "provenance", "provenance_id", with(), with());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/ResearchStudyDaoJdbc.java

@@ -13,7 +13,7 @@ public class ResearchStudyDaoJdbc extends AbstractResourceDaoJdbc<ResearchStudy>
 	public ResearchStudyDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
 		super(dataSource, fhirContext, ResearchStudy.class, "research_studies", "research_study", "research_study_id",
-				ResearchStudyIdentifier::new, ResearchStudyEnrollment::new);
+				with(ResearchStudyIdentifier::new, ResearchStudyEnrollment::new), with());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/SubscriptionDaoJdbc.java

@@ -27,8 +27,9 @@ public class SubscriptionDaoJdbc extends AbstractResourceDaoJdbc<Subscription> i
 	public SubscriptionDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
 		super(dataSource, fhirContext, Subscription.class, "subscriptions", "subscription", "subscription_id",
-				SubscriptionCriteria::new, SubscriptionStatus::new, SubscriptionChannelType::new,
-				SubscriptionChannelPayload::new);
+				with(SubscriptionCriteria::new, SubscriptionStatus::new, SubscriptionChannelType::new,
+						SubscriptionChannelPayload::new),
+				with());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/TaskDaoJdbc.java

@@ -13,8 +13,8 @@ public class TaskDaoJdbc extends AbstractResourceDaoJdbc<Task> implements TaskDa
 {
 	public TaskDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
-		super(dataSource, fhirContext, Task.class, "tasks", "task", "task_id", TaskIdentifier::new, TaskRequester::new,
-				TaskStatus::new);
+		super(dataSource, fhirContext, Task.class, "tasks", "task", "task_id",
+				with(TaskIdentifier::new, TaskRequester::new, TaskStatus::new), with());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/ValueSetDaoJdbc.java

@@ -19,10 +19,10 @@ public class ValueSetDaoJdbc extends AbstractResourceDaoJdbc<ValueSet> implement
 	public ValueSetDaoJdbc(BasicDataSource dataSource, FhirContext fhirContext)
 	{
 		super(dataSource, fhirContext, ValueSet.class, "value_sets", "value_set", "value_set_id",
-				ValueSetIdentifier::new, ValueSetUrl::new, ValueSetVersion::new);
+				with(ValueSetIdentifier::new, ValueSetUrl::new, ValueSetVersion::new), with());
 
-		readByUrl = new ReadByUrlDaoJdbc<>(this::getDataSource, this::getResource, getResourceTable(), getResourceColumn(),
-				getResourceIdColumn());
+		readByUrl = new ReadByUrlDaoJdbc<>(this::getDataSource, this::getResource, getResourceTable(),
+				getResourceColumn(), getResourceIdColumn());
 	}
 
 	@Override

dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/function/BiConsumerWithSqlException.java

@@ -0,0 +1,40 @@
+package org.highmed.dsf.fhir.function;
+
+import java.sql.SQLException;
+import java.util.Objects;
+
+@FunctionalInterface
+public interface BiConsumerWithSqlException<T, U>
+{
+	void accept(T t, U u) throws SQLException;
+
+	default BiConsumerWithSqlException<T, U> andThen(BiConsumerWithSqlException<? super T, ? super U> after)
+	{
+		Objects.requireNonNull(after);
+		return (T t, U u) ->
+		{
+			SQLException suppressed = null;
+			try
+			{
+				accept(t, u);
+			}
+			catch (SQLException e)
+			{
+				suppressed = e;
+			}
+			finally
+			{
+				try
+				{
+					after.accept(t, u);
+				}
+				catch (SQLException e)
+				{
+					if (suppressed != null)
+						e.addSuppressed(suppressed);
+					throw e;
+				}
+			}
+		};
+	}
+}