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Merge pull request #322 from patryllus/feat/PullingLimsLabResults
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Feat/pulling lims lab results
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@ojwanganto
ojwanganto authored Nov 8, 2024
2 parents 77ae720 + 4d1a6d8 commit 7227c4b
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Showing 6 changed files with 342 additions and 78 deletions.
77 changes: 53 additions & 24 deletions ...g/openmrs/module/kenyaemrorderentry/labDataExchange/LabwareFacilityWideResultsMapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
*/
public class LabwareFacilityWideResultsMapper {
public static final String LAB_TEST_RESULT_SET_PROPERTY = "result";
String LAB_ENCOUNTER_TYPE_UUID = "e1406e88-e9a9-11e8-9f32-f2801f1b9fd1";
public static String LAB_ENCOUNTER_TYPE_UUID = "e1406e88-e9a9-11e8-9f32-f2801f1b9fd1";

public LabwareFacilityWideResultsMapper() {
}
Expand Down Expand Up @@ -64,7 +64,7 @@ public LabwareFacilityWideResultsMapper() {
* }
* @return
*/
public ObjectNode readLabTestMappingConfiguration(){
public static ObjectNode readLabTestMappingConfiguration(){
AdministrationService administrationService = Context.getAdministrationService();
String limsConfiguration = (administrationService.getGlobalProperty("kenyaemrorderentry.facilitywidelims.mapping"));
ObjectMapper mapper = new ObjectMapper();
Expand All @@ -83,12 +83,14 @@ public ObjectNode readLabTestMappingConfiguration(){
* @param resultPayload
* @return
*/
public ResponseEntity<String> processResultsFromLims(String resultPayload) {
public static ResponseEntity<String> processResultsFromLims(String resultPayload) {
System.out.println("Start Processing results from LIMs" + resultPayload);
JsonElement rootNode = JsonParser.parseString(resultPayload);
JsonObject resultsObj = null;
try {
if (rootNode.isJsonObject()) {
resultsObj = rootNode.getAsJsonObject();
System.out.println("Result object" + resultPayload);
} else {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body("The payload could not be understood. An object is expected!");
}
Expand All @@ -100,15 +102,18 @@ public ResponseEntity<String> processResultsFromLims(String resultPayload) {
if (resultsObj != null) {
Map<String,String> resultMap = new HashMap<>();
JsonArray resultArray = resultsObj.get("data").getAsJsonArray();
System.out.println("Data Array" + resultArray);
Integer orderId = null;
for (int i = 0; i < resultArray.size(); i++) {
try {
JsonObject o = resultArray.get(i).getAsJsonObject();
orderId = o.get("labRequestId").getAsInt();
System.out.println("Lab request ID " + orderId);
String testName = !o.isJsonNull() && !o.get("resultName").isJsonNull() ? o.get("resultName").getAsString() : "";
String result = !o.isJsonNull() && !o.get("resultValue").isJsonNull() ? o.get("resultValue").getAsString() : "";
if (StringUtils.isNotBlank(testName) && StringUtils.isNotBlank(result)) {
resultMap.put(testName, result);
System.out.println("Result Map" + resultMap);
}
} catch (Exception ex) {
ex.printStackTrace();
Expand All @@ -117,6 +122,7 @@ public ResponseEntity<String> processResultsFromLims(String resultPayload) {
}
}
// update results and complete the order
System.out.println("Map" + resultMap + "OrderID " +orderId);
return mapLimsResultsInEmr(orderId, resultMap);
} else {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body("The system could not extract the test results from LIMS details");
Expand All @@ -132,7 +138,9 @@ public ResponseEntity<String> processResultsFromLims(String resultPayload) {
* For lab sets i.e. complete blood count, the map entry is a test and the value
* Results for lab sets are handled as grouped observations with a reference to the parent order.
*/
public ResponseEntity<String> mapLimsResultsInEmr(Integer orderId, Map<String,String> limsResult) {
public static ResponseEntity<String> mapLimsResultsInEmr(Integer orderId, Map<String,String> limsResult) {
System.out.println("Inside mapper");
System.out.println("Inside mapper" + limsResult);
if (limsResult == null || limsResult.isEmpty()) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body("The system encountered empty results from LIMS");
}
Expand All @@ -145,17 +153,22 @@ public ResponseEntity<String> mapLimsResultsInEmr(Integer orderId, Map<String,St
Concept orderConcept = order.getConcept();

if (orderConcept != null) {

System.out.println("Order Concept" + orderConcept);
ObjectNode mapping = readLabTestMappingConfiguration();
if (mapping == null) {
return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body("LIMS-EMR mapping configuration is missing or invalid!");
}
// Get mapping for the test concept
System.out.println("Starting concept mapping ==>");
System.out.println("Order Concept UUID==> " + orderConcept.getUuid());
ObjectNode testConceptMapping = (ObjectNode) mapping.get(orderConcept.getUuid());
System.out.println("Concept map ==>"+testConceptMapping);
if (testConceptMapping == null) {
System.out.println("Concept mapping ==> "+testConceptMapping);
System.out.println("Mapping does not exists ==>");
return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body("LIMS lab test configuration doesn't support result mapping for test " + orderConcept.getUuid());
}

System.out.println("Mapping exists ==>");
// setup lab result encounter
Encounter enc = new Encounter();
enc.setEncounterType(labEncounterType);
Expand Down Expand Up @@ -187,33 +200,45 @@ public ResponseEntity<String> mapLimsResultsInEmr(Integer orderId, Map<String,St
* "WBC": 123, "RDW": 679, "someQualitativeTest":"Positive"
*/
if (orderConcept.isSet() && orderConcept.getSetMembers().size() > 0) {
System.out.println("Test is a set ==>");
ObjectNode resultSet = (ObjectNode) testConceptMapping.get(LAB_TEST_RESULT_SET_PROPERTY);
// loop through the results and create an obs group
for (Map.Entry<String, String> entry : limsResult.entrySet()) {
limsTestName = entry.getKey();
limsTestResult = entry.getValue();

System.out.println("Test Name ==>"+limsTestName);
System.out.println("Test Result ==>"+limsTestResult);

if (StringUtils.isBlank(limsTestResult) || StringUtils.isBlank(limsTestName)) {
return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body("The system extracted NULL test name or results from LIMS data for lab set " + orderConcept.getUuid());
}
String memberConceptUuid = resultSet.get(limsTestName).asText();
Concept memberObsConcept = conceptService.getConceptByUuid(memberConceptUuid);
Obs memberObs = constructObs(order);
if (memberObsConcept != null) {
memberObs.setConcept(memberObsConcept);
if (memberObsConcept.getDatatype().isNumeric() || memberObsConcept.getDatatype().isText()) {
setObsValue(memberObs, memberObsConcept, limsTestResult);
} else if (memberObsConcept.getDatatype().isCoded()) {
String memberTestConceptUuid = resultSet.get(limsTestName).asText();
Concept codedAnswer = Context.getConceptService().getConceptByUuid(memberTestConceptUuid);
setObsValue(memberObs, memberObsConcept, codedAnswer);
}
}
o.addGroupMember(memberObs);
if(resultSet.get(limsTestName) != null) {
String memberConceptUuid = resultSet.get(limsTestName).asText();
Concept memberObsConcept = conceptService.getConceptByUuid(memberConceptUuid);
System.out.println("Member Name ==>" + memberConceptUuid);
System.out.println("Member Result ==>" + memberObsConcept);
Obs memberObs = constructObs(order);
if (memberObsConcept != null) {
System.out.println("Setting conceptMembers ==>" + memberObsConcept);
memberObs.setConcept(memberObsConcept);
if (memberObsConcept.getDatatype().isNumeric() || memberObsConcept.getDatatype().isText()) {
System.out.println("Member concept is Numeric or Text ==>");
setObsValue(memberObs, memberObsConcept, limsTestResult);
} else if (memberObsConcept.getDatatype().isCoded()) {
System.out.println("Member concept is Coded ==>");
String memberTestConceptUuid = resultSet.get(limsTestName).asText();
Concept codedAnswer = Context.getConceptService().getConceptByUuid(memberTestConceptUuid);
setObsValue(memberObs, memberObsConcept, codedAnswer);
}
}
o.addGroupMember(memberObs);
}
}

} else { // this is for a non-set test.
for (Map.Entry<String, String> entry : limsResult.entrySet()) {
System.out.println("Is non set ==>");
limsTestName = entry.getKey();
limsTestResult = entry.getValue();
}
Expand All @@ -223,6 +248,7 @@ public ResponseEntity<String> mapLimsResultsInEmr(Integer orderId, Map<String,St
}

if (orderConcept.getDatatype().isNumeric() || orderConcept.getDatatype().isText()) {
System.out.println("Setting obs value for Numeric or text==>");
setObsValue(o, orderConcept, limsTestResult);
} else if (orderConcept.getDatatype().isCoded()) {
/*
Expand All @@ -236,16 +262,19 @@ public ResponseEntity<String> mapLimsResultsInEmr(Integer orderId, Map<String,St
}
We expect results in the form of "Malaria Smear":"Positive"
*/
System.out.println("Setting obs value for Coded==>");
ObjectNode resultSet = (ObjectNode) testConceptMapping.get(LAB_TEST_RESULT_SET_PROPERTY);
String codedAnswerConceptUuid = resultSet.get(limsTestResult).asText();
Concept codedAnswer = Context.getConceptService().getConceptByUuid(codedAnswerConceptUuid);
setObsValue(o, orderConcept, codedAnswer);
}
}
try {
System.out.println("Saving encounter");
enc.addObs(o);
encounterService.saveEncounter(enc);
orderService.discontinueOrder(order, "Results received", new Date(), order.getOrderer(), enc);
orderService.discontinueOrder(order, "Results received", new Date(), order.getOrderer(), enc);
order.setFulfillerStatus(Order.FulfillerStatus.COMPLETED);
return ResponseEntity.status(HttpStatus.OK).body("Lab results updated successfully");

} catch (Exception e) {
Expand All @@ -262,7 +291,7 @@ public ResponseEntity<String> mapLimsResultsInEmr(Integer orderId, Map<String,St
* @param concept
* @param obsValue
*/
private void setObsValue(Obs obs, Concept concept, String obsValue) {
private static void setObsValue(Obs obs, Concept concept, String obsValue) {
if (concept.isNumeric()) {
obs.setValueNumeric(Double.valueOf(obsValue));
} else if (concept.getDatatype().isText()) {
Expand All @@ -276,7 +305,7 @@ private void setObsValue(Obs obs, Concept concept, String obsValue) {
* @param concept
* @param obsValue
*/
private void setObsValue(Obs obs, Concept concept, Concept obsValue) {
private static void setObsValue(Obs obs, Concept concept, Concept obsValue) {
if (concept.getDatatype().isCoded()) {
obs.setValueCoded(obsValue);
}
Expand All @@ -287,7 +316,7 @@ private void setObsValue(Obs obs, Concept concept, Concept obsValue) {
* @param order
* @return
*/
private Obs constructObs(Order order){
private static Obs constructObs(Order order){
Obs o = new Obs();
o.setDateCreated(new Date());
o.setCreator(Context.getUserService().getUser(1));
Expand Down
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