import csv

import json

import os 

import re

path = '/home/josh/code/healthanon/CRT MGH 950 cohort/'

file_template = 'cl491_092315161707361168_'

def anonymize_doc(patient, doc):

    replacements = []

    replacements.append((patient['First_Name'], 'First_Name'))

    replacements.append((patient['Last_Name'], 'Last_Name'))

    replacements.append((patient['Last_Name'], 'Last_Name'))

    replacements.append((patient['EMPI'], patient['NEW_EMPI']))

    for mrn in patient['MRNS']:

        replacements.append((mrn, 'MRN'))

    for (regex, sub) in replacements:

        pattern = re.compile(regex, re.IGNORECASE)

        doc = re.sub(pattern, sub, doc)

    return doc

def get_docs_empi_map(doc_type):

    doc_file = path + file_template + doc_type + '.txt'

    with open(doc_file, 'r') as f:

        doc_text = f.read()

        doc_array = doc_text.split('[report_end]')

    doc_map = {}

    for doc in doc_array:

        empi = doc.split('\n')[1].split('|')[0]

        if empi not in doc_map:

            doc_map[empi] = []

        doc_map[empi].append(doc)

    return doc_map

def get_struct_empi_map(doc_type):

    doc_file = path + file_template + doc_type + '.txt'

    with open(doc_file, 'r') as f:

        doc_text = f.read()

        doc_array = doc_text.split('\n')

    doc_map = {}

    keys = doc_array[0].split('|')

    for row in doc_array[1:]:

        cols = row.split('|')

        empi = cols[0]

        record = {}

        try:

            for i in range(3, len(keys)):

                key = keys[i]

                record[key] = cols[i]

        except:

            print 'Error for type:' + doc_type + ' column:' + str(i) + ' row:' + row

        if empi not in doc_map:

            doc_map[empi] = []

        doc_map[empi].append(record)

    return doc_map

def get_patient_dem_info():

    # Get demographic text

    dem_file = path + file_template + 'Dem.txt'

    with open(dem_file, 'r') as f:

        dem_text = f.read()

        dem_array = dem_text.split('\n')

    # Get contact text

    contact_file = path + file_template + 'Con.txt'

    with open(contact_file, 'r') as f:

        contact_text = f.read()

        contact_array = contact_text.split('\n')

    # Build dictionary

    patients = {}

    for (i, row) in enumerate(contact_array[1:]):

        cols = row.strip().split('|')

        patient = {}

        try:

            patient['NEW_EMPI'] = 'FAKE_EMPI_' + str(i)

            patient['EMPI'] = cols[0].strip()

            patient['MRNS'] = map(lambda x: x.strip(), cols[2].strip().split(','))

            patient['Last_Name'] = cols[3].strip()

            patient['First_Name'] = cols[4].strip()

            patient['Middle_Name'] = cols[5].strip()

            # store in dict

            patients[patient['EMPI']] = patient

        except:

            print('Error in contact dict build for row:')

            print row

    for row in dem_array[1:]:

        cols = row.strip().split('|')

        try:

            empi = cols[0].strip()

            patient = patients[empi]

            patient['Vital_status'] = cols[13].strip()

            patient['Date_Of_Death'] = cols[14].strip()

        except:

            print('Error in dem build for row:')

            print row

    return patients

def get_mrn_to_empi(patients):

    mrn_empi = {}

    for empi in patients.keys():

        patient = patients[empi]

        for mrn in patient['MRNS']:

            mrn_empi[mrn] = empi

    return mrn_empi

def parse_procedure_date_file(patients):

    proc_file = path + 'additional data/PATIENT_LIST_with_appointment_dates.csv'

    mrn_to_empi = get_mrn_to_empi(patients)

    patients_procs = {}

    with open(proc_file, 'r') as f:

        reader = csv.DictReader(f)

        for row in reader:

            mrn = row['MR#'].strip().replace('-','')

            if mrn != '':

                try:

                    empi = mrn_to_empi[mrn]

                    patient = patients[empi]

                    del row['Name']

                    del row['MR#']

                    patients[empi]['Procedure'] = row

                except KeyError:

                    print "Error parsing procedure date for MRN:" + mrn

    write_null_if_empty(patients, 'Procedure')

def write_null_if_empty(patients, key):

    for empi in patients.keys():

        if key not in patients[empi]:

            patients[empi][key] = None

def parse_response_file(patients):

    resp_file = path + 'additional data/9 24 14 CRT Database for Charlotta.csv'

    mrn_to_empi = get_mrn_to_empi(patients)

    patients_procs = {}

    with open(resp_file, 'r') as f:

        reader = csv.DictReader(f)

        for row in reader:

            mrn = row['Patient_ID'].strip()

            if mrn != '':

                try:

                    empi = mrn_to_empi[mrn]

                    patient = patients[empi]

                    del row['First_Name']

                    del row['Last_Name']

                    del row['Patient_ID']

                    del row['DOB']

                    patients[empi]['Supplemental'] = row

                except KeyError:

                    print "Error parsing supplemental data for MRN:" + mrn

    write_null_if_empty(patients, 'Supplemental')

if __name__ == "__main__":

    # Do the anonymization!

    patients = get_patient_dem_info()

    parse_procedure_date_file(patients)

    parse_response_file(patients)

    report_types = ['Car', 'Dis', 'End', 'Lno', 'Mic', 'Opn', 'Pat', 'Pul', 'Rad']

    for report_type in report_types:

        report_map = get_docs_empi_map(report_type)

        for key in patients.keys():

            try:

                docs = report_map[key]

                for doc in docs:

                    if report_type not in patients[key]:

                        patients[key][report_type] = []

                    patients[key][report_type].append(anonymize_doc(patients[key], doc))

            except:

                patients[key][report_type] = []

                print('Patient with empi:' + key + ' doesnt have report for report_type:' + report_type)

    struct_reports = ['Dia', 'Enc', 'Lab', 'Lhm', 'Lme', 'Lpr', 'Lvs', 'Med', 'Phy', 'Prc', 'Prv', 'Rdt', 'Rnd', 'Trn']

    for report_type in struct_reports:

        report_map = get_struct_empi_map(report_type)

        for key in patients.keys():

            try:

                patients[key][report_type] = report_map[key]

            except:

                patients[key][report_type] = []

                print('Patient with empi:' + key + ' doesnt have report for report_type:' + report_type)

    # Final delete of info

    anon_patients = {}

    old_mapping = {}

    for key in patients.keys():

        patient = patients[key]

        old_mapping[patient['EMPI']] = patient['NEW_EMPI']

        del patient['EMPI']

        del patient['MRNS']

        del patient['Last_Name']

        del patient['First_Name']

        del patient['Middle_Name']

        anon_patients[patient['NEW_EMPI']] = patient

    out_path = '/home/josh/code/healthanon/data/'

    if not os.path.exists(out_path):

        os.makedirs(out_path)

    with open(out_path + 'mapping.csv', 'w') as f:

        for key in old_mapping.keys():

            f.write(key + ',' + old_mapping[key] + '\n')

    for key in anon_patients.keys():

        with open(out_path + key + '.json','w') as f:

            json.dump(anon_patients[key], f)