Imahara edition ready for testing

zymoTransmit.py

@@ -29,7 +29,7 @@
 
 class CheckArgs(object):
 
-    __slots__ = ["input", "noTransmit", "hl7Directory"]
+    __slots__ = ["input", "noTransmit", "hl7Directory", "cdph"]
 
     def __init__(self):
         parser = argparse.ArgumentParser()
@@ -40,6 +40,7 @@ def __init__(self):
         parser.add_argument("-e", "--editConfig", help = "Edit configuration file", action = 'store_true')
         parser.add_argument("-n", "--noTransmit", help = "Do not attempt to transmit data", action = 'store_true')
         parser.add_argument("-d", "--hl7Directory", help = "Upload a directory of HL7 files", action = 'store_true')
+        parser.add_argument("--cdph", help = "Read CDPH format with header line", action = 'store_true')
         parser.add_argument("input", help = "Input file", type = str, nargs='?')
         rawArgs = parser.parse_args()
         testConnection = rawArgs.testConnection
@@ -50,6 +51,7 @@ def __init__(self):
         inputValue = rawArgs.input
         self.noTransmit = rawArgs.noTransmit
         self.hl7Directory = rawArgs.hl7Directory
+        self.cdph = rawArgs.cdph
         if self.hl7Directory and convertCertificate:
             raise RuntimeError("Error: Program cannot be set to both process a certificate AND take in a directory for upload")
         if testConnection or loinc or snomed:
@@ -108,8 +110,8 @@ def convertPFX(pfxPath:str, pfxPassword:str=None):
     return pemPath
 
 
-def getTestResults(testResultPath:str="results.txt"):
-    resultList = zymoTransmitSupport.inputOutput.resultReader.loadRawDataTable(testResultPath)
+def getTestResults(testResultPath:str="results.txt", cdphCSV:bool=False):
+    resultList = zymoTransmitSupport.inputOutput.resultReader.loadRawDataTable(testResultPath, cdphCSV)
     return resultList
 
 
@@ -120,7 +122,7 @@ def makeHL7Codes(resultList:typing.List[zymoTransmitSupport.inputOutput.resultRe
         specimenID = result.specimenID
         hl7Sets[(patientID, specimenID)] = []
         currentSet = hl7Sets[(patientID, specimenID)]
-        currentSet.append(zymoTransmitSupport.hl7Encoder.encoders.makeMSHLine())
+        currentSet.append(zymoTransmitSupport.hl7Encoder.encoders.makeMSHLine(result))
         currentSet.append(zymoTransmitSupport.hl7Encoder.encoders.makeSFTLine())
         currentSet.append(zymoTransmitSupport.hl7Encoder.encoders.makePIDLine(result))
         currentSet.append(zymoTransmitSupport.hl7Encoder.encoders.makeORCLine(result))
@@ -176,7 +178,7 @@ def prepareAndSendResults(args:CheckArgs):
             print("Using raw HL7 from file %s" %args.input)
             hl7TextBlocks = zymoTransmitSupport.inputOutput.rawHL7.textBlocksFromRawHL7(args.input)
         else:
-            resultList = getTestResults(args.input)
+            resultList = getTestResults(args.input, args.cdph)
             hl7Sets = makeHL7Codes(resultList)
             hl7TextBlocks = makeHL7Blocks(hl7Sets)
     hl7TextRecord = makeHL7TextRecord(hl7TextBlocks)

zymoTransmitSupport/hl7Encoder/encoders.py

@@ -14,13 +14,13 @@
 
 config = defaultConfig
 
-def makeMSHLine():
+def makeMSHLine(result:inputOutput.resultReader.TestResult):
     uniqueID = header.UniqueID(config.LabInfo.name, prependTime=True)
-    return header.MSHFromObject(config.Configuration.MSH, uniqueID, config.Configuration.productionReady)
+    return header.MSHFromObject(config.Configuration.MSH, uniqueID, config.Configuration.productionReady, result.auxiliaryData)
 
 
-def makeSFTLine():
-    return software.SoftwareLine()
+def makeSFTLine(passThruMode:bool=False):
+    return software.SoftwareLine(passThruMode)
 
 
 def makePIDLine(result:inputOutput.resultReader.TestResult):
@@ -61,12 +61,22 @@ def makePIDLine(result:inputOutput.resultReader.TestResult):
 
 
 def makeORCLine(result:inputOutput.resultReader.TestResult):
-    fillerOrderNumber = orderHeader.FillerOrderNumber(
-        "%s.%s" %(result.patientID, result.specimenID),
-        config.LabInfo.name,
-        config.LabInfo.clia,
-        "CLIA"
-    )
+    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),
+            result.auxiliaryData["labName"],
+            result.auxiliaryData["labCLIA"],
+            "CLIA"
+        )
+    else:
+        fillerOrderNumber = orderHeader.FillerOrderNumber(
+            "%s.%s" % (result.patientID, result.specimenID),
+            config.LabInfo.name,
+            config.LabInfo.clia,
+            "CLIA"
+        )
     orderingProvider = orderHeader.OrderingProvider(
         result.providerLastName,
         result.providerFirstName,
@@ -76,25 +86,49 @@ def makeORCLine(result:inputOutput.resultReader.TestResult):
     orderingFacilityAssigningAuthority = orderHeader.OrderingFacilityAssigningAuthority(
         "CLIA"
     )
-    orderingFacilityName = orderHeader.OrderingFacilityName(
-        config.LabInfo.name,
-        orderingFacilityAssigningAuthority,
-        config.LabInfo.clia
-    )
-    orderingFacilityAddress = orderHeader.OrderingFacilityAddress(
-        config.LabInfo.street,
-        config.LabInfo.city,
-        config.LabInfo.state,
-        config.LabInfo.zip
-    )
-    orderingFacilityPhone = orderHeader.OrderingFacilityPhone(config.LabInfo.phone)
+    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")
+        orderingFacilityName = orderHeader.OrderingFacilityName(
+            result.auxiliaryData["labName"],
+            orderingFacilityAssigningAuthority,
+            result.auxiliaryData["labCLIA"]
+        )
+    else:
+        orderingFacilityName = orderHeader.OrderingFacilityName(
+            config.LabInfo.name,
+            orderingFacilityAssigningAuthority,
+            config.LabInfo.clia,
+        )
+    if "labStreet" in result.auxiliaryData or "labCity" in result.auxiliaryData or "labState" in result.auxiliaryData or "labZip" in result.auxiliaryData:
+        if not (
+                "labStreet" in result.auxiliaryData and "labCity" in result.auxiliaryData and "labState" and result.auxiliaryData or "labZip" in result.auxiliaryData):
+            raise ValueError(
+                "All or no elements of lab address (street, city, state, zip) must be defined in auxiliary data")
+        orderingFacilityAddress = orderHeader.OrderingFacilityAddress(
+            result.auxiliaryData["labStreet"],
+            result.auxiliaryData["labCity"],
+            result.auxiliaryData["labState"],
+            result.auxiliaryData["labZip"]
+        )
+    else:
+        orderingFacilityAddress = orderHeader.OrderingFacilityAddress(
+            config.LabInfo.street,
+            config.LabInfo.city,
+            config.LabInfo.state,
+            config.LabInfo.zip
+        )
+    if "labPhone" in result.auxiliaryData:
+        orderingFacilityPhone = orderHeader.OrderingFacilityPhone(result.auxiliaryData["labPhone"])
+    else:
+        orderingFacilityPhone = orderHeader.OrderingFacilityPhone(config.LabInfo.phone)
+
     orderingProviderAddress = orderHeader.ProviderAddress(
         result.providerStreet,
         result.providerCity,
         result.providerState,
         result.providerZip
     )
-
     return orderHeader.OrderHeaderLine(
         fillerOrderNumber,
         orderingProvider,
@@ -107,12 +141,22 @@ def makeORCLine(result:inputOutput.resultReader.TestResult):
 
 
 def makeOBRLine(result:inputOutput.resultReader.TestResult):
-    fillerOrderNumber = orderRequest.FillerOrderNumber(
-        "%s.%s" %(result.patientID, result.specimenID),
-        config.LabInfo.name,
-        config.LabInfo.clia,
-        "CLIA"
-    )
+    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),
+            result.auxiliaryData["labName"],
+            result.auxiliaryData["labCLIA"],
+            "CLIA"
+        )
+    else:
+        fillerOrderNumber = orderRequest.FillerOrderNumber(
+            "%s.%s" % (result.patientID, result.specimenID),
+            config.LabInfo.name,
+            config.LabInfo.clia,
+            "CLIA"
+        )
     serviceData = loinc.loincTable[result.testLOINC]
     universalServiceIdentifier = orderRequest.UniversalServiceIdentifier(
         result.testLOINC,
@@ -192,16 +236,34 @@ def makeObservationValueAndAbnormalityObjects(resultString:str):
         result.analysisDateTime.minute,
         result.analysisDateTime.second
     )
-    performingOrganization = observedResults.PerformingOrganization(
-        config.LabInfo.name,
-        config.LabInfo.clia
-    )
-    labAddress = observedResults.PerformingOrganizationLabAddress(
-        config.LabInfo.street,
-        config.LabInfo.city,
-        config.LabInfo.state,
-        config.LabInfo.zip
-    )
+    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")
+        performingOrganization = observedResults.PerformingOrganization(
+            result.auxiliaryData["labName"],
+            result.auxiliaryData["labCLIA"]
+        )
+    else:
+        performingOrganization = observedResults.PerformingOrganization(
+            config.LabInfo.name,
+            config.LabInfo.clia
+        )
+    if "labStreet" in result.auxiliaryData or "labCity" in result.auxiliaryData or "labState" in result.auxiliaryData or "labZip" in result.auxiliaryData:
+        if not ("labStreet" in result.auxiliaryData and "labCity" in result.auxiliaryData and "labState" and result.auxiliaryData or "labZip" in result.auxiliaryData):
+            raise ValueError("All or no elements of lab address (street, city, state, zip) must be defined in auxiliary data")
+        labAddress = observedResults.PerformingOrganizationLabAddress(
+            result.auxiliaryData["labStreet"],
+            result.auxiliaryData["labCity"],
+            result.auxiliaryData["labState"],
+            result.auxiliaryData["labZip"]
+        )
+    else:
+        labAddress = observedResults.PerformingOrganizationLabAddress(
+            config.LabInfo.street,
+            config.LabInfo.city,
+            config.LabInfo.state,
+            config.LabInfo.zip
+        )
     if config.LabDirectorInfo.assigningAuthority:
         medicalDirectorAssignmentAuthority = observedResults.MedicalDirectorNumberAssignmentAuthority(
             config.LabDirectorInfo.assigningAuthority
@@ -232,16 +294,30 @@ def makeObservationValueAndAbnormalityObjects(resultString:str):
 
 def makeSPMLine(result:inputOutput.resultReader.TestResult):
     specimenData = snomed.snomedTable[result.specimenSNOMED]
+    if "labName" in result.auxiliaryData:
+        assignerName = result.auxiliaryData["labName"]
+    else:
+        assignerName = config.LabInfo.name
     specimenIDNumber = specimen.SpecimenIDNumber(
         result.specimenID,
-        config.LabInfo.name
-    )
-    fillerAssignedIdentifier = specimen.FillerAssignedIdentifier(
-        "%s.%s" %(result.patientID, result.specimenID),
-        config.LabInfo.name,
-        config.LabInfo.clia,
-        "CLIA"
-    )
+        assignerName
+    )
+    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")
+        fillerAssignedIdentifier = specimen.FillerAssignedIdentifier(
+            "%s.%s" % (result.patientID, result.specimenID),
+            result.auxiliaryData["labName"],
+            result.auxiliaryData["labCLIA"],
+            "CLIA"
+        )
+    else:
+        fillerAssignedIdentifier = specimen.FillerAssignedIdentifier(
+            "%s.%s" % (result.patientID, result.specimenID),
+            config.LabInfo.name,
+            config.LabInfo.clia,
+            "CLIA"
+        )
     specimenID = specimen.SpecimenID(
         specimenIDNumber,
         fillerAssignedIdentifier

zymoTransmitSupport/hl7Encoder/header.py

@@ -1,6 +1,8 @@
 from .generics import Hl7Field
 from . import generics
 from .. import config
+
+
 fieldSeparator = "|"
 
 encodingCharacters = r"^~\&"
@@ -324,9 +326,17 @@ def __init__(self,
                  mshObject:config.Configuration.MSH,
                  uniqueID: UniqueID,
                  production:bool,
+                 resultAuxiliary:dict = None
                  ):
+        if not resultAuxiliary:
+            resultAuxiliary = {}
         self.sendingApplication = SendingApplication()
-        self.sendingFacility = SendingFacility.fromObject(mshObject.SendingFacility)
+        if "labName" in resultAuxiliary or "labCLIA"  in resultAuxiliary:
+            if not ("labName" in resultAuxiliary and "labCLIA"  in resultAuxiliary):
+                raise ValueError("Both lab name and lab CLIA must be present or absent from the resultAuxiliary")
+            self.sendingFacility = SendingFacility(resultAuxiliary["labName"], resultAuxiliary["labCLIA"])
+        else:
+            self.sendingFacility = SendingFacility.fromObject(mshObject.SendingFacility)
         self.receivingAppliation = ReceivingApplication.fromObject(mshObject.ReceivingApplication)
         self.receivingFacility = ReceivingFacility.fromObject(mshObject.ReceivingFacility)
         self.messageDateTime = TimeStamp()

zymoTransmitSupport/hl7Encoder/software.py

@@ -12,7 +12,7 @@ class VendorOrg(Hl7Field):
 
     def __init__(self):
         self.orgName = "Zymo Research"
-        self.orgType = "L"  #TODO: Make sure JC is good with this being listed as our legal name
+        self.orgType = "L"
         self.idNumber = ""
         self.checkDigit = ""
         self.checkDigitScheme = ""
@@ -50,8 +50,10 @@ def __init__(self):
 
 class Name(Hl7Field):
 
-    def __init__(self):
+    def __init__(self, passThruMode:bool=False):
         self.softwareName = "Zymo Transmission"
+        if passThruMode:
+            self.softwareName += " - Pass Thru"
         self.subfields = [self.softwareName]
 
 
@@ -80,10 +82,10 @@ def __init__(self):
 
 class SoftwareLine(generics.Hl7Line):
 
-    def __init__(self):
+    def __init__(self, passThruMode:bool=False):
         self.vendorOrg = VendorOrg()
         self.version = Version()
-        self.name = Name()
+        self.name = Name(passThruMode=passThruMode)
         self.binaryID = BinaryID()
         self.productInformation = ProductInformation()
         self.installDate = InstallDate()