def main():
if len(sys.argv) == 2:
filepath = sys.argv[1]
else:
filepath = None
utils.load_settings(filepath=filepath)
utils.init_db()
application = get_application()
application.listen(settings["PORT"], xheaders=True)
pid = os.getpid()
if settings["PIDFILE"]:
with open(settings["PIDFILE"], "w") as pf:
pf.write(str(pid))
logging.info(f"web server PID {pid} at {settings['BASE_URL']}")
tornado.ioloop.IOLoop.instance().start()
with PublicationSaver(doc=publ, db=db) as saver:
labels = publ['labels'].copy()
labels[label] = qualifier
saver['labels'] = labels
count += 1
print("Label '%s/%s' added to %i publications" % (label, qualifier, count))
for error in errors:
print(error)
if __name__ == '__main__':
parser = utils.get_command_line_parser(
'Add a label to all publications in a list.')
parser.add_argument('--label', action='store', dest='label',
default=None, help='label to add')
parser.add_argument('--qualifier', action='store', dest='qualifier',
default=None, help='qualifier of label to add')
parser.add_argument('--file', action='store', dest='idfile',
metavar='IDFILE',
help='path to file containing publication identifiers')
args = parser.parse_args()
utils.load_settings(filepath=args.settings)
db = utils.get_db()
identifiers = []
with open(args.idfile) as infile:
for line in infile:
line = line.strip()
if line: identifiers.append(line)
print(len(identifiers), 'identifiers')
add_label_to_publications(db, args.label, args.qualifier, identifiers)
count_files += 1
else:
doc = json.loads(itemdata)
atts = doc.pop('_attachments', dict())
db.save(doc)
count_items += 1
for attname, attinfo in list(atts.items()):
key = "{0}_att/{1}".format(doc['_id'], attname)
attachments[key] = dict(filename=attname,
content_type=attinfo['content_type'])
if count_items % 100 == 0:
logging.info("%s items loaded...", count_items)
infile.close()
designs.regenerate_indexes(db)
logging.info("undumped %s items and %s files from %s", count_items,
count_files, filepath)
if __name__ == '__main__':
parser = utils.get_command_line_parser('Load tar.gz dump file'
' into the database.')
parser.add_argument('dumpfile',
metavar='FILE',
type=str,
help='Dump file to load into the database.')
args = parser.parse_args()
utils.load_settings(filepath=args.settings, ignore_logging_filepath=True)
db = utils.get_db()
utils.initialize(db)
undump(db, args.dumpfile)
def cli(settings, log):
utils.load_settings(settings, log=log)
symdifference = pp.Literal("^").set_parse_action(_Symdifference)
intersection = pp.Literal("#").set_parse_action(_Intersection)
difference = pp.Literal("-").set_parse_action(_Difference)
operator = union | symdifference | difference | intersection
expression = pp.Forward()
atom = function | identifier | pp.Group(left + expression + right)
expression <<= atom + (operator + atom)[...]
expression.set_parse_action(_Expression)
expression.ignore("!" + pp.rest_of_line)
return expression
if __name__ == "__main__":
logging.getLogger().disabled = True
utils.load_settings()
db = utils.get_db()
parser = get_parser()
variables = dict(blah=Subset(db, year="2010"))
line = """((label(Clinical Genomics Linköping) +
label(Clinical Genomics Gothenburg)) +
label(Clinical Genomics Lund) +
label(Clinical Genomics Uppsala) +
label(Clinical Genomics Stockholm) +
label(Clinical Genomics Umeå) +
label(Clinical Genomics Örebro)) #
(year(2020) + year(2019) +year(2018) + year(2017)) + blah"""
print(">>>", get_subset(db, line, variables=variables))
def main():
args = get_args()
utils.load_settings(filepath=args.settings)
utils.initialize()
url = tornado.web.url
handlers = [
url(r'/', Home, name='home'),
url(r'/site/([^/]+)',
tornado.web.StaticFileHandler, {'path': settings['SITE_DIR']},
name='site'),
url(r'/publication/(.+).json',
PublicationJson,
name='publication_json'),
url(r'/publication/(.+)', Publication, name='publication'),
url(r'/publications/(\d{4})', Publications, name='publications_year'),
url(r'/publications/(\d{4}).json',
PublicationsJson,
name='publications_year_json'),
url(r'/publications', Publications, name='publications'),
url(r'/publications.json', PublicationsJson, name='publications_json'),
url(r'/publications/csv', PublicationsCsv, name='publications_csv'),
url(r'/publications/xlsx', PublicationsXlsx, name='publications_xlsx'),
url(r'/publications/table/(\d{4})',
PublicationsTable,
name='publications_table_year'),
url(r'/publications/table',
PublicationsTable,
name='publications_table'),
url(r'/publications/acquired',
PublicationsAcquired,
name='publications_acquired'),
url(r'/publications/no_pmid',
PublicationsNoPmid,
name='publications_no_pmid'),
url(r'/publications/no_doi',
PublicationsNoDoi,
name='publications_no_doi'),
url(r'/publications/no_label',
PublicationsNoLabel,
name='publications_no_label'),
url(r'/publications/duplicates',
PublicationsDuplicates,
name='publications_duplicates'),
url(r'/publications/modified',
PublicationsModified,
name='publications_modified'),
url(r'/edit/([^/]+)', PublicationEdit, name='publication_edit'),
url(r'/xrefs/([^/]+)', PublicationXrefs, name='publication_xrefs'),
url(r'/add', PublicationAdd, name='publication_add'),
url(r'/fetch', PublicationFetch, name='publication_fetch'),
url(r'/blacklist/([^/]+)',
PublicationBlacklist,
name='publication_blacklist'),
url(r'/acquire/([^/]+)',
PublicationAcquire,
name='publication_acquire'),
url(r'/release/([^/]+)',
PublicationRelease,
name='publication_release'),
url(r'/qc/([^/]+)', PublicationQc, name='publication_qc'),
url(r'/update/([^/]+)/pmid',
PublicationUpdatePmid,
name='publication_update_pmid'),
url(r'/update/([^/]+)/doi',
PublicationUpdateDoi,
name='publication_update_doi'),
url(r'/journals', Journals, name='journals'),
url(r'/journals.json', JournalsJson, name='journals_json'),
url(r'/journal/([^/]+).json', JournalJson, name='journal_json'),
url(r'/journal/([^/]+)', Journal, name='journal'),
url(r'/journal/([^/]+)/edit', JournalEdit, name='journal_edit'),
url(r'/labels', LabelsList, name='labels'),
url(r'/labels.json', LabelsJson, name='labels_json'),
url(r'/labels/table', LabelsTable, name='labels_table'),
# These two label path patterns need to be checked first.
url(r'/label/([^\.]+)/edit', LabelEdit, name='label_edit'),
url(r'/label/([^\.]+)/merge', LabelMerge, name='label_merge'),
url(r'/label/([^\.]+).json', LabelJson, name='label_json'),
url(r'/label/([^\.]+)', Label, name='label'),
url(r'/label', LabelAdd, name='label_add'),
url(r'/account/reset', AccountReset, name='account_reset'),
url(r'/account/password', AccountPassword, name='account_password'),
url(r'/account/([^/]+).json', AccountJson, name='account_json'),
url(r'/account/([^/]+)', Account, name='account'),
url(r'/account/([^/]+)/edit', AccountEdit, name='account_edit'),
url(r'/account/([^/]+)/disable',
AccountDisable,
name='account_disable'),
url(r'/account/([^/]+)/enable', AccountEnable, name='account_enable'),
url(r'/accounts', Accounts, name='accounts'),
url(r'/accounts.json', AccountsJson, name='accounts_json'),
url(r'/account', AccountAdd, name='account_add'),
url(r'/search', Search, name='search'),
url(r'/search.json', SearchJson, name='search_json'),
url(r'/logs/([^/]+)', Logs, name='logs'),
url(r'/contact', Contact, name='contact'),
url(r'/settings', Settings, name='settings'),
url(r'/login', Login, name='login'),
url(r'/logout', Logout, name='logout'),
url(r'/api/publication',
ApiPublicationFetch,
name='api_publication_fetch'),
]
os.chdir(settings['ROOT'])
application = tornado.web.Application(
handlers=handlers,
debug=settings.get('TORNADO_DEBUG', False),
cookie_secret=settings['COOKIE_SECRET'],
xsrf_cookies=True,
ui_modules=uimodules,
template_path='templates',
static_path='static',
login_url=r'/login')
application.listen(settings['PORT'], xheaders=True)
pid = os.getpid()
logging.info("web server PID %s at %s", pid, settings['BASE_URL'])
if args.pidfile:
with open(args.pidfile, 'w') as pf:
pf.write(str(pid))
tornado.ioloop.IOLoop.instance().start()