Take in and properly handle accession numbers as primary sample ident…

…ifiers.

templateSubmission.txt

@@ -1,2 +1,2 @@
-#PatientID	Patient Last Name	Patient First Name	Patient Middle Name	Patient Date of Birth	Patient Sex	Patient Street Address	Patient City	Patient State	Patient Zip	Patient Phone	Provider Last Name	Provider First Name	Provider Middle Name	Provider Street	Provider City	Provider State	Provider Zip	Provider Phone	Specimen ID	Collection Date	Collection Time	Received Date	Received Time	Specimen SNOMED Code	Test LOINC Code	Analysis Date	Analysis Time	Result	Reported Date	Reported Time	Notes	Race	Ethnicity
-#1K94U	Weinstein	Andrew	P	8/15/2017	M	17062 Murphy Ave. #1	Irvine	CA	92614	888-882-9682	Rain	Leo		13842 Tustin East Drive	Tustin	CA	92780	(818) 344-3434	1234567	6/8/2020	0:00	6/8/2020	13:00	258529004	94306-8	6/9/2020	11:00	Negative	6/10/2020	14:00	"Phone is pretty flexible for formatting, just be reasonable.  Email address is also an acceptable entry there, if needed. Please stick to mm/dd/yyyy formatting for dates.  Having a # at the start of a line will cause that line to be ignored as a comment or header."	unknown	unk
+#PatientID	Patient Last Name	Patient First Name	Patient Middle Name	Patient Date of Birth	Patient Sex	Patient Street Address	Patient City	Patient State	Patient Zip	Patient Phone	Provider Last Name	Provider First Name	Provider Middle Name	Provider Street	Provider City	Provider State	Provider Zip	Provider Phone	Specimen ID	Collection Date	Collection Time	Received Date	Received Time	Specimen SNOMED Code	Test LOINC Code	Analysis Date	Analysis Time	Result	Reported Date	Reported Time	Notes	Race	Ethnicity	Accession ID
+#1K94U	Weinstein	Andrew	P	8/15/2017	M	17062 Murphy Ave. #1	Irvine	CA	92614	888-882-9682	Rain	Leo		13842 Tustin East Drive	Tustin	CA	92780	(818) 344-3434	1234567	6/8/2020	0:00	6/8/2020	13:00	258529004	94306-8	6/9/2020	11:00	Negative	6/10/2020	14:00	"Phone is pretty flexible for formatting, just be reasonable.  Email address is also an acceptable entry there, if needed. Please stick to mm/dd/yyyy formatting for dates.  Having a # at the start of a line will cause that line to be ignored as a comment or header."	unknown	unk	1A2B3C4D5E

zymoTransmitSupport/hl7Encoder/encoders.py

@@ -67,18 +67,22 @@ def makePIDLine(result:inputOutput.resultReader.TestResult):
 
 
 def makeORCLine(result:inputOutput.resultReader.TestResult):
+    if result.accession:
+        orderID = result.accession
+    else:
+        orderID = "%s.%s" % (result.patientID, result.specimenID)
     if "labName" in result.auxiliaryData or "labCLIA" in result.auxiliaryData:
         if not ("labName" in result.auxiliaryData and "labCLIA" in result.auxiliaryData):
             raise ValueError("Lab name and lab CLIA must both be either present or absent in auxiliary data")
         fillerOrderNumber = orderHeader.FillerOrderNumber(
-            "%s.%s" % (result.patientID, result.specimenID),
+            orderID,
             result.auxiliaryData["labName"],
             result.auxiliaryData["labCLIA"],
             "CLIA"
         )
     else:
         fillerOrderNumber = orderHeader.FillerOrderNumber(
-            "%s.%s" % (result.patientID, result.specimenID),
+            orderID,
             config.LabInfo.name,
             config.LabInfo.clia,
             "CLIA"
@@ -147,18 +151,22 @@ def makeORCLine(result:inputOutput.resultReader.TestResult):
 
 
 def makeOBRLine(result:inputOutput.resultReader.TestResult):
+    if result.accession:
+        orderID = result.accession
+    else:
+        orderID = "%s.%s" % (result.patientID, result.specimenID)
     if "labName" in result.auxiliaryData or "labCLIA" in result.auxiliaryData:
         if not ("labName" in result.auxiliaryData and "labCLIA" in result.auxiliaryData):
             raise ValueError("Lab name and lab CLIA must both be either present or absent in auxiliary data")
         fillerOrderNumber = orderRequest.FillerOrderNumber(
-            "%s.%s" % (result.patientID, result.specimenID),
+            orderID,
             result.auxiliaryData["labName"],
             result.auxiliaryData["labCLIA"],
             "CLIA"
         )
     else:
         fillerOrderNumber = orderRequest.FillerOrderNumber(
-            "%s.%s" % (result.patientID, result.specimenID),
+            orderID,
             config.LabInfo.name,
             config.LabInfo.clia,
             "CLIA"
@@ -305,6 +313,10 @@ def makeObservationValueAndAbnormalityObjects(resultString:str):
 
 def makeSPMLine(result:inputOutput.resultReader.TestResult):
     specimenData = snomed.snomedTable[result.specimenSNOMED]
+    if result.accession:
+        orderID = result.accession
+    else:
+        orderID = "%s.%s" % (result.patientID, result.specimenID)
     if "labName" in result.auxiliaryData:
         assignerName = result.auxiliaryData["labName"]
     else:
@@ -317,14 +329,14 @@ def makeSPMLine(result:inputOutput.resultReader.TestResult):
         if not ("labName" in result.auxiliaryData and "labCLIA" in result.auxiliaryData):
             raise ValueError("Lab name and lab CLIA must both be either present or absent in auxiliary data")
         fillerAssignedIdentifier = specimen.FillerAssignedIdentifier(
-            "%s.%s" % (result.patientID, result.specimenID),
+            orderID,
             result.auxiliaryData["labName"],
             result.auxiliaryData["labCLIA"],
             "CLIA"
         )
     else:
         fillerAssignedIdentifier = specimen.FillerAssignedIdentifier(
-            "%s.%s" % (result.patientID, result.specimenID),
+            orderID,
             config.LabInfo.name,
             config.LabInfo.clia,
             "CLIA"

zymoTransmitSupport/inputOutput/caResultReader.py

@@ -87,13 +87,6 @@ def __init__(self, rawLine: [str, collections.Iterable], delimiter: str = "\t"):
          self.resultCode,
          self.unused
          ) = self.elementArray
-        if self.accession:
-            if self.specimenID:
-                holder = self.specimenID
-                self.specimenID = self.accession
-                self.accession = holder
-            else:
-                self.specimenID = self.accession
         self.patientDateOfBirth = self.processDateAndTime(patientDateOfBirth, "")
         self.collectionDateTime = self.processDateAndTime(collectionDate, "")
         self.reportedDateTime = self.processDateAndTime(reportedDateAndTime, "")
@@ -348,6 +341,7 @@ def convertToStandardResultObject(self):
              self.note,
              self.race,
              self.ethnicity,
+             self.accession
          ]
          resultObject = resultReader.TestResult(resultArray)
          auxiliaryData = {

zymoTransmitSupport/inputOutput/resultReader.py

@@ -9,7 +9,7 @@
 
 
 class TestResult(object):
-    expectedElements = 34
+    expectedElements = 35
 
     def __init__(self, rawLine: [str, collections.Iterable], delimiter: str = "\t"):
         self.rawLine = rawLine
@@ -52,6 +52,7 @@ def __init__(self, rawLine: [str, collections.Iterable], delimiter: str = "\t"):
          self.note,
          self.race,
          self.ethnicity,
+         self.accession
          ) = self.elementArray
         self.patientDateOfBirth = self.processDateAndTime(patientDateOfBirth, "")
         self.collectionDateTime = self.processDateAndTime(collectionDate, collectionTime)