ETOR Processing Tag

.run/Debug TI.run.xml

@@ -0,0 +1,16 @@
+<!--Configuration settings to add to IntelliJ for debugging the application when running in docker container-->
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="Debug TI" type="Remote">
+    <option name="USE_SOCKET_TRANSPORT" value="true" />
+    <option name="SERVER_MODE" value="false" />
+    <option name="SHMEM_ADDRESS" />
+    <option name="HOST" value="localhost" />
+    <option name="PORT" value="6006" />
+    <option name="AUTO_RESTART" value="false" />
+    <RunnerSettings RunnerId="Debug">
+      <option name="DEBUG_PORT" value="6006" />
+      <option name="LOCAL" value="false" />
+    </RunnerSettings>
+    <method v="2" />
+  </configuration>
+</component>

.secrets.baseline

@@ -138,23 +138,23 @@
         "filename": "README.md",
         "hashed_secret": "367e3228ed16bf72b36de9a4134ee8b825cafacb",
         "is_verified": false,
-        "line_number": 279,
+        "line_number": 285,
         "is_secret": false
       },
       {
         "type": "Secret Keyword",
         "filename": "README.md",
         "hashed_secret": "40bd7d88eae0468b048e62e1056ac390970b2b51",
         "is_verified": false,
-        "line_number": 284,
+        "line_number": 290,
         "is_secret": false
       },
       {
         "type": "Secret Keyword",
         "filename": "README.md",
         "hashed_secret": "0d46754ae17642645ca041edaac9a1c1569f5edc",
         "is_verified": false,
-        "line_number": 289,
+        "line_number": 295,
         "is_secret": false
       }
     ],
@@ -269,5 +269,5 @@
       }
     ]
   },
-  "generated_at": "2024-02-09T15:36:39Z"
+  "generated_at": "2024-02-09T23:44:14Z"
 }

README.md

@@ -112,6 +112,12 @@ the swarm parameters for the test and the local url where the app is running
 
 ### Debugging
 
+#### Attached JVM Config for IntelliJ
+The project comes with an attached remote jvm configuration for debuging the container.
+If you check your remote JVM settings, under `Run/Edit Configurations`,
+you will see the `Debug TI`. If you want to add a new remote JVM configuration, follow the steps below,
+under "**Docker Container Debugging Using Java Debug Wire Protocal**"
+
 #### Docker Container Debugging Using Java Debug Wire Protocal (JDWP)
 
 Go into the `Dockerfile` file and change `CMD ["java", "-jar", "app.jar"]` to `CMD ["java", "-agentlib:jdwp=transport=dt_socket,address=*:6006,server=y,suspend=n", "-jar", "app.jar"]`

e2e/src/test/groovy/gov/hhs/cdc/trustedintermediary/e2e/OrderTest.groovy

@@ -40,6 +40,27 @@ class OrderTest extends Specification {
         parsedSentPayload.entry[24].resource.contact.name.text.contains("SADIE S SMITH")
     }
 
+    def "check that ETOR processing code is added to the order before sending to report stream"() {
+        given:
+        var loginFirst = true
+        def expectedSystem = "http://localcodes.org/ETOR"
+        def expectedCode = "ETOR"
+        def expectedDisplay = "Processed by ETOR"
+
+        when:
+        orderClient.submit(labOrderJsonFileString, submissionId, loginFirst)
+        def sentPayload = SentPayloadReader.read()
+        def parsedSentPayLoad = JsonParsing.parse(sentPayload)
+        def actualSystem = parsedSentPayLoad.entry[0].resource.meta.tag[1].system
+        def actualCode = parsedSentPayLoad.entry[0].resource.meta.tag[1].code
+        def actualDisplay = parsedSentPayLoad.entry[0].resource.meta.tag[1].display
+
+        then:
+        actualSystem == expectedSystem
+        actualCode == expectedCode
+        actualDisplay == expectedDisplay
+    }
+
     def "check that the rest of the message is unchanged except the parts we changed"() {
         when:
         orderClient.submit(labOrderJsonFileString, submissionId, true)
@@ -48,10 +69,11 @@ class OrderTest extends Specification {
         def parsedLabOrderJsonFile = JsonParsing.parse(labOrderJsonFileString)
 
         then:
-        //test that everything else is the same except the MessageHeader's event and Patient contact
+        //test that everything else is the same except the MessageHeader's event, Patient contact, and etor processing tag
         parsedSentPayload.entry[0].resource.remove("eventCoding")
         parsedLabOrderJsonFile.entry[0].resource.remove("eventCoding")
         parsedSentPayload.entry[24].resource.remove("contact")
+        parsedSentPayload.entry[0].resource.meta.tag.remove(1)
 
         parsedSentPayload == parsedLabOrderJsonFile
     }

etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/EtorDomainRegistration.java

@@ -25,13 +25,16 @@
 import gov.hhs.cdc.trustedintermediary.etor.orders.SendOrderUseCase;
 import gov.hhs.cdc.trustedintermediary.etor.results.Result;
 import gov.hhs.cdc.trustedintermediary.etor.results.ResultController;
+import gov.hhs.cdc.trustedintermediary.etor.results.ResultConverter;
 import gov.hhs.cdc.trustedintermediary.etor.results.ResultResponse;
 import gov.hhs.cdc.trustedintermediary.etor.results.ResultSender;
 import gov.hhs.cdc.trustedintermediary.etor.results.SendResultUseCase;
 import gov.hhs.cdc.trustedintermediary.external.database.DatabasePartnerMetadataStorage;
 import gov.hhs.cdc.trustedintermediary.external.database.DbDao;
 import gov.hhs.cdc.trustedintermediary.external.database.PostgresDao;
+import gov.hhs.cdc.trustedintermediary.external.hapi.HapiMessageConverterHelper;
 import gov.hhs.cdc.trustedintermediary.external.hapi.HapiOrderConverter;
+import gov.hhs.cdc.trustedintermediary.external.hapi.HapiResultConverter;
 import gov.hhs.cdc.trustedintermediary.external.localfile.FilePartnerMetadataStorage;
 import gov.hhs.cdc.trustedintermediary.external.localfile.MockRSEndpointClient;
 import gov.hhs.cdc.trustedintermediary.external.reportstream.ReportStreamEndpointClient;
@@ -90,20 +93,28 @@ public class EtorDomainRegistration implements DomainConnector {
 
     @Override
     public Map<HttpEndpoint, Function<DomainRequest, DomainResponse>> domainRegistration() {
+        // Demographics
         ApplicationContext.register(
                 PatientDemographicsController.class, PatientDemographicsController.getInstance());
         ApplicationContext.register(
                 ConvertAndSendDemographicsUsecase.class,
                 ConvertAndSendDemographicsUsecase.getInstance());
+        // Orders
         ApplicationContext.register(OrderConverter.class, HapiOrderConverter.getInstance());
         ApplicationContext.register(OrderController.class, OrderController.getInstance());
         ApplicationContext.register(SendOrderUseCase.class, SendOrderUseCase.getInstance());
         ApplicationContext.register(OrderSender.class, ReportStreamOrderSender.getInstance());
-        ApplicationContext.register(
-                PartnerMetadataOrchestrator.class, PartnerMetadataOrchestrator.getInstance());
-        ApplicationContext.register(ResultSender.class, ReportStreamResultSender.getInstance());
+        // Results
+        ApplicationContext.register(ResultConverter.class, HapiResultConverter.getInstance());
         ApplicationContext.register(ResultController.class, ResultController.getInstance());
         ApplicationContext.register(SendResultUseCase.class, SendResultUseCase.getInstance());
+        ApplicationContext.register(ResultSender.class, ReportStreamResultSender.getInstance());
+        // Message
+        ApplicationContext.register(
+                HapiMessageConverterHelper.class, HapiMessageConverterHelper.getInstance());
+        // Metadata
+        ApplicationContext.register(
+                PartnerMetadataOrchestrator.class, PartnerMetadataOrchestrator.getInstance());
 
         if (ApplicationContext.getProperty("DB_URL") != null) {
             ApplicationContext.register(DbDao.class, PostgresDao.getInstance());

etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/metadata/EtorMetadataStep.java

@@ -1,12 +1,10 @@
 package gov.hhs.cdc.trustedintermediary.etor.metadata;
 
-/** Etor specific steps from the general shared metadata steps */
+/** Etor specific steps from the general shared metadata steps. Keep enum in alphabetical order */
 public enum EtorMetadataStep {
-    RECEIVED_FROM_REPORT_STREAM,
-
-    ORDER_CONVERTED_TO_OML,
-
     CONTACT_SECTION_ADDED_TO_PATIENT,
-
+    ETOR_PROCESSING_TAG_ADDED_TO_MESSAGE_HEADER,
+    ORDER_CONVERTED_TO_OML,
+    RECEIVED_FROM_REPORT_STREAM,
     SENT_TO_REPORT_STREAM
 }

etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/orders/OrderConverter.java

@@ -12,6 +12,8 @@ public interface OrderConverter {
 
     Order<?> addContactSectionToPatientResource(Order<?> order);
 
+    Order<?> addEtorProcessingTag(Order<?> message);
+
     FhirMetadata<?> extractPublicMetadataToOperationOutcome(
             PartnerMetadata metadata, String requestedId);
 }

etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/orders/SendOrderUseCase.java

@@ -34,6 +34,11 @@ public void convertAndSend(final Order<?> order, String receivedSubmissionId)
         omlOrder = converter.addContactSectionToPatientResource(omlOrder);
         metadata.put(order.getFhirResourceId(), EtorMetadataStep.CONTACT_SECTION_ADDED_TO_PATIENT);
 
+        omlOrder = converter.addEtorProcessingTag(omlOrder);
+        metadata.put(
+                order.getFhirResourceId(),
+                EtorMetadataStep.ETOR_PROCESSING_TAG_ADDED_TO_MESSAGE_HEADER);
+
         String sentSubmissionId = sender.send(omlOrder).orElse(null);
 
         saveSentOrderSubmissionId(receivedSubmissionId, sentSubmissionId);

etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/results/ResultConverter.java

@@ -0,0 +1,6 @@
+package gov.hhs.cdc.trustedintermediary.etor.results;
+
+/** Interface for converting things to results and things in results. */
+public interface ResultConverter {
+    Result<?> addEtorProcessingTag(Result<?> message);
+}

etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/results/SendResultUseCase.java

@@ -7,6 +7,9 @@
 /** Use case for converting and sending a lab result message. */
 public class SendResultUseCase implements SendMessageUseCase<Result<?>> {
     private static final SendResultUseCase INSTANCE = new SendResultUseCase();
+
+    @Inject ResultConverter converter;
+
     @Inject ResultSender sender;
 
     private SendResultUseCase() {}
@@ -17,6 +20,13 @@ public static SendResultUseCase getInstance() {
 
     @Override
     public void convertAndSend(Result<?> result) throws UnableToSendMessageException {
-        sender.send(result);
+
+        // savePartnerMetadataForReceivedResult(receivedSubmissionId, result)
+        var convertedResult = converter.addEtorProcessingTag(result);
+        // metadata.put(result.getFhirResourceId(),
+        // EtorMetadataStep.ETOR_PROCESSING_TAG_ADDED_TO_MESSAGE_HEADER);
+        sender.send(convertedResult); // var bundleId = sender.send(convertedResult).orElse(null),
+        // thoughts?
+        // saveSentResultSubmissionId(receivedSubmissionId, bundleId)
     }
 }

etor/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiMessageConverterHelper.java

@@ -0,0 +1,55 @@
+package gov.hhs.cdc.trustedintermediary.external.hapi;
+
+import gov.hhs.cdc.trustedintermediary.wrappers.Logger;
+import javax.inject.Inject;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.MessageHeader;
+import org.hl7.fhir.r4.model.Meta;
+
+/**
+ * Helper class with a variety of utilities to use on a FHIR bundle message. It adds the 'ETOR' tag
+ * to a FHIR bundle of type: OML, ORU It also creates the messageHeader resource in a FHIR bundle
+ * message.
+ */
+public class HapiMessageConverterHelper {
+
+    private static final HapiMessageConverterHelper INSTANCE = new HapiMessageConverterHelper();
+
+    public static HapiMessageConverterHelper getInstance() {
+        return INSTANCE;
+    }
+
+    @Inject Logger logger;
+
+    private HapiMessageConverterHelper() {}
+
+    /**
+     * Adds the `ETOR` code to any message provided
+     *
+     * @param messageBundle the in coming message in a FHIR bundle
+     */
+    public void addEtorTagToBundle(Bundle messageBundle) {
+        var messageHeader = findOrInitializeMessageHeader(messageBundle);
+        var meta = messageHeader.hasMeta() ? messageHeader.getMeta() : new Meta();
+
+        meta.addTag(new Coding("http://localcodes.org/ETOR", "ETOR", "Processed by ETOR"));
+        messageHeader.setMeta(meta);
+    }
+
+    /**
+     * Checks if the FHIR bundle has a messageHeader, and it creates one if it is missing
+     *
+     * @param bundle the in coming message in a FHIR bundle
+     * @return returns existing MessageHeader resource or a newly created one
+     */
+    public MessageHeader findOrInitializeMessageHeader(Bundle bundle) {
+        var messageHeader =
+                HapiHelper.resourcesInBundle(bundle, MessageHeader.class).findFirst().orElse(null);
+        if (messageHeader == null) {
+            messageHeader = new MessageHeader();
+            bundle.addEntry(new Bundle.BundleEntryComponent().setResource(messageHeader));
+        }
+        return messageHeader;
+    }
+}

etor/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiOrderConverter.java

@@ -45,6 +45,8 @@ public class HapiOrderConverter implements OrderConverter {
 
     @Inject Logger logger;
 
+    @Inject HapiMessageConverterHelper hapiMessageConverterHelper;
+
     public static HapiOrderConverter getInstance() {
         return INSTANCE;
     }
@@ -99,16 +101,7 @@ public Order<?> convertToOmlOrder(Order<?> order) {
 
         var hapiOrder = (Order<Bundle>) order;
         var orderBundle = hapiOrder.getUnderlyingOrder();
-
-        var messageHeader =
-                HapiHelper.resourcesInBundle(orderBundle, MessageHeader.class)
-                        .findFirst()
-                        .orElse(null);
-
-        if (messageHeader == null) {
-            messageHeader = new MessageHeader();
-            orderBundle.addEntry(new Bundle.BundleEntryComponent().setResource(messageHeader));
-        }
+        var messageHeader = hapiMessageConverterHelper.findOrInitializeMessageHeader(orderBundle);
 
         messageHeader.setEvent(OML_CODING);
 
@@ -152,13 +145,12 @@ private MessageHeader createMessageHeader() {
 
         messageHeader.setEvent(OML_CODING);
 
-        messageHeader.setMeta(
-                new Meta()
-                        .addTag(
-                                new Coding(
-                                        "http://terminology.hl7.org/CodeSystem/v2-0103",
-                                        "P",
-                                        "Production")));
+        var meta = new Meta();
+
+        // Adding processing id of 'P'
+        meta.addTag("http://terminology.hl7.org/CodeSystem/v2-0103", "P", "Production");
+
+        messageHeader.setMeta(meta);
 
         messageHeader.setSource(
                 new MessageHeader.MessageSourceComponent(
@@ -168,6 +160,16 @@ private MessageHeader createMessageHeader() {
         return messageHeader;
     }
 
+    @Override
+    public Order<?> addEtorProcessingTag(Order<?> message) {
+        var hapiOrder = (Order<Bundle>) message;
+        var messageBundle = hapiOrder.getUnderlyingOrder();
+
+        hapiMessageConverterHelper.addEtorTagToBundle(messageBundle);
+
+        return new HapiOrder(messageBundle);
+    }
+
     private ServiceRequest createServiceRequest(final Patient patient, final Date orderDateTime) {
         logger.logInfo("Creating new ServiceRequest");
 

etor/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiResultConverter.java

@@ -0,0 +1,36 @@
+package gov.hhs.cdc.trustedintermediary.external.hapi;
+
+import gov.hhs.cdc.trustedintermediary.etor.results.Result;
+import gov.hhs.cdc.trustedintermediary.etor.results.ResultConverter;
+import gov.hhs.cdc.trustedintermediary.wrappers.Logger;
+import javax.inject.Inject;
+import org.hl7.fhir.r4.model.Bundle;
+
+/**
+ * Converts {@link Result} to a Hapi-specific FHIR lab result {@link Result <Bundle>}) with proper
+ * identifying message headers.
+ */
+public class HapiResultConverter implements ResultConverter {
+
+    private static final HapiResultConverter INSTANCE = new HapiResultConverter();
+
+    @Inject HapiMessageConverterHelper hapiMessageConverterHelper;
+
+    @Inject Logger logger;
+
+    public static HapiResultConverter getInstance() {
+        return INSTANCE;
+    }
+
+    private HapiResultConverter() {}
+
+    @Override
+    public Result<?> addEtorProcessingTag(final Result<?> message) {
+        var hapiResult = (Result<Bundle>) message;
+        var messageBundle = hapiResult.getUnderlyingResult();
+
+        hapiMessageConverterHelper.addEtorTagToBundle(messageBundle);
+
+        return new HapiResult(messageBundle);
+    }
+}

etor/src/test/groovy/gov/hhs/cdc/trustedintermediary/ResultMock.groovy

@@ -10,9 +10,9 @@ class ResultMock<T> implements Result<T> {
     private String fhirResourceId
     private T underlyingResult
 
-    ResultMock(String fhirResourceId, T underlyingOrders) {
+    ResultMock(String fhirResourceId, T underlyingResults) {
         this.fhirResourceId = fhirResourceId
-        this.underlyingResult = underlyingOrders
+        this.underlyingResult = underlyingResults
     }
 
     @Override