def pmcid_article(ref, user=None):
article_array = []
fetch = PubMedFetcher()
for pmcid in Reference.pmcid(ref):
article = fetch.article_by_pmcid(pmcid)
article_array.append(article)
return article
def pmcid_article(ref, user=None):
article_array = []
fetch = PubMedFetcher()
for pmcid in Reference.pmcid(ref):
article = fetch.article_by_pmcid(pmcid)
article_array.append(article)
return article
def processPMID(self, description, document, text):
"""XXX"""
pmid = re.compile('PMID *(\d+)')
list_pmid = pmid.findall(description)
description = re.sub(r'\[PMID *\d+\]', '', description)
pmcid = re.compile('PMCID *(\d+)')
list_pmcid = pmcid.findall(description)
description = re.sub(r'\[PMCID *\d+\]', '', description)
para = description.split(ur'\n')
for para_str in para:
#print para_str
p = document.add_paragraph(' ')
p.add_run(para_str)
std_str = u"我们通过检测您的基因位点，使用PUBMED等国际公认参考系统，我们认为" + text + u"。"
p = document.add_paragraph(' ')
p.add_run(std_str)
fetch = PubMedFetcher()
for pmid in list_pmid:
# http://www.ncbi.nlm.nih.gov/pubmed/26471457
pm = fetch.article_by_pmid(pmid)
title = pm.title
title = re.sub('\.', '', title)
citation = '. '.join([title, pm.journal])
p = document.add_paragraph()
p.add_run(citation).italic = True
for pmcid in list_pmcid:
pm = fetch.article_by_pmcid(pmcid)
title = pm.title
title = re.sub('\.', '', title)
citation = '. '.join([title, pm.journal])
p = document.add_paragraph()
p.add_run(citation).italic = True
def fetch_pubmed(pub_id, id_type = "pmid"):
"""
Fetches and formats pub data from
pubmed
"""
pm = PubMedFetcher()
if id_type == 'doi':
try:
result = pm.article_by_doi(pub_id)
except (AttributeError, MetaPubError, EutilsNCBIError):
return None
elif id_type == "pmid":
try:
result = pm.article_by_pmid(pub_id)
except (AttributeError, InvalidPMID, EutilsNCBIError):
return None
elif id_type == "pmc":
try:
result = pm.article_by_pmcid('PMC' + str(pub_id))
except (AttributeError, MetaPubError, EutilsNCBIError):
return None
result = result.to_dict()
# Set link using DOI
if result.get('doi'):
result['url'] = "http://dx.doi.org/" + result.get('doi')
else:
result['url'] = result.get('url')
# Provide PDF if possible
if result.get('pmc'):
result['pdf_url'] = f"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC{result['pmc']}/pdf"
out = {"pub_title": result.get('title'),
"pub_authors": result.get('authors'),
"pub_abstract": result.get('abstract'),
"pub_doi": result.get('doi'),
"pub_pmid": result.get('pmid'),
"pub_pmc": pub_id if id_type == 'pmc' else None,
"pub_url": result.get('url'),
"pub_pdf_url": result.get('pdf_url') or 'searching',
"pub_journal": result.get('journal'),
"pub_date": result['history'].get('pubmed')}
return out
def search(entry):
fetch = PubMedFetcher()
try:
article = fetch.article_by_pmid(entry['pmid'])
except:
try:
article = fetch.article_by_pmcid(entry['pmcid'])
except:
try:
article = fetch.article_by_doi(entry['doi'])
except:
try:
pmids = fetch.pmids_for_citation(authors=entry['author'], journal=entry['journal'], year=entry['year'], volume=entry['volume'])
# pmids2 = fetch.pmids_for_query(entry['title'])
article = fetch.article_by_pmid(pmids[0])
except:
return None
return article
from metapub import PubMedFetcher
fetch = PubMedFetcher()
print "Get paper information by PMID"
article = fetch.article_by_pmid('21931568')
print article.title
print article.journal, article.year, article.volume, article.issue
print article.authors
print '\nGet paper information by PMCID'
article = fetch.article_by_pmcid(2674488)
print article.title
print article.journal, article.year, article.volume, article.issue
print article.authors
from __future__ import absolute_import, print_function, unicode_literals
import sys, logging
from metapub import PubMedFetcher
logging.loglevel = logging.INFO
try:
someid = sys.argv[1]
except IndexError:
print('Supply a PMCID or DOI (example: ./blah.py PMC3479421)')
sys.exit()
fetch = PubMedFetcher()
article = fetch.article_by_pmcid(someid)
print(article.title)
print(', '.join(article.authors))
print()
print(article.journal, article.volume_issue)
print()
print('Pubmed ID: ' + article.pmid)
"""
<pmcids status="ok">
<request idtype="pmcid" pmcids="" versions="yes" showaiid="no">
<echo>tool=medgen-python;email=naomi.most%40invitae.com;ids=PMC3479421</echo>
</request>
<record requested-id="PMC3479421" pmcid="PMC3479421" pmid="22676651" doi="10.1186/1750-1172-7-35"><versions><version pmcid="PMC3479421.1" current="true"/></versions></record>
</pmcids>
"""