Source code for pypath.inputs.pubmed

#!/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/
#

from future.utils import iteritems
from past.builtins import xrange, range

import sys
import json
import webbrowser

import pypath.resources.urls as urls
import pypath.share.curl as curl
import pypath_common._constants as _const
import pypath.share.progress as progress
import pypath.inputs.eutils as eutils




def open_pubmed(pmid):
    """
    Opens PubMed record in web browser.

    @pmid : str or int
        PubMed ID
    """

    pmid = str(pmid)
    url = urls.urls['pubmed']['url'] % pmid
    webbrowser.open(url)





def only_pmids(idList, strict = True):
    """
    Return elements unchanged which comply with the PubMed ID format,
    and attempts to translate the DOIs and PMC IDs using NCBI
    E-utils.
    Returns list containing only PMIDs.

    @idList : list, str
        List of IDs or one single ID.
    @strict : bool
        Whether keep in the list those IDs which are not PMIDs,
        neither DOIs or PMC IDs or NIH manuscript IDs.
    """
    if type(idList) in _const.SIMPLE_TYPES:
        idList = [idList]

    pmids = {i for i in idList if isinstance(i, int) or i.isdigit()}
    pmcids = [i for i in idList if i.startswith('PMC')]
    dois = [i for i in idList if '/' in i]
    manuscids = [i for i in idList if i.startswith('NIHMS')]

    if not strict:
        pmids = set(pmids) | set(dois) | set(pmcids) | set(manuscids)

    if len(pmcids) > 0:
        pmids = pmids | set(pmids_list(pmcids))

    if len(dois) > 0:
        pmids = pmids | set(pmids_list(dois))

    return list(pmids)





def get_pmid(idList):
    """
    For a list of doi or PMC IDs
    fetches the corresponding PMIDs.
    """

    if type(idList) in _const.SIMPLE_TYPES:
        idList = [idList]

    url = urls.urls['eutils']['pmc-idconv'] % ','.join(str(i) for i in idList)
    c = curl.Curl(url, silent = True)
    data = c.result

    try:
        js = json.loads(data)

    except:
        js = {}

    return js





def pmids_dict(idList):

    jsn = get_pmid(idList)
    result = {'doi': {}, 'pmc': {}}

    if 'records' in jsn:
        for r in jsn['records']:
            if 'pmid' in r:
                if 'doi' in r:
                    result['doi'][r['pmid']] = r['doi']

                if 'pmcid' in r:
                    result['pmc'][r['pmid']] = r['pmcid']

    return result





def pmids_list(idList):

    jsn = get_pmid(idList)
    result = []

    if 'records' in jsn:
        for r in jsn['records']:
            if 'pmid' in r:
                result.append(r['pmid'])

    return result





def get_pubmeds(pmids: list[str], cache_small: int = 10) -> dict:
    """
    Metadata about PubMed records.

    Args:
        pmids:
            One or more PubMed IDs.
        cache_small:
            Small requests querying less than 10 IDs by default are not cached,
            except if this parameter is True or is set to a lower number.
    """

    return eutils.esummary(
        ids = pmids,
        db = 'pubmed',
        cache_small = cache_small,
    )