49 add fhir resource bundle to cda doc (#60)

* Added debugging messages

* Restored ability to attach documents to SOAP requests

* Fixed HL7 parsing error resulting from additional time parameter on the birthdate

* Added provision to filter getMessages request by facility sitecode

* Code formatting changes

* Removed unused unit test

* Replaced invalid characters in the Config file

* COde formatting changes

* Added method override to attach more than 1 additional documents

* Added method override to attach more than 1 additional documents

* Added method override to attach more than 1 additional documents

* Added code stubs for the fhir document builder

* Added jnuit & upgraded maven jaxb version

* Added unit tests

* Code clean-up

* Fixing a failing unit test

* Fixed failing unit tests

* Added a System Identifier to the Patient Resource

* Updated hoe the System Identifier type is handled to support OpenCR MPI integration

* Finalizing 2.1.0

* Finalizing 2.1.1

* Added code stubs for the fhir document builder

* Added a System Identifier to the Patient Resource

* updated local pid global property name

* Assign placeholder System Identifier

* Added code stubs for the fhir document builder

* Added unit tests and provided lnsp-workflow fixes

* Updated unit tests and fixed dependency issues

* Changes to allow attaching FHIR resource to the Xds document

* Fixed the bug preventing processing of Pull Point notification documents

* Added base64 decoding for pull point documents.

* Resolve possisble duplication of ECID identifier types on the XDS document

* Fixed general Lab-lnsp workflow issues and updated

* Fixed merge conflicts

* Updated gitignore file

* Removed test files

* Removed test files and updated gitignore

* Delete settings.json

* Delete id_file

* Updated gitignore

.gitignore

@@ -16,4 +16,12 @@ target
 .DS_Store
 
 # Log Files
-*.log
+*.log
+
+# test files
+api/null/*
+null/*
+
+#vs Code
+.vscode/*
+api/id_file

api/pom.xml

@@ -18,6 +18,7 @@
 		<dependency>
 			<groupId>org.openmrs.module</groupId>
 			<artifactId>fhir2-api</artifactId>
+			<version>${fhirModuleVersion}</version>
 		</dependency>
 		<dependency>
 			<groupId>org.openmrs.module</groupId>
@@ -67,10 +68,6 @@
 			<groupId>javax.servlet</groupId>
 			<artifactId>javax.servlet-api</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>javax.xml.ws</groupId>
-			<artifactId>jaxws-api</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>org.springframework.ws</groupId>
 			<artifactId>spring-ws-core</artifactId>

api/src/main/java/org/openmrs/module/xdssender/XdsSenderConstants.java

@@ -485,7 +485,17 @@ public final class XdsSenderConstants {
 	public static final String SCT_TEMPLATE_HISTORY_OF_BLOOD_TRANSFUSIONS = "1.3.6.1.4.1.19376.1.5.3.1.1.9.12";
 
 	public static final String LOCATION_SITECODE_ATTRIBUTE_UUID = "6242bf19-207e-4076-9d28-9290525b8ed9";
-
+
+	public static final String SYSTEM_IDENTIFIER_TYPE_NAME = "SYSTEM";
+
+	public static final String PROP_PID_LOCAL = "fhir2.uriPrefix";
+
+	public static final String IDENTIFIER_SYSTEM = "http://openclientregistry.org/fhir/sourceid";
+
+	public static final String SYSTEM_IDENTIFIER_TYPE_UUID = "99F5A4C3-CEEA-4F5F-ABE6-399CD4C9FE24";
+
+	public static final String ECID_IDENTIFIER_TYPE_NAME = "ECID";
+
 	private XdsSenderConstants() {
 	}
 }

api/src/main/java/org/openmrs/module/xdssender/api/cda/CdaDataUtil.java

@@ -67,6 +67,7 @@
 import org.openmrs.api.context.Context;
 import org.openmrs.module.xdssender.XdsSenderConfig;
 import org.openmrs.module.xdssender.XdsSenderConstants;
+import org.openmrs.module.xdssender.api.xds.XdsUtil;
 import org.openmrs.util.OpenmrsConstants;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
@@ -88,7 +89,7 @@
  */
 @Component("xdssender.CdaDataUtil")
 public class CdaDataUtil {
-	
+
 	// NOK codes
 	private static final List<String> nextOfKinRelations = Arrays.asList("MTH", "FTH", "GRMTH", "GRFTH", "SIB", "CHILD",
 	    "AUNT", "UNCLE", "PGRMTH", "MGRMTH", "PGRFTH", "MGRFTH", "SON", "DAU", "BRO", "SIS", "DOMPART", "FAMMEMB");
@@ -464,22 +465,44 @@ public RecordTarget createRecordTarget(Patient patient) {
 		// Identifiers
 		patientRole.setId(new SET<II>());
 		for (PatientIdentifier pid : patient.getActiveIdentifiers()) {
-			II ii = new II(pid.getIdentifierType().getName(), pid.getIdentifier());
-			if (!patientRole.getId().contains(ii))
-				patientRole.getId().add(ii);
+			// To cater for old records assigned ECID by OpenEMPI, we will Skip adding the ECID identifier type
+			// if it already exists
+			if (!pid.getIdentifierType().getName().equals(XdsSenderConstants.ECID_IDENTIFIER_TYPE_NAME) ) {
+				II ii = new II(pid.getIdentifierType().getName(), pid.getIdentifier());
+				if (!patientRole.getId().contains(ii))
+					patientRole.getId().add(ii);
+			}
 		}
-
+
+		// Add system identifier
+		II ii = null;
+		II iii = null;
+		try {
+			ii = new II(XdsSenderConstants.SYSTEM_IDENTIFIER_TYPE_NAME, XdsUtil.getPlaceholderSystemIdentifier(patient).getIdentifier());
+			patientRole.getId().add(ii);
+			// Adding an ECID to allow for processing by xds-b-repository in the SHR
+			iii = new II(XdsSenderConstants.ECID_IDENTIFIER_TYPE_NAME, XdsUtil.getPlaceholderSystemIdentifier(patient).getIdentifier());
+			patientRole.getId().add(iii);
+		}
+		catch (Exception e) {
+			e.printStackTrace();
+		}
+
 		// Address?
 		patientRole.setAddr(createAddressSet(patient));
 
 		// Telecom?
 		patientRole.setTelecom(createTelecomSet(patient));
 
 		// Marital status?
-		PersonAttribute civilStatusCode = patient.getAttribute(XdsSenderConstants.ATTRIBUTE_NAME_CIVIL_STATUS);
-		if (civilStatusCode != null)
-			hl7Patient.setMaritalStatusCode(metadataUtil.getStandardizedCode((Concept) civilStatusCode.getHydratedObject(),
-			    XdsSenderConstants.CODE_SYSTEM_MARITAL_STATUS, CE.class));
+		try {
+			PersonAttribute civilStatusCode = patient.getAttribute(XdsSenderConstants.ATTRIBUTE_NAME_CIVIL_STATUS);
+			if (civilStatusCode != null)
+				hl7Patient.setMaritalStatusCode(metadataUtil.getStandardizedCode((Concept) civilStatusCode.getHydratedObject(),
+						XdsSenderConstants.CODE_SYSTEM_MARITAL_STATUS, CE.class));
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
 
 		// Names
 		hl7Patient.setName(createNameSet(patient));

api/src/main/java/org/openmrs/module/xdssender/api/cda/ClinicalDocumentBuilder.java

@@ -68,11 +68,14 @@ public DocumentModel buildDocument(Patient patient, Encounter encounter) throws
 			//relevantObs = Context.getObsService().getObservationsByPerson(builder.getRecordTarget());
 
 		for (Obs obs : relevantObs) {
-			//we want to have all obs groups at the end of the list
-			if (obs.hasGroupMembers()) {
-				medicationObs.add(obs);
-			} else {
-				medicationObs.add(0, obs);	//this probably is some group member
+			// Ensure that only obs relating to Tests are eliminated from the list
+			if (!obs.getConcept().getConceptClass().getName().equals("Test")) {
+				//we want to have all obs groups at the end of the list
+				if (obs.hasGroupMembers()) {
+					medicationObs.add(obs);
+				} else {
+					medicationObs.add(0, obs);	//this probably is some group member
+				}
 			}
 		}
 

api/src/main/java/org/openmrs/module/xdssender/api/cda/EncounterEventListener.java

@@ -103,8 +103,9 @@ private void exportEncounter(String encounterUuid) {
 			LOGGER.warn("Skipped sending Encounter %s (formId is NULL " + "-> probably it's the creating encounter)");
 		} else {
 			Patient patient = Context.getPatientService().getPatient(encounter.getPatient().getPatientId());
-
-			ecidUpdater.fetchEcidIfRequired(patient);
+
+			// TODO: Replace this with a method that queries OpenCR and fetches/updates the patient data
+			// ecidUpdater.fetchEcidIfRequired(patient);
 
 			XdsExportService service = Context.getService(XdsExportService.class);
 

api/src/main/java/org/openmrs/module/xdssender/api/fhir/FhirResourceDocumentBuilderImpl.java

@@ -4,6 +4,7 @@
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.Resource;
 import org.marc.everest.datatypes.NullFlavor;
 import org.marc.everest.datatypes.TS;
@@ -14,10 +15,12 @@
 import org.openmrs.api.impl.BaseOpenmrsService;
 import org.openmrs.module.fhir2.api.translators.PatientTranslator;
 import org.openmrs.module.fhir2.api.translators.impl.PatientTranslatorImpl;
+import org.openmrs.module.xdssender.XdsSenderConfig;
 import org.openmrs.module.xdssender.XdsSenderConstants;
 import org.openmrs.module.xdssender.api.cda.CdaDataUtil;
 import org.openmrs.module.xdssender.api.cda.model.DocumentModel;
 import org.openmrs.module.xdssender.api.fhir.exceptions.ResourceGenerationException;
+import org.openmrs.module.xdssender.api.xds.XdsUtil;
 import org.springframework.beans.BeansException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
@@ -82,13 +85,10 @@ public Resource generateFhirResource(Object openmrsEntity) throws ResourceGenera
     	if (openmrsEntity instanceof Patient) {
     		Patient patient = (Patient)openmrsEntity;
     		resource = patientTranslator.toFhirResource(patient);
-    		localPatientId = Context.getAdministrationService().getGlobalProperty(PROP_PID_LOCAL);
-    		if (localPatientId == null) {
-    			throw new ResourceGenerationException("Unable to retrieve the Local PID, ensure that the MPI client module is installed and the \"PID LOCAL\" global property has been set");
-		    }
-		    org.hl7.fhir.r4.model.Patient patientResource = (org.hl7.fhir.r4.model.Patient) resource;
-		    patientResource.addIdentifier().setSystem(IDENTIFIER_SYSTEM).setValue(localPatientId + patient.getUuid());
-			resource = patientResource;
+		    org.hl7.fhir.r4.model.Patient patientResource;
+		    patientResource = checkAndSetSystemIdentifier(patient, (org.hl7.fhir.r4.model.Patient) resource);
+
+		    resource = patientResource;
 	    } else {
     		log.error(String.format("Entity %s not yet implemented", openmrsEntity.getClass().getName()));
     		throw new ResourceGenerationException("Entity not implemented");
@@ -97,7 +97,35 @@ public Resource generateFhirResource(Object openmrsEntity) throws ResourceGenera
 		return resource;
     }
 
-    /**
+	private org.hl7.fhir.r4.model.Patient checkAndSetSystemIdentifier(Patient patient, org.hl7.fhir.r4.model.Patient patientResource)
+			throws ResourceGenerationException {
+		Boolean isSystemIdentifierDefined = false;
+		for (Identifier identifer: patientResource.getIdentifier()) {
+			if(identifer.getSystem() != null) {
+				if (identifer.getSystem().equals(XdsSenderConstants.IDENTIFIER_SYSTEM)) {
+					isSystemIdentifierDefined = true;
+					break;
+				}
+			}
+		}
+
+		if (!isSystemIdentifierDefined) {
+			PatientIdentifier systemPatientIdentifier = null;
+			try {
+				systemPatientIdentifier = XdsUtil.getPlaceholderSystemIdentifier(patient);
+			}
+			catch (Exception e) {
+				throw new ResourceGenerationException("Unable to retrieve the Local PID, ensure that the \"PID LOCAL\" global property has been set");
+			}
+
+			patientResource.addIdentifier().setSystem(XdsSenderConfig.getInstance().getEcidRoot()).setValue(systemPatientIdentifier.getIdentifier());
+			// qpatientResource.addIdentifier().setSystem(XdsSenderConstants.IDENTIFIER_SYSTEM).setValue(systemPatientIdentifier.getIdentifier());
+		}
+
+		return patientResource;
+	}
+
+	/**
      * @should return valid document
      */
     @Override