def publications_page():
global publications
if request.method == 'POST':
publication_ids = parse_pubmed_ids(request.form['pubmed_ids'])
logging.debug("Request to add publications: %s" % "; ".join(map(str, publication_ids)))
new_publications = Publications.from_pubmed_ids(publication_ids)
for publication in new_publications.values():
publication.update_authors(users)
logging.debug("Found %s potential authors for %s" %
(len(publication.most_likely_affiliated_authors()),
publication.pubmed_id))
flash(message_about_new_publications(new_publications))
publications = Publications.merge(publications, new_publications)
return redirect(url_for('publications_page'))
return render_template('affiliated.html',
publications=publications.not_denied(),
users=users,
user_title="All affiliated publications",
download_link=url_for('download'))
def publications_page():
global publications
if request.method == 'POST':
publication_ids = parse_pubmed_ids(request.form['pubmed_ids'])
logging.debug("Request to add publications: %s" %
"; ".join(map(str, publication_ids)))
new_publications = Publications.from_pubmed_ids(publication_ids)
for publication in new_publications.values():
publication.update_authors(users)
logging.debug("Found %s potential authors for %s" %
(len(publication.most_likely_affiliated_authors()),
publication.pubmed_id))
flash(message_about_new_publications(new_publications))
publications = Publications.merge(publications, new_publications)
return redirect(url_for('publications_page'))
return render_template('affiliated.html',
publications=publications.not_denied(),
users=users,
user_title="All affiliated publications",
download_link=url_for('download'))
pubmed_ids = set()
logging.info("Searching pubmed for publications")
for user in users.values():
new_pubmed_ids = Searcher.get_pubmed_ids_for_user(user, options.start, options.end)
pubmed_ids.update(new_pubmed_ids)
pubmed_id_count = len(pubmed_ids)
logging.info("Found %s citations by searching pubmed" % pubmed_id_count)
logging.info("Getting pubmed_ids from the Library")
new_pubmed_ids = LibrarySearcher.get_pubmed_ids(options.start, options.end)
pubmed_ids.update(new_pubmed_ids)
logging.info("Found additional %s publications in Library" % (len(pubmed_ids) - pubmed_id_count))
new_publications = Publications.from_pubmed_ids(list(pubmed_ids))
publications = Publications.merge(publications, new_publications)
for publication in publications.values():
publication.update_authors(users)
if options.outputfile != "":
with open(options.outputfile, "wb") as output:
affiliated_publications = publications.not_denied()
affiliated_publications.to_csv(output)
logging.info("%s citations with at least one user matching the input queries have been printed to %s" % (
len(affiliated_publications), options.outputfile))
try:
with open(options.publicationsfile, 'w') as publications_output:
publications_output.write(publications.to_yaml())
except IOError:
# The file is missing
logging.info("Searching pubmed for publications")
for user in users.values():
new_pubmed_ids = Searcher.get_pubmed_ids_for_user(
user, options.start, options.end)
pubmed_ids.update(new_pubmed_ids)
pubmed_id_count = len(pubmed_ids)
logging.info("Found %s citations by searching pubmed" % pubmed_id_count)
logging.info("Getting pubmed_ids from the Library")
new_pubmed_ids = LibrarySearcher.get_pubmed_ids(options.start, options.end)
pubmed_ids.update(new_pubmed_ids)
logging.info("Found additional %s publications in Library" %
(len(pubmed_ids) - pubmed_id_count))
new_publications = Publications.from_pubmed_ids(list(pubmed_ids))
publications = Publications.merge(publications, new_publications)
for publication in publications.values():
publication.update_authors(users)
if options.outputfile != "":
with open(options.outputfile, "wb") as output:
affiliated_publications = publications.not_denied()
affiliated_publications.to_csv(output)
logging.info(
"%s citations with at least one user matching the input queries have been printed to %s"
% (len(affiliated_publications), options.outputfile))
try:
with open(options.publicationsfile, 'w') as publications_output:
publications_output.write(publications.to_yaml())
except IOError: