csv_to_json.py

# Script for decoding of CSV-file with medical cards of patients and recording them to json files
import sys
from mongodb import put
from mongodb import connect

apriory = [
            'not mentioned', 
            'ambiguous',
            'diagnosed', 
            'inconclusive', 
            'ruled out', 
            'symptoms present', 
            'other'
            ]

formulas = [
            'CHF', 
            'MI'
            ]

def csv_to_json(mongo):
    csv_file_name = 'cci/data/TrainingCases2016-11-16.txt' # CSV-file  
    #json_directory = 'cci/documents' # Directory for JSON-files and file dir.list with id of cards
    print('Decoding of csv file "' + csv_file_name + '".')
    for formula in formulas:
        try:
            f = open(csv_file_name,  'r')
        except IOError:
            print('File "' + csv_file_name + '" not found.')
            sys.exit()
        else:
            print('Formula: ' + formula)
            ids = [] # List of id of cards
            chf_ids = {}
            for stat in apriory:
                chf_ids[stat] = []
            for line in f:
                card = line.split('\t')
                try:
                    number_of_card = card[0]
                    ids.append(int(number_of_card))
                except ValueError:
                    continue
                else:
                    print('Card #' + number_of_card)
                    # Read every card and record to a dictionary  
                    dict = {}
                    key = ''
                    h = True
                    for field in card[2:]:
                        if field.isspace():  continue
                        if key == '':
                            key = field
                        else:
                            dict[key] = field
                            if key.find(formula) != -1:
                                h = False
                                for stat in apriory:
                                    if key.find(stat) != -1:
                                        chf_ids[stat].append(number_of_card)
                                        break
                            key = ''
                    if h:
                        print(number_of_card)
                    # Record dictionary to JSON-file
                    put("doc.json", dict, number_of_card=number_of_card,  mongo=mongo)
            # Record of id of cards
            f.close()
            ids.sort()
            #print(str(len(chf_ids))+ ' documents apriory have diagnosis CHF.')
            put('results_apriory',  chf_ids,  formula = formula,  mongo=mongo)

if __name__ == '__main__':
    mongo = connect()
    csv_to_json(mongo)
    print('OK.')