Source code for pypath.inputs.biomodels

#!/usr/bin/env python
# -*- coding: utf-8 -*-

#
#  This file is part of the `pypath` python module
#
#  Copyright 2014-2023
#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University
#
#  Authors: see the file `README.rst`
#  Contact: Dénes Türei (turei.denes@gmail.com)
#
#  Distributed under the GPLv3 License.
#  See accompanying file LICENSE.txt or copy at
#      https://www.gnu.org/licenses/gpl-3.0.html
#
#  Website: https://pypath.omnipathdb.org/
#

"""
This file collects all available models from the biomodels repository
using the bioservices python module, then downloads the individual
models to parse for the relevant information to enter into pypath.
"""

import time
import json

import pycurl
import requests

import pypath.resources.urls as urls
import pypath.share.curl as curl
import pypath.share.settings as settings
import pypath.share.session as session

_logger = session.Logger(name = 'biomodels_input')
_log = _logger._log

try:

    import bioservices.biomodels as biom

except ModuleNotFoundError:

    _log(
        'Module `bioservices` not available. '
        'Install it by: pip install bioservices'
    )



[docs]
def get_single_model(model_id):
    """
    Get single BioModel using bioservices.
    
    Args
        model_id (str): ID of model

    Returns
        dict: dictionary containing model specifics, eg name/id,
        description, associated files
    """
    bm = biom.BioModels()
    model = bm.get_model(model_id)

    return model



[docs]
def get_all_models():
    """
    Fetch list of available models using bioservices.

    Returns 
        dict: A dictionary of models with model identifiers as keys and
        model attributes as values. Model attributes include format
        (SMBL being most common), model id, name,
        submission/modification date and author.
    """

    bm = biom.BioModels()
    # CAUTION: Below function has a bug causing an infinite loop (Mar22)
    models = bm.get_all_models()

    return models



[docs]
def download_single_model(model_id):
    """
    Download the main file of a single model to extract relevant data 
    for pypath integration. Downloaded models should be cached.
    """



def _get_biomodels():

    def init_fun(resp_hdr):

        return ['Cookie: access-token=%s' % resp_hdr['token']]


    t = int(time.time() * 1000) - 3600000

    loginurl = urls.urls['biomodels']['login'] % t

    hdrs = [
        'Host: www.intomics.com',
        'X-Requested-With: XMLHttpRequest',
        settings.get('user_agent'),
        'Accept-Language: en-US,en;q=0.5',
        'DNT: 1',
        'Connection: keep-alive',
        'Referer: https://www.intomics.com/inbio/map/',
        'Accept: */*'
    ]

    c0 = curl.Curl(loginurl, silent = False, large = False,
                   cache = False, req_headers = hdrs)

    hdrs = hdrs[:-2]

    hdrs.extend([
        'Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8',
        'Upgrade-Insecure-Requests: 1',
        'Accept-Encoding: gzip'
    ])

    # 'Host: www.intomics.com' -H 'User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:52.0) Gecko/20100101 Firefox/52.0' -H 'Accept: text/html,application/xhtml+xml,application/xml;q = 0.9,*/*;q = 0.8' -H 'Accept-Language: en-US,en;q = 0.5' --compressed -H 'Cookie: access_token = '"$token" -H 'DNT: 1' -H 'Connection: keep-alive' -H 'Upgrade-Insecure-Requests: 1'

    hdrs.append('Cookie: access-token=%s' % json.loads(c0.result)['token'])

    url = urls.urls['biomodels']['url']

    time.sleep(1)

    c2 = curl.Curl(
        url,
        silent = False,
        large = True,
        req_headers = hdrs,
        cache = False,
        compressed = True,
    )

    return c0, c2



[docs]
def get_biomodels(verbose = 0):

    t = int(time.time() * 1000) - 3600000

    url   = 'https://www.intomics.com/inbio/map/api/'\
            'get_data?file=InBio_Map_core_2016_09_12.tar.gz'
    login = 'https://www.intomics.com/inbio/api/login_guest?ref=&_= %u' % t

    fp_login = open('biomodels.login.tmp', 'wb')
    fp_biomodels = open('biomodels.tmp.tar.gz', 'wb')

    c0 = pycurl.Curl()
    c0.setopt(pycurl.URL, login)
    c0.setopt(pycurl.WRITEFUNCTION, fp_login.write)

    c0.perform()

    fp_login.close()

    with open('biomodels.login.tmp', 'r') as fp:

        token = json.loads(fp.read())['token']

    _log('Token: %s' % token)

    hdrs = ['Cookie: access-token=%s' % token]

    c1 = pycurl.Curl()
    c1.setopt(pycurl.URL, url)
    c1.setopt(pycurl.WRITEFUNCTION, fp_biomodels.write)
    c1.setopt(pycurl.HTTPHEADER, [h.encode('ascii') for h in hdrs])
    c1.setopt(pycurl.VERBOSE, 1)
    c1.setopt(pycurl.DEBUGFUNCTION, print)

    c1.perform()

    fp_biomodels.close()




[docs]
def get_biomodels_req():

    t = int(time.time() * 1000) - 3600000

    url   = 'https://www.intomics.com/inbio/map/api/'\
            'get_data?file=InBio_Map_core_2016_09_12.tar.gz'
    login = 'https://www.intomics.com/inbio/api/login_guest?ref=&_=%u' % t

    r0 = requests.get(login)
    token = json.loads(r0.text)['token']
    hdrs = {'Cookie': 'access-token=%s' % token}

    with open('biomodels.tmp.tar.gz', 'wb') as fp:

        r1 = requests.get(url, headers = hdrs, stream = True)

        for block in r1.iter_content(4096):

            fp.write(block)