Story/672/marshal results into fhir (#755)

* Initial commit with the needed FHIR resources created in the HapiOrderConverter * Updating Orchestrator with WIP of converter call * Fixed postgres DAO issues and added marshaling to metadata handler * Reverting Azure client registration * Fixing other test * Fixing test * Fixing formatting * Adding test for Domain Response helper methods * Re-adding constructor temporarily * Fixing e2e test and linting * Removing commented code * Updated openapi docs for metadata response * Adding wrapper class * Adding java docs --------- Co-authored-by: Basilio Bogado <[email protected]> Co-authored-by: halprin <[email protected]>
CDCgov · Jan 9, 2024 · 921f82a · 921f82a
1 parent b368cec
commit 921f82a
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Showing 16 changed files with 166 additions and 34 deletions.
diff --git a/.github/workflows/terraform-deploy_reusable.yml b/.github/workflows/terraform-deploy_reusable.yml
@@ -74,7 +74,7 @@ jobs:
       - name: Run Db migration
         run: |
           export PGPASSWORD=$(az account get-access-token --resource-type oss-rdbms --query "[accessToken]" -o tsv)
-          psql "host=$(terraform output -raw database_hostname) port=5432 dbname=postgres user=cdcti-github sslmode=require" -c "CREATE TABLE IF NOT EXISTS metadata (message_id varchar(30), sender varchar(30), receiver varchar(30), hash_of_order varchar(1000), time_received timestamptz); GRANT ALL ON metadata TO azure_pg_admin; ALTER TABLE metadata OWNER TO azure_pg_admin;"
+          psql "host=$(terraform output -raw database_hostname) port=5432 dbname=postgres user=cdcti-github sslmode=require" -c "CREATE TABLE IF NOT EXISTS metadata (message_id varchar(30) PRIMARY KEY, sender varchar(30), receiver varchar(30), hash_of_order varchar(1000), time_received timestamptz); GRANT ALL ON metadata TO azure_pg_admin; ALTER TABLE metadata OWNER TO azure_pg_admin;"
 
       - id: export-terraform-output
         name: Export Terraform Output

diff --git a/e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/e2e/MetadataTest.groovy b/e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/e2e/MetadataTest.groovy
@@ -32,7 +32,7 @@ class MetadataTest extends Specification {
 
         then:
         metadataResponse.getCode() == expectedStatusCode
-        parsedJsonBody.receivedSubmissionId == submissionId
+        parsedJsonBody.get("id") == submissionId
     }
 
     def "a 404 is returned when there is no metadata for a given ID"() {

diff --git a/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/EtorDomainRegistration.java b/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/EtorDomainRegistration.java
@@ -15,6 +15,7 @@
 import gov.hhs.cdc.trustedintermediary.etor.metadata.PartnerMetadataException;
 import gov.hhs.cdc.trustedintermediary.etor.metadata.PartnerMetadataOrchestrator;
 import gov.hhs.cdc.trustedintermediary.etor.metadata.PartnerMetadataStorage;
+import gov.hhs.cdc.trustedintermediary.etor.operationoutcomes.FhirMetadata;
 import gov.hhs.cdc.trustedintermediary.etor.orders.Order;
 import gov.hhs.cdc.trustedintermediary.etor.orders.OrderController;
 import gov.hhs.cdc.trustedintermediary.etor.orders.OrderConverter;
@@ -34,6 +35,7 @@
 import gov.hhs.cdc.trustedintermediary.external.reportstream.ReportStreamOrderSender;
 import gov.hhs.cdc.trustedintermediary.wrappers.DbDao;
 import gov.hhs.cdc.trustedintermediary.wrappers.FhirParseException;
+import gov.hhs.cdc.trustedintermediary.wrappers.HapiFhir;
 import gov.hhs.cdc.trustedintermediary.wrappers.Logger;
 import gov.hhs.cdc.trustedintermediary.wrappers.SqlDriverManager;
 import java.io.IOException;
@@ -62,6 +64,10 @@ public class EtorDomainRegistration implements DomainConnector {
     @Inject DomainResponseHelper domainResponseHelper;
     @Inject PartnerMetadataOrchestrator partnerMetadataOrchestrator;
 
+    @Inject OrderConverter orderConverter;
+
+    @Inject HapiFhir fhir;
+
     private final Map<HttpEndpoint, Function<DomainRequest, DomainResponse>> endpoints =
             Map.of(
                     new HttpEndpoint("POST", DEMOGRAPHICS_API_ENDPOINT, true),
@@ -175,7 +181,11 @@ DomainResponse handleMetadata(DomainRequest request) {
                         404, "Metadata not found for ID: " + metadataId);
             }
 
-            return domainResponseHelper.constructOkResponse(metadata.get());
+            FhirMetadata<?> responseObject =
+                    orderConverter.extractPublicMetadataToOperationOutcome(metadata.get());
+
+            return domainResponseHelper.constructOkResponseFromString(
+                    fhir.encodeResourceToJson(responseObject.getUnderlyingOutcome()));
         } catch (PartnerMetadataException e) {
             String errorMessage = "Unable to retrieve requested metadata";
             logger.logError(errorMessage, e);

diff --git a/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/metadata/PartnerMetadata.java b/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/metadata/PartnerMetadata.java
@@ -25,6 +25,15 @@ public PartnerMetadata(
         this(receivedSubmissionId, null, sender, null, timeReceived, hash);
     }
 
+    public PartnerMetadata(
+            String receivedSubmissionId,
+            String sender,
+            String receiver,
+            Instant timeReceived,
+            String hash) {
+        this(receivedSubmissionId, null, sender, receiver, timeReceived, hash);
+    }
+
     public PartnerMetadata(String receivedSubmissionId, String hash) {
         this(receivedSubmissionId, null, null, null, null, hash);
     }

diff --git a/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/operationoutcomes/FhirMetadata.java b/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/operationoutcomes/FhirMetadata.java
@@ -0,0 +1,12 @@
+package gov.hhs.cdc.trustedintermediary.etor.operationoutcomes;
+
+/**
+ * Wrapper interface for our public facing metadata. Wraps an operation outcomes object to be
+ * returned to our ReST API
+ *
+ * @param <T>
+ */
+public interface FhirMetadata<T> {
+
+    T getUnderlyingOutcome();
+}
diff --git a/...rc/main/java/gov/hhs/cdc/trustedintermediary/etor/operationoutcomes/HapiFhirMetadata.java b/...rc/main/java/gov/hhs/cdc/trustedintermediary/etor/operationoutcomes/HapiFhirMetadata.java
@@ -0,0 +1,18 @@
+package gov.hhs.cdc.trustedintermediary.etor.operationoutcomes;
+
+import org.hl7.fhir.r4.model.OperationOutcome;
+
+/** Implementation of our wrapper for public facing metadata. Returns an operation outcomes */
+public class HapiFhirMetadata implements FhirMetadata<OperationOutcome> {
+
+    private final OperationOutcome innerOutcome;
+
+    public HapiFhirMetadata(OperationOutcome outcome) {
+        this.innerOutcome = outcome;
+    }
+
+    @Override
+    public OperationOutcome getUnderlyingOutcome() {
+        return innerOutcome;
+    }
+}
diff --git a/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/orders/OrderConverter.java b/etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/orders/OrderConverter.java
@@ -1,6 +1,8 @@
 package gov.hhs.cdc.trustedintermediary.etor.orders;
 
 import gov.hhs.cdc.trustedintermediary.etor.demographics.Demographics;
+import gov.hhs.cdc.trustedintermediary.etor.metadata.PartnerMetadata;
+import gov.hhs.cdc.trustedintermediary.etor.operationoutcomes.FhirMetadata;
 
 /** Interface for converting things to orders and things in orders. */
 public interface OrderConverter {
@@ -9,4 +11,6 @@ public interface OrderConverter {
     Order<?> convertMetadataToOmlOrder(Order<?> order);
 
     Order<?> addContactSectionToPatientResource(Order<?> order);
+
+    FhirMetadata<?> extractPublicMetadataToOperationOutcome(PartnerMetadata metadata);
 }
diff --git a/etor/src/main/java/gov/hhs/cdc/trustedintermediary/external/database/PostgresDao.java b/etor/src/main/java/gov/hhs/cdc/trustedintermediary/external/database/PostgresDao.java
@@ -69,7 +69,7 @@ protected Connection connect() throws SQLException {
 
         // If the below prop isn't set to require and we just set ssl=true it will expect a CA cert
         // in azure which breaks it
-        props.setProperty("sslmode", ssl);
+        props.setProperty("ssl", ssl);
         conn = driverManager.getConnection(url, props);
         logger.logInfo("DB Connected Successfully");
         return conn;
@@ -90,9 +90,12 @@ public synchronized void upsertMetadata(
 
         try (Connection conn = connect();
                 PreparedStatement statement =
-                        conn.prepareStatement("INSERT INTO metadata VALUES (?, ?, ?, ?, ?)")) {
-            // TODO: Update the below statement to handle on conflict, after we figure out what that
-            // behavior should be
+                        conn.prepareStatement(
+                                """
+                                INSERT INTO metadata VALUES (?, ?, ?, ?, ?)
+                                ON CONFLICT (message_id) DO UPDATE SET receiver = EXCLUDED.receiver
+                                """)) {
+
             statement.setString(1, receivedSubmissionId);
             statement.setString(2, sender);
             statement.setString(3, receiver);
@@ -120,6 +123,7 @@ public synchronized PartnerMetadata fetchMetadata(String receivedSubmissionId)
 
             return new PartnerMetadata(
                     result.getString("message_id"),
+                    result.getString("sender"),
                     result.getString("receiver"),
                     result.getTimestamp("time_received").toInstant(),
                     result.getString("hash_of_order"));

diff --git a/etor/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiOrderConverter.java b/etor/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiOrderConverter.java
@@ -1,6 +1,9 @@
 package gov.hhs.cdc.trustedintermediary.external.hapi;
 
 import gov.hhs.cdc.trustedintermediary.etor.demographics.Demographics;
+import gov.hhs.cdc.trustedintermediary.etor.metadata.PartnerMetadata;
+import gov.hhs.cdc.trustedintermediary.etor.operationoutcomes.FhirMetadata;
+import gov.hhs.cdc.trustedintermediary.etor.operationoutcomes.HapiFhirMetadata;
 import gov.hhs.cdc.trustedintermediary.etor.orders.Order;
 import gov.hhs.cdc.trustedintermediary.etor.orders.OrderConverter;
 import gov.hhs.cdc.trustedintermediary.wrappers.Logger;
@@ -15,6 +18,7 @@
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.MessageHeader;
 import org.hl7.fhir.r4.model.Meta;
+import org.hl7.fhir.r4.model.OperationOutcome;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Provenance;
 import org.hl7.fhir.r4.model.Reference;
@@ -200,4 +204,36 @@ private Provenance createProvenanceResource(Date orderDate) {
 
         return provenance;
     }
+
+    @Override
+    public FhirMetadata<?> extractPublicMetadataToOperationOutcome(PartnerMetadata metadata) {
+        var operation = new OperationOutcome();
+
+        operation.setId(metadata.receivedSubmissionId());
+        operation.getIssue().add(createInformationIssueComponent("sender name", metadata.sender()));
+        operation
+                .getIssue()
+                .add(createInformationIssueComponent("receiver name", metadata.receiver()));
+        operation
+                .getIssue()
+                .add(
+                        createInformationIssueComponent(
+                                "order ingestion", metadata.timeReceived().toString()));
+        operation.getIssue().add(createInformationIssueComponent("payload hash", metadata.hash()));
+
+        return new HapiFhirMetadata(operation);
+    }
+
+    protected OperationOutcome.OperationOutcomeIssueComponent createInformationIssueComponent(
+            String details, String diagnostics) {
+        OperationOutcome.OperationOutcomeIssueComponent issue =
+                new OperationOutcome.OperationOutcomeIssueComponent();
+
+        issue.setSeverity(OperationOutcome.IssueSeverity.INFORMATION);
+        issue.setCode(OperationOutcome.IssueType.INFORMATIONAL);
+        issue.getDetails().setText(details);
+        issue.setDiagnostics(diagnostics);
+
+        return issue;
+    }
 }
diff --git a/etor/src/main/resources/openapi_etor.yaml b/etor/src/main/resources/openapi_etor.yaml
@@ -92,7 +92,7 @@ paths:
           content:
             application/json:
             schema:
-              $ref: '#/components/schemas/MetadataResponse'
+              $ref: 'https://github.com/LinuxForHealth/FHIR/blob/main/fhir-openapi/src/main/webapp/META-INF/openapi.json?raw=true#/components/schemas/OperationOutcome'
         '401':
           description: Authentication failed due to invalid token or unknown organization
           content:
@@ -125,24 +125,6 @@ components:
         patientId:
           type: string
           example: MRN7465737865
-    MetadataResponse:
-      type: object
-      properties:
-        uniqueId:
-          type: string
-          example: abc123
-        sender:
-          type: string
-          example: simulated-hospital
-        receiver:
-          type: string
-          example: simulated-lab
-        timeReceived:
-          type: string
-          example: 2023-12-01T12:00:00.000000Z
-        hash:
-          type: string
-          example: abc123
     BadRequestError:
       description: Bad Request
       type: object

diff --git a/etor/src/test/groovy/gov/hhs/cdc/trustedintermediary/etor/EtorDomainRegistrationTest.groovy b/etor/src/test/groovy/gov/hhs/cdc/trustedintermediary/etor/EtorDomainRegistrationTest.groovy
@@ -14,15 +14,18 @@ import gov.hhs.cdc.trustedintermediary.etor.demographics.PatientDemographicsResp
 import gov.hhs.cdc.trustedintermediary.etor.metadata.PartnerMetadata
 import gov.hhs.cdc.trustedintermediary.etor.metadata.PartnerMetadataException
 import gov.hhs.cdc.trustedintermediary.etor.metadata.PartnerMetadataOrchestrator
+import gov.hhs.cdc.trustedintermediary.etor.operationoutcomes.FhirMetadata
 import gov.hhs.cdc.trustedintermediary.etor.orders.Order
 import gov.hhs.cdc.trustedintermediary.etor.orders.OrderController
+import gov.hhs.cdc.trustedintermediary.etor.orders.OrderConverter
 import gov.hhs.cdc.trustedintermediary.etor.orders.OrderResponse
 import gov.hhs.cdc.trustedintermediary.etor.orders.SendOrderUseCase
 import gov.hhs.cdc.trustedintermediary.etor.orders.UnableToSendOrderException
-import gov.hhs.cdc.trustedintermediary.external.jackson.Jackson
 import gov.hhs.cdc.trustedintermediary.wrappers.FhirParseException
+import gov.hhs.cdc.trustedintermediary.wrappers.HapiFhir
 import gov.hhs.cdc.trustedintermediary.wrappers.Logger
-import gov.hhs.cdc.trustedintermediary.wrappers.formatter.Formatter
+import org.hl7.fhir.r4.model.OperationOutcome
+
 import java.time.Instant
 import spock.lang.Specification
 
@@ -325,10 +328,16 @@ class EtorDomainRegistrationTest extends Specification {
         TestApplicationContext.register(PartnerMetadataOrchestrator, mockPartnerMetadataOrchestrator)
 
         def mockResponseHelper = Mock(DomainResponseHelper)
-        mockResponseHelper.constructOkResponse(_ as PartnerMetadata) >> new DomainResponse(expectedStatusCode)
+        mockResponseHelper.constructOkResponseFromString(_ as String) >> new DomainResponse(expectedStatusCode)
         TestApplicationContext.register(DomainResponseHelper, mockResponseHelper)
 
-        TestApplicationContext.register(Formatter, Jackson.getInstance())
+        def mockOrderConverter = Mock(OrderConverter)
+        mockOrderConverter.extractPublicMetadataToOperationOutcome(_ as PartnerMetadata) >> Mock(FhirMetadata)
+        TestApplicationContext.register(OrderConverter, mockOrderConverter)
+
+        def mockFhir = Mock(HapiFhir)
+        mockFhir.encodeResourceToJson(_) >> ""
+        TestApplicationContext.register(HapiFhir, mockFhir)
         TestApplicationContext.injectRegisteredImplementations()
 
         when:

diff --git a/...oovy/gov/hhs/cdc/trustedintermediary/etor/metadata/PartnerMetadataOrchestratorTest.groovy b/...oovy/gov/hhs/cdc/trustedintermediary/etor/metadata/PartnerMetadataOrchestratorTest.groovy
@@ -2,6 +2,9 @@ package gov.hhs.cdc.trustedintermediary.etor.metadata
 
 import gov.hhs.cdc.trustedintermediary.context.TestApplicationContext
 import gov.hhs.cdc.trustedintermediary.etor.RSEndpointClient
+import gov.hhs.cdc.trustedintermediary.etor.orders.Order
+import gov.hhs.cdc.trustedintermediary.etor.orders.OrderConverter
+import gov.hhs.cdc.trustedintermediary.external.hapi.HapiOrderConverter
 import gov.hhs.cdc.trustedintermediary.external.jackson.Jackson
 import gov.hhs.cdc.trustedintermediary.external.reportstream.ReportStreamEndpointClientException
 import gov.hhs.cdc.trustedintermediary.wrappers.formatter.Formatter
@@ -25,9 +28,12 @@ class PartnerMetadataOrchestratorTest extends Specification {
         mockClient = Mock(RSEndpointClient)
 
         TestApplicationContext.register(PartnerMetadataOrchestrator, PartnerMetadataOrchestrator.getInstance())
+        TestApplicationContext.register(OrderConverter, HapiOrderConverter.getInstance())
         TestApplicationContext.register(PartnerMetadataStorage, mockPartnerMetadataStorage)
+
         TestApplicationContext.register(RSEndpointClient, mockClient)
         TestApplicationContext.register(Formatter, mockFormatter)
+
         TestApplicationContext.injectRegisteredImplementations()
     }
 

diff --git a/.../src/test/groovy/gov/hhs/cdc/trustedintermediary/external/database/PostgresDaoTest.groovy b/.../src/test/groovy/gov/hhs/cdc/trustedintermediary/external/database/PostgresDaoTest.groovy
@@ -148,17 +148,18 @@ class PostgresDaoTest extends Specification {
     def "fetchMetadata returns partnermetadata when rows exist"() {
         given:
         def messageId = "12345"
-        def receiver = "DogCow"
+        def sender = "DogCow"
         Timestamp timestampForMock = Timestamp.from(Instant.parse("2024-01-03T15:45:33.30Z"))
         Instant timeReceived = timestampForMock.toInstant()
-        def hash = receiver.hashCode().toString()
-        def expected = new PartnerMetadata(messageId, receiver, timeReceived, hash)
+        def hash = sender.hashCode().toString()
+        def expected = new PartnerMetadata(messageId, sender, null, timeReceived, hash)
 
         mockDriver.getConnection(_ as String, _ as Properties) >> mockConn
         mockConn.prepareStatement(_ as String) >>  mockPreparedStatement
         mockResultSet.next() >> true
         mockResultSet.getString("message_id") >> messageId
-        mockResultSet.getString("receiver") >> receiver
+        mockResultSet.getString("sender") >> sender
+        mockResultSet.getString("receiver") >> null
         mockResultSet.getTimestamp("time_received") >> timestampForMock
         mockResultSet.getString("hash_of_order") >> hash
         mockPreparedStatement.executeQuery() >> mockResultSet

diff --git a/...c/test/groovy/gov/hhs/cdc/trustedintermediary/external/hapi/HapiOrderConverterTest.groovy b/...c/test/groovy/gov/hhs/cdc/trustedintermediary/external/hapi/HapiOrderConverterTest.groovy
@@ -3,11 +3,13 @@ package gov.hhs.cdc.trustedintermediary.external.hapi
 import gov.hhs.cdc.trustedintermediary.DemographicsMock
 import gov.hhs.cdc.trustedintermediary.OrderMock
 import gov.hhs.cdc.trustedintermediary.context.TestApplicationContext
+import gov.hhs.cdc.trustedintermediary.etor.metadata.PartnerMetadata
 import gov.hhs.cdc.trustedintermediary.etor.orders.OrderConverter
 import org.hl7.fhir.r4.model.Address
 import org.hl7.fhir.r4.model.ContactPoint
 import org.hl7.fhir.r4.model.Extension
 import org.hl7.fhir.r4.model.HumanName
+import org.hl7.fhir.r4.model.OperationOutcome
 import org.hl7.fhir.r4.model.StringType
 
 import java.time.Instant
@@ -242,6 +244,17 @@ class HapiOrderConverterTest extends Specification {
         !contactSection.hasName()
     }
 
+
+    def "creating an issue returns a valid OperationOutcomeIssueComponent with Information level severity and code" () {
+        when:
+        def output = HapiOrderConverter.getInstance().createInformationIssueComponent("test_details", "test_diagnostics")
+        then:
+        output.getSeverity() == OperationOutcome.IssueSeverity.INFORMATION
+        output.getCode() == OperationOutcome.IssueType.INFORMATIONAL
+        output.getDetails().getText() == "test_details"
+        output.getDiagnostics() == "test_diagnostics"
+    }
+
     Patient fakePatientResource(boolean addHumanName) {
 
         def patient = new Patient()

diff --git a/...d/src/main/java/gov/hhs/cdc/trustedintermediary/domainconnector/DomainResponseHelper.java b/...d/src/main/java/gov/hhs/cdc/trustedintermediary/domainconnector/DomainResponseHelper.java
@@ -40,10 +40,24 @@ public DomainResponse constructResponse(int httpStatus, Object objectResponseBod
         return response;
     }
 
+    public DomainResponse constructResponseFromString(int httpStatus, String jsonResponseBody) {
+        logger.logInfo("Constructing the response");
+        var response = new DomainResponse(httpStatus);
+        response.setBody(jsonResponseBody);
+
+        response.setHeaders(Map.of(CONTENT_TYPE_LITERAL, APPLICATION_JSON_LITERAL));
+
+        return response;
+    }
+
     public DomainResponse constructOkResponse(Object objectResponseBody) {
         return constructResponse(200, objectResponseBody);
     }
 
+    public DomainResponse constructOkResponseFromString(String jsonBody) {
+        return constructResponseFromString(200, jsonBody);
+    }
+
     public DomainResponse constructErrorResponse(int httpStatus, String errorString) {
         return constructResponse(httpStatus, Map.of("error", errorString));
     }