From 1e9b76105c0faaa8f95a4e89e95cc2c765a01232 Mon Sep 17 00:00:00 2001
From: Megan Henning <meganhenning@flywheel.io>
Date: Thu, 21 Jul 2016 17:48:24 -0500
Subject: [PATCH] Fix most pylint warnings
---
api/api.py | 2 +-
api/base.py | 8 ++--
api/centralclient.py | 28 +++----------
api/dao/liststorage.py | 2 +-
api/handlers/collectionshandler.py | 50 +++++++++++------------
api/handlers/grouphandler.py | 12 +-----
api/handlers/listhandler.py | 65 +++++++++++++-----------------
api/handlers/reporthandler.py | 8 ++--
api/handlers/schemahandler.py | 3 +-
api/handlers/searchhandler.py | 5 ++-
api/handlers/userhandler.py | 20 +++------
api/jobs/jobs.py | 2 +-
api/jobs/queue.py | 4 +-
api/placer.py | 6 +--
api/search/queryprocessor.py | 3 +-
15 files changed, 85 insertions(+), 133 deletions(-)
diff --git a/api/api.py b/api/api.py
index f18db054..b6d92dd6 100644
--- a/api/api.py
+++ b/api/api.py
@@ -169,7 +169,7 @@ routing_regexes = {
'note_id_re': '[0-9a-f]{24}',
# schema regex
# example: schema_path/schema.json
- 'schema_re': '[^/.]{3,60}/[^/.]{3,60}\.json'
+ 'schema_re': r'[^/.]{3,60}/[^/.]{3,60}\.json'
}
def _format(route):
diff --git a/api/base.py b/api/base.py
index 1e2a01ce..0cb67415 100644
--- a/api/base.py
+++ b/api/base.py
@@ -132,10 +132,10 @@ class RequestHandler(webapp2.RequestHandler):
if cached_token:
uid = cached_token['uid']
- log.debug('looked up cached token in %dms' % ((datetime.datetime.utcnow() - timestamp).total_seconds() * 1000.))
+ log.debug('looked up cached token in %dms', ((datetime.datetime.utcnow() - timestamp).total_seconds() * 1000.))
else:
uid = self.validate_oauth_token(access_token, timestamp)
- log.debug('looked up remote token in %dms' % ((datetime.datetime.utcnow() - timestamp).total_seconds() * 1000.))
+ log.debug('looked up remote token in %dms', ((datetime.datetime.utcnow() - timestamp).total_seconds() * 1000.))
# Cache the token for future requests
config.db.authtokens.replace_one({'_id': access_token}, {'uid': uid, 'timestamp': timestamp}, upsert=True)
@@ -296,7 +296,7 @@ class RequestHandler(webapp2.RequestHandler):
site_id = config.get_item('site', 'id')
target_site = self.get_param('site', site_id)
if target_site == site_id:
- log.debug('from %s %s %s %s %s' % (self.source_site, self.uid, self.request.method, self.request.path, str(self.request.GET.mixed())))
+ log.debug('from %s %s %s %s %s', self.source_site, self.uid, self.request.method, self.request.path, str(self.request.GET.mixed()))
return super(RequestHandler, self).dispatch()
else:
if not site_id:
@@ -318,7 +318,7 @@ class RequestHandler(webapp2.RequestHandler):
params = self.request.GET.mixed()
if 'user' in params: del params['user']
del params['site']
- log.debug(' for %s %s %s %s %s' % (target_site, self.uid, self.request.method, self.request.path, str(self.request.GET.mixed())))
+ log.debug(' for %s %s %s %s %s', target_site, self.uid, self.request.method, self.request.path, str(self.request.GET.mixed()))
target_uri = target['api_uri'] + self.request.path.split('/api')[1]
r = requests.request(
self.request.method,
diff --git a/api/centralclient.py b/api/centralclient.py
index 711289fd..5c2294a5 100644
--- a/api/centralclient.py
+++ b/api/centralclient.py
@@ -44,8 +44,8 @@ def update(db, api_uri, site_name, site_id, ssl_cert, central_url):
response = (json.loads(r.content))
sites = response.get('sites')
users = response.get('users')
- log.debug('recieved sites: %s ' % ', '.join(s['_id'] for s in sites))
- log.debug('recieved users: %s' % ', '.join([key for key in users]))
+ log.debug('recieved sites: %s ', ', '.join(s['_id'] for s in sites))
+ log.debug('recieved users: %s', ', '.join([key for key in users]))
if response.get('users'):
for _id, remotes in response['users'].iteritems():
db.users.update_one({'_id': _id}, {'$set': {'remotes': remotes}})
@@ -57,10 +57,10 @@ def update(db, api_uri, site_name, site_id, ssl_cert, central_url):
{'remotes': {'$exists': True}, '_id': {'$nin': users.keys()}},
{'$unset': {'remotes': ''}},
)
- log.info('%3d users with remote data, %3d remotes' % (
+ log.info('%3d users with remote data, %3d remotes' ,
len([u['_id'] for u in db.users.find({'remotes': {'$exists': True}}, {'_id': True})]),
len([s['_id'] for s in db.sites.find({}, {'_id': True})])
- ))
+ )
return True
else:
# r.reason contains generic description for the specific error code
@@ -70,7 +70,7 @@ def update(db, api_uri, site_name, site_id, ssl_cert, central_url):
msg = reason.group(1)
else:
msg = r.reason
- log.warning('%s - %s' % (r.status_code, msg))
+ log.warning('%s - %s', r.status_code, msg)
return False
@@ -139,21 +139,3 @@ class CentralClient(base.RequestHandler):
self.abort(404, 'register endpoint is not implemented')
# every request to this route is aborted at the moment
- if not config.get_item('site', 'registered'):
- self.abort(400, 'Site not registered with central')
- if not config.get_item('site', 'ssl_cert'):
- self.abort(400, 'SSL cert not configured')
- if not config.get_item('site', 'central_url'):
- self.abort(400, 'Central URL not configured')
- if not update(db=config.db,
- api_uri=config.get_item('site', 'api_url'),
- site_name=config.get_item('site', 'name'),
- site_id=config.get_item('site', 'id'),
- ssl_cert=config.get_item('site', 'ssl_cert'),
- central_url=config.get_item('site', 'central_url'),):
- fail_count += 1
- else:
- fail_count = 0
- if fail_count == 3:
- log.warning('scitran central unreachable, purging all remotes info')
- clean_remotes(db=config.db, site_id=config.get_item('site', 'id'))
diff --git a/api/dao/liststorage.py b/api/dao/liststorage.py
index 1bd902d7..c4f0ac74 100644
--- a/api/dao/liststorage.py
+++ b/api/dao/liststorage.py
@@ -270,7 +270,7 @@ class AnalysesStorage(ListStorage):
files.append(file_)
q = {'analyses._id': analysis['_id']}
- u = {'$set': {'analyses.$.job': job._id, 'analyses.$.files': files}}
+ u = {'$set': {'analyses.$.job': job.id_, 'analyses.$.files': files}}
config.db.sessions.update_one(q, u)
analysis['job'] = job
diff --git a/api/handlers/collectionshandler.py b/api/handlers/collectionshandler.py
index 24b52ff8..a740fca4 100644
--- a/api/handlers/collectionshandler.py
+++ b/api/handlers/collectionshandler.py
@@ -6,12 +6,13 @@ from ..auth import containerauth, always_ok
from ..dao import containerstorage
from ..dao import APIStorageException
-from containerhandler import ContainerHandler
+from .containerhandler import ContainerHandler
log = config.log
class CollectionsHandler(ContainerHandler):
+ # pylint: disable=arguments-differ
container_handler_configurations = ContainerHandler.container_handler_configurations
@@ -23,9 +24,13 @@ class CollectionsHandler(ContainerHandler):
'list_projection': {'metadata': 0}
}
+ def __init__(self, request=None, response=None):
+ super(CollectionsHandler, self).__init__(request, response)
+
+
+
def post(self, **kwargs):
- self.config = self.container_handler_configurations['collections']
- self.storage = self.config['storage']
+ storage = self.container_handler_configurations['collections']['storage']
mongo_validator, payload_validator = self._get_validators()
payload = self.request.json_body
@@ -38,7 +43,7 @@ class CollectionsHandler(ContainerHandler):
}]
payload['curator'] = self.uid
payload['created'] = payload['modified'] = datetime.datetime.utcnow()
- result = mongo_validator(self.storage.exec_op)('POST', payload=payload)
+ result = mongo_validator(storage.exec_op)('POST', payload=payload)
if result.acknowledged:
return {'_id': result.inserted_id}
@@ -47,8 +52,7 @@ class CollectionsHandler(ContainerHandler):
def put(self, **kwargs):
_id = kwargs.pop('cid')
- self.config = self.container_handler_configurations['collections']
- self.storage = self.config['storage']
+ storage = self.container_handler_configurations['collections']['storage']
container = self._get_container(_id)
mongo_validator, payload_validator = self._get_validators()
@@ -58,7 +62,7 @@ class CollectionsHandler(ContainerHandler):
permchecker = self._get_permchecker(container)
payload['modified'] = datetime.datetime.utcnow()
try:
- result = mongo_validator(permchecker(self.storage.exec_op))('PUT', _id=_id, payload=payload)
+ result = mongo_validator(permchecker(storage.exec_op))('PUT', _id=_id, payload=payload)
except APIStorageException as e:
self.abort(400, e.message)
@@ -66,7 +70,7 @@ class CollectionsHandler(ContainerHandler):
self._add_contents(contents, _id)
return {'modified': result.modified_count}
else:
- self.abort(404, 'Element not updated in collection {} {}'.format(self.storage.cont_name, _id))
+ self.abort(404, 'Element not updated in collection {} {}'.format(storage.cont_name, _id))
def _add_contents(self, contents, _id):
if not contents:
@@ -95,20 +99,18 @@ class CollectionsHandler(ContainerHandler):
config.db.acquisitions.update_many({'collections': bson.ObjectId(_id)}, {'$pull': {'collections': bson.ObjectId(_id)}})
def get_all(self, cont_name):
- self.config = self.container_handler_configurations[cont_name]
- self.storage = self.config['storage']
- projection = self.config['list_projection']
+ storage = self.container_handler_configurations['collections']['storage']
+ projection = self.container_handler_configurations['collections']['list_projection']
if self.superuser_request:
permchecker = always_ok
elif self.public_request:
permchecker = containerauth.list_public_request
else:
- admin_only = self.is_true('admin')
- permchecker = containerauth.list_permission_checker(self, admin_only)
+ permchecker = containerauth.list_permission_checker(self)
query = {}
- results = permchecker(self.storage.exec_op)('GET', query=query, public=self.public_request, projection=projection)
+ results = permchecker(storage.exec_op)('GET', query=query, public=self.public_request, projection=projection)
if results is None:
- self.abort(404, 'Element not found in collection {}'.format(self.storage.cont_name))
+ self.abort(404, 'Element not found in collection {}'.format(storage.cont_name))
self._filter_all_permissions(results, self.uid, self.user_site)
if self.is_true('counts'):
self._add_results_counts(results)
@@ -136,16 +138,15 @@ class CollectionsHandler(ContainerHandler):
curator_ids = list(set((c['curator'] for c in self.get_all('collections'))))
return list(config.db.users.find({'_id': {'$in': curator_ids}}, ['firstname', 'lastname']))
- def get_sessions(self, cont_name, cid):
+ def get_sessions(self, cid):
"""Return the list of sessions in a collection."""
- # FIXME use storage and permission checking abstractions
- self.config = self.container_handler_configurations['collections']
- self.storage = self.config['storage']
+ # TODO use storage and permission checking abstractions
+ storage = self.container_handler_configurations['collections']['storage']
if not bson.ObjectId.is_valid(cid):
self.abort(400, 'not a valid object id')
_id = bson.ObjectId(cid)
- if not self.storage.dbc.find_one({'_id': _id}):
+ if not storage.dbc.find_one({'_id': _id}):
self.abort(404, 'no such Collection')
agg_res = config.db.acquisitions.aggregate([
{'$match': {'collections': _id}},
@@ -168,16 +169,15 @@ class CollectionsHandler(ContainerHandler):
sess['debug']['acquisitions'] = self.uri_for('coll_acq', cont_name='collections', cid=cid, _full=True) + '?session=%s&user=%s' % (sid, self.get_param('user', ''))
return sessions
- def get_acquisitions(self, cid, **kwargs):
+ def get_acquisitions(self, cid):
"""Return the list of acquisitions in a collection."""
- # FIXME use storage and permission checking abstractions
- self.config = self.container_handler_configurations['collections']
- self.storage = self.config['storage']
+ # TODO use storage and permission checking abstractions
+ storage = self.container_handler_configurations['collections']['storage']
if not bson.ObjectId.is_valid(cid):
self.abort(400, 'not a valid object id')
_id = bson.ObjectId(cid)
- if not self.storage.dbc.find_one({'_id': _id}):
+ if not storage.dbc.find_one({'_id': _id}):
self.abort(404, 'no such Collection')
query = {'collections': _id}
sid = self.get_param('session', '')
diff --git a/api/handlers/grouphandler.py b/api/handlers/grouphandler.py
index 6d1e0785..07f56893 100644
--- a/api/handlers/grouphandler.py
+++ b/api/handlers/grouphandler.py
@@ -5,7 +5,7 @@ from .. import util
from .. import config
from .. import debuginfo
from .. import validators
-from ..auth import groupauth, always_ok
+from ..auth import groupauth
from ..dao import containerstorage
log = config.log
@@ -15,9 +15,9 @@ class GroupHandler(base.RequestHandler):
def __init__(self, request=None, response=None):
super(GroupHandler, self).__init__(request, response)
+ self.storage = containerstorage.GroupStorage('groups', use_object_id=False)
def get(self, _id):
- self._init_storage()
group = self._get_group(_id)
if not group:
self.abort(404, 'no such Group: ' + _id)
@@ -30,7 +30,6 @@ class GroupHandler(base.RequestHandler):
def delete(self, _id):
if _id == 'unknown':
self.abort(400, 'The group "unknown" can\'t be deleted as it is integral within the API')
- self._init_storage()
group = self._get_group(_id)
if not group:
self.abort(404, 'no such Group: ' + _id)
@@ -43,8 +42,6 @@ class GroupHandler(base.RequestHandler):
return result
def get_all(self, uid=None):
- self._init_storage()
- query = None
projection = {'name': 1, 'created': 1, 'modified': 1, 'roles': [], 'tags': []}
permchecker = groupauth.list_permission_checker(self, uid)
results = permchecker(self.storage.exec_op)('GET', projection=projection)
@@ -57,7 +54,6 @@ class GroupHandler(base.RequestHandler):
return results
def put(self, _id):
- self._init_storage()
group = self._get_group(_id)
if not group:
self.abort(404, 'no such Group: ' + _id)
@@ -75,7 +71,6 @@ class GroupHandler(base.RequestHandler):
self.abort(404, 'Group {} not updated'.format(_id))
def post(self):
- self._init_storage()
permchecker = groupauth.default(self, None)
payload = self.request.json_body
mongo_schema_uri = validators.schema_uri('mongo', 'group.json')
@@ -95,9 +90,6 @@ class GroupHandler(base.RequestHandler):
else:
self.abort(404, 'Group {} not updated'.format(payload['_id']))
- def _init_storage(self):
- self.storage = containerstorage.GroupStorage('groups', use_object_id=False)
-
def _get_group(self, _id):
group = self.storage.get_container(_id)
if group is not None:
diff --git a/api/handlers/listhandler.py b/api/handlers/listhandler.py
index 1b0f0ae0..962bf2cc 100644
--- a/api/handlers/listhandler.py
+++ b/api/handlers/listhandler.py
@@ -9,10 +9,7 @@ import zipfile
from .. import base
from .. import config
-from .. import files
-from ..jobs import rules
from ..jobs.jobs import Job
-from .. import tempdir as tempfile
from .. import upload
from .. import download
from .. import util
@@ -73,7 +70,7 @@ def initialize_list_configurations():
'input_schema_file': 'analysis.json'
}
}
- list_handler_configurations = {
+ list_container_configurations = {
'groups': {
'roles':{
'storage': liststorage.ListStorage,
@@ -97,7 +94,7 @@ def initialize_list_configurations():
'collections': copy.deepcopy(container_default_configurations)
}
# preload the Storage instances for all configurations
- for cont_name, cont_config in list_handler_configurations.iteritems():
+ for cont_name, cont_config in list_container_configurations.iteritems():
for list_name, list_config in cont_config.iteritems():
storage_class = list_config['storage']
storage = storage_class(
@@ -106,7 +103,7 @@ def initialize_list_configurations():
use_object_id=list_config.get('use_object_id', False)
)
list_config['storage'] = storage
- return list_handler_configurations
+ return list_container_configurations
list_handler_configurations = initialize_list_configurations()
@@ -130,7 +127,7 @@ class ListHandler(base.RequestHandler):
def get(self, cont_name, list_name, **kwargs):
_id = kwargs.pop('cid')
- container, permchecker, storage, _, _, keycheck = self._initialize_request(cont_name, list_name, _id, query_params=kwargs)
+ permchecker, storage, _, _, keycheck = self._initialize_request(cont_name, list_name, _id, query_params=kwargs)
try:
result = keycheck(permchecker(storage.exec_op))('GET', _id, query_params=kwargs)
except APIStorageException as e:
@@ -142,7 +139,7 @@ class ListHandler(base.RequestHandler):
def post(self, cont_name, list_name, **kwargs):
_id = kwargs.pop('cid')
- container, permchecker, storage, mongo_validator, payload_validator, keycheck = self._initialize_request(cont_name, list_name, _id)
+ permchecker, storage, mongo_validator, payload_validator, keycheck = self._initialize_request(cont_name, list_name, _id)
payload = self.request.json_body
payload_validator(payload, 'POST')
@@ -155,7 +152,7 @@ class ListHandler(base.RequestHandler):
def put(self, cont_name, list_name, **kwargs):
_id = kwargs.pop('cid')
- container, permchecker, storage, mongo_validator, payload_validator, keycheck = self._initialize_request(cont_name, list_name, _id, query_params=kwargs)
+ permchecker, storage, mongo_validator, payload_validator, keycheck = self._initialize_request(cont_name, list_name, _id, query_params=kwargs)
payload = self.request.json_body
payload_validator(payload, 'PUT')
@@ -171,7 +168,7 @@ class ListHandler(base.RequestHandler):
def delete(self, cont_name, list_name, **kwargs):
_id = kwargs.pop('cid')
- container, permchecker, storage, _, _, keycheck = self._initialize_request(cont_name, list_name, _id, query_params=kwargs)
+ permchecker, storage, _, _, keycheck = self._initialize_request(cont_name, list_name, _id, query_params=kwargs)
try:
result = keycheck(permchecker(storage.exec_op))('DELETE', _id, query_params=kwargs)
except APIStorageException as e:
@@ -191,11 +188,11 @@ class ListHandler(base.RequestHandler):
5) the mongo_validator that will check what will be sent to mongo against a json schema
6) the keycheck decorator validating the request key
"""
- config = list_handler_configurations[cont_name][list_name]
- storage = config['storage']
- permchecker = config['permchecker']
- if config.get('get_full_container'):
- query_params = None
+ conf = list_handler_configurations[cont_name][list_name]
+ storage = conf['storage']
+ permchecker = conf['permchecker']
+ if conf.get('get_full_container'):
+ query_params = None
container = storage.get_container(_id, query_params)
if container is not None:
if self.superuser_request:
@@ -206,12 +203,12 @@ class ListHandler(base.RequestHandler):
permchecker = permchecker(self, container)
else:
self.abort(404, 'Element {} not found in container {}'.format(_id, storage.cont_name))
- mongo_schema_uri = validators.schema_uri('mongo', config.get('storage_schema_file'))
+ mongo_schema_uri = validators.schema_uri('mongo', conf.get('storage_schema_file'))
mongo_validator = validators.decorator_from_schema_path(mongo_schema_uri)
- input_schema_uri = validators.schema_uri('input', config.get('input_schema_file'))
+ input_schema_uri = validators.schema_uri('input', conf.get('input_schema_file'))
input_validator = validators.from_schema_path(input_schema_uri)
keycheck = validators.key_check(mongo_schema_uri)
- return container, permchecker, storage, mongo_validator, input_validator, keycheck
+ return permchecker, storage, mongo_validator, input_validator, keycheck
class PermissionsListHandler(ListHandler):
@@ -248,7 +245,7 @@ class PermissionsListHandler(ListHandler):
'permissions': config.db.projects.find_one({'_id': oid},{'permissions': 1})['permissions']
}}
hierarchy.propagate_changes(cont_name, oid, {}, update)
- except:
+ except APIStorageException:
self.abort(500, 'permissions not propagated from project {} to sessions'.format(_id))
@@ -260,7 +257,7 @@ class NotesListHandler(ListHandler):
def post(self, cont_name, list_name, **kwargs):
_id = kwargs.pop('cid')
- container, permchecker, storage, mongo_validator, input_validator, keycheck = self._initialize_request(cont_name, list_name, _id)
+ permchecker, storage, mongo_validator, input_validator, keycheck = self._initialize_request(cont_name, list_name, _id)
payload = self.request.json_body
input_validator(payload, 'POST')
@@ -278,7 +275,7 @@ class NotesListHandler(ListHandler):
def put(self, cont_name, list_name, **kwargs):
_id = kwargs.pop('cid')
- container, permchecker, storage, mongo_validator, input_validator, keycheck = self._initialize_request(cont_name, list_name, _id, query_params=kwargs)
+ permchecker, storage, mongo_validator, input_validator, keycheck = self._initialize_request(cont_name, list_name, _id, query_params=kwargs)
payload = self.request.json_body
input_validator(payload, 'PUT')
@@ -327,7 +324,7 @@ class TagsListHandler(ListHandler):
"""
try:
hierarchy.propagate_changes(cont_name, _id, query, update)
- except:
+ except APIStorageException:
self.abort(500, 'tag change not propagated from group {}'.format(_id))
@@ -406,7 +403,7 @@ class FileListHandler(ListHandler):
"""
_id = kwargs.pop('cid')
- container, permchecker, storage, _, _, keycheck = self._initialize_request(cont_name, list_name, _id)
+ permchecker, storage, _, _, keycheck = self._initialize_request(cont_name, list_name, _id)
list_name = storage.list_name
filename = kwargs.get('name')
@@ -464,12 +461,6 @@ class FileListHandler(ListHandler):
self.response.headers['Content-Type'] = 'application/octet-stream'
self.response.headers['Content-Disposition'] = 'attachment; filename="' + filename + '"'
- def delete(self, cont_name, list_name, **kwargs):
- filename = kwargs.get('name')
- _id = kwargs.get('cid')
- result = super(FileListHandler, self).delete(cont_name, list_name, **kwargs)
- return result
-
def post(self, cont_name, list_name, **kwargs):
_id = kwargs.pop('cid')
@@ -481,10 +472,10 @@ class FileListHandler(ListHandler):
cont_name_plural = cont_name + 's'
# Authorize
- container, permchecker, storage, mongo_validator, payload_validator, keycheck = self._initialize_request(cont_name_plural, list_name, _id)
+ permchecker, _, _, _, _ = self._initialize_request(cont_name_plural, list_name, _id)
permchecker(noop)('POST', _id=_id)
- return upload.process_upload(self.request, upload.Strategy.targeted, container_type=cont_name, id=_id, origin=self.origin)
+ return upload.process_upload(self.request, upload.Strategy.targeted, container_type=cont_name, id_=_id, origin=self.origin)
def _check_packfile_token(self, project_id, token_id, check_user=True):
"""
@@ -563,7 +554,7 @@ class FileListHandler(ListHandler):
'token': str(result.inserted_id)
}
- def packfile(self, cont_name, **kwargs):
+ def packfile(self, **kwargs):
"""
Add files to an in-progress packfile.
"""
@@ -574,7 +565,7 @@ class FileListHandler(ListHandler):
return upload.process_upload(self.request, upload.Strategy.token, origin=self.origin, context={'token': token_id})
- def packfile_end(self, cont_name, **kwargs):
+ def packfile_end(self, **kwargs):
"""
Complete and save an uploaded packfile.
"""
@@ -678,7 +669,7 @@ class AnalysesHandler(ListHandler):
"""
_id = kwargs.pop('cid')
- container, permchecker, storage, mongo_validator, _, keycheck = self._initialize_request(cont_name, list_name, _id)
+ permchecker, storage, mongo_validator, _, keycheck = self._initialize_request(cont_name, list_name, _id)
permchecker(noop)('POST', _id=_id)
if self.is_true('job'):
@@ -840,7 +831,7 @@ class AnalysesHandler(ListHandler):
"""
_id = kwargs.pop('cid')
- container, permchecker, storage, _, _, _ = self._initialize_request(cont_name, list_name, _id)
+ permchecker, storage, _, _, _ = self._initialize_request(cont_name, list_name, _id)
filename = kwargs.get('name')
ticket_id = self.get_param('ticket')
if not ticket_id:
@@ -910,7 +901,7 @@ class AnalysesHandler(ListHandler):
def delete_note(self, cont_name, list_name, **kwargs):
_id = kwargs.pop('cid')
analysis_id = kwargs.pop('_id')
- container, permchecker, storage, _, _, _ = self._initialize_request(cont_name, list_name, _id)
+ permchecker, storage, _, _, _ = self._initialize_request(cont_name, list_name, _id)
note_id = kwargs.get('note_id')
permchecker(noop)('DELETE', _id=_id)
result = storage.delete_note(_id=_id, analysis_id=analysis_id, note_id=note_id)
@@ -922,7 +913,7 @@ class AnalysesHandler(ListHandler):
def add_note(self, cont_name, list_name, **kwargs):
_id = kwargs.pop('cid')
analysis_id = kwargs.get('_id')
- container, permchecker, storage, mongo_validator, input_validator, keycheck = self._initialize_request(cont_name, list_name, _id)
+ permchecker, storage, _, input_validator, _ = self._initialize_request(cont_name, list_name, _id)
payload = self.request.json_body
input_validator(payload, 'POST')
payload['_id'] = str(bson.objectid.ObjectId())
diff --git a/api/handlers/reporthandler.py b/api/handlers/reporthandler.py
index 52347e51..6855d13e 100644
--- a/api/handlers/reporthandler.py
+++ b/api/handlers/reporthandler.py
@@ -1,11 +1,9 @@
-import json
import bson
import dateutil
import copy
from .. import base
from .. import config
-from .. import util
log = config.log
@@ -19,7 +17,7 @@ class ReportHandler(base.RequestHandler):
def __init__(self, request=None, response=None):
super(ReportHandler, self).__init__(request, response)
- def get(self, report_type, **kwargs):
+ def get(self, report_type):
report = None
if report_type == 'site':
report = SiteReport()
@@ -38,7 +36,7 @@ class ReportHandler(base.RequestHandler):
if end_date is not None and start_date is not None and end_date < start_date:
self.abort(400, 'End date {} is before start date {}'.format(end_date, start_date))
- report = ProjectReport(map(bson.ObjectId, project_list),
+ report = ProjectReport([bson.ObjectId(id_) for id_ in project_list],
start_date=start_date,
end_date=end_date)
@@ -193,7 +191,7 @@ class ProjectReport(Report):
if perm.get('access') == 'admin':
admins.append(perm.get('_id'))
admin_objs = config.db.users.find({'_id': {'$in': admins}})
- project['admins'] = map(lambda x: x.get('firstname','')+' '+x.get('lastname',''), admin_objs)
+ project['admins'] = map(lambda x: x.get('firstname','')+' '+x.get('lastname',''), admin_objs) # pylint: disable=bad-builtin, deprecated-lambda
base_query = self._base_query(p['_id'])
project['session_count'] = config.db.sessions.count(base_query)
diff --git a/api/handlers/schemahandler.py b/api/handlers/schemahandler.py
index 18eb4a00..f672e38b 100644
--- a/api/handlers/schemahandler.py
+++ b/api/handlers/schemahandler.py
@@ -1,6 +1,5 @@
import os
import json
-import datetime
from .. import base
from .. import config
@@ -12,7 +11,7 @@ class SchemaHandler(base.RequestHandler):
def __init__(self, request=None, response=None):
super(SchemaHandler, self).__init__(request, response)
- def get(self, schema, **kwargs):
+ def get(self, schema):
schema_path = os.path.join(config.get_item('persistent', 'schema_path'), schema)
try:
with open(schema_path, 'ru') as f:
diff --git a/api/handlers/searchhandler.py b/api/handlers/searchhandler.py
index eca3f677..891e04f2 100644
--- a/api/handlers/searchhandler.py
+++ b/api/handlers/searchhandler.py
@@ -67,8 +67,9 @@ class SearchHandler(base.RequestHandler):
def __init__(self, request=None, response=None):
super(SearchHandler, self).__init__(request, response)
+ self.search_containers = None
- def advanced_search(self, **kwargs):
+ def advanced_search(self):
if self.public_request:
self.abort(403, 'search is available only for authenticated users')
queries = self.request.json_body
@@ -113,7 +114,7 @@ class SearchHandler(base.RequestHandler):
parents.update(self._get_parents(parent_container, parent_name))
return parents
- def get_datatree(self, **kwargs):
+ def get_datatree(self):
if self.public_request:
self.abort(403, 'search is available only for authenticated users')
size = self.get_param('size')
diff --git a/api/handlers/userhandler.py b/api/handlers/userhandler.py
index 1ef7f4db..73fe2e72 100644
--- a/api/handlers/userhandler.py
+++ b/api/handlers/userhandler.py
@@ -7,9 +7,9 @@ from .. import base
from .. import util
from .. import config
from .. import validators
-from ..auth import userauth, always_ok, ROLES
+from ..auth import userauth
from ..dao import containerstorage
-from ..dao import noop
+from ..dao import noop, APIStorageException
log = config.log
@@ -18,9 +18,9 @@ class UserHandler(base.RequestHandler):
def __init__(self, request=None, response=None):
super(UserHandler, self).__init__(request, response)
+ self.storage = containerstorage.ContainerStorage('users', use_object_id=False)
def get(self, _id):
- self._init_storage()
user = self._get_user(_id)
permchecker = userauth.default(self, user)
result = permchecker(self.storage.exec_op)('GET', _id, projection={'api_key': 0} or None)
@@ -30,7 +30,6 @@ class UserHandler(base.RequestHandler):
def self(self):
"""Return details for the current User."""
- self._init_storage()
if not self.uid:
self.abort(400, 'no user is logged in')
user = self.storage.exec_op('GET', self.uid)
@@ -47,7 +46,6 @@ class UserHandler(base.RequestHandler):
return result
def delete(self, _id):
- self._init_storage()
user = self._get_user(_id)
permchecker = userauth.default(self, user)
# Check for authZ before cleaning up user permissions
@@ -94,8 +92,6 @@ class UserHandler(base.RequestHandler):
{"modified": 1}
"""
-
- self._init_storage()
user = self._get_user(_id)
permchecker = userauth.default(self, user)
payload = self.request.json_body
@@ -159,9 +155,6 @@ class UserHandler(base.RequestHandler):
else:
self.abort(404, 'User {} not updated'.format(payload['_id']))
- def _init_storage(self):
- self.storage = containerstorage.ContainerStorage('users', use_object_id=False)
-
def _cleanup_user_permissions(self, uid):
try:
config.db.collections.delete_many({'curator': uid})
@@ -172,17 +165,15 @@ class UserHandler(base.RequestHandler):
config.db.projects.update_many(query, update)
config.db.sessions.update_many(query, update)
config.db.acquisitions.update_many(query, update)
- except:
+ except APIStorageException:
self.abort(500, 'Site-wide user permissions for {} were unabled to be removed'.format(uid))
def avatar(self, uid):
- self._init_storage()
self.resolve_avatar(uid, default=self.request.GET.get('default'))
def self_avatar(self):
if self.uid is None:
self.abort(404, 'not a logged-in user')
- self._init_storage()
self.resolve_avatar(self.uid, default=self.request.GET.get('default'))
def resolve_avatar(self, email, default=None):
@@ -194,11 +185,10 @@ class UserHandler(base.RequestHandler):
# Storage throws a 404; we want to catch that and handle it separately in the case of a provided default.
try:
user = self._get_user(email)
- except:
+ except APIStorageException:
user = {}
avatar = user.get('avatar', None)
- avatars = user.get('avatars', {})
# If the user exists but has no set avatar, try to get one
if user and avatar is None:
diff --git a/api/jobs/jobs.py b/api/jobs/jobs.py
index 0f320d28..dc5a3b4c 100644
--- a/api/jobs/jobs.py
+++ b/api/jobs/jobs.py
@@ -97,7 +97,7 @@ class Job(object):
d['_id'] = str(d['_id'])
- return cls(d['name'], d.get('inputs', None), destination=d.get('destination', None), tags=d['tags'], attempt=d['attempt'], previous_job_id=d.get('previous_job_id', None), created=d['created'], modified=d['modified'], state=d['state'], request=d.get('request', None), _id=d['_id'])
+ return cls(d['name'], d.get('inputs', None), destination=d.get('destination', None), tags=d['tags'], attempt=d['attempt'], previous_job_id=d.get('previous_job_id', None), created=d['created'], modified=d['modified'], state=d['state'], request=d.get('request', None), id_=d['_id'])
@classmethod
def get(cls, _id):
diff --git a/api/jobs/queue.py b/api/jobs/queue.py
index 91179067..fccb3b65 100644
--- a/api/jobs/queue.py
+++ b/api/jobs/queue.py
@@ -83,7 +83,7 @@ class Queue(object):
"""
if job.attempt >= max_attempts() and not force:
- log.info('Permanently failed job %s (after %d attempts)' % (job.id_, job.attempt))
+ log.info('Permanently failed job %s (after %d attempts)', job.id_, job.attempt)
return
if job.state != 'failed':
@@ -109,7 +109,7 @@ class Queue(object):
new_job.modified = now
new_id = new_job.insert()
- log.info('respawned job %s as %s (attempt %d)' % (job.id_, new_id, new_job.attempt))
+ log.info('respawned job %s as %s (attempt %d)', job.id_, new_id, new_job.attempt)
return new_id
diff --git a/api/placer.py b/api/placer.py
index 5e894500..b1c927c8 100644
--- a/api/placer.py
+++ b/api/placer.py
@@ -161,9 +161,9 @@ class UIDPlacer(Placer):
container = target['container']
r_metadata = target['metadata']
- self.container_type = container.level
- self.id = container._id
- self.container = container.container
+ self.container_type = container['level']
+ self.id = container['_id']
+ self.container = container['container']
info.update(r_metadata)
diff --git a/api/search/queryprocessor.py b/api/search/queryprocessor.py
index bf76bb0b..82896896 100644
--- a/api/search/queryprocessor.py
+++ b/api/search/queryprocessor.py
@@ -148,9 +148,8 @@ class TargetProperty(object):
class TargetInAnalysis(TargetProperty):
def __init__(self, name, query, analyses_query):
+ super(TargetInAnalysis, self).__init__(name, query)
self.target_analysys = TargetProperty('analyses', analyses_query)
- self.name = name
- self.query = query
def get_results(self, parent_name, parent_results):
analysis_list = self.target_analysys.get_results(parent_name, parent_results)
--
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