def load_users():
try:
with open(app.config['USERS_FILE'], 'r') as user_data_file:
users = User.from_yaml(user_data_file.read())
logging.info("Loaded %s users from %s" % (len(users),
app.config['USERS_FILE']))
except IOError:
logging.warning("Could not open %s to read users" %
app.config['USERS_FILE'])
users = {}
except Exception as e:
logging.error("There was a problem parsing users from %s" %
app.config['USERS_FILE'], exc_info=e)
users = {}
publication_users = publications.get_users()
publication_users.update(users)
users = publication_users
def by_name(user_id__user):
user_id, user = user_id__user
return user.ordered_name()
users = OrderedDict(sorted(users.items(), key=by_name))
logging.info("Merge users from userfile with users from publications, %s found" % len(users))
return users
def load_users():
try:
with open(app.config['USERS_FILE'], 'r') as user_data_file:
users = User.from_yaml(user_data_file.read())
logging.info("Loaded %s users from %s" %
(len(users), app.config['USERS_FILE']))
except IOError:
logging.warning("Could not open %s to read users" %
app.config['USERS_FILE'])
users = {}
except Exception as e:
logging.error("There was a problem parsing users from %s" %
app.config['USERS_FILE'],
exc_info=e)
users = {}
publication_users = publications.get_users()
publication_users.update(users)
users = publication_users
def by_name(user_id__user):
user_id, user = user_id__user
return user.ordered_name()
users = OrderedDict(sorted(users.items(), key=by_name))
logging.info(
"Merge users from userfile with users from publications, %s found" %
len(users))
return users
(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():
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))
(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():
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)