Imahara edition able to submit results.

CDPH.bat

@@ -0,0 +1 @@
+python zymoTransmit.py --cdph

raceEthnicityCodes.txt

@@ -9,4 +9,4 @@
 PHC1369	not obtainable			
 PHC1367	refused			
 ASKU	asked but unknown			
-UNK	unknown			
+UNK	unknown	u		

zymoTransmit.py

@@ -29,7 +29,7 @@
 
 class CheckArgs(object):
 
-    __slots__ = ["input", "noTransmit", "hl7Directory", "cdph"]
+    __slots__ = ["input", "noTransmit", "hl7Directory", "cdph", "debug"]
 
     def __init__(self):
         parser = argparse.ArgumentParser()
@@ -41,6 +41,7 @@ def __init__(self):
         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("--debug", help="Running in debugging mode", action='store_true')
         parser.add_argument("input", help = "Input file", type = str, nargs='?')
         rawArgs = parser.parse_args()
         testConnection = rawArgs.testConnection
@@ -52,6 +53,7 @@ def __init__(self):
         self.noTransmit = rawArgs.noTransmit
         self.hl7Directory = rawArgs.hl7Directory
         self.cdph = rawArgs.cdph
+        self.debug = rawArgs.debug
         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:
@@ -197,12 +199,20 @@ def makeDirectoriesIfNeeded():
         os.mkdir(os.path.join(contentRoot, config.Configuration.logFolder))
 
 
+class PlaceHolderException(Exception):
+    pass
+
+
 def main():
+    if "--debug" in sys.argv:
+        allOrNothingException = PlaceHolderException
+    else:
+        allOrNothingException = Exception
     try:
         makeDirectoriesIfNeeded()
         args = CheckArgs()
         prepareAndSendResults(args)
-    except Exception as err:
+    except allOrNothingException as err:
         print("Encountered an unhandled error as follows:")
         traceback.print_exc()
         input("Run was not successful. Press enter to quit")

zymoTransmitSupport/config.py

@@ -139,6 +139,6 @@ class Facility:
 
 class ResultTerms:
     positiveResultTerms = ["POSITIVE", "DETECTED", "POS"]
-    indeterminateResultTerms = ["INDETERMINATE", "N/A", "UNKNOWN"]
+    indeterminateResultTerms = ["INDETERMINATE", "N/A", "UNKNOWN", "INCONCLUSIVE", "INVALID"]
     negativeResultTerms = ["ND", "NEG", "NEGATIVE", "NOT DETECTED"]
     unsatisfactorySpecimenResultTerms = ["UNSATISFACTORY SPECIMEN", "SPECIMEN UNSATISFACTORY", "UNSATISFACTORY"]

zymoTransmitSupport/hl7Encoder/patient.py

@@ -95,7 +95,9 @@ def __init__(self, sex:str=None):
             "M": "M",
             "F": "F",
             "MALE": "M",
-            "FEMALE": "F"
+            "FEMALE": "F",
+            "U": "",
+            "UNKNOWN": ""
         }
         if not sex:
             sexString = ""

zymoTransmitSupport/inputOutput/caResultReader.py

@@ -129,29 +129,30 @@ def processDateAndTime(self, dateString: str, timeString: str, possibleDateDelim
                 break
         if not dateDelimiter:
             if len(dateString) == 8:
-                month = dateString[:4]
-                day = dateString[4:6]
-                year = dateString[6:]
+                year = dateString[:4]
+                month = dateString[4:6]
+                day = dateString[6:]
             elif len(dateString) == 14:
-                month = dateString[:4]
-                day = dateString[4:6]
-                year = dateString[6:8]
+                year = dateString[:4]
+                month = dateString[4:6]
+                day = dateString[6:8]
                 hour = dateString[8:10]
                 minute = dateString[10:12]
                 second = dateString[12:14]
                 timeString = ":".join([hour, minute, second])
             elif len(dateString) == 19 and "-" in dateString:
-                month = dateString[:4]
-                day = dateString[4:6]
-                year = dateString[6:8]
+                year = dateString[:4]
+                month = dateString[4:6]
+                day = dateString[6:8]
                 hour = dateString[8:10]
                 minute = dateString[10:12]
                 second = dateString[12:14]
                 timeString = ":".join([hour, minute, second])
-                offset = timeString.split("-")[1]
+                offset = dateString.split("-")[1]
                 offset = offset[:2]
                 offset = int(offset)
                 tzInfo = datetime.timedelta(hours=offset)
+                tzInfo = datetime.timezone(tzInfo)
             else:
                 errorMessageLines = []
                 errorMessageLines.append("Unable to process date value")
@@ -235,6 +236,8 @@ def revertDateTimeObject(self, revertant:[datetime.datetime, datetime.date, date
             dateString = ""
             timeString = "%s:%s:%s" %(revertant.hour, revertant.minute, revertant.second)
         else:
+            if type(revertant) == tuple:
+                return revertant[0], revertant[1]
             raise ValueError("Got an invalid value trying to revert a datetime object to a string: %s of type %s" %(revertant, type(revertant)))
         return (dateString, timeString)
 

zymoTransmitSupport/inputOutput/resultReader.py

@@ -103,9 +103,9 @@ def processDateAndTime(self, dateString: str, timeString: str, possibleDateDelim
                 break
         if not dateDelimiter:
             if len(dateString) == 8:
-                month = dateString[:2]
-                day = dateString[2:4]
-                year = dateString[4:]
+                year = dateString[:4]
+                month = dateString[4:6]
+                day = dateString[6:]
             else:
                 errorMessageLines = []
                 errorMessageLines.append("Unable to process date value")