From bbfec8187527d74233e8a80c041647022a19b44d Mon Sep 17 00:00:00 2001
From: Michael Weinstein <michael.weinstein@ucla.edu>
Date: Mon, 20 Jul 2020 16:21:32 -0700
Subject: [PATCH] Now checks for valid SNOMED code in CDPH CSV fields before
 trying anything else and uses that if present.

---
 zymoTransmitSupport/hl7Encoder/snomed.py      |  8 +++----
 .../inputOutput/caResultReader.py             | 21 +++++++++++++++++++
 zymoTransmitSupport/supportData.py            |  2 +-
 3 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/zymoTransmitSupport/hl7Encoder/snomed.py b/zymoTransmitSupport/hl7Encoder/snomed.py
index b97ae37..a44b2bb 100644
--- a/zymoTransmitSupport/hl7Encoder/snomed.py
+++ b/zymoTransmitSupport/hl7Encoder/snomed.py
@@ -39,18 +39,16 @@ def loadRawDataTable():
     dataTable = []
     for line in data:
         line = [element.strip() for element in line]
-        if len(line) == 7:
-            line.append("")
         dataTable.append(line)
     return dataTable
 
 
 def makeSnomedTable(data:list):
-    loincTable = {}
+    snomedTable = {}
     for line in data:
         code, fullName, preferredName = line
-        loincTable[code] = SNOMED(code, fullName, preferredName)
-    return loincTable
+        snomedTable[code] = SNOMED(code, fullName, preferredName)
+    return snomedTable
 
 
 def makeLookupTables(loincTable:typing.Dict[str, SNOMED]):
diff --git a/zymoTransmitSupport/inputOutput/caResultReader.py b/zymoTransmitSupport/inputOutput/caResultReader.py
index f46b3b5..210eabd 100644
--- a/zymoTransmitSupport/inputOutput/caResultReader.py
+++ b/zymoTransmitSupport/inputOutput/caResultReader.py
@@ -19,6 +19,24 @@ def makeSpecimenRegexes():
 swabRegex = re.compile("SWAB", re.IGNORECASE)
 
 
+def getSnomedList(): # Doing this to avoid circular references and because SNOMED format is not specific enough
+    inputFileDirectory = os.path.split(os.path.abspath(__file__))[0]
+    inputFileDirectory = os.path.split(inputFileDirectory)[0]
+    inputFileDirectory = os.path.split(inputFileDirectory)[0]
+    inputFile = "snomedSpecimens.txt"
+    inputPath = os.path.join(inputFileDirectory, inputFile)
+    data = open(inputPath, 'r').readlines()
+    data = [line.strip() for line in data if line and not line.startswith("#")]
+    data = [line.split("\t") for line in data if line]
+    codeTable = []
+    for line in data:
+        line = [element.strip() for element in line]
+        codeTable.append(line[0])
+    return codeTable
+
+snomedList = getSnomedList()
+
+
 class CATestResult(object):
     expectedElements = 40
 
@@ -263,6 +281,9 @@ def checkFields(regexList:list):
         bloodSNOMED = "788707000"
         swabNotOtherwiseSpecifiedSNOMED = "257261003"
         fields = [self.specimenType, self.specimenSite]
+        for field in fields:
+            if field in snomedList:
+                return field
         nasal = checkFields(nasalRegexList)
         swab = checkFields([swabRegex])
         oral = checkFields(oralRegexList)
diff --git a/zymoTransmitSupport/supportData.py b/zymoTransmitSupport/supportData.py
index 8db4a7b..49e74cb 100644
--- a/zymoTransmitSupport/supportData.py
+++ b/zymoTransmitSupport/supportData.py
@@ -1,4 +1,4 @@
 
-softwareVersion = "1.0.0"
+softwareVersion = "1.0.1"
 
 softwareDate = "20200719"
\ No newline at end of file