def get_dbserver():
"Return the CouchDB2 handle for the CouchDB server."
kwargs = dict(href=settings["DATABASE_SERVER"])
if settings.get("DATABASE_ACCOUNT") and settings.get("DATABASE_PASSWORD"):
kwargs["username"] = settings["DATABASE_ACCOUNT"]
kwargs["password"] = settings["DATABASE_PASSWORD"]
return couchdb2.Server(**kwargs)
def __init__(self):
"""Open the connection to the email server.
Raise ValueError if no email server host has been defined.
"""
try:
host = settings["EMAIL"]["HOST"]
if not host:
raise ValueError
self.email = settings.get("SITE_EMAIL") or settings["EMAIL"]["SENDER"]
except (KeyError, TypeError):
raise ValueError("email server host is not properly defined")
port = settings["EMAIL"].get("PORT") or 0
if settings["EMAIL"].get("SSL"):
self.server = smtplib.SMTP_SSL(host, port=port)
else:
self.server = smtplib.SMTP(host, port=port)
if settings["EMAIL"].get("TLS"):
self.server.starttls()
self.server.ehlo()
try:
user = settings["EMAIL"]["USER"]
password = settings["EMAIL"]["PASSWORD"]
except KeyError:
pass
else:
self.server.login(user, password)
def get(self):
if self.is_admin():
account = self.get_argument("account", self.current_user["email"])
elif self.current_user:
account = self.current_user["email"]
else:
account = None
if settings.get("EMAIL") and settings["EMAIL"].get("HOST"):
self.render("account_reset.html", account=account)
else:
self.set_error_flash(
"Cannot reset password since"
" no email server configuration."
" Contact the system administrator."
)
self.see_other("home")
def load_settings(filepath=None, log=True):
"""Load the settings. The file path first specified is used:
1) The argument to this procedure (possibly from a command line argument).
2) The environment variable PUBLICATIONS_SETTINGS.
3) The file '../site/settings.yaml' relative to this directory.
If 'log' is True, activate logging according to DEBUG settings.
Raise IOError if settings file could not be read.
Raise KeyError if a settings variable is missing.
Raise ValueError if a settings variable value is invalid.
"""
site_dir = settings["SITE_DIR"]
if not os.path.exists(site_dir):
raise IOError(f"The required site directory '{site_dir}' does not exist.")
if not os.path.isdir(site_dir):
raise IOError(f"The site directory path '{site_dir}' is not a directory.")
# Find and read the settings file, updating the defaults.
if not filepath:
try:
filename = os.environ["PUBLICATIONS_SETTINGS"]
except KeyError:
filepath = os.path.join(site_dir, "settings.yaml")
with open(filepath) as infile:
settings.update(yaml.safe_load(infile))
settings["SETTINGS_FILE"] = filepath
# Setup logging.
if settings.get("LOGGING_DEBUG"):
kwargs = dict(level=logging.DEBUG)
else:
kwargs = dict(level=logging.INFO)
try:
kwargs["format"] = settings["LOGGING_FORMAT"]
except KeyError:
pass
try:
kwargs["filename"] = settings["LOGGING_FILEPATH"]
except KeyError:
pass
else:
try:
kwargs["filemode"] = settings["LOGGING_FILEMODE"]
except KeyError:
pass
settings["LOG"] = log
if log:
logging.basicConfig(**kwargs)
logging.info(f"Publications version {constants.VERSION}")
logging.info(f"ROOT: {constants.ROOT}")
logging.info(f"SITE_DIR: {settings['SITE_DIR']}")
logging.info(f"settings: {settings['SETTINGS_FILE']}")
logging.info(f"logging debug: {settings['LOGGING_DEBUG']}")
logging.info(f"tornado debug: {settings['TORNADO_DEBUG']}")
# Check some settings.
for key in ["BASE_URL", "PORT", "DATABASE_SERVER", "DATABASE_NAME"]:
if key not in settings:
raise KeyError(f"No settings['{key}'] item.")
if not settings[key]:
raise ValueError(f"Settings['{key}'] has invalid value.")
if len(settings.get("COOKIE_SECRET") or "") < 10:
raise ValueError("settings['COOKIE_SECRET'] not set, or too short.")
if len(settings.get("PASSWORD_SALT") or "") < 10:
raise ValueError("Settings['PASSWORD_SALT'] not set, or too short.")
for key in ["PUBMED_DELAY", "PUBMED_TIMEOUT", "CROSSREF_DELAY", "CROSSREF_TIMEOUT"]:
if not isinstance(settings[key], (int, float)) or settings[key] <= 0.0:
raise ValueError(f"Invalid '{key}' value: must be positive number.")
# Set up the xref templates URLs.
settings["XREF_TEMPLATE_URLS"] = NocaseDict(settings["XREF_TEMPLATE_URLS"])
settings["XREF_TEMPLATE_URLS"]["URL"] = "%s"
def get_application():
url = tornado.web.url
handlers = [
url(r"/", publications.home.Home, name="home"),
url(r"/status", publications.home.Status, name="status"),
url(r"/docs/([^/]+)", publications.home.Doc, name="doc"),
url(
r"/site/([^/]+)",
tornado.web.StaticFileHandler,
{"path": settings["SITE_STATIC_DIR"]},
name="site",
),
url(
r"/publication/([^/]{32,32})",
publications.publication.Publication,
name="publication",
),
url(
r"/publication/([^/]{32,32}).json",
publications.publication.PublicationJson,
name="publication_json",
),
url(
r"/publications/(\d{4})",
publications.publication.Publications,
name="publications_year",
),
url(
r"/publications/(\d{4}).json",
publications.publication.PublicationsJson,
name="publications_year_json",
),
url(r"/publications",
publications.publication.Publications,
name="publications"),
url(
r"/publications.json",
publications.publication.PublicationsJson,
name="publications_json",
),
url(
r"/publications/csv",
publications.publication.PublicationsCsv,
name="publications_csv",
),
url(
r"/publications/xlsx",
publications.publication.PublicationsXlsx,
name="publications_xlsx",
),
url(
r"/publications/txt",
publications.publication.PublicationsTxt,
name="publications_txt",
),
url(
r"/publications/table/(\d{4})",
publications.publication.PublicationsTable,
name="publications_table_year",
),
url(
r"/publications/table",
publications.publication.PublicationsTable,
name="publications_table",
),
url(
r"/publications/no_pmid",
publications.publication.PublicationsNoPmid,
name="publications_no_pmid",
),
url(
r"/publications/no_pmid.json",
publications.publication.PublicationsNoPmidJson,
name="publications_no_pmid_json",
),
url(
r"/publications/no_doi",
publications.publication.PublicationsNoDoi,
name="publications_no_doi",
),
url(
r"/publications/no_doi.json",
publications.publication.PublicationsNoDoiJson,
name="publications_no_doi_json",
),
url(
r"/publications/no_label",
publications.publication.PublicationsNoLabel,
name="publications_no_label",
),
url(
r"/publications/no_label.json",
publications.publication.PublicationsNoLabelJson,
name="publications_no_label_json",
),
url(
r"/publications/duplicates",
publications.publication.PublicationsDuplicates,
name="publications_duplicates",
),
url(
r"/publications/modified",
publications.publication.PublicationsModified,
name="publications_modified",
),
url(
r"/edit/([^/]{32,32})",
publications.publication.PublicationEdit,
name="publication_edit",
),
url(
r"/researchers/([^/]{32,32})",
publications.publication.PublicationResearchers,
name="publication_researchers",
),
url(
r"/xrefs/([^/]{32,32})",
publications.publication.PublicationXrefs,
name="publication_xrefs",
),
url(r"/add",
publications.publication.PublicationAdd,
name="publication_add"),
url(
r"/fetch",
publications.publication.PublicationFetch,
name="publication_fetch",
),
url(r"/blacklist/([^/]+)",
publications.blacklist.Blacklist,
name="blacklist"),
url(r"/blacklisted",
publications.blacklist.Blacklisted,
name="blacklisted"),
url(
r"/update/([^/]{32,32})/pmid",
publications.publication.PublicationUpdatePmid,
name="publication_update_pmid",
),
url(
r"/update/([^/]{32,32})/find_pmid",
publications.publication.PublicationFindPmid,
name="publication_find_pmid",
),
url(
r"/update/([^/]{32,32})/doi",
publications.publication.PublicationUpdateDoi,
name="publication_update_doi",
),
url(r"/researcher",
publications.researcher.ResearcherAdd,
name="researcher_add"),
url(
r"/researchers_json",
publications.researcher.ResearchersJson,
name="researchers_json",
),
url(r"/researchers",
publications.researcher.Researchers,
name="researchers"),
url(
r"/researcher/([^/]+).json",
publications.researcher.ResearcherJson,
name="researcher_json",
),
url(
r"/researcher/([^/]+)",
publications.researcher.Researcher,
name="researcher",
),
url(
r"/researcher/([^/]+)/edit",
publications.researcher.ResearcherEdit,
name="researcher_edit",
),
url(
r"/researcher/([^/]+)/publications.csv",
publications.researcher.ResearcherPublicationsCsv,
name="researcher_publications_csv",
),
url(
r"/researcher/([^/]+)/publications.xlsx",
publications.researcher.ResearcherPublicationsXlsx,
name="researcher_publications_xlsx",
),
url(
r"/researcher/([^/]+)/publications.txt",
publications.researcher.ResearcherPublicationsTxt,
name="researcher_publications_txt",
),
url(
r"/researcher/([^/]+)/publications/edit",
publications.researcher.ResearcherPublicationsEdit,
name="researcher_publications_edit",
),
url(r"/journals", publications.journal.Journals, name="journals"),
url(r"/journals.json",
publications.journal.JournalsJson,
name="journals_json"),
url(
r"/journal/([^/]+).json",
publications.journal.JournalJson,
name="journal_json",
),
url(r"/journal/([^/]+)", publications.journal.Journal, name="journal"),
url(
r"/journal/([^/]+)/edit",
publications.journal.JournalEdit,
name="journal_edit",
),
url(r"/labels", publications.label.LabelsList, name="labels"),
url(r"/labels.json", publications.label.LabelsJson,
name="labels_json"),
url(r"/labels/table",
publications.label.LabelsTable,
name="labels_table"),
# These two label path patterns need to be checked first.
url(r"/label/([^\.]+)/edit",
publications.label.LabelEdit,
name="label_edit"),
url(r"/label/([^\.]+)/merge",
publications.label.LabelMerge,
name="label_merge"),
url(r"/label/([^\.]+).json",
publications.label.LabelJson,
name="label_json"),
url(r"/label/([^\.]+)", publications.label.Label, name="label"),
url(r"/label", publications.label.LabelAdd, name="label_add"),
url(r"/account/reset",
publications.account.AccountReset,
name="account_reset"),
url(
r"/account/password",
publications.account.AccountPassword,
name="account_password",
),
url(
r"/account/([^/]+).json",
publications.account.AccountJson,
name="account_json",
),
url(r"/account/([^/]+)", publications.account.Account, name="account"),
url(
r"/account/([^/]+)/edit",
publications.account.AccountEdit,
name="account_edit",
),
url(
r"/account/([^/]+)/disable",
publications.account.AccountDisable,
name="account_disable",
),
url(
r"/account/([^/]+)/enable",
publications.account.AccountEnable,
name="account_enable",
),
url(r"/accounts", publications.account.Accounts, name="accounts"),
url(r"/accounts.json",
publications.account.AccountsJson,
name="accounts_json"),
url(r"/account", publications.account.AccountAdd, name="account_add"),
url(r"/search", publications.search.Search, name="search"),
url(r"/search.json",
publications.search.SearchJson,
name="search_json"),
url(r"/subset", publications.subset.SubsetDisplay, name="subset"),
url(r"/logs/([^/]+)", publications.log.Logs, name="logs"),
url(r"/contact", publications.home.Contact, name="contact"),
url(r"/settings", publications.home.Settings, name="settings"),
url(r"/software", publications.home.Software, name="software"),
url(r"/login", publications.login.Login, name="login"),
url(r"/logout", publications.login.Logout, name="logout"),
url(
r"/api/publication",
publications.publication.ApiPublicationFetch,
name="api_publication_fetch",
),
url(
r"/api/publication/([^/]{32,32})/labels",
publications.publication.ApiPublicationLabels,
name="api_publication_labels",
),
]
return tornado.web.Application(
handlers=handlers,
debug=settings.get("TORNADO_DEBUG", False),
cookie_secret=settings["COOKIE_SECRET"],
xsrf_cookies=True,
ui_modules=uimodules,
template_path=os.path.join(constants.ROOT, "templates"),
static_path=os.path.join(constants.ROOT, "static"),
login_url=r"/login",
)
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()