#!/usr/bin/python

"""

Utility functions.

"""

import time

import logging

import requests

import json

from config import settings

from Authentication import Authentication

# API-kEY FOR UMLS REST TICKET SERVICES

umls_api = settings['apis']['umls']

# UMLS REST SERVICES INITIALIZATION OF CLIENT AND TICKET

# GRANTING SERVICE TO BE USED IN ALL CASES

AuthClient = Authentication(umls_api)

tgt = AuthClient.gettgt()

# To supress some kind of warning?!

logging.getLogger("requests").setLevel(logging.WARNING)

logging.getLogger("urllib3").setLevel(logging.WARNING)

# logging.basicConfig(

#     format="%(asctime)s [%(threadName)-12.12s] [%(levelname)-5.5s]  %(message)s",

#     handlers=[

#         #logging.FileHandler("%s" % settings['log_path']),

#         logging.StreamHandler()

#     ])

# logging.info('lala')

# # create logger

# logger = logging.getLogger()

# formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')

# ch = logging.StreamHandler()

# ch.setFormatter(formatter)

# logger.addHandler(ch)

# fh = logging.FileHandler(settings['log_path'])

# fh.setFormatter(formatter)

# logger.addHandler(fh)

def get_umls_ticket2(tgt=tgt, AuthClient=AuthClient, apikey=umls_api):

    """

    Get a single use ticket for the UMLS REST services.

    It is supposed that an Author Client and a Ticket

    Granting Service have already been set-up in case

    the apikey = None. If an api-key is given, create the

    above needed instances and generate a new ticket.

    Input:

        - apikey: str,

        UMLS REST services api-key. Default is None and

        the already establised service is used

    Output:

        - string of the generated ticket

    """

    # Get ticket from the already establised service

    if not(tgt) and not(AuthClient):

        AuthClient = Authentication(umls_api)

        tgt = AuthClient.gettgt()

    return AuthClient.getst(tgt)

def get_umls_ticket(apikey=None, AuthClient=AuthClient, tgt=tgt):

    """

    Get a single use ticket for the UMLS REST services.

    It is supposed that an Author Client and a Ticket

    Granting Service have already been set-up in case

    the apikey = None. If an api-key is given, create the

    above needed instances and generate a new ticket.

    Input:

        - apikey: str,

        UMLS REST services api-key. Default is None and

        the already establised service is used

    Output:

        - string of the generated ticket

    """

    # Get ticket from the already establised service

    if apikey is None:

        return AuthClient.getst(tgt)

    else:

        # Establish new Client and Ticket granting service

        AuthClient = Authentication(apikey)

        tgt = AuthClient.gettgt()

        return AuthClient.getst(tgt)

def time_log(phrase, time_start=None):

    """

    A time_logger function so as to print info with time since elapsed if wanted,

    alongside with the current logging config.

    """

    # If we want to also print time_elapsed

    if time_start:

        logging.info('%s in : %.2f seconds.' % (phrase, time.time() - time_start))

    else:

        logging.info('%s' % (phrase))

    return 1

def get_concept_from_source(source_id, source, apikey=tgt):

    """

    Function that maps an entity from another source to UMLS concepts.

    Input:

        - source_id: str,

        string of the unique id from the source knowledge base

        - source: str,

        string code-name of the knowledge base, as used by the

        UMLS REST services (e.g. drugbank -> DRUGBANK, MESH->MSH)

        - apikey: str,

        UMLS REST services api-key. Default is None and

        the already establised service is used. Check get_umls_ticket

        function for details

    Output:

        - concepts: list,

        list of dictionaries representing concepts mapped to the

        source_id entity. Each dictionary has keys "label", "cuid", "sem_types"

        Check get_concept_from_cui for more details

    """

    ticket = get_umls_ticket2()

    #ticket = get_umls_ticket(apikey)

    url = "https://uts-ws.nlm.nih.gov/rest/search/current"

    passed = False

    times = 0

    while not(passed):

        params = {'string': source_id, 'sabs': source, 'searchType': 'exact',

              'inputType': 'sourceUi', 'ticket': ticket}

        r = requests.get(url, params=params)

        r.encoding = 'utf-8'

        concepts = []

        if r.ok:

            items = json.loads(r.text)

            jsonData = items["result"]

            # Get cuis related to source_id

            cuis = [res['ui']for res in jsonData['results']]

            # Get concepts from cuis

            concepts = [get_concept_from_cui(cui) for cui in cuis if cui != 'NONE']

            passed = True

        else:

            time_log(r.url)

            time_log('Error getting concept from: Source %s   | ID: %s' % (source, source_id))

            time_log('~'*25 + ' GETTING NEW TICKET SERVICE' + '~'*24)

            ticket = get_umls_ticket2(None, None, umls_api)

            times += 1

            if times >= 2:

                passed = True

                time_log('Error getting concept from: Source %s   | ID: %s' % (source, source_id))

                time_log('~'*25 + ' EXITING AFTER TRYING TWICE WITH NEW TICKET  ' + '~'*25)

                #exit(1)

                raise Exception

    return concepts

def get_concept_from_cui(cui, apikey=None):

    """

    Function that fetches a concept's attributes from the corresponding cui.

    Input:

        - cui: str,

        string of cui that will be looked up

        - apikey: str,

        UMLS REST services api-key. Default is None and

        the already establised service is used. Check get_umls_ticket

        function for details

    Output:

        - res: dictionary,

        dictionary with the concepts attributes as fetched. Specifically,

        "label", "cuid"(cui) and "sem_types"(comma delimited string of

        the semantic types us returned)

    """

    ticket = get_umls_ticket2()

    #ticket = get_umls_ticket(apikey)

    url = "https://uts-ws.nlm.nih.gov/rest/content/current/CUI/" + cui

    passed = False

    times = 0

    while not(passed):

        try:

            r = requests.get(url, params={'ticket': ticket}, timeout=120)

            passed = True

        except requests.exceptions.Timeout:

            time_log('~'*25 + ' TIMEOUT ERROR 120 SECONDS'+'~'*25)

            time_log('~'*25 + ' GETTING NEW TICKET SERVICE' + '~'*24)

            ticket = get_umls_ticket2(None, None, umls_api)

            times += 1

            if times >= 2:

                passed = True

                time_log('Error getting concept from: CUI %s' % cui)

                time_log('~'*25 + ' EXITING AFTER TRYING TWICE WITH NEW TICKET  ' + '~'*25)

                raise Exception

                #exit(1)

    r.encoding = 'utf-8'

    res = {}

    if r.ok:

        items = json.loads(r.text)

        jsonData = items["result"]

        res = {'label': jsonData['name'], 'cuid': cui}

        sem_types = []

        # For each semantic type of the entity

        for stys in jsonData["semanticTypes"]:

            # Keep only the TUI code from the uri e.g.

            # https://uts-ws.nlm.nih.gov/rest/semantic-network/current/TUI/T116

            code_tui = stys['uri'].split('/')[-1]

            # Fetch the abbreviation of this TUI code

            sem_types.append(get_sem_type_abbr(code_tui))

        # Comma separated string

        sem_types = ",".join(sem_types)

        res['sem_types'] = sem_types

    else:

        time_log(r.url)

        time_log('Error getting concept from cui : %s' % cui)

        raise ValueError

    return res

def get_sem_type_abbr(code_tui, apikey=None):

    """

    Function that fetches a semantic-type's abbreviation.

    Input:

        - code_tui: str,

        string of TUI code that will be looked up

        - apikey: str,

        UMLS REST services api-key. Default is None and

        the already establised service is used. Check get_umls_ticket

        function for details

    Output:

        string, abbreviation of the code (e.g. "gngm")

    """

    ticket = get_umls_ticket2()

    #ticket = get_umls_ticket(apikey)

    url = "https://uts-ws.nlm.nih.gov/rest/semantic-network/current/TUI/" + code_tui

    passed = False

    times = 0

    while not(passed):

        try:

            r = requests.get(url, params={'ticket': ticket}, timeout=120)

            passed = True

        except requests.exceptions.Timeout:

            time_log('~'*25 + ' TIMEOUT ERROR 120 SECONDS'+'~'*25)

            time_log('~'*25 + ' GETTING NEW TICKET SERVICE' + '~'*24)

            ticket = get_umls_ticket2(None, None, umls_api)

        times += 1

        if times >= 2:

            passed = True

            time_log('Error getting semantic type abbreviation: %s' % code_tui)

            time_log('~'*25 + ' EXITING AFTER TRYING TWICE WITH NEW TICKET  ' + '~'*25)

            raise Exception

            #exit(1)

    r.encoding = 'utf-8'

    res = ' '

    if r.ok:

        items = json.loads(r.text)

        jsonData = items["result"]

        res = jsonData['abbreviation']

    else:

        time_log(r.url)

        time_log('Error getting sem-type from TUI : %s' % code_tui)

        raise ValueError

    return res