Merge pull request #3

Security improvement and data update

templateSubmission.csv

@@ -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,Accession ID,Test Ordered Date,Test Ordered Time,Test Equipment Code,Test Equipment Description,Test Equipment ID Number,Provider NPI
-#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,6/8/2020,0:00,qPCR,Zymo Research Quick SARS-CoV-2 rRT-PCR Kit,R3011,
+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,6/8/2020,0:00,qPCR,Zymo Research Quick SARS-CoV-2 rRT-PCR Kit,R3011,

zymoTransmitSupport/config.py

@@ -56,6 +56,7 @@ class LabInfo:
     phone = configDict.setdefault("lab phone", "")
     email = configDict.setdefault("lab email", "")
     street = configDict.setdefault("lab street", "")
+    suite = configDict.setdefault("lab suite", "")
     city = configDict.setdefault("lab city", "")
     state = configDict.setdefault("lab state", "")
     zip = configDict.setdefault("lab zip", "")

zymoTransmitSupport/configClean.txt

@@ -12,6 +12,7 @@ Lab Name:
 Lab Phone:
 Lab Email:
 Lab Street:
+Lab Suite:
 Lab City:
 Lab State:
 Lab Zip:

zymoTransmitSupport/hl7Encoder/encoders.py

@@ -125,7 +125,8 @@ def makeORCLine(result:inputOutput.resultReader.TestResult):
             config.LabInfo.street,
             config.LabInfo.city,
             config.LabInfo.state,
-            config.LabInfo.zip
+            config.LabInfo.zip,
+            otherDesignation=config.LabInfo.suite
         )
     if "labPhone" in result.auxiliaryData:
         orderingFacilityPhone = orderHeader.OrderingFacilityPhone(result.auxiliaryData["labPhone"])
@@ -303,7 +304,8 @@ def makeObservationValueAndAbnormalityObjects(resultString:str):
             config.LabInfo.street,
             config.LabInfo.city,
             config.LabInfo.state,
-            config.LabInfo.zip
+            config.LabInfo.zip,
+            otherDesignation=config.LabInfo.suite
         )
     if config.LabDirectorInfo.assigningAuthority:
         medicalDirectorAssignmentAuthority = observedResults.MedicalDirectorNumberAssignmentAuthority(

zymoTransmitSupport/hl7Encoder/generics.py

@@ -252,9 +252,9 @@ class Address(Hl7Field):
 
     defaultAddressType = "H"
 
-    def __init__(self, streetAddress:str, city:str, state:str, zip:str, country:str="USA", addressType:str=None):
+    def __init__(self, streetAddress:str, city:str, state:str, zip:str, country:str="USA", addressType:str=None, otherDesignation:str=""):
         self.streetAddress = streetAddress
-        self.otherDesignation = ""
+        self.otherDesignation = otherDesignation
         self.city = city
         self.state = state
         self.zip = correctLostLeadingZeroZipcode(zip, state)

zymoTransmitSupport/hl7Encoder/observedResults.py

@@ -67,13 +67,13 @@ def getAbnormalityObject(result:str):
     if not result in validResults:
         raise ValueError("Result type must be in: " %validResults)
     if result == "detected":
-        return generics.SystemCode(code="260373001", text="Detected", coding="SNOMED", codingSystemDateOrVersion="2.7")
+        return generics.SystemCode(code="A", text="Abnormal", coding="HL70078", codingSystemDateOrVersion="2.7")
     elif result == "indeterminate":
-        return generics.SystemCode(code="419984006", text="Inconclusive", coding="SNOMED", codingSystemDateOrVersion="2.7")
+        return generics.SystemCode(code="A", text="Abnormal", coding="HL70078", codingSystemDateOrVersion="2.7")
     elif result == "negative":
-        return generics.SystemCode(code="260415000", text="Not detected", coding="SNOMED", codingSystemDateOrVersion="2.7")
+        return generics.SystemCode(code="N", text="Normal", coding="HL70078", codingSystemDateOrVersion="2.7")
     elif result == "unsatisfactory":
-        return generics.SystemCode(code="125154007", text="Specimen unsatisfactory", coding="SNOMED", codingSystemDateOrVersion="2.7")
+        return generics.SystemCode(code="A", text="Abnormal", coding="HL70078", codingSystemDateOrVersion="2.7")
     elif result == "":
         return ""
     else:

zymoTransmitSupport/inputOutput/connection.py

@@ -1,10 +1,30 @@
 import requests
 import os
 import zeep
+import ssl
+import requests.adapters
+import requests.packages.urllib3
+
+strongSSLCipherSuiteEnforcement = True
+permittedCipherSuites = 'ECDHE-RSA-AES256-GCM-SHA384:ECDHE-RSA-AES256-GCM-SHA256:ECDHE-RSA-AES128-GCM-SHA384:ECDHE-RSA-AES128-GCM-SHA256'
+defaultSSLRules = (ssl.OP_NO_SSLv2 | ssl.OP_NO_SSLv3 | ssl.OP_NO_TLSv1 | ssl.OP_NO_TLSv1_1)
+
+
+class TLSEnforcer(requests.adapters.HTTPAdapter):
+    def __init__(self, sslRules=defaultSSLRules, **kwargs):
+        self.sslRules = sslRules
+        super(TLSEnforcer, self).__init__(**kwargs)
+
+    def init_poolmanager(self, *pool_args, **pool_kwargs):
+        sslSettings = requests.packages.urllib3.util.ssl_.create_urllib3_context(ciphers=permittedCipherSuites, cert_reqs=ssl.CERT_REQUIRED, options=self.sslRules)
+        self.poolmanager = requests.packages.urllib3.poolmanager.PoolManager(*pool_args, ssl_context=sslSettings, **pool_kwargs)
+
 
 
 def getSOAPClient(wsdlURL:str, clientCertificatePath:str=None, dumpClientInfo:bool=False, testOnly:bool=False):
     session = requests.Session()
+    if strongSSLCipherSuiteEnforcement:
+        session.mount("https://", adapter=TLSEnforcer())
     if clientCertificatePath:
         if not os.path.isfile(clientCertificatePath):
             raise FileNotFoundError("Unable to find client certificate path at %s" %clientCertificatePath)

zymoTransmitSupport/supportData.py

@@ -1,4 +1,4 @@
 
-softwareVersion = "1.3.0"
+softwareVersion = "1.4.0"
 
-softwareDate = "20200805"
+softwareDate = "20201201"