Re-upload pyEdc

from string import Template

import pandas as pd
from fuzzywuzzy import fuzz
from pandas import DataFrame, ExcelWriter

# pip install openpyxl
# pip install xlsxwriter
# pip install Pandas

# define global variables
folder = ''
safetyfiles = folder + "safetyfile1.xlsx"
edcfile = folder + "edc5.xlsx"
safety_df = DataFrame
edc_df = DataFrame
sheetlen = 0
query_temp = "Sponsor DM: per EDC $column is $val However, per Safety database $column is $value please clarify"
query_temp = Template(query_temp)


# configurations ***you can tweak these settings to adjust accuracy***
similarity_threshold = 40

# field Mapping Object
# TODO: complete the mappings
table = {
    "Patient_ID": {
        'edc': 2,
        'safety': 1,

    },
    "Protocol #": {
        'edc': 1,
        'safety': 3,

    },
    "SAE Term": {
        'edc': 6,
        'safety': 4,

    },
    # "Preferred Term": {
    #     'edc': 0,
    #     'safety': 0,
    #
    # },
    # "Date site became aware of event": {
    #     'edc': 0,
    #     'safety': 0,
    #
    # },
    # "Stop Date": {
    #     'edc': 0,
    #     'safety': 0,
    #
    # },
    # "Toxicity Grade": {
    #     'edc': 0,
    #     'safety': 0,
    #
    # },
    # "Event Outcome": {
    #     'edc': 0,
    #     'safety': 0,
    #
    # },
    # "Relationship to study treatment": {
    #     'edc': 0,
    #     'safety': 0,
    #
    # },
    # "Action taken with study": {
    #     'edc': 0,
    #     'safety': 0,
    #
    # },
    # "SAE criteria": {
    #     'edc': 0,
    #     'safety': 0,
    #
    # },
    # "Date of death": {
    #     'edc': 0,
    #     'safety': 0,
    #
    # },
    # "Date of Hospitalization": {
    #     'edc': 0,
    #     'safety': 0,
    #
    # },

}


# funtion definations
def main():
    global sheetlen
    data_array = []
    patient_id = edc_df = pd.read_excel(edcfile, index_col=[2])
    for k in table:
        edc_col = table[k]['edc']
        safety_col = table[k]['safety']
        # query_template = table[k]['query']
        # ------------------------------------------------------
        edc_df = pd.read_excel(edcfile, index_col=[edc_col])
        sheetlen = len(edc_df.index)
        safety_df = pd.read_excel(safetyfiles, index_col=[safety_col])
        print("**************generating .xlsx for ************")
        print(k)
        print("*****************Done!*************************")
        for row in range(sheetlen):
            res = fuzzySmiles(patient_id.index[row],
                              edc_df.index[row], safety_df.index[row], similarity_threshold, k)
            data_array.append(res)
        # write new sheet to output file
        create_or_append_xlsx("output.xlsx", k, data_array)
        data_array.clear()


# using fuzzywuzzy for similarity check
def fuzzySmiles(patient_id, str1, str2, threshold, col):
    query = ''
    val = fuzz.token_sort_ratio(str1, str2)
    str1_len = len(str(str1))
    str2_len = len(str(str2))

    r_val = False
    if val >= threshold:
        r_val = True
    else:
        r_val = False
        query = query_temp.substitute(
            {'column': col, "val": str1, "value": str2})
        if val == 0:
            l = str1_len > str2_len
            if l:
                query = query_temp.substitute(
                    {'column': col, "val": str1, "value": "Missing"})
    return [patient_id, str1, str2, r_val, val, query, ]


def create_or_append_xlsx(filepath, sheetname, data):

    df = pd.DataFrame(
        data, columns=["Patient_ID", "Edc_field", "Safety_field", "Similarity", "Score", "Query"])
    with ExcelWriter(sheetname + "_gen_.xlsx", engine="xlsxwriter", mode='w') as writer:
        df.to_excel(writer, sheet_name=sheetname)
        writer.close()


# python run as main script
if __name__ == "__main__":
    main()