def load_publications():
try:
with open(app.config['PUBLICATIONS_FILE'],
'r') as publication_data_file:
publications = Publications.from_yaml(publication_data_file.read())
logging.info("Loaded publications from %s" %
app.config['PUBLICATIONS_FILE'])
except IOError:
logging.warning("Could not open %s to read publications" %
app.config['PUBLICATIONS_FILE'])
publications = Publications([])
except Exception as e:
logging.error("There was a problem parsing publications from %s" %
app.config['PUBLICATIONS_FILE'],
exc_info=e)
publications = Publications([])
return publications
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'))
def user_page(user_id):
if not user_id in users:
return render_template('affiliated.html',
publications=Publications(),
users=users,
user_title="Unknown user",
download_link='#'), 404
return render_template(
'affiliated.html',
publications=publications.filter_by_user_id(user_id),
users=users,
user_title="Publications for %s" % users[user_id].full_name(),
download_link=url_for('download', user_id=user_id))
def load_publications():
try:
with open(app.config['PUBLICATIONS_FILE'], 'r') as publication_data_file:
publications = Publications.from_yaml(publication_data_file.read())
logging.info("Loaded publications from %s" %
app.config['PUBLICATIONS_FILE'])
except IOError:
logging.warning("Could not open %s to read publications" %
app.config['PUBLICATIONS_FILE'])
publications = Publications([])
except Exception as e:
logging.error("There was a problem parsing publications from %s" %
app.config['PUBLICATIONS_FILE'], exc_info=e)
publications = Publications([])
return publications
def missing():
"""Hidden URL for missing publications
I've intentionally not publicised this feature because it makes lots of HTTP
requests to the Sanger website and I probably only want me / administrators to
use it on an infrequent basis.
This endpoint lists all of the publicatons which are currently not in the
Sanger Library's dataset"""
library_pubmed_ids = set(LibrarySearcher.get_pubmed_ids())
possible_pubmed_ids = set(publications.not_denied().keys())
missing_pubmed_ids = possible_pubmed_ids.difference(library_pubmed_ids)
missing_publications = Publications(
[publications[pubmed_id] for pubmed_id in missing_pubmed_ids])
return render_template('affiliated.html',
publications=missing_publications,
users=users,
user_title="Publications not in the Sanger Library")
logging.basicConfig(level=logging.WARN)
if do_exit:
print"Exiting"
print
sys.exit(1)
if __name__=="__main__":
(options, args)=main()
check_command_line()
try:
with open(options.publicationsfile, 'r') as publications_input:
publications = Publications.from_yaml(publications_input.read())
except IOError:
# The file is missing
logging.info("Could not load existing publications from %s, skipping" %
options.publicationsfile)
publications={}
users={}
with open(options.usersfile, "r") as usersfile:
users = User.from_yaml(usersfile.read())
users_count = len(users)
logging.info("Loaded %s users from %s" % (users_count, options.usersfile))
pubmed_ids = set()
logging.info("Searching pubmed for publications")
for user in users.values():
logging.basicConfig(level=logging.WARN)
if do_exit:
print "Exiting"
print
sys.exit(1)
if __name__ == "__main__":
(options, args) = main()
check_command_line()
try:
with open(options.publicationsfile, 'r') as publications_input:
publications = Publications.from_yaml(publications_input.read())
except IOError:
# The file is missing
logging.info("Could not load existing publications from %s, skipping" %
options.publicationsfile)
publications = {}
users = {}
with open(options.usersfile, "r") as usersfile:
users = User.from_yaml(usersfile.read())
users_count = len(users)
logging.info("Loaded %s users from %s" % (users_count, options.usersfile))
pubmed_ids = set()
logging.info("Searching pubmed for publications")
for user in users.values():
