Add "realistic" test and fix handling of string-coded systemless results

IsantePlus · Dec 17, 2024 · b996fed · b996fed
1 parent d5bf7b9
commit b996fed
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Showing 3 changed files with 46 additions and 11 deletions.
diff --git a/api/src/main/java/org/openmrs/module/labintegration/api/hl7/handler/OruR01Handler.java b/api/src/main/java/org/openmrs/module/labintegration/api/hl7/handler/OruR01Handler.java
@@ -95,7 +95,7 @@ public Message processMessage(Message message) throws ApplicationException, HL7E
 			return response;
 		}
 		catch (ClassCastException ex) {
-			LOGGER.warn("Error casting " + message.getClass().getName() + " to ORU_R01", ex);
+            LOGGER.warn("Error casting {} to ORU_R01", message.getClass().getName(), ex);
 			throw new ApplicationException(Context.getMessageSourceService().getMessage("ORUR01.error.invalidMessageType ",
 			    new Object[] { message.getClass().getName() }, null), ex);
 		}
@@ -104,7 +104,7 @@ public Message processMessage(Message message) throws ApplicationException, HL7E
 			throw new ApplicationException(Context.getMessageSourceService().getMessage("ORUR01.error.WhileProcessing"), ex);
 		}
 		catch (Exception e) {
-			LOGGER.error("Could not process message!\n" + e.getMessage());
+            LOGGER.error("Could not process message! {}", e.getMessage(), e);
 		}
 
 		return null;
@@ -137,7 +137,7 @@ private Message processOruR01(ORU_R01 message) throws HL7Exception, ApplicationE
 
 		ORU_R01_PATIENT_RESULT patientResult = message.getPATIENT_RESULT();
 		int numObr = patientResult.getORDER_OBSERVATIONReps();
-		LOGGER.debug("Patient result {}", patientResult.toString());
+		LOGGER.debug("Patient result {}", patientResult);
 		LOGGER.debug("# Observation results returned {}", numObr);
 		PV1 pv1 = patientResult.getPATIENT().getVISIT().getPV1();
 		LOGGER.debug("PV1 Time {}", pv1.getAdmitDateTime().getTime());
@@ -149,10 +149,8 @@ private Message processOruR01(ORU_R01 message) throws HL7Exception, ApplicationE
 		LOGGER.debug("Alternate Visit Id - Identifier type code {}", pv1.getAlternateVisitID()
 			.getCx5_IdentifierTypeCode().getValue());
 		for (int i = 0; i < numObr; i++) {
-
-			LOGGER.debug("Processing OBR {}", i);
-			LOGGER.debug(" of {}", numObr);
-
+			LOGGER.debug("Processing OBR {} of {}", i + 1, numObr);
+
 			ORU_R01_ORDER_OBSERVATION orderObs = patientResult.getORDER_OBSERVATION(i);
 			OBR obr = orderObs.getOBR();
 			// OBR values
@@ -271,14 +269,15 @@ protected Concept getConcept(String hl7ConceptId, String codingSystem, String ui
 			try {
 				conceptId = Integer.valueOf(hl7ConceptId);
 			} catch (NumberFormatException e) {
-				 if (hl7ConceptId.equals("D??tect??")) {
+				 if (hl7ConceptId.equals("Détecté")) {
 					LOGGER.info("this is the value text 2 : " + hl7ConceptId);
 					conceptId = Integer.valueOf(DETECTED_CODED_VALUE);
-					} else if (hl7ConceptId.equals("Non-D??tect??")) {
+				 } else if (hl7ConceptId.equals("Non-Détecté")) {
 					LOGGER.info("this is the value text 3 : " + hl7ConceptId);
 					conceptId = Integer.valueOf(NOT_DETECTED_CODED_VALUE);
-					} 
-				}
+				 }
+			}
+
 			return Context.getConceptService().getConcept(conceptId);
 		} else {
 			// the concept is not local, look it up in our mapping

diff --git a/api/src/test/java/org/openmrs/module/labintegration/api/hl7/handler/OruR01HandlerTest.java b/api/src/test/java/org/openmrs/module/labintegration/api/hl7/handler/OruR01HandlerTest.java
@@ -50,4 +50,25 @@ public void processMessage_shouldParseObsAndNotReturnNull() throws HL7Exception,
 		Message message1 = oruR01Handler.processMessage(message);
 		assertNotNull(message);
 	}
+
+	@Test
+	public void processMessage_shouldProcessMessageToObs() throws Exception {
+		executeDataSet(DATASET);
+
+		String hl7Message = "MSH|^~\\&|||||20241216090516-0500||ORU^R01|00000000|P|2.5\n" +
+				"PID||33118500^^^^MR^112123|33118500^^^^MR^112123||WASHINGTONN^GLENN||20000601|M||U|^4èME LA MONTAGNE^JEAN RABEL^NRO|||||||^7a732da7-f3a8-40fe-b9eb-c8a058de9497\n" +
+				"PV1||R|11223||||11223^OPAP^PRESTATAIRE^^^^^^^^^^L||||||||||^^^^^^^^^^^^L|||||||||||||||||||||||||||20241216||||||290fb4d0-2ae6-40bd-a058-436acea3d881^f037e97b-471e-4898-a07c-b8e169e0ddc4^^b181ab58-e4fb-4b47-bc69-f0c05dd473cd^7a732da7-f3a8-40fe-b9eb-c8a058de9497\n" +
+				"ORC|RE|11223-53-440|1|C8160001|||^^^202412160558-0500^^R||202412160558|HISTC||11223^OPAP^PRESTATAIRE^^^^^^^^^^L|11223\n" +
+				"OBR|1|11223-53-440|1|f037e97b-471e-4898-a07c-b8e169e0ddc4|||202412160558|||HISTC|N|||202412160600||11223^OPAP^PRESTATAIRE^^^^^^^^^^L||||||202412160905-0500|||F||^^^202412160558-0500^^R|||||||DIG\n" +
+				"OBX|1|CE|44871-2^^LN^LVH2P^ADN VIH-1, PCR-2^L|0|Détecté|||*|||F|||202412160601||DIG|||202412160905";
+		hl7Message = hl7Message.replaceFirst(ORUR01_ORU_R01, ORU_R01);
+		hl7Message = hl7Message.replaceFirst(VERSION_251, VERSION_25);
+		hl7Message = hl7Message.replace("\n", Character.toString((char) 13));
+		hl7Message = hl7Message.replaceAll("\\[[0-9]{4}\\]", "");
+
+		Message message = new PipeParser().parse(hl7Message);
+		OruR01Handler oruR01Handler = new OruR01Handler();
+
+		Message ack = oruR01Handler.processMessage(message);
+	}
 }
diff --git a/api/src/test/resources/lab-dataset.xml b/api/src/test/resources/lab-dataset.xml
@@ -67,6 +67,14 @@
         concept_id="162929" uuid="278664ABBBBBBBBBBBBBBBBBBBBBBBBBBBBB" concept_map_type_id="1"
         creator="1" date_created="2005-01-06 00:00:00"/>
 
+    <concept_reference_term concept_reference_term_id="278666" creator="1" date_created="2005-01-06 00:00:00"
+                            concept_source_id="6" code="44871-2" uuid=" 3cd1e7d8-0645-4469-bdd2-4c7b607eedc0 "
+                            retired="0"/>
+
+    <concept_reference_map concept_reference_term_id="278666" concept_map_id="278666"
+                           concept_id="856" uuid="278666ABBBBBBBBBBBBBBBBBBBBBBBBBBBBB" concept_map_type_id="1"
+                           creator="1" date_created="2005-01-06 00:00:00"/>
+
     <!-- Birth Place -->
     <concept concept_id="21399" retired="0" date_created="2005-01-06 00:00:00" is_set="1"/>
     <concept concept_id="21400" retired="0" date_created="2005-01-06 00:00:00" is_set="0"/>
@@ -184,5 +192,12 @@
                location_id="2"
                uuid="549c78dc-31da-11e8-acac-c3add5b19973"/>
 
+    <encounter encounter_id="22"
+               patient_id="10" encounter_type="22"
+               encounter_datetime="2018-03-28 17:16:07"
+               creator="1" date_created="2005-01-06 00:00:00" voided="0"
+               location_id="2"
+               uuid="7a732da7-f3a8-40fe-b9eb-c8a058de9497"/>
+
 
 </dataset>