Me/dpc 4324 hapi jpa eval

docker-compose.override.yml

@@ -1,5 +1,3 @@
-version: '3'
-
 services:
   db:
     ports:
@@ -12,9 +10,6 @@ services:
   aggregation:
     ports:
       - "5006:5005"
-  attribution:
-    ports:
-      - "5007:5005"
   consent:
     ports:
       - "5008:5005"

docker-compose.yml

@@ -4,7 +4,7 @@ services:
     image: postgres:14
     command: postgres -c 'max_connections=250'
     environment:
-      - POSTGRES_MULTIPLE_DATABASES=dpc_attribution,dpc_queue,dpc_auth,dpc_consent,dpc-website_development,bcda,dpc-portal_development
+      - POSTGRES_MULTIPLE_DATABASES=dpc_queue,dpc_auth,dpc_consent,dpc-website_development,bcda,dpc-portal_development,hapi
       - POSTGRES_USER=postgres
       - POSTGRES_PASSWORD=dpc-safe
     volumes:
@@ -33,20 +33,6 @@ services:
       - export-volume:/app/data
       - ./jacocoReport/dpc-aggregation:/jacoco-report
 
-  attribution:
-    image: ${ECR_HOST:-755619740999.dkr.ecr.us-east-1.amazonaws.com/dpc-attribution}:latest
-    depends_on:
-      - db
-    environment:
-      - ENV=local
-      - JACOCO=${REPORT_COVERAGE}
-      - DEBUG_MODE=${DEBUG_MODE:-false}
-    ports:
-      - "3500:8080"
-      - "9902:9902"
-    volumes:
-      - ./jacocoReport/dpc-attribution:/jacoco-report
-
   api:
     image: ${ECR_HOST:-755619740999.dkr.ecr.us-east-1.amazonaws.com/dpc-api}:latest
     ports:
@@ -58,10 +44,11 @@ services:
       - ENV=local
       - JACOCO=${REPORT_COVERAGE}
       - EXPORT_PATH=/app/data
-      - AUTH_DISABLED=${AUTH_DISABLED:-false}
+      #- AUTH_DISABLED=${AUTH_DISABLED:-false}
+      - AUTH_DISABLED=true
       - DEBUG_MODE=${DEBUG_MODE:-false}
     depends_on:
-      - attribution
+      - fhir
     volumes:
       - export-volume:/app/data
       - ./jacocoReport/dpc-api:/jacoco-report
@@ -89,9 +76,10 @@ services:
   start_api_dependencies:
     image: dadarek/wait-for-dependencies
     depends_on:
-      - attribution
+      #- attribution
+      - fhir
       - aggregation
-    command: attribution:8080 aggregation:9901
+    command: fhir:8080 aggregation:9901
 
   start_api:
     image: dadarek/wait-for-dependencies
@@ -116,6 +104,20 @@ services:
     command: sh -c "mvn test -Pintegration-tests -am -ntp"
     network_mode: host
 
+  fhir:
+    image: "hapiproject/hapi:latest"
+    ports:
+      - "8080:8080"
+    configs:
+      - source: hapi
+        target: /app/config/application.yaml
+    depends_on:
+      - db
+
+configs:
+  hapi:
+    file: ./hapi.application.yaml
+
 volumes:
   pgdata14:
   export-volume:

dpc-aggregation/src/main/java/gov/cms/dpc/aggregation/AggregationAppModule.java

@@ -14,7 +14,6 @@
 import gov.cms.dpc.aggregation.service.*;
 import gov.cms.dpc.common.annotations.ExportPath;
 import gov.cms.dpc.common.annotations.JobTimeout;
-import gov.cms.dpc.common.hibernate.attribution.DPCManagedSessionFactory;
 import gov.cms.dpc.fhir.configuration.FHIRClientConfiguration;
 import gov.cms.dpc.fhir.hapi.ContextUtils;
 import gov.cms.dpc.queue.models.JobQueueBatch;
@@ -114,7 +113,7 @@ public int provideJobTimeoutInSeconds() {
     }
 
     @Provides
-    LookBackService provideLookBackService(DPCManagedSessionFactory sessionFactory, OperationsConfig operationsConfig) {
+    LookBackService provideLookBackService(OperationsConfig operationsConfig) {
         //Configuring to skip look back when look back months is less than 0
         if (operationsConfig.getLookBackMonths() < 0) {
             return new EveryoneGetsDataLookBackServiceImpl();

dpc-aggregation/src/main/java/gov/cms/dpc/aggregation/DPCAggregationConfiguration.java

@@ -3,7 +3,6 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 import gov.cms.dpc.bluebutton.config.BBClientConfiguration;
 import gov.cms.dpc.bluebutton.config.BlueButtonBundleConfiguration;
-import gov.cms.dpc.common.hibernate.attribution.IDPCDatabase;
 import gov.cms.dpc.common.hibernate.queue.IDPCQueueDatabase;
 import gov.cms.dpc.fhir.configuration.FHIRClientConfiguration;
 import gov.cms.dpc.queue.config.DPCAwsQueueConfiguration;
@@ -20,13 +19,7 @@
 import java.time.ZoneId;
 import java.util.List;
 
-public class DPCAggregationConfiguration extends Configuration implements BlueButtonBundleConfiguration, IDPCDatabase, IDPCQueueDatabase, DPCQueueConfig {
-
-    @Valid
-    @NotNull
-    @JsonProperty("database")
-    private final DataSourceFactory database = new DataSourceFactory();
-
+public class DPCAggregationConfiguration extends Configuration implements BlueButtonBundleConfiguration, IDPCQueueDatabase, DPCQueueConfig {
     @Valid
     @NotNull
     @JsonProperty("queuedb")
@@ -81,11 +74,6 @@ public class DPCAggregationConfiguration extends Configuration implements BlueBu
     @NotNull
     private final YearMonth lookBackDate = YearMonth.now(ZoneId.systemDefault());
 
-    @Override
-    public DataSourceFactory getDatabase() {
-        return this.database;
-    }
-
     @Override
     public DataSourceFactory getQueueDatabase() {
         return queueDatabase;

dpc-aggregation/src/main/java/gov/cms/dpc/aggregation/DPCAggregationService.java

@@ -2,8 +2,6 @@
 
 import com.squarespace.jersey2.guice.JerseyGuiceUtils;
 import gov.cms.dpc.bluebutton.BlueButtonClientModule;
-import gov.cms.dpc.common.hibernate.attribution.DPCHibernateBundle;
-import gov.cms.dpc.common.hibernate.attribution.DPCHibernateModule;
 import gov.cms.dpc.common.hibernate.queue.DPCQueueHibernateBundle;
 import gov.cms.dpc.common.hibernate.queue.DPCQueueHibernateModule;
 import gov.cms.dpc.common.utils.EnvironmentParser;
@@ -21,7 +19,6 @@
 public class DPCAggregationService extends Application<DPCAggregationConfiguration> {
 
     private final DPCQueueHibernateBundle<DPCAggregationConfiguration> queueHibernateBundle = new DPCQueueHibernateBundle<>();
-    private final DPCHibernateBundle<DPCAggregationConfiguration> hibernateBundle = new DPCHibernateBundle<>();
 
     public static void main(final String[] args) throws Exception {
         new DPCAggregationService().run(args);
@@ -45,7 +42,7 @@ public void initialize(Bootstrap<DPCAggregationConfiguration> bootstrap) {
         GuiceBundle guiceBundle = GuiceBundle.builder()
                 .modules(new AggregationAppModule(),
                         new DPCQueueHibernateModule<>(queueHibernateBundle),
-                        new DPCHibernateModule<>(hibernateBundle),
+                        //new DPCHibernateModule<>(hibernateBundle),
                         new JobQueueModule<DPCAggregationConfiguration>(),
                         new BlueButtonClientModule<DPCAggregationConfiguration>())
                 .build();
@@ -54,7 +51,6 @@ public void initialize(Bootstrap<DPCAggregationConfiguration> bootstrap) {
         // The Hibernate Guice module requires an initialized SessionFactory,
         // so Dropwizard needs to initialize the HibernateBundle first to create the SessionFactory.
         bootstrap.addBundle(queueHibernateBundle);
-        bootstrap.addBundle(hibernateBundle);
 
         bootstrap.addBundle(guiceBundle);
         bootstrap.addBundle(new MigrationsBundle<>() {

dpc-aggregation/src/main/resources/application.yml

@@ -1,15 +1,3 @@
-database:
-  driverClass: org.postgresql.Driver
-  url: ${DATABASE_URL:-"jdbc:postgresql://db:5432/dpc_attribution"}
-  user: "${ATTRIBUTION_DB_USER:-postgres}"
-  password: "${ATTRIBUTION_DB_PASS:-dpc-safe}"
-  initialSize: 5
-  minSize: 5
-  maxSize: 10
-  properties:
-    charSet: UTF-8
-    hibernate.dialect: org.hibernate.dialect.PostgreSQL10Dialect
-
 queuedb:
   driverClass: org.postgresql.Driver
   url: ${QUEUE_DB_URL:-"jdbc:postgresql://db:5432/dpc_queue"}

dpc-api/src/main/java/gov/cms/dpc/api/APIHelpers.java

@@ -31,21 +31,14 @@ public static <T extends BaseResource> Bundle bulkResourceClient(Class<T> clazz,
                 .getEntry()
                 .stream()
                 .filter(Bundle.BundleEntryComponent::hasResource)
+                .map(component -> component.setRequest(new Bundle.BundleEntryRequestComponent().setMethod(Bundle.HTTPVerb.POST)))
                 .map(Bundle.BundleEntryComponent::getResource)
                 .filter(resource -> resource.getClass().equals(clazz))
                 .map(clazz::cast)
                 .forEach(entryConsumer);
+        resourceBundle.setType(Bundle.BundleType.TRANSACTION);
 
-        final Parameters params = new Parameters();
-        params.addParameter().setResource(resourceBundle);
-        return client
-                .operation()
-                .onType(clazz)
-                .named("submit")
-                .withParameters(params)
-                .returnResourceType(Bundle.class)
-                .encodedJson()
-                .execute();
+        return client.transaction().withBundle(resourceBundle).execute();
     }
 
     public static String formatValidationMessages(List<SingleValidationMessage> messages) {

dpc-api/src/main/java/gov/cms/dpc/api/DPCAPIModule.java

@@ -187,7 +187,9 @@ SessionFactory provideSessionFactory(DPCAuthManagedSessionFactory factory) {
     @Singleton
     @Named("fhirContextAttributionSTU3")
     public FhirContext provideAttributionSTU3Context() {
-        return FhirContext.forDstu3();
+        FhirContext ctx = FhirContext.forDstu3();
+        ctx.getParserOptions().setOverrideResourceIdWithBundleEntryFullUrl(false);
+        return ctx;
     }
 
     @Provides

dpc-api/src/main/java/gov/cms/dpc/api/DPCAPIService.java

@@ -107,7 +107,8 @@ public void run(final DPCAPIConfiguration configuration,
         environment.healthChecks().register("api-self-check",
             new HttpHealthCheck(UrlGenerator.generateVersionUrl(configuration.getServicePort(), configuration.getAppContextPath()))
         );
-        environment.healthChecks().register("dpc-attribution", new HttpHealthCheck(configuration.getAttributionHealthCheckURL()));
+        // TODO: Turned off for PoC since I don't want to create a healthcheck for the new FHIR server
+        //environment.healthChecks().register("dpc-attribution", new HttpHealthCheck(configuration.getAttributionHealthCheckURL()));
     }
 
     private GuiceBundle setupGuiceBundle() {

dpc-api/src/main/java/gov/cms/dpc/api/auth/macaroonauth/MacaroonsAuthenticator.java

@@ -50,25 +50,23 @@ public Optional<OrganizationPrincipal> authenticate(DPCAuthCredentials credentia
         logger.debug("Looking up resource {} in path authorizer. With value: {}", credentials.getPathAuthorizer().type(), credentials.getPathAuthorizer().pathParam());
         Map<String, List<String>> searchParams = new HashMap<>();
         searchParams.put("_id", Collections.singletonList(credentials.getPathValue()));
-        searchParams.put("organization", Collections.singletonList(credentials.getOrganization().getId()));
 
-        // Special handling of Group resources, which use tags instead of resource properties.
-        // TODO: Remove with DPC-552
-        if (credentials.getPathAuthorizer().type() == DPCResourceType.Group) {
-            searchParams.put("_tag", Collections.singletonList(String.format("%s|%s", DPCIdentifierSystem.DPC.getSystem(), credentials.getOrganization().getId())));
+        var query = this.client
+            .search()
+            .forResource(credentials.getPathAuthorizer().type().toString())
+            .returnBundle(Bundle.class)
+            .encodedJson();
+
+        if ( List.of(DPCResourceType.Group, DPCResourceType.Practitioner).contains(credentials.getPathAuthorizer().type()) ) {
+            query.withTag(DPCIdentifierSystem.DPC.getSystem(), credentials.getOrganization().getIdPart());
+        } else {
+            searchParams.put("organization", Collections.singletonList(credentials.getOrganization().getId()));
         }
-        final Bundle bundle = this.client
-                .search()
-                .forResource(credentials.getPathAuthorizer().type().toString())
-                .whereMap(searchParams)
-                .returnBundle(Bundle.class)
-                .encodedJson()
-                .execute();
+        final Bundle bundle = query.whereMap(searchParams).execute();
 
         if (bundle.getTotal() == 0) {
             return Optional.empty();
         }
-
         return Optional.of(principal);
     }
 

dpc-api/src/main/java/gov/cms/dpc/api/cli/organizations/OrganizationDelete.java

@@ -1,12 +1,23 @@
 package gov.cms.dpc.api.cli.organizations;
 
+import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.util.BundleBuilder;
 import gov.cms.dpc.api.cli.AbstractAttributionCommand;
 import io.dropwizard.core.setup.Bootstrap;
 import net.sourceforge.argparse4j.inf.Namespace;
 import net.sourceforge.argparse4j.inf.Subparser;
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.Endpoint;
 import org.hl7.fhir.dstu3.model.IdType;
 
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import static gov.cms.dpc.fhir.helpers.FHIRHelpers.getPages;
+
 public class OrganizationDelete extends AbstractAttributionCommand {
 
     public OrganizationDelete() {
@@ -33,11 +44,27 @@ public void run(Bootstrap<?> bootstrap, Namespace namespace) {
 
         final IGenericClient client = ctx.newRestfulGenericClient(attributionService);
 
-        client
-                .delete()
-                .resourceById(new IdType(orgReference))
-                .encodedJson()
-                .execute();
+        // The org and its endpoints must be deleted together since they reference each other
+        Map<String, List<String>> searchParams = new HashMap<>();
+        searchParams.put("organization", Collections.singletonList(orgReference));
+
+        Bundle endpointBundle = client
+            .search()
+            .forResource(Endpoint.class)
+            .encodedJson()
+            .returnBundle(Bundle.class)
+            .whereMap(searchParams)
+            .cacheControl(CacheControlDirective.noCache())
+            .execute();
+        endpointBundle = getPages(client, endpointBundle);
+
+        // Build a transaction for all of our deletes
+        BundleBuilder bundleBuilder = new BundleBuilder(client.getFhirContext());
+        bundleBuilder.addTransactionDeleteEntry(new IdType("Organization", orgReference));
+        endpointBundle.getEntry().stream()
+            .map(entry -> (Endpoint) entry.getResource())
+            .forEach(bundleBuilder::addTransactionDeleteEntry);
+        client.transaction().withBundle(bundleBuilder.getBundle()).execute();
 
         System.out.println("Successfully deleted Organization");
     }

dpc-api/src/main/java/gov/cms/dpc/api/cli/organizations/OrganizationList.java

@@ -1,8 +1,10 @@
 package gov.cms.dpc.api.cli.organizations;
 
+import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import com.jakewharton.fliptables.FlipTable;
 import gov.cms.dpc.api.cli.AbstractAttributionCommand;
+import gov.cms.dpc.fhir.helpers.FHIRHelpers;
 import io.dropwizard.core.setup.Bootstrap;
 import net.sourceforge.argparse4j.inf.Namespace;
 import net.sourceforge.argparse4j.inf.Subparser;
@@ -36,7 +38,9 @@ public void run(Bootstrap<?> bootstrap, Namespace namespace) {
                 .forResource(Organization.class)
                 .encodedJson()
                 .returnBundle(Bundle.class)
+                .cacheControl(CacheControlDirective.noCache())
                 .execute();
+        FHIRHelpers.getPages(client, organizations);
 
         // Generate the table
         final String[] headers = {"ID", "NPI", "NAME"};