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fileImport.py
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fileImport.py
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import csv
import globals as g
import pandas as pd
import DBModule as db
if g.mode == "I":
import constants as con
else:
import constantsMed as con
import os
class fileClass:
def __init__(self):
self.filePath = "input/"
self.inputFileName = ""
def __numIn(self, s):
return any(i.isdigit() for i in s)
def setPath(self, path):
self.filePath = path
def openInput(self, inputFileName):
with open(self.filePath + inputFileName, 'r') as file:
fileData = file.read()
fileData = fileData.replace('"', '')
with open('scratch/cleaned.csv', 'w') as file:
file.write(fileData)
file.close()
def parseForMed(self, issue, fileName):
with open('scratch/' + fileName, 'r') as csvfile:
# creating a csv reader object
csvreader = csv.reader(csvfile)
with open('scratch/parsed1.csv', "w", newline='') as result:
writer = csv.writer(result)
for row in csvreader:
if "PALMETTO" not in row[1]:
writer.writerow(row)
result.close()
def parseForBlankIns(self, issue, fileName):
with open('scratch/parsed1.csv', 'r') as csvfile:
# creating a csv reader object
csvreader = csv.reader(csvfile)
with open('scratch/parsed2.csv', "w", newline='') as result:
writer = csv.writer(result)
for row in csvreader:
if len(row[1]) == 0:
row[1] = "Insurance Info Missing"
writer.writerow(row)
result.close()
def parseForBadSubID(self, issue, fileName):
with open('scratch/parsed2.csv', 'r') as csvfile:
# creating a csv reader object
csvreader = csv.reader(csvfile)
with open('scratch/parsed3.csv', "w", newline='') as result:
writer = csv.writer(result)
for row in csvreader:
if self.__numIn(row[15]) == True:
writer.writerow(row)
result.close()
def parseForBadAddress(self, issue, fileName):
with open('scratch/parsed3.csv', 'r') as csvfile:
# creating a csv reader object
csvreader = csv.reader(csvfile)
with open('scratch/parsed4.csv', "w", newline='') as result:
writer = csv.writer(result)
for row in csvreader:
if "SUITE" in row[con.SUITE_FIX_1]:
row[con.SUITE_FIX_1 - 1] = row[con.SUITE_FIX_1 - 1] + row[con.SUITE_FIX_1]
del row[con.SUITE_FIX_1]
writer.writerow(row)
result.close()
def parseForRan(self, _accession):
database = db.database_class()
with open('scratch/parsed4.csv', 'r') as csvfile:
# creating a csv reader object
csvreader = csv.reader(csvfile)
with open('scratch/addressFixed.csv', "w", newline='') as result:
writer = csv.writer(result)
for row in csvreader:
if database.didRun(row[con.ACCESSION_NUMBER]) == False:
writer.writerow(row)
else:
print("Accession " + row[con.ACCESSION_NUMBER] + " Ran")
def fixAddress(self, fileName):
with open('scratch/' + fileName, 'r') as csvfile:
# creating a csv reader object
csvreader = csv.reader(csvfile)
with open('scratch/addressFixed.csv', "w", newline='') as result:
writer = csv.writer(result)
for row in csvreader:
if self.__numIn(row[con.NUM_FIX_1]) == True:
row[con.NUM_FIX_1 - 1] = row[con.NUM_FIX_1 - 1] + row[con.NUM_FIX_1]
del row[con.NUM_FIX_1]
if self.__numIn(row[con.NUM_FIX_2]) == True:
row[con.NUM_FIX_2 - 1] = row[con.NUM_FIX_2 - 1] + row[con.NUM_FIX_2]
del row[con.NUM_FIX_2]
if self.__numIn(row[con.NUM_FIX_3]) == True:
row[con.NUM_FIX_3 - 1] = row[con.NUM_FIX_3 - 1] + row[con.NUM_FIX_3]
del row[con.NUM_FIX_3]
if "SUITE" in row[con.SUITE_FIX_1]:
row[con.SUITE_FIX_1 - 1] = row[con.SUITE_FIX_1 - 1] + row[con.SUITE_FIX_1]
del row[con.SUITE_FIX_1]
if "SUITE" in row[con.SUITE_FIX_2]:
row[con.SUITE_FIX_2 - 1] = row[con.SUITE_FIX_2 - 1] + row[con.SUITE_FIX_2]
del row[con.SUITE_FIX_2]
if "MD" in row[con.MD_FIX]:
del row[con.MD_FIX]
if "MD" in row[con.MD_FIX2]:
del row[con.MD_FIX2]
writer.writerow(row)
result.close()
def get(self):
try:
self.dataset = pd.read_csv("scratch/addressFixed.csv", header=None)
return (self.dataset)
except:
print("There is no Accessions number to run")
exit(10)