def pubmed_citation(args=sys.argv[1:], out=sys.stdout):
"""Get a citation via the command line using a PubMed ID or PubMed URL"""
parser = argparse.ArgumentParser(
description='Get a citation using a PubMed ID or PubMed URL')
parser.add_argument('query', help='PubMed ID or PubMed URL')
parser.add_argument('-m',
'--mini',
action='store_true',
help='get mini citation')
parser.add_argument('-e',
'--email',
action='store',
help='set user email',
default='')
args = parser.parse_args(args=args)
lookup = PubMedLookup(args.query, args.email)
publication = Publication(lookup, resolve_doi=False)
if args.mini:
out.write(publication.cite_mini() + '\n')
else:
out.write(publication.cite() + '\n')
def search(PubMedID):
# Retrieve a PubMed record:
# NCBI will contact user by email if excessive queries are detected
"""
Retrieve a PubMed record using its PubMed ID or PubMed URL.
(e.g., '22331878' or 'http://www.ncbi.nlm.nih.gov/pubmed/22331878')
"""
email = ''
#url = 'http://www.ncbi.nlm.nih.gov/pubmed/22331878'
#lookup = PubMedLookup(url, email)
#print(type(PubMedID))
lookup = PubMedLookup(PubMedID, email)
# Create a Publication object:
publication = Publication(
lookup) # Use 'resolve_doi=False' to keep DOI URL
# Access the Publication object's attributes:
tupleoutput = [(
PubMedID,
publication.title,
publication.authors,
publication.journal,
publication.year,
publication.month,
publication.day,
#publication.url, # doesn't seem to work w/ dataframe
publication.pubmed_url,
publication.cite(),
publication.cite_mini(),
repr(publication.abstract),
0,
)]
return tupleoutput
def search(PubMedID):
# Retrieve a PubMed record:
# NCBI will contact user by email if excessive queries are detected
"""
Retrieve a PubMed record using its PubMed ID or PubMed URL.
(e.g., '22331878' or 'http://www.ncbi.nlm.nih.gov/pubmed/22331878')
"""
email = ''
#url = 'http://www.ncbi.nlm.nih.gov/pubmed/22331878'
#lookup = PubMedLookup(url, email)
lookup = PubMedLookup(PubMedID, email)
# Create a Publication object:
publication = Publication(
lookup) # Use 'resolve_doi=False' to keep DOI URL
# Access the Publication object's attributes:
tupleoutput = ("""
TITLE:\n{title}\n
AUTHORS:\n{authors}\n
JOURNAL:\n{journal}\n
YEAR:\n{year}\n
MONTH:\n{month}\n
DAY:\n{day}\n
URL:\n{url}\n
PUBMED:\n{pubmed}\n
CITATION:\n{citation}\n
MINICITATION:\n{mini_citation}\n
ABSTRACT:\n{abstract}\n
""".format(
**{
'title': publication.title,
'authors': publication.authors,
'journal': publication.journal,
'year': publication.year,
'month': publication.month,
'day': publication.day,
'url': publication.url,
'pubmed': publication.pubmed_url,
'citation': publication.cite(),
'mini_citation': publication.cite_mini(),
'abstract': repr(publication.abstract),
}))
return tupleoutput
def pubmed_citation(args=sys.argv[1:], out=sys.stdout):
"""Get a citation via the command line using a PubMed ID or PubMed URL"""
parser = argparse.ArgumentParser(
description='Get a citation using a PubMed ID or PubMed URL')
parser.add_argument('query', help='PubMed ID or PubMed URL')
parser.add_argument(
'-m', '--mini', action='store_true', help='get mini citation')
parser.add_argument(
'-e', '--email', action='store', help='set user email', default='')
args = parser.parse_args(args=args)
lookup = PubMedLookup(args.query, args.email)
publication = Publication(lookup, resolve_doi=False)
if args.mini:
out.write(publication.cite_mini() + '\n')
else:
out.write(publication.cite() + '\n')
def pubmed_search(request):
publications = LabPublication.objects.all().order_by('-year')
if 'pubmed_id' in request.GET:
paper_id = request.GET['pubmed_id']
if not paper_id:
message = '<strong>No PubMed ID or PubMed URL provided!</strong>'
else:
email = request.user.email
url = paper_id
try:
lookup = PubMedLookup(url, email)
except Exception:
message = '<strong>Error using your PubMed ID/URL</strong>'
return render(request, 'public_pages/publications.html', {'publications': publications, 'message': message})
publication = Publication(lookup)
if publication == '':
message = '<strong>No match found for your pubmed ID</strong>'
return render(request, 'public_pages/publications.html', {'publications': publications, 'message': message})
user = request.user
title = publication.title
authors = publication.authors
journal = publication.journal
year = publication.year
journal_url = publication.url
pubmed = publication.pubmed_url
citation = publication.cite()
mini_citation = publication.cite_mini()
abstract = repr(publication.abstract)
try:
new_publication, created = LabPublication.objects.get_or_create(user = user, title = title, authors = authors, journal = journal, year = year, journal_url = journal_url, pubmed = pubmed, citation = citation, mini_citation = mini_citation, abstract = abstract)
except:
message = '<strong>Could not add your publication. Are you trying to add a duplicate entry?</strong>'
return render(request, 'public_pages/publications.html', {'publications': publications, 'message': message})
if created == '':
message = '<strong>Could not add your publication. Are you trying to add a duplicate entry?</strong>'
return render(request, 'public_pages/publications.html', {'publications': publications, 'message': message})
else:
return HttpResponseRedirect('publications')
return render(request, 'public_pages/publications.html', {'publications': publications, 'message': message})
def handle(self, *args, **options):
print('importing {0}'.format(options['path']))
file = os.path.normpath(options['path'])
df = pd.read_csv(file, header=None)
with open(options['search_function'], "r") as sf_file:
search_function = sf_file.readlines()
import_record = PubmedImport()
import_record.import_date = timezone.now()
import_record.search_function = search_function
import_record.save()
import_id = import_record.id
failed_ids = list()
for index, record in tqdm(df.iterrows(), total=df.shape[0]):
pmid = record[0]
find_pmid = PubmedImportedArticle.objects.filter(pmid=pmid)
if len(find_pmid) > 0:
continue
try:
email = ''
url = 'http://www.ncbi.nlm.nih.gov/pubmed/{0}'.format(pmid)
lookup = PubMedLookup(url, email)
publication = Publication(lookup, resolve_doi=False)
pia = PubmedImportedArticle()
pia.pmid = pmid
year = self.get_int(publication.year)
month = self.get_int(publication.month)
day = self.get_int(publication.day)
pia.pub_date = datetime(year,
month,
day,
0,
0,
0,
0,
tzinfo=pytz.UTC)
pia.title = publication.title
pia.authors = publication.authors
pia.journal = publication.journal
pia.citation = publication.cite()
# pia.mini_citation = publication.cite_mini()
pia.url = publication.url
pia.pubmed_url = publication.pubmed_url
pia.abstract = repr(publication.abstract)
pia.screened = False
pia.tagged = False
pia.landmark = False
pia.pmimport = import_record
pia.save()
except:
print('\nPMID {0} failed'.format(pmid))
failed_ids.append(pmid)
np.savetxt('failed_ids.txt', np.asarray(failed_ids), fmt='%d')
print('finished')
np.savetxt(np.asarray(pmid))
publication = Publication(lookup) # Use 'resolve_doi=False' to keep DOI URL
#Access the Publication object’s attributes:
print(
"""
TITLE:\n{title}\n
AUTHORS:\n{authors}\n
JOURNAL:\n{journal}\n
YEAR:\n{year}\n
MONTH:\n{month}\n
DAY:\n{day}\n
URL:\n{url}\n
PUBMED:\n{pubmed}\n
CITATION:\n{citation}\n
MINICITATION:\n{mini_citation}\n
ABSTRACT:\n{abstract}\n
"""
.format(**{
'title': publication.title,
'authors': publication.authors,
'journal': publication.journal,
'year': publication.year,
'month': publication.month,
'day': publication.day,
'url': publication.url,
'pubmed': publication.pubmed_url,
'citation': publication.cite(),
'mini_citation': publication.cite_mini(),
'abstract': repr(publication.abstract),
}))