# -*- coding: utf-8 -*-
"""Utilities to merge multiple BEL documents on the same topic"""
import logging
from xml.etree import ElementTree
import requests
from pybel.resources.constants import *
from pybel.resources.document import make_knowledge_header
from pybel_tools.constants import abstract_url_fmt, title_url_fmt
__all__ = [
'write_boilerplate',
]
log = logging.getLogger(__name__)
def make_pubmed_abstract_group(pmids):
"""Builds a skeleton for the citations' statements
:param pmids: A list of PubMed identifiers
:type pmids: iter[str] or iter[int]
:return: An iterator over the lines of the citation section
:rtype: iter[str]
"""
for pmid in set(pmids):
yield ''
res = requests.get(title_url_fmt.format(pmid))
title = res.content.decode('utf-8').strip()
yield citation_format.format(title, pmid)
res = requests.get(abstract_url_fmt.format(pmid))
abstract = res.content.decode('utf-8').strip()
yield evidence_format.format(abstract)
yield '\nUNSET Evidence\nUNSET Citation'
def _sanitize(s):
if s is None:
return None
return s.strip().replace('\n', '')
#: Allows for querying the Entrez Gene Summary utility by formatting with an entrez id or list of comma seperated ids
PUBMED_GENE_QUERY_URL = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={}'
def get_entrez_gene_data(entrez_ids):
"""Gets gene info from Entrez"""
url = PUBMED_GENE_QUERY_URL.format(','.join(str(x).strip() for x in entrez_ids))
response = requests.get(url)
tree = ElementTree.fromstring(response.content)
return {
element.attrib['uid']: {
'summary': _sanitize(element.find('Summary').text),
'description': element.find('Description').text
}
for element in tree.findall('./DocumentSummarySet/DocumentSummary')
}
def make_pubmed_gene_group(entrez_ids):
"""Builds a skeleton for gene summaries
:param list[str] entrez_ids: A list of entrez id's to query the pubmed service
:return: An iterator over statement lines for NCBI entrez gene summaries
:rtype: iter[str]
"""
url = PUBMED_GENE_QUERY_URL.format(','.join(str(x).strip() for x in entrez_ids))
response = requests.get(url)
tree = ElementTree.fromstring(response.content)
for x in tree.findall('./DocumentSummarySet/DocumentSummary'):
yield '\n# {}'.format(x.find('Description').text)
yield 'SET Citation = {{"Other", "PubMed Gene", "{}"}}'.format(x.attrib['uid'])
yield 'SET Evidence = "{}"'.format(x.find('Summary').text.strip().replace('\n', ''))
yield '\nUNSET Evidence\nUNSET Citation'
[docs]def write_boilerplate(name, version=None, description=None, authors=None, contact=None, copyright=None, licenses=None,
disclaimer=None, namespace_url=None, namespace_patterns=None, annotation_url=None,
annotation_patterns=None, annotation_list=None, pmids=None, entrez_ids=None, file=None):
"""Writes a boilerplate BEL document, with standard document metadata, definitions.
:param str name: The unique name for this BEL document
:param str contact: The email address of the maintainer
:param str description: A description of the contents of this document
:param str authors: The authors of this document
:param str version: The version. Defaults to current date in format ``YYYYMMDD``.
:param str copyright: Copyright information about this document
:param str licenses: The license applied to this document
:param str disclaimer: The disclaimer for this document
:param dict[str,str] namespace_url: an optional dictionary of {str name: str URL} of namespaces
:param dict[str,str] namespace_patterns: An optional dictionary of {str name: str regex} namespaces
:param dict[str,str] annotation_url: An optional dictionary of {str name: str URL} of annotations
:param dict[str,str] annotation_patterns: An optional dictionary of {str name: str regex} of regex annotations
:param dict[str,set[str]] annotation_list: An optional dictionary of {str name: set of names} of list annotations
:param iter[str] or iter[int] pmids: A list of PubMed identifiers to auto-populate with citation and abstract
:param iter[str] or iter[int] entrez_ids: A list of Entrez identifiers to autopopulate the gene summary as evidence
:param file file: A writable file or file-like. If None, defaults to :data:`sys.stdout`
"""
lines = make_knowledge_header(
name=name,
version=version or '1.0.0',
description=description,
authors=authors,
contact=contact,
copyright=copyright,
licenses=licenses,
disclaimer=disclaimer,
namespace_url=namespace_url,
namespace_patterns=namespace_patterns,
annotation_url=annotation_url,
annotation_patterns=annotation_patterns,
annotation_list=annotation_list,
)
for line in lines:
print(line, file=file)
if pmids is not None:
for line in make_pubmed_abstract_group(pmids):
print(line, file=file)
if entrez_ids is not None:
for line in make_pubmed_gene_group(entrez_ids):
print(line, file=file)