def ukpmc(ids=None):
"""
Given a pubmed id, Load entities into DB from UKPMC
"""
ids = ids.split(",") if ids else demo_pubmeds
url = 'http://ukpmc.ac.uk/abstract/MED/'
import requests, re
col = mongo.getCollection('publication')
for id in ids:
print "#### proceesing %s" % id
p = col.find_one({'_id': 'publ%s' % id})
pub = Publication(p)
u = "%s%s" % (url, id)
r = requests.get(u)
if r.status_code == 200:
from django.utils.encoding import smart_str, smart_unicode
content = smart_str(r.text)
entities = {}
for m in re.finditer(
r'<span class="(disease|protein|geneOntology|species|chemical)".*?_blank">(.*?)</a></span>',
content):
group = m.group(1)
group = 'go' if group == 'geneOntology' else group.lower()
e = {'name': m.group(2).lower(), 'group': group}
entities[e['name']] = e
pub.entities = []
for en, item in entities.items():
pub.entities.append(item)
if (pub.entities):
pub.save()
print("Saved %d items" % (len(entities)))
def ukpmc(ids=None):
"""
Given a pubmed id, Load entities into DB from UKPMC
"""
ids = ids.split(",") if ids else demo_pubmeds
url = 'http://ukpmc.ac.uk/abstract/MED/'
import requests,re
col = mongo.getCollection('publication')
for id in ids:
print "#### proceesing %s" %id
p = col.find_one({'_id':'publ%s'%id})
pub = Publication( p )
u = "%s%s" %(url, id)
r = requests.get(u)
if r.status_code == 200:
from django.utils.encoding import smart_str, smart_unicode
content = smart_str(r.text)
entities = {}
for m in re.finditer(r'<span class="(disease|protein|geneOntology|species|chemical)".*?_blank">(.*?)</a></span>', content):
group = m.group(1)
group = 'go' if group == 'geneOntology' else group.lower()
e = {'name': m.group(2).lower(), 'group': group}
entities[e['name']] = e
pub.entities = []
for en, item in entities.items():
pub.entities.append(item)
if(pub.entities):
pub.save()
print("Saved %d items" %(len(entities)))
