Imahara edition will not crash out when result string is uninterpreta…

…ble, but will throw multiple warnings and explanations when encountering one. Will also remove it from the submission to avoid submitting a sample with blank results.

zymoTransmit.py

@@ -133,6 +133,11 @@ def makeHL7Codes(resultList:typing.List[zymoTransmitSupport.inputOutput.resultRe
         currentSet.append(zymoTransmitSupport.hl7Encoder.encoders.makeSPMLine(result))
         if result.note:
             currentSet.append(zymoTransmitSupport.hl7Encoder.encoders.makeNTELine(result))
+        if not result.okToTransmit:
+            print("Skipping preparation of %s:%s for the following reasons:" %(result.patientID, result.specimenID))
+            for reason in result.reasonsNotToTransmit:
+                print("\t%s" %reason)
+            del hl7Sets[(patientID, specimenID)]
     return hl7Sets
 
 

zymoTransmitSupport/config.py

@@ -138,7 +138,7 @@ class Facility:
             idType = "CLIA"
 
 class ResultTerms:
-    positiveResultTerms = ["POSITIVE", "DETECTED", "POS"]
-    indeterminateResultTerms = ["INDETERMINATE", "N/A", "UNKNOWN", "INCONCLUSIVE", "INVALID"]
-    negativeResultTerms = ["ND", "NEG", "NEGATIVE", "NOT DETECTED"]
-    unsatisfactorySpecimenResultTerms = ["UNSATISFACTORY SPECIMEN", "SPECIMEN UNSATISFACTORY", "UNSATISFACTORY"]
+    positiveResultTerms = ["POSITIVE", "DETECTED", "POS", "260373001", "SARS-COV-2 NUCLEIC ACID DETECTED BY BDMAX", "POSITIVE SARS-COV-2", "DETECT", "REACTIVE", "DETECT", "2019-NCOV NUCLEIC ACID DETECTED BY GENEXPERT"]
+    indeterminateResultTerms = ["INDETERMINATE", "N/A", "UNKNOWN", "INCONCLUSIVE", "INVALID", "419984006"]
+    negativeResultTerms = ["ND", "NEG", "NEGATIVE", "NOT DETECTED", "260415000", "NOTDET", "NONE DETECTED", "NONREACTIVE", "NON-REACTIVE", "NOT_DETECTED", "COVID-19 (SARS-COV-2) RNA: NOT DETECTED"]
+    unsatisfactorySpecimenResultTerms = ["UNSATISFACTORY SPECIMEN", "SPECIMEN UNSATISFACTORY", "UNSATISFACTORY", "125154007"]

zymoTransmitSupport/hl7Encoder/encoders.py

@@ -200,7 +200,9 @@ def makeOBRLine(result:inputOutput.resultReader.TestResult):
 def makeOBXLine(result:inputOutput.resultReader.TestResult):
     def makeObservationValueAndAbnormalityObjects(resultString:str):
         resultStringUpper = resultString.upper()
-        if resultStringUpper in config.ResultTerms.indeterminateResultTerms:
+        if "NOT DETECTED" in resultStringUpper:
+            resultTerm = "negative"
+        elif resultStringUpper in config.ResultTerms.indeterminateResultTerms:
             resultTerm = "indeterminate"
         elif resultStringUpper in config.ResultTerms.positiveResultTerms:
             resultTerm = "detected"
@@ -209,7 +211,10 @@ def makeObservationValueAndAbnormalityObjects(resultString:str):
         elif resultStringUpper in config.ResultTerms.unsatisfactorySpecimenResultTerms:
             resultTerm = "unsatisfactory"
         else:
-            raise ValueError("Unable to classify result '%s'. Preferred terms are: detected, indeterminate, negative, and unsatisfactory specimen." %resultString)
+            print("Unable to classify result '%s' for patient %s specimen %s. Preferred terms are: detected, indeterminate, negative, and unsatisfactory specimen." %(resultString, result.patientID, result.specimenID))
+            resultTerm = ""
+            result.okToTransmit = False
+            result.reasonsNotToTransmit.append("Failed to interpret result value")
         return (observedResults.getObservationValue(resultTerm),
                 observedResults.getAbnormalityObject(resultTerm))
 

zymoTransmitSupport/hl7Encoder/observedResults.py

@@ -32,7 +32,7 @@ def getObservationValue(result:str):
     :param result: String describing the result. Must be in ["detected", "indeterminate", "negative"]
     :return: An appropriate result as a generics.SystemCode object
     '''
-    validResults = ["detected", "indeterminate", "negative", "unsatisfactory"]
+    validResults = ["detected", "indeterminate", "negative", "unsatisfactory", ""]
     if not result in validResults:
         raise ValueError("Result type must be in: " %validResults)
     if result == "detected":
@@ -43,6 +43,8 @@ def getObservationValue(result:str):
         return generics.SystemCode(code="260415000", text="Not detected", coding="SNOMED", codingSystemDateOrVersion="2.7")
     elif result == "unsatisfactory":
         return generics.SystemCode(code="125154007", text="Specimen unsatisfactory", coding="SNOMED", codingSystemDateOrVersion="2.7")
+    elif result == "":
+        return ""
     else:
         raise RuntimeError("This code should be unreachable if result validations is working properly and how we got here needs to be investigated")
 
@@ -61,7 +63,7 @@ def getAbnormalityObject(result:str):
     :param result: String describing the result. Must be in ["detected", "indeterminate", "negative"]
     :return: An appropriate result as a generics.SystemCode object
     '''
-    validResults = ["detected", "indeterminate", "negative", "unsatisfactory"]
+    validResults = ["detected", "indeterminate", "negative", "unsatisfactory", ""]
     if not result in validResults:
         raise ValueError("Result type must be in: " %validResults)
     if result == "detected":
@@ -72,6 +74,8 @@ def getAbnormalityObject(result:str):
         return generics.SystemCode(code="260415000", text="Not detected", coding="SNOMED", codingSystemDateOrVersion="2.7")
     elif result == "unsatisfactory":
         return generics.SystemCode(code="125154007", text="Specimen unsatisfactory", coding="SNOMED", codingSystemDateOrVersion="2.7")
+    elif result == "":
+        return ""
     else:
         raise RuntimeError("This code should be unreachable if result validations is working properly and how we got here needs to be investigated")
 

zymoTransmitSupport/inputOutput/resultReader.py

@@ -58,6 +58,8 @@ def __init__(self, rawLine: [str, collections.Iterable], delimiter: str = "\t"):
         self.analysisDateTime = self.processDateAndTime(analysisDate, analysisTime)
         self.reportedDateTime = self.processDateAndTime(reportedDate, reportedTime)
         self.auxiliaryData = {}
+        self.okToTransmit = True
+        self.reasonsNotToTransmit = []
 
     def processRawLine(self, delimiter):
         rawLine = self.rawLine.strip()