# -*- coding: utf-8 -*- 

'''

input:  348k data  

    1. ClinicalTrialGov/NCTxxxx/xxxxxx.xml & all_xml    

    1. data/diseases.csv  

    2. data/drug2smiles.pkl          

output: data/raw_data.csv

processing:  

    0.1 Interventional: 273k data (348k total, e.g., observatorial, surgery, )

    0.2 intervention_type == Drug  (drug not empty)

    0.3 drop_set  96k data (273k),  (we don't use drop_set to filter out)

    0.4 -1 -> 0 based on "why_stop" 

    0.5 filter out -1(invalid)

    1. disease -> icd

    2. drug -> smiles  

    3. inclusive / exclusive criteria ---- to do 

requires ~10 minutes. 

'''

##### standard library

import os, csv, pickle   

from xml.dom import minidom

from xml.etree import ElementTree as ET

from collections import defaultdict

from time import time 

import re 

from tqdm import tqdm 

from utils import get_path_of_all_xml_file, walkData

drop_set = ['Active, not recruiting', 'Enrolling by invitation', 'No longer available',  

            'Not yet recruiting', 'Recruiting', 'Temporarily not available', 'Unknown status']

'''

14 overall_status 

     Active, not recruiting

     Approved for marketing

     Available

     Completed

     Enrolling by invitation

     No longer available

     Not yet recruiting

     Recruiting

     Suspended

     Temporarily not available

     Terminated

     Unknown status

     Withdrawn

     Withheld

'''

def root2outcome(root):

    result_list = []

    walkData(root, prefix = '', result_list = result_list) 

    filter_func = lambda x:'p_value' in x[0] 

    outcome_list = list(filter(filter_func, result_list))

    if len(outcome_list)==0:

        return None 

    outcome = outcome_list[0][1]

    if outcome[0]=='<':

        return 1

    if outcome[0]=='>':

        return 0 

    if outcome[0]=='=':

        outcome = outcome[1:]

    try:

        label = float(outcome)

        if label < 0.05:

            return 1

        else:

            return 0

    except:

        return None 

def xmlfile_2_label(xml_file):

    tree = ET.parse(xml_file)

    root = tree.getroot()

    nctid = root.find('id_info').find('nct_id').text    ### nctid: 'NCT00000102'

    label = root2outcome(root)

    label = -1 if label is None else label 

    return label