def get_args(self):
parser = utils.get_command_line_parser(description=
'Fix documents in CouchDB.')
parser.add_option('-d', '--dry-run',
action='store_true', dest='dry_run', default=False,
help='do not perform save; for debug')
return parser.parse_args()
def get_args():
parser = utils.get_command_line_parser(description='Send unsent messages.')
parser.add_option('-d',
'--dry-run',
action='store_true',
dest='dry_run',
default=False,
help='do not send messages; for debug')
return parser.parse_args()
def get_command_line_parser():
parser = utils.get_command_line_parser(
description='Dump all data into a tar file.')
parser.add_option('-d',
'--dumpfile',
action='store',
dest='dumpfile',
metavar='DUMPFILE',
help='name of dump file')
return parser
def get_args():
parser = utils.get_command_line_parser(
description='Get document(s) from CouchDB and write to JSON file.')
parser.add_option("-w",
"--write",
action='store',
dest='FILE',
default=None,
metavar="FILE",
help="filepath of file to write")
return parser.parse_args()
def get_args():
parser = utils.get_command_line_parser(
description='Send info message to all users.')
parser.add_option('-d', '--dry-run',
action='store_true', dest='dry_run', default=False,
help='do not send messages; for debug')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
send_info_email('accounts.csv',
sender='Per Kraulis <*****@*****.**>',
options=options)
def __init__(self):
parser = utils.get_command_line_parser(
description='Fix documents in CouchDB.')
parser.add_option('-d', '--dry-run',
action='store_true', dest='dry_run', default=False,
help='do not perform save; for debug')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
self.dry_run = options.dry_run
self.db = utils.get_db()
self.args = args
self.prepare()
def get_args():
parser = utils.get_command_line_parser(
description='Initialize the database, deleting all old data,'
' optionally load from dump file.')
parser.add_option("-L",
"--load",
action='store',
dest='FILE',
default=None,
metavar="FILE",
help="filepath of dump file to load")
return parser.parse_args()
import yaml
from orderportal import constants
from orderportal import settings
from orderportal import utils
def load_order_messages(db):
"Load the order messages document."
for key in ['ORDER_MESSAGES_FILEPATH', 'INITIAL_ORDER_MESSAGES_FILEPATH']:
filepath = settings.get(key)
if filepath: break
else:
raise KeyError('no order messages file specified')
print('Order messages from', filepath)
with open(filepath) as infile:
doc = yaml.safe_load(infile)
doc['_id'] = 'order_messages'
doc[constants.DOCTYPE] = constants.META
print('saving order messages in database')
db.save(doc)
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Load the order messages document.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
db = utils.get_db()
load_order_messages(db)
" Get the previous version of the document and save it as new. "
from __future__ import print_function, absolute_import
import sys
from orderportal import utils
def revert(db, docid):
revisions = list(db.revisions(docid))
if len(revisions) < 2:
sys.exit('no previous version to revert to')
latest = revisions[0]
previous = revisions[1]
new = previous.copy()
new['_rev'] = latest['_rev']
db.save(new)
if __name__ == '__main__':
parser = utils.get_command_line_parser(description=
'Get the previous version of the document and save it as new.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
db = utils.get_db()
for docid in args:
revert(db, docid)
for filename in os.listdir(path):
name, ext = os.path.splitext(filename)
if ext != '.js': continue
if name.startswith('map_'):
name = name[len('map_'):]
elif name.startswith('reduce_'):
name = name[len('reduce_'):]
viewname = design + '/' + name
if viewname not in viewnames:
viewnames.append(viewname)
for field in settings['ORDERS_SEARCH_FIELDS']:
if constants.ID_RX.match(field):
viewnames.append("fields/%s" % field)
for viewname in viewnames:
print('regenerating view', viewname)
view = db.view(viewname)
count = 0
for row in view:
count += 1
if count > 4: break
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Reload all CouchDB design documents.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
db = utils.get_db()
load_designs(db)
regenerate_views(db)
def set_password(email, password, verbose=False):
db = utils.get_db()
view = db.view('account/email', include_docs=True)
rows = list(view[email])
if len(rows) != 1:
raise ValueError("no such account %s" % email)
doc = rows[0].doc
with AccountSaver(doc=doc, db=db) as saver:
saver.set_password(password)
if verbose: print('Password was set for', email)
if saver['status'] != constants.ENABLED:
saver['status'] = constants.ENABLED
if verbose: print('Account was enabled.')
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Set the password for an account.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
email = input('Email address (=account name) > ')
if not email:
sys.exit('no email address provided')
password = getpass.getpass('Password > ')
if not password:
sys.exit('no password provided')
try:
utils.check_password(password)
except ValueError as msg:
sys.exit(str(msg))
again_password = getpass.getpass('Password again > ')
if password != again_password:
sys.exit('passwords do not match')
def set_role(email, role):
assert role in constants.ACCOUNT_ROLES
db = utils.get_db()
view = db.view('account/email', include_docs=True)
rows = list(view[email])
if len(rows) != 1:
raise ValueError("no such account %s" % email)
doc = rows[0].doc
with AccountSaver(doc=doc, db=db) as saver:
saver['role'] = role
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Set the role for an account.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
email = input('Email address (=account name) > ')
if not email:
sys.exit('no email address provided')
role = input("role [%s] > " % '|'.join(constants.ACCOUNT_ROLES))
if not role:
sys.exit('no role provided')
if role not in constants.ACCOUNT_ROLES:
sys.exit("invalid role; must be one of %s" %
', '.join(constants.ACCOUNT_ROLES))
set_role(email, role)
print('Set role for', email)
except KeyError:
pass
else:
with MessageSaver(db=db) as saver:
saver.set_params(
account=account['email'],
password_url=absolute_reverse_url('password'),
password_code_url=absolute_reverse_url(
'password',
email=account['email'],
code=account['code']),
code=account['code'])
saver.set_template(template)
saver['recipients'] = [account['email']]
print(account['email'])
time.sleep(PAUSE)
def absolute_reverse_url(path, **kwargs):
url = "https://ngisweden.scilifelab.se/{0}".format(path)
if kwargs:
url += '?' + urllib.urlencode(kwargs)
return url
if __name__ == '__main__':
parser = utils.get_command_line_parser(description=
"Enable all pending accounts.")
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
enable_accounts(utils.get_db())
def main():
parser = utils.get_command_line_parser(description='OrderPortal server.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
url = tornado.web.url
handlers = [url(r'/', Home, name='home')]
try:
regexp = settings['ORDER_IDENTIFIER_REGEXP']
except KeyError:
pass
else:
handlers.append(url(r"/order/({0})".format(regexp),
Order, name='order_id'))
handlers.append(url(r"/api/v1/order/({0})".format(regexp),
OrderApiV1, name='order_id_api'))
handlers.extend([
url(r'/order/([0-9a-f]{32})', Order, name='order'),
url(r'/api/v1/order/([0-9a-f]{32})', OrderApiV1, name='order_api'),
url(r'/order/([^/]+).csv', OrderCsv, name='order_csv'),
url(r'/order/([^/]+).zip', OrderZip, name='order_zip'),
url(r'/order/([0-9a-f]{32})/logs', OrderLogs, name='order_logs'),
url(r'/order', OrderCreate, name='order_create'),
url(r'/api/v1/order', OrderCreateApiV1, name='order_create_api'),
url(r'/order/([0-9a-f]{32})/edit', OrderEdit, name='order_edit'),
url(r'/order/([0-9a-f]{32})/transition/(\w+)',
OrderTransition, name='order_transition'),
url(r'/api/v1/order/([0-9a-f]{32})/transition/(\w+)',
OrderTransitionApiV1, name='order_transition_api'),
url(r'/order/([0-9a-f]{32})/clone', OrderClone, name='order_clone'),
url(r'/order/([0-9a-f]{32})/file', OrderFile, name='order_file_add'),
url(r'/order/([0-9a-f]{32})/file/([^/]+)',OrderFile,name='order_file'),
url(r'/order/([0-9a-f]{32})/report', OrderReport, name='order_report'),
url(r'/api/v1/order/([0-9a-f]{32})/report',
OrderReportApiV1, name='order_report_api'),
url(r'/order/([0-9a-f]{32})/report/edit',
OrderReportEdit, name='order_report_edit'),
url(r'/orders', Orders, name='orders'),
url(r'/api/v1/orders', OrdersApiV1, name='orders_api'),
url(r'/orders.csv', OrdersCsv, name='orders_csv'),
url(r'/accounts', Accounts, name='accounts'),
url(r'/api/v1/accounts', AccountsApiV1, name='accounts_api'),
url(r'/accounts.csv', AccountsCsv, name='accounts_csv'),
url(r'/account/([^/]+)', Account, name='account'),
url(r'/api/v1/account/([^/]+)', AccountApiV1, name='account_api'),
url(r'/account/([^/]+)/orders', AccountOrders, name='account_orders'),
url(r'/api/v1/account/([^/]+)/orders',
AccountOrdersApiV1, name='account_orders_api'),
url(r'/account/([^/]+)/groups/orders',
AccountGroupsOrders, name='account_groups_orders'),
url(r'/api/v1/account/([^/]+)/groups/orders',
AccountGroupsOrdersApiV1, name='account_groups_orders_api'),
url(r'/account/([^/]+)/logs', AccountLogs, name='account_logs'),
url(r'/account/([^/]+)/messages',
AccountMessages, name='account_messages'),
url(r'/account/([^/]+)/edit', AccountEdit, name='account_edit'),
url(r'/group', GroupCreate, name='group_create'),
url(r'/group/([0-9a-f]{32})', Group, name='group'),
url(r'/group/([0-9a-f]{32})/edit', GroupEdit, name='group_edit'),
url(r'/group/([0-9a-f]{32})/accept', GroupAccept, name='group_accept'),
url(r'/group/([0-9a-f]{32})/decline',
GroupDecline, name='group_decline'),
url(r'/group/([0-9a-f]{32})/logs', GroupLogs, name='group_logs'),
url(r'/groups', Groups, name='groups'),
url(r'/search', Search, name='search'),
url(r'/login', Login, name='login'),
url(r'/logout', Logout, name='logout'),
url(r'/reset', Reset, name='reset'),
url(r'/password', Password, name='password'),
url(r'/register', Register, name='register'),
url(r'/registered', Registered, name='registered'),
url(r'/account/([^/]+)/enable', AccountEnable, name='account_enable'),
url(r'/account/([^/]+)/disable', AccountDisable,name='account_disable'),
url(r'/account/([^/]+)/updateinfo',
AccountUpdateInfo, name='account_update_info'),
url(r'/forms', Forms, name='forms'),
url(r'/form/([0-9a-f]{32})', Form, name='form'),
url(r'/api/v1/form/([0-9a-f]{32})', FormApiV1, name='form_api'),
url(r'/form/([0-9a-f]{32})/logs', FormLogs, name='form_logs'),
url(r'/form', FormCreate, name='form_create'),
url(r'/form/([0-9a-f]{32})/edit', FormEdit, name='form_edit'),
url(r'/form/([0-9a-f]{32})/clone', FormClone, name='form_clone'),
url(r'/form/([0-9a-f]{32})/pending', FormPending, name='form_pending'),
url(r'/form/([0-9a-f]{32})/testing', FormTesting, name='form_testing'),
url(r'/form/([0-9a-f]{32})/enable', FormEnable, name='form_enable'),
url(r'/form/([0-9a-f]{32})/disable', FormDisable, name='form_disable'),
url(r'/form/([0-9a-f]{32})/field', FormFieldCreate,name='field_create'),
url(r'/form/([0-9a-f]{32})/field/([a-zA-Z][_a-zA-Z0-9]*)',
FormFieldEdit, name='field_edit'),
url(r'/form/([0-9a-f]{32})/field/([a-zA-Z][_a-zA-Z0-9]*)/descr',
FormFieldEditDescr, name='field_edit_descr'),
url(r'/form/([0-9a-f]{32})/orders', FormOrders, name='form_orders'),
url(r'/form/([0-9a-f]{32})/orders.csv',
FormOrdersCsv, name='form_orders_csv'),
url(r'/news', News, name='news'),
url(r'/new/([0-9a-f]{32})', NewsEdit, name='news_edit'),
url(r'/new', NewsCreate, name='news_create'),
url(r'/events', Events, name='events'),
url(r'/event/([0-9a-f]{32})', Event, name='event'),
url(r'/event', EventCreate, name='event_create'),
url(r'/contact', Contact, name='contact'),
url(r'/about', About, name='about'),
url(r'/software', Software, name='software'),
url(r'/infos', Infos, name='infos'),
url(r'/info', InfoCreate, name='info_create'),
url(r'/info/([^/]+)', Info, name='info'),
url(r'/info/([^/]+)/edit', InfoEdit, name='info_edit'),
url(r'/info/([^/]+)/logs', InfoLogs, name='info_logs'),
url(r'/files', Files, name='files'),
url(r'/file', FileCreate, name='file_create'),
url(r'/file/([^/]+)', File, name='file'),
url(r'/file/([^/]+)/meta', FileMeta, name='file_meta'),
url(r'/file/([^/]+)/download', FileDownload, name='file_download'),
url(r'/file/([^/]+)/edit', FileEdit, name='file_edit'),
url(r'/api/v1/file/([^/]+)/edit', FileEditApiV1, name='file_edit_api'),
url(r'/file/([0-9a-f]{32})/logs', FileLogs, name='file_logs'),
url(r'/log/([0-9a-f]{32})', Log, name='log'),
url(r'/([0-9a-f]{32})', Entity, name='entity'),
url(r'/nsc/package/([0-9a-f]{32})', NscOrderPkgV1, name='nsc_order_package'),
url(r'/admin/global_modes', GlobalModes, name='global_modes'),
url(r'/admin/settings', Settings, name='settings'),
url(r'/admin/text/([^/]+)', Text, name='text'),
url(r'/admin/texts', Texts, name='texts'),
url(r'/admin/order_statuses', OrderStatuses, name='order_statuses'),
url(r'/admin/order_messages',
AdminOrderMessages, name='admin_order_messages'),
url(r'/admin/account_messages',
AdminAccountMessages, name='admin_account_messages'),
url(r'/site/([^/]+)', tornado.web.StaticFileHandler,
{'path': utils.expand_filepath(settings['SITE_DIR'])},
name='site'),
])
handlers.append(url(r'/api/v1/(.*)', NoSuchEntityApiV1))
handlers.append(url(r'/(.*)', NoSuchEntity))
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=os.path.join(settings['ROOT_DIR'], 'html'),
static_path=os.path.join(settings['ROOT_DIR'], 'static'),
login_url=r'/login')
# Add href URLs for the status icons.
# This depends on order status setup.
for key, value in settings['ORDER_STATUSES_LOOKUP'].iteritems():
value['href'] = application.reverse_url('site', key + '.png')
application.listen(settings['PORT'], xheaders=True)
pid = os.getpid()
logging.info("web server PID %s on port %s", pid, settings['PORT'])
if options.pidfile:
with open(options.pidfile, 'w') as pf:
pf.write(str(pid))
tornado.ioloop.IOLoop.instance().start()
try:
doc = db[docid]
except couchdb.ResourceNotFound:
print('no such document', docid, file=sys.stderr)
else:
docs.append(doc)
if docs:
if filepath:
outfile = open(filepath, 'w')
print('writing to', filepath)
else:
outfile = sys.stdout
json.dump(docs, outfile, indent=2)
else:
print('no such document(s)', file=sys.stderr)
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Get document(s) from CouchDB and write to JSON file.')
parser.add_option("-w",
"--write",
action='store',
dest='FILE',
default=None,
metavar="FILE",
help="filepath of file to write")
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
get_documents(utils.get_db(), docids=args, filepath=options.FILE)
def get_args():
parser = utils.get_command_line_parser(
description=
'Get the previous version of the document and save it as new.')
return parser.parse_args()
def get_args():
parser = utils.get_command_line_parser(
description='Reload all CouchDB design documents.')
return parser.parse_args()
def get_args():
parser = utils.get_command_line_parser(
description='Set the password for an account.')
return parser.parse_args()
except KeyError:
pass
else:
with MessageSaver(db=db) as saver:
saver.set_params(account=account['email'],
password_url=absolute_reverse_url('password'),
password_code_url=absolute_reverse_url(
'password',
email=account['email'],
code=account['code']),
code=account['code'])
saver.set_template(template)
saver['recipients'] = [account['email']]
print(account['email'])
time.sleep(PAUSE)
def absolute_reverse_url(path, **kwargs):
url = "https://ngisweden.scilifelab.se/{0}".format(path)
if kwargs:
url += '?' + urllib.urlencode(kwargs)
return url
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description="Enable all pending accounts.")
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
enable_accounts(utils.get_db())
def add_text(db, name, textfilepath, force=False):
"Load the text from file, overwriting the current."
with open(utils.expand_filepath(textfilepath)) as infile:
text = infile.read()
docs = [
r.doc for r in db.view('text/name', include_docs=True, key=name)
]
try:
doc = docs[0]
if not force:
sys.exit('text exists; not overwritten')
except IndexError:
doc = None
with admin.TextSaver(doc=doc, db=db) as saver:
saver['name'] = name
saver['text'] = text
print("Text '{0}' loaded".format(name))
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Load a named text from file into the database.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
if len(args) != 2:
sys.exit('Error: give name and filepath')
add_text(utils.get_db(),
name=args[0],
textfilepath=args[1],
force=options.force)
for filename in os.listdir(path):
name, ext = os.path.splitext(filename)
if ext != '.js': continue
if name.startswith('map_'):
name = name[len('map_'):]
elif name.startswith('reduce_'):
name = name[len('reduce_'):]
viewname = design + '/' + name
if viewname not in viewnames:
viewnames.append(viewname)
for field in settings['ORDERS_SEARCH_FIELDS']:
if constants.ID_RX.match(field):
viewnames.append("fields/%s" % field)
for viewname in viewnames:
print('regenerating view', viewname)
view = db.view(viewname)
count = 0
for row in view:
count += 1
if count > 4: break
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Reload all CouchDB design documents.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
db = utils.get_db()
load_designs(db)
regenerate_views(db)
except KeyError:
pass
try:
other_data.append(u"old portal uid: {0}".format(account['uid']))
except KeyError:
pass
doc['other_data'] = '\n'.join(other_data)
doc['update_info'] = True
doc['password'] = None
# Role '2' is Drupal admin
doc['role'] = set(account['roles']).difference(set([2])) \
and constants.ADMIN or constants.USER
doc['owner'] = email
doc['created'] = utils.epoch_to_iso(account['created'])
doc['modified'] = utils.epoch_to_iso(account.get('last_access') or account['created'])
print('loaded', email)
db.save(doc)
counter += 1
print(counter, 'accounts loaded')
if __name__ == '__main__':
parser = utils.get_command_line_parser(description=
"Load accounts from old Drupal site JSON dump 'users.json'.")
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
db = utils.get_db()
load_accounts(db)
regenerate_views(db)
db.save(doc)
count_items += 1
for attname, attinfo in atts.items():
# Handle problematic non-ASCII filenames
attname2 = utils.to_ascii(attname)
key = "{0}_att/{1}".format(doc['_id'], attname2)
attachments[key] = dict(filename=attname2,
content_type=attinfo['content_type'])
infile.close()
# This will be executed on the command line, so output to console, not log.
print('undumped', count_items, 'items and',
count_files, 'files from', filepath)
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Dump all data into a tar file.')
parser.add_option('-d', '--dumpfile',
action='store', dest='dumpfile',
metavar='DUMPFILE', help='name of dump file')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
db = utils.get_db()
if options.dumpfile:
filepath = options.dumpfile
else:
filepath = "dump_{0}.tar.gz".format(time.strftime("%Y-%m-%d"))
if os.path.basename(filepath) == filepath:
try:
filepath = os.path.join(settings['BACKUP_DIR'], filepath)
except KeyError:
pass
def set_role(email, role):
assert role in constants.ACCOUNT_ROLES
db = utils.get_db()
view = db.view('account/email', include_docs=True)
rows = list(view[email])
if len(rows) != 1:
raise ValueError("no such account %s" % email)
doc = rows[0].doc
with AccountSaver(doc=doc, db=db) as saver:
saver['role'] = role
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Set the role for an account.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
email = raw_input('Email address (=account name) > ')
if not email:
sys.exit('no email address provided')
role = raw_input("role [%s] > " % '|'.join(constants.ACCOUNT_ROLES))
if not role:
sys.exit('no role provided')
if role not in constants.ACCOUNT_ROLES:
sys.exit("invalid role; must be one of %s" %
', '.join(constants.ACCOUNT_ROLES))
set_role(email, role)
print('Set role for', email)
attname2 = utils.to_ascii(attname)
key = "{0}_att/{1}".format(doc['_id'], attname2)
attachments[key] = dict(filename=attname2,
content_type=attinfo['content_type'])
infile.close()
print('undumped',
count_items,
'items and',
count_files,
'files from',
filepath,
file=sys.stderr)
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Dump all data into a tar file.')
parser.add_option('-d',
'--dumpfile',
action='store',
dest='dumpfile',
metavar='DUMPFILE',
help='name of dump file')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
db = utils.get_db()
if options.dumpfile:
filepath = options.dumpfile
else:
filepath = "dump_{0}.tar.gz".format(time.strftime("%Y-%m-%d"))
if os.path.basename(filepath) == filepath:
try:
del project['history']['undefined']
except KeyError:
pass
else:
changed = True
if changed:
print('saving', project['identifier'],
project['fields']['lims_id'], project['status'],
project['title'])
db.save(project)
else:
print('no change for', project['identifier'])
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Load project info from Clarity LIMS into OrderPortal.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
db = utils.get_db()
projects_lookup = get_old_portal_projects(db)
print(len(projects_lookup), 'projects from old portal requiring more info')
projects = projects_lookup.values()
projects.sort(lambda i, j: cmp(i['modified'], j['modified']))
for project in projects:
print(project['identifier'], project['modified'])
clarity = Clarity()
clarity_projects = clarity.get_all_projects()
print(len(clarity_projects), 'projects in Clarity')
for record in clarity_projects:
undump(db, dumpfilepath)
designs.regenerate_views_indexes(db)
except IOError:
print('Warning: could not load', dumpfilepath)
else:
print('no dump file loaded')
# Load texts from the initial texts YAML file. Only if missing in db!
print('loading any missing texts from', INIT_TEXTS_FILEPATH)
try:
with open(INIT_TEXTS_FILEPATH) as infile:
texts = yaml.safe_load(infile)
except IOError:
print('Warning: could not load', INIT_TEXTS_FILEPATH)
texts = dict()
for name in constants.TEXTS:
if len(list(db.view('text/name', key=name))) == 0:
with admin.TextSaver(db=db) as saver:
saver['name'] = name
saver['text'] = texts.get(name, '')
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Initialize the database, optionally load from dump file.')
parser.add_option("-L", "--load",
action='store', dest='FILE', default=None,
metavar="FILE", help="filepath of dump file to load")
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
init_database(dumpfilepath=options.FILE)
def main():
parser = utils.get_command_line_parser(description='OrderPortal server.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
utils.initialize()
url = tornado.web.url
handlers = [
url(r'/', Home, name='home'),
url(r'/status', Status, name="status")
]
try:
regexp = settings['ORDER_IDENTIFIER_REGEXP']
except KeyError:
pass
else:
handlers.append(
url(r"/order/({0})".format(regexp), Order, name='order_id'))
handlers.append(
url(r"/api/v1/order/({0})".format(regexp),
OrderApiV1,
name='order_id_api'))
handlers.extend([
url(r'/order/([0-9a-f]{32})', Order, name='order'),
url(r'/api/v1/order/([0-9a-f]{32})', OrderApiV1, name='order_api'),
url(r'/order/([^/]+).csv', OrderCsv, name='order_csv'),
url(r'/order/([^/]+).xlsx', OrderXlsx, name='order_xlsx'),
url(r'/order/([^/]+).zip', OrderZip, name='order_zip'),
url(r'/order/([0-9a-f]{32})/logs', OrderLogs, name='order_logs'),
url(r'/order', OrderCreate, name='order_create'),
url(r'/api/v1/order', OrderCreateApiV1, name='order_create_api'),
url(r'/order/([0-9a-f]{32})/edit', OrderEdit, name='order_edit'),
url(r'/order/([0-9a-f]{32})/transition/(\w+)',
OrderTransition,
name='order_transition'),
url(r'/api/v1/order/([0-9a-f]{32})/transition/(\w+)',
OrderTransitionApiV1,
name='order_transition_api'),
url(r'/order/([0-9a-f]{32})/owner', OrderOwner, name='order_owner'),
url(r'/order/([0-9a-f]{32})/clone', OrderClone, name='order_clone'),
url(r'/order/([0-9a-f]{32})/file', OrderFile, name='order_file_add'),
url(r'/order/([0-9a-f]{32})/file/([^/]+)',
OrderFile,
name='order_file'),
url(r'/order/([0-9a-f]{32})/report', OrderReport, name='order_report'),
url(r'/api/v1/order/([0-9a-f]{32})/report',
OrderReportApiV1,
name='order_report_api'),
url(r'/order/([0-9a-f]{32})/report/edit',
OrderReportEdit,
name='order_report_edit'),
url(r'/orders', Orders, name='orders'),
url(r'/api/v1/orders', OrdersApiV1, name='orders_api'),
url(r'/orders.csv', OrdersCsv, name='orders_csv'),
url(r'/orders.xlsx', OrdersXlsx, name='orders_xlsx'),
url(r'/accounts', Accounts, name='accounts'),
url(r'/api/v1/accounts', AccountsApiV1, name='accounts_api'),
url(r'/accounts.csv', AccountsCsv, name='accounts_csv'),
url(r'/accounts.xlsx', AccountsXlsx, name='accounts_xlsx'),
url(r'/account/([^/]+)', Account, name='account'),
url(r'/api/v1/account/([^/]+)', AccountApiV1, name='account_api'),
url(r'/account/([^/]+)/orders', AccountOrders, name='account_orders'),
url(r'/api/v1/account/([^/]+)/orders',
AccountOrdersApiV1,
name='account_orders_api'),
url(r'/account/([^/]+)/groups/orders',
AccountGroupsOrders,
name='account_groups_orders'),
url(r'/api/v1/account/([^/]+)/groups/orders',
AccountGroupsOrdersApiV1,
name='account_groups_orders_api'),
url(r'/account/([^/]+)/logs', AccountLogs, name='account_logs'),
url(r'/account/([^/]+)/messages',
AccountMessages,
name='account_messages'),
url(r'/account/([^/]+)/edit', AccountEdit, name='account_edit'),
url(r'/group', GroupCreate, name='group_create'),
url(r'/group/([0-9a-f]{32})', Group, name='group'),
url(r'/group/([0-9a-f]{32})/edit', GroupEdit, name='group_edit'),
url(r'/group/([0-9a-f]{32})/accept', GroupAccept, name='group_accept'),
url(r'/group/([0-9a-f]{32})/decline',
GroupDecline,
name='group_decline'),
url(r'/group/([0-9a-f]{32})/logs', GroupLogs, name='group_logs'),
url(r'/groups', Groups, name='groups'),
url(r'/search', Search, name='search'),
url(r'/login', Login, name='login'),
url(r'/logout', Logout, name='logout'),
url(r'/reset', Reset, name='reset'),
url(r'/password', Password, name='password'),
url(r'/register', Register, name='register'),
url(r'/registered', Registered, name='registered'),
url(r'/account/([^/]+)/enable', AccountEnable, name='account_enable'),
url(r'/account/([^/]+)/disable',
AccountDisable,
name='account_disable'),
url(r'/account/([^/]+)/updateinfo',
AccountUpdateInfo,
name='account_update_info'),
url(r'/forms', Forms, name='forms'),
url(r'/form/([0-9a-f]{32})', Form, name='form'),
url(r'/api/v1/form/([0-9a-f]{32})', FormApiV1, name='form_api'),
url(r'/form/([0-9a-f]{32})/logs', FormLogs, name='form_logs'),
url(r'/form', FormCreate, name='form_create'),
url(r'/form/([0-9a-f]{32})/edit', FormEdit, name='form_edit'),
url(r'/form/([0-9a-f]{32})/clone', FormClone, name='form_clone'),
url(r'/form/([0-9a-f]{32})/pending', FormPending, name='form_pending'),
url(r'/form/([0-9a-f]{32})/testing', FormTesting, name='form_testing'),
url(r'/form/([0-9a-f]{32})/enable', FormEnable, name='form_enable'),
url(r'/form/([0-9a-f]{32})/disable', FormDisable, name='form_disable'),
url(r'/form/([0-9a-f]{32})/field',
FormFieldCreate,
name='field_create'),
url(r'/form/([0-9a-f]{32})/field/([a-zA-Z][_a-zA-Z0-9]*)',
FormFieldEdit,
name='field_edit'),
url(r'/form/([0-9a-f]{32})/field/([a-zA-Z][_a-zA-Z0-9]*)/descr',
FormFieldEditDescr,
name='field_edit_descr'),
url(r'/form/([0-9a-f]{32})/orders', FormOrders, name='form_orders'),
url(r'/form/([0-9a-f]{32})/aggregate',
FormOrdersAggregate,
name='form_orders_aggregate'),
url(r'/news', News, name='news'),
url(r'/new/([0-9a-f]{32})', NewsEdit, name='news_edit'),
url(r'/new', NewsCreate, name='news_create'),
url(r'/events', Events, name='events'),
url(r'/event/([0-9a-f]{32})', Event, name='event'),
url(r'/event', EventCreate, name='event_create'),
url(r'/contact', Contact, name='contact'),
url(r'/about', About, name='about'),
url(r'/software', Software, name='software'),
url(r'/infos', Infos, name='infos'),
url(r'/info', InfoCreate, name='info_create'),
url(r'/info/([^/]+)', Info, name='info'),
url(r'/info/([^/]+)/edit', InfoEdit, name='info_edit'),
url(r'/info/([^/]+)/logs', InfoLogs, name='info_logs'),
url(r'/files', Files, name='files'),
url(r'/file', FileCreate, name='file_create'),
url(r'/file/([^/]+)', File, name='file'),
url(r'/file/([^/]+)/meta', FileMeta, name='file_meta'),
url(r'/file/([^/]+)/download', FileDownload, name='file_download'),
url(r'/file/([^/]+)/edit', FileEdit, name='file_edit'),
url(r'/api/v1/file/([^/]+)/edit', FileEditApiV1, name='file_edit_api'),
url(r'/file/([0-9a-f]{32})/logs', FileLogs, name='file_logs'),
url(r'/log/([0-9a-f]{32})', Log, name='log'),
url(r'/([0-9a-f]{32})', Entity, name='entity'),
url(r'/admin/global_modes', GlobalModes, name='global_modes'),
url(r'/admin/settings', Settings, name='settings'),
url(r'/admin/text/([^/]+)', Text, name='text'),
url(r'/admin/texts', Texts, name='texts'),
url(r'/admin/order_statuses', OrderStatuses, name='order_statuses'),
url(r'/admin/order_messages',
AdminOrderMessages,
name='admin_order_messages'),
url(r'/admin/account_messages',
AdminAccountMessages,
name='admin_account_messages'),
url(r'/site/([^/]+)',
tornado.web.StaticFileHandler,
{'path': utils.expand_filepath(settings['SITE_DIR'])},
name='site'),
])
handlers.append(url(r'/api/v1/(.*)', NoSuchEntityApiV1))
handlers.append(url(r'/(.*)', NoSuchEntity))
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=os.path.join(settings['ROOT_DIR'], 'templates'),
static_path=os.path.join(settings['ROOT_DIR'], 'static'),
login_url=(settings['BASE_URL_PATH_PREFIX'] or '') + '/login')
# Add href URLs for the status icons.
# This depends on order status setup.
for key, value in settings['ORDER_STATUSES_LOOKUP'].items():
value['href'] = application.reverse_url('site', key + '.png')
application.listen(settings['PORT'], xheaders=True)
pid = os.getpid()
url = settings['BASE_URL']
if settings['BASE_URL_PATH_PREFIX']:
url += settings['BASE_URL_PATH_PREFIX']
logging.info("web server %s (PID %s)", url, pid)
if options.pidfile:
with open(options.pidfile, 'w') as pf:
pf.write(str(pid))
tornado.ioloop.IOLoop.instance().start()
docs = []
for docid in docids:
try:
doc = db[docid]
except couchdb.ResourceNotFound:
print('no such document', docid, file=sys.stderr)
else:
docs.append(doc)
if docs:
if filepath:
outfile = open(filepath, 'w')
print('writing to', filepath)
else:
outfile = sys.stdout
json.dump(docs, outfile, indent=2)
else:
print('no such document(s)', file=sys.stderr)
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Get document(s) from CouchDB and write to JSON file.')
parser.add_option("-w", "--write",
action='store', dest='FILE', default=None,
metavar="FILE", help="filepath of file to write")
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
get_documents(utils.get_db(),
docids=args,
filepath=options.FILE)
else:
try:
del doc['_rev']
except KeyError:
pass
db.save(doc)
print('saved', doc['_id'])
def add_docs(docs, data):
if isinstance(data, dict):
if not '_id' in data: raise KeyError
docs.append(data)
elif isinstance(data, list):
for item in data:
if isinstance(item, dict):
if not '_id' in item: raise KeyError
docs.append(item)
else:
raise ValueError
else:
raise ValueError
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Put document(s) to CouchDB from JSON file.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
put_documents(utils.get_db(), filepaths=args)
for field in fields:
if field['type'] == constants.GROUP: continue
value = record.get(field['identifier'])
if isinstance(value, list):
value = '\n'.join(value)
values[field['identifier']] = value
saver['fields'] = values
saver['identifier'] = \
settings['ORDER_IDENTIFIER_FORMAT'].format(int(record['nid']))
counter = max(counter, int(record['nid']))
saver['history'] = {}
saver.set_status('undefined')
saver.check_fields_validity(fields)
print('loaded', saver.doc['identifier'], saver.doc['title'])
total += 1
print(total, 'orders loaded, counter', counter)
meta['counter'] = counter
db.save(meta)
if __name__ == '__main__':
parser = utils.get_command_line_parser(description=
"Load orders from old Drupal site JSON dump 'orders.json'.")
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
db = utils.get_db()
load_orders(db,
authors=load_users(),
form_iuid='ed37e428cd0e4b43894c9686555018a1')
regenerate_views(db)
def get_args():
parser = utils.get_command_line_parser(
description='Load the account messages document.')
return parser.parse_args()
pass
else:
changed = True
if changed:
print('saving',
project['identifier'],
project['fields']['lims_id'],
project['status'],
project['title'])
db.save(project)
else:
print('no change for', project['identifier'])
if __name__ == '__main__':
parser = utils.get_command_line_parser(description=
'Load project info from Clarity LIMS into OrderPortal.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
db = utils.get_db()
projects_lookup = get_old_portal_projects(db)
print(len(projects_lookup), 'projects from old portal requiring more info')
projects = projects_lookup.values()
projects.sort(lambda i,j: cmp(i['modified'], j['modified']))
for project in projects:
print(project['identifier'], project['modified'])
clarity = Clarity()
clarity_projects = clarity.get_all_projects()
print(len(clarity_projects), 'projects in Clarity')
for record in clarity_projects:
" Get the previous version of the document and save it as new. "
from __future__ import print_function, absolute_import
import sys
from orderportal import utils
def revert(db, docid):
revisions = list(db.revisions(docid))
if len(revisions) < 2:
sys.exit('no previous version to revert to')
latest = revisions[0]
previous = revisions[1]
new = previous.copy()
new['_rev'] = latest['_rev']
db.save(new)
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description=
'Get the previous version of the document and save it as new.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
db = utils.get_db()
for docid in args:
revert(db, docid)
def set_password(email, password):
db = utils.get_db()
view = db.view('account/email', include_docs=True)
rows = list(view[email])
if len(rows) != 1:
raise ValueError("no such account %s" % email)
doc = rows[0].doc
with AccountSaver(doc=doc, db=db) as saver:
saver.set_password(password)
print('Set password for', email)
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Set the password for an account.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
email = raw_input('Email address (=account name) > ')
if not email:
sys.exit('no email address provided')
password = getpass.getpass('Password > ')
if not password:
sys.exit('no password provided')
try:
utils.check_password(password)
except ValueError, msg:
sys.exit(str(msg))
again_password = getpass.getpass('Password again > ')
if password != again_password:
sys.exit('passwords do not match')
saver.set_email(email)
saver['first_name'] = first_name
saver['last_name'] = last_name
saver['address'] = dict()
saver['invoice_address'] = dict()
saver['university'] = university
saver['department'] = None
saver['owner'] = email
saver.set_password(password)
saver['role'] = constants.ADMIN
saver['status'] = constants.ENABLED
print('Created admin account', email)
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Create a new admin account.')
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
email = raw_input('Email address (=account name) > ')
if not email:
sys.exit('no email address provided')
password = getpass.getpass('Password > ')
if not password:
sys.exit('no password provided')
try:
utils.check_password(password)
except ValueError, msg:
sys.exit(str(msg))
again_password = getpass.getpass('Password again > ')
if password != again_password:
sys.exit('passwords do not match')
def get_args():
parser = utils.get_command_line_parser(
description='Put document(s) to CouchDB from JSON file.')
return parser.parse_args()
undump(db, dumpfilepath)
designs.regenerate_views_indexes(db)
except IOError:
print('Warning: could not load', dumpfilepath)
else:
print('no dump file loaded')
# Load texts from the initial texts YAML file. Only if missing in db!
print('loading any missing texts from', INIT_TEXTS_FILEPATH)
try:
with open(INIT_TEXTS_FILEPATH) as infile:
texts = yaml.safe_load(infile)
except IOError:
print('Warning: could not load', INIT_TEXTS_FILEPATH)
texts = dict()
for name in constants.TEXTS:
if len(list(db.view('text/name', key=name))) == 0:
with admin.TextSaver(db=db) as saver:
saver['name'] = name
saver['text'] = texts.get(name, '')
if __name__ == '__main__':
parser = utils.get_command_line_parser(
description='Initialize the database, optionally load from dump file.')
parser.add_option("-L", "--load",
action='store', dest='FILE', default=None,
metavar="FILE", help="filepath of dump file to load")
(options, args) = parser.parse_args()
utils.load_settings(filepath=options.settings)
init_database(dumpfilepath=options.FILE)
def get_args():
parser = utils.get_command_line_parser(
description='Create a new admin account.')
return parser.parse_args()
