import csv

import json

import os 

path1 = '/PHShome/ju601/crt/data/patients_10_2015/'

path2 = '/PHShome/ju601/crt/data/added_patients_4_2016/'

file_template1 = 'cl491_092315161707361168_'

file_template2 = 'cl491_04071618244390383_'

out_path = '/PHShome/ju601/crt/data/json/'

procedure_file = '/PHShome/ju601/crt/data/procedure_dates_updated.csv'

def get_docs_empi_map(doc_type, path, file_template):

    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]')

    # Get structured data fields from each report

    doc0_split = doc_array[0].split('\r\n')

    keys = doc0_split[0].split('|')

    doc_array[0] = '\r\n'.join(doc0_split[1:])

    doc_map = {}

    for doc_text in doc_array:

        doc = {}

        structured = doc_text.split('\r\n')[1].split('|')

        for (i, val) in enumerate(structured):

            doc[keys[i]] = val

        doc['free_text'] = doc_text

        empi = structured[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, path, file_template):

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

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

        doc_text = f.read()

        doc_array = doc_text.split('\r\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(dem_file, patients = {}):

    # Get demographic text

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

        dem_text = f.read()

        dem_array = dem_text.split('\r\n')

    # Build dictionary

    key_arr = dem_array[0].split('|')

    for row in dem_array[1:]:

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

        if len(cols) == len(key_arr):

            patient = {}

            for (i, col) in enumerate(cols):

                try:

                    if i == 2:

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

                    else:

                        patient[key_arr[i]] = col

                except:

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

                    print row

            if patient['EMPI'] in patients:

                print "DEMFILE- Duplicate patient: " + patient['EMPI']

            else:

                patients[patient['EMPI']] = patient

    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(proc_file, patients):

    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['MRN']

            if mrn != '':

                try:

                    empi = mrn_to_empi[mrn]

                    patient = patients[empi]

                    proc = {}

                    proc['Implant Status'] = row['ImplantDate']

                    proc['1 Mo. Appt'] = ''

                    proc['3 Mo. Appt'] = ''

                    patient['Procedure'] = proc

                except KeyError:

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

    write_null_if_empty(patients, 'Procedure')

def add_reports(patients, report_types, is_structured, paths):

    if is_structured:

        report_id_key = 'Encounter_number'

    else:

        report_id_key = 'Report_Number'

    for report_type in report_types:

        patients_no_report = set(patients.keys())

        for (path, file_template) in paths:

            if is_structured:

                report_map = get_struct_empi_map(report_type, path, file_template)

            else:

                report_map = get_docs_empi_map(report_type, path, file_template)

            for patient in patients.keys():

                # Patient does not have any of these reports yet

                if report_type not in patients[patient]:

                    if patient in report_map and report_map[patient] != []:

                        patients[patient][report_type] = report_map[patient]

                        patients_no_report.remove(patient)

                # Patient already has some of these reports:

                else:

                    if patient in report_map:

                        for report in report_map[patient]:

                            # Only add unique reports

                            if report not in patients[patient][report_type]:

                                patients[patient][report_type].append(report)

        for patient in patients_no_report:

            patients[patient][report_type] = []

        print "Patients without report: " + report_type

        print patients_no_report

def write_null_if_empty(patients, key):

    for empi in patients.keys():

        if key not in patients[empi]:

            patients[empi][key] = None

            print "No " + key + " for patient: " + str(empi)

if __name__ == "__main__":

    paths = [(path1, file_template1), (path2, file_template2)]

    # Do the conversion!

    patients = get_patient_dem_info(path1 + file_template1 + 'Dem.txt')

    patients = get_patient_dem_info(path2 + file_template2 + 'Dem.txt', patients)

    parse_procedure_date_file(procedure_file, patients)

    # All unstructured report types:

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

    # Only include the ones you anticipate using in the following array:

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

    report_types = ['Car', 'Dis', 'Lno', 'Rad']

    add_reports(patients, report_types, False, paths)

    # All structured report types:

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

    # Only include the ones you anticipate using in the following array:

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

    struct_reports = ['Dia', 'Enc', 'Lab', 'Med']

    add_reports(patients, struct_reports, True, paths)

    # Final write of info

    if not os.path.exists(out_path):

        os.makedirs(out_path)

    for key in patients.keys():

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

            json.dump(patients[key], f)