Merge pull request #13759 from SORMAS-Foundation/task-update_external_message_autoprocessing

Updated automatic processing for lab messages and some other fixes

Author: raulbob

sormas-api/src/main/java/de/symeda/sormas/api/epipulse/EpipulseExportFacade.java

@@ -40,5 +40,5 @@ public interface EpipulseExportFacade extends DeletableFacade {
 
 	void deleteEpipulseExport(String uuid);
 
-	boolean configured();
+	boolean isConfigured();
 }

sormas-api/src/main/java/de/symeda/sormas/api/externalmessage/ExternalMessageDto.java

@@ -255,6 +255,9 @@ public class ExternalMessageDto extends SormasToSormasShareableDto {
 	private Integer tuberculosisInfectionYear;
 	private YesNoUnknown previousTuberculosisTreatment;
 	private ComplianceWithTreatment complianceWithTreatment;
+	private Boolean tuberculosisDirectlyObservedTreatment;
+	private Boolean tuberculosisMdrXdrTuberculosis;
+	private Boolean tuberculosisBeijingLineage;
 
 	public ExternalMessageType getType() {
 		return type;
@@ -901,4 +904,28 @@ public ComplianceWithTreatment getComplianceWithTreatment() {
 	public void setComplianceWithTreatment(ComplianceWithTreatment complianceWithTreatment) {
 		this.complianceWithTreatment = complianceWithTreatment;
 	}
+
+	public Boolean getTuberculosisDirectlyObservedTreatment() {
+		return tuberculosisDirectlyObservedTreatment;
+	}
+
+	public void setTuberculosisDirectlyObservedTreatment(Boolean tuberculosisDirectlyObservedTreatment) {
+		this.tuberculosisDirectlyObservedTreatment = tuberculosisDirectlyObservedTreatment;
+	}
+
+	public Boolean getTuberculosisMdrXdrTuberculosis() {
+		return tuberculosisMdrXdrTuberculosis;
+	}
+
+	public void setTuberculosisMdrXdrTuberculosis(Boolean tuberculosisMdrXdrTuberculosis) {
+		this.tuberculosisMdrXdrTuberculosis = tuberculosisMdrXdrTuberculosis;
+	}
+
+	public Boolean getTuberculosisBeijingLineage() {
+		return tuberculosisBeijingLineage;
+	}
+
+	public void setTuberculosisBeijingLineage(Boolean tuberculosisBeijingLineage) {
+		this.tuberculosisBeijingLineage = tuberculosisBeijingLineage;
+	}
 }

sormas-api/src/main/java/de/symeda/sormas/api/externalmessage/processing/AbstractMessageProcessingFlowBase.java

@@ -381,16 +381,63 @@ private FlowThen<ExternalMessageProcessingResult> doSinglePickOrCreateSampleFlow
 
     }
 
+    /**
+     * Retrieves similar cases based on the selected person and lab message.
+     * This method will call getSimilarCases(PersonReferenceDto selectedPerson, Disease disease) with the disease of the external message by
+     * default.
+     * 
+     * @param selectedPerson
+     * @param externalMessage
+     * @return
+     */
+    protected List<CaseSelectionDto> getSimilarCases(PersonReferenceDto selectedPerson, ExternalMessageDto externalMessage) {
+        return getSimilarCases(selectedPerson, externalMessage.getDisease());
+    }
+
+    protected List<CaseSelectionDto> getSimilarCases(PersonReferenceDto selectedPerson, Disease disease) {
+        return getExternalMessageProcessingFacade().getSimilarCases(selectedPerson, disease);
+    }
+
+    /**
+     * Retrieves similar contacts based on the selected person and lab message.
+     * This method will call getSimilarContacts(PersonReferenceDto selectedPerson, Disease disease) with the disease of the external message
+     * by default.
+     * 
+     * @param selectedPerson
+     * @param externalMessage
+     * @return
+     */
+    protected List<SimilarContactDto> getSimilarContacts(PersonReferenceDto selectedPerson, ExternalMessageDto externalMessage) {
+        return getSimilarContacts(selectedPerson, externalMessage.getDisease());
+    }
+
+    protected List<SimilarContactDto> getSimilarContacts(PersonReferenceDto selectedPerson, Disease disease) {
+        return getExternalMessageProcessingFacade().getSimilarContacts(selectedPerson, disease);
+    }
+
+    /**
+     * Retrieves similar event participants based on the selected person and lab message.
+     * This method will call getSimilarEventParticipants(PersonReferenceDto selectedPerson, Disease disease) with the disease of the
+     * external message by default.
+     * 
+     * @param selectedPerson
+     * @param externalMessage
+     * @return
+     */
+    protected List<SimilarEventParticipantDto> getSimilarEventParticipants(PersonReferenceDto selectedPerson, ExternalMessageDto externalMessage) {
+        return getSimilarEventParticipants(selectedPerson, externalMessage.getDisease());
+    }
+
     /**
      * Retrieves similar event participants based on the selected person and lab message.
      *
      * @param selectedPerson
      *            The selected person reference.
-     * @param labMessage
+     * @param externalMessage
      *            The external lab message.
      * @return A list of similar event participants.
      */
-    protected List<SimilarEventParticipantDto> getSimilarEventParticipants(PersonReferenceDto selectedPerson, ExternalMessageDto labMessage) {
+    protected List<SimilarEventParticipantDto> getSimilarEventParticipants(PersonReferenceDto selectedPerson, Disease disease) {
 
         if (getExternalMessageProcessingFacade().isFeatureDisabled(FeatureType.EVENT_SURVEILLANCE)
             || !getExternalMessageProcessingFacade().hasAllUserRights(UserRight.EVENTPARTICIPANT_CREATE, UserRight.EVENTPARTICIPANT_EDIT)) {
@@ -399,7 +446,7 @@ protected List<SimilarEventParticipantDto> getSimilarEventParticipants(PersonRef
 
         EventParticipantCriteria eventParticipantCriteria = new EventParticipantCriteria();
         eventParticipantCriteria.setPerson(selectedPerson);
-        eventParticipantCriteria.setDisease(labMessage.getDisease());
+        eventParticipantCriteria.setDisease(disease);
 
         return getExternalMessageProcessingFacade().getMatchingEventParticipants(eventParticipantCriteria);
     }
@@ -436,8 +483,9 @@ protected CompletionStage<ProcessingResult<PickOrCreateEntryResult>> pickOrCreat
         ExternalMessageDto externalMessage) {
 
         PersonReferenceDto personRef = previousResult.getPerson().toReference();
-        List<CaseSelectionDto> similarCases = getExternalMessageProcessingFacade().getSimilarCases(personRef, externalMessage.getDisease());
-        List<SimilarContactDto> similarContacts = getExternalMessageProcessingFacade().getSimilarContacts(personRef, externalMessage.getDisease());
+
+        List<CaseSelectionDto> similarCases = getSimilarCases(personRef, externalMessage);
+        List<SimilarContactDto> similarContacts = getSimilarContacts(personRef, externalMessage);
         List<SimilarEventParticipantDto> similarEventParticipants = getSimilarEventParticipants(personRef, externalMessage);
 
         HandlerCallback<PickOrCreateEntryResult> callback = new HandlerCallback<>();
@@ -982,42 +1030,41 @@ protected abstract void markExternalMessageAsProcessed(
         ProcessingResult<ExternalMessageProcessingResult> result,
         SurveillanceReportDto surveillanceReport);
 
-
     protected void doPersonUpdates(EntitySelection<PersonDto> personSelection) {
         // requested for #13589
         // TODO: we need to find a better way to handle this
 
-        if(personSelection.isNew()) {
+        if (personSelection.isNew()) {
             // no updates for new persons
             return;
         }
 
         final PersonDto person = personSelection.getEntity();
-        if(person == null) {
+        if (person == null) {
             return;
         }
 
         final LocationDto personAddress = person.getAddress();
 
-        if(personAddress != null) {
+        if (personAddress != null) {
             final String houseNumber = getExternalMessage().getPersonHouseNumber();
-            if(houseNumber != null ) {
+            if (houseNumber != null) {
                 personAddress.setHouseNumber(houseNumber);
             }
             final String street = getExternalMessage().getPersonStreet();
-            if(street != null) {
+            if (street != null) {
                 personAddress.setStreet(street);
             }
             final String city = getExternalMessage().getPersonCity();
-            if(city != null) {
+            if (city != null) {
                 personAddress.setCity(city);
             }
             final String postalCode = getExternalMessage().getPersonPostalCode();
-            if(postalCode != null) {
+            if (postalCode != null) {
                 personAddress.setPostalCode(postalCode);
             }
             final CountryReferenceDto country = getExternalMessage().getPersonCountry();
-            if(country != null) {
+            if (country != null) {
                 personAddress.setCountry(country);
             }
 

sormas-api/src/main/java/de/symeda/sormas/api/externalmessage/processing/ExternalMessageProcessingFacade.java

@@ -153,6 +153,10 @@ public FacilityReferenceDto getFacilityReferenceByUuid(String uuid) {
 		return facilityFacade.getReferenceByUuid(uuid);
 	}
 
+	public List<SampleDto> getSamplesByCaseUuids(List<String> caseUuids) {
+		return sampleFacade.getByCaseUuids(caseUuids);
+	}
+
 	public List<SampleDto> getSamplesByCriteria(SampleCriteria sampleCriteria) {
 		return sampleFacade.getSamplesByCriteria(sampleCriteria);
 	}