def get_authenticated_idx_and_idx_types(user=None, idx_keys=None, idx_type_keys=None):
''' Check permissions on elastic indexes and returns indexes that the given user can see'''
# get all public idx_keys and idx_type_keys
(idx_keys_public, idx_type_keys_public) = elastic_factory.get_idx_and_idx_type_keys(auth_public=True)
# get all the private idx_keys and idx_type_keys
(idx_keys_private, idx_type_keys_private) = elastic_factory.get_idx_and_idx_type_keys(auth_public=False)
# user is None...return all public keys
if user is None:
return idx_keys_public, idx_type_keys_public
idx_keys_auth = []
idx_type_keys_auth = []
# idx_keys or idx_type_keys is None, first fetch and add public keys
# if idx_keys is None or idx_type_keys is None:
if idx_keys is None:
# First add all the public idx keys
idx_keys_auth.extend(idx_keys_public)
# Assign the idx keys that need to be checked
idx_keys = idx_keys_private
else:
# don't add all, limit the one that the user has passed
idx_keys_auth = [idx_key for idx_key in idx_keys if idx_key in idx_keys_public]
if idx_type_keys is None:
# First add all the public idx type keys
idx_type_keys_auth.extend(idx_type_keys_public)
# Assign the idx type keys that need to be checked
idx_type_keys = idx_type_keys_private
else:
# don't add all, limit the one that the user has passed
idx_type_keys_auth = [idx_key for idx_key in idx_type_keys if idx_key in idx_type_keys_public]
# get elastic model names for the idx_keys and types
(model_names_idx, model_names_idx_types) = elastic_factory.get_elastic_model_names(idx_keys=idx_keys,
idx_type_keys=idx_type_keys) # @IgnorePep8
# check if the user has permissions to see the idx model
model_names_idx_auth = _check_content_type_perms(model_names_idx, user)
# check if the user has permissions to see the idx type model
model_names_idx_types_auth = _check_content_type_perms(model_names_idx_types, user)
# finally get the actual idx keys from model names and return them
(idx_auth, idx_types_auth) = elastic_factory.get_keys_from_model_names(model_names_idx_auth,
model_names_idx_types_auth)
if idx_auth is not None and len(idx_auth) > 0:
for idx in idx_auth:
if idx not in idx_keys_auth:
idx_keys_auth.append(idx)
if idx_types_auth is not None and len(idx_types_auth) > 0:
for idx in idx_types_auth:
if idx not in idx_type_keys_auth:
idx_type_keys_auth.append(idx)
return (idx_keys_auth, idx_type_keys_auth)
def test_elastic_model_names_round_trip(self):
# getting the private ones
(model_names_idx, model_names_idx_types) = elastic_factory.get_elastic_model_names(auth_public=False)
self.assertIn('target_mifsud_idx', model_names_idx, 'target_mifsud_idx found')
self.assertIn('cp_stats_gwas-gwas-anderson_idx_type', model_names_idx_types,
'cp_stats_gwas-gwas-anderson_idx_type found')
(idx_keys, idx_type_keys) = elastic_factory.get_keys_from_model_names(model_names_idx, model_names_idx_types)
self.assertIn('TARGET_MIFSUD', idx_keys, 'TARGET_MIFSUD found')
self.assertIn('CP_STATS_IC.IC-NAR_FARACO', idx_type_keys, 'CP_STATS_IC.IC-NAR_FARACO found')
def test_get_keys_from_model_names(self):
idx_model_names = ['disease_idx', 'gene_idx']
idx_type_model_names = ['gene-interactions_idx_type', 'marker-ic_idx_type', 'publication-publication_idx_type']
(idx_keys, idx_type_keys) = elastic_factory.get_keys_from_model_names(idx_model_names,
idx_type_model_names)
self.assertTrue('DISEASE' in idx_keys, 'got right idx key : DISEASE')
self.assertTrue('GENE' in idx_keys, 'got right idx key : GENE')
self.assertTrue('GENE.INTERACTIONS' in idx_type_keys, 'got right idx type key : GENE.INTERACTIONS')
self.assertTrue('MARKER.IC' in idx_type_keys, 'got right idx type key : MARKER.IC')
self.assertTrue('PUBLICATION.PUBLICATION' in idx_type_keys, 'got right idx type key : PUBLICATION.PUBLICATION')
def test_elastic_model_names_round_trip(self):
# getting the private ones
(model_names_idx,
model_names_idx_types) = elastic_factory.get_elastic_model_names(
auth_public=False)
self.assertIn('target_mifsud_idx', model_names_idx,
'target_mifsud_idx found')
self.assertIn('cp_stats_gwas-gwas-anderson_idx_type',
model_names_idx_types,
'cp_stats_gwas-gwas-anderson_idx_type found')
(idx_keys, idx_type_keys) = elastic_factory.get_keys_from_model_names(
model_names_idx, model_names_idx_types)
self.assertIn('TARGET_MIFSUD', idx_keys, 'TARGET_MIFSUD found')
self.assertIn('CP_STATS_IC.IC-NAR_FARACO', idx_type_keys,
'CP_STATS_IC.IC-NAR_FARACO found')
def test_get_keys_from_model_names(self):
idx_model_names = ['disease_idx', 'gene_idx']
idx_type_model_names = [
'gene-interactions_idx_type', 'marker-ic_idx_type',
'publication-publication_idx_type'
]
(idx_keys, idx_type_keys) = elastic_factory.get_keys_from_model_names(
idx_model_names, idx_type_model_names)
self.assertTrue('DISEASE' in idx_keys, 'got right idx key : DISEASE')
self.assertTrue('GENE' in idx_keys, 'got right idx key : GENE')
self.assertTrue('GENE.INTERACTIONS' in idx_type_keys,
'got right idx type key : GENE.INTERACTIONS')
self.assertTrue('MARKER.IC' in idx_type_keys,
'got right idx type key : MARKER.IC')
self.assertTrue('PUBLICATION.PUBLICATION' in idx_type_keys,
'got right idx type key : PUBLICATION.PUBLICATION')
def get_authenticated_idx_and_idx_types(user=None,
idx_keys=None,
idx_type_keys=None):
''' Check permissions on elastic indexes and returns indexes that the given user can see'''
# get all public idx_keys and idx_type_keys
(idx_keys_public,
idx_type_keys_public) = elastic_factory.get_idx_and_idx_type_keys(
auth_public=True)
# get all the private idx_keys and idx_type_keys
(idx_keys_private,
idx_type_keys_private) = elastic_factory.get_idx_and_idx_type_keys(
auth_public=False)
# user is None...return all public keys
if user is None:
return idx_keys_public, idx_type_keys_public
idx_keys_auth = []
idx_type_keys_auth = []
# idx_keys or idx_type_keys is None, first fetch and add public keys
# if idx_keys is None or idx_type_keys is None:
if idx_keys is None:
# First add all the public idx keys
idx_keys_auth.extend(idx_keys_public)
# Assign the idx keys that need to be checked
idx_keys = idx_keys_private
else:
# don't add all, limit the one that the user has passed
idx_keys_auth = [
idx_key for idx_key in idx_keys if idx_key in idx_keys_public
]
if idx_type_keys is None:
# First add all the public idx type keys
idx_type_keys_auth.extend(idx_type_keys_public)
# Assign the idx type keys that need to be checked
idx_type_keys = idx_type_keys_private
else:
# don't add all, limit the one that the user has passed
idx_type_keys_auth = [
idx_key for idx_key in idx_type_keys
if idx_key in idx_type_keys_public
]
# get elastic model names for the idx_keys and types
(model_names_idx,
model_names_idx_types) = elastic_factory.get_elastic_model_names(
idx_keys=idx_keys, idx_type_keys=idx_type_keys) # @IgnorePep8
# check if the user has permissions to see the idx model
model_names_idx_auth = _check_content_type_perms(model_names_idx, user)
# check if the user has permissions to see the idx type model
model_names_idx_types_auth = _check_content_type_perms(
model_names_idx_types, user)
# finally get the actual idx keys from model names and return them
(idx_auth, idx_types_auth) = elastic_factory.get_keys_from_model_names(
model_names_idx_auth, model_names_idx_types_auth)
if idx_auth is not None and len(idx_auth) > 0:
for idx in idx_auth:
if idx not in idx_keys_auth:
idx_keys_auth.append(idx)
if idx_types_auth is not None and len(idx_types_auth) > 0:
for idx in idx_types_auth:
if idx not in idx_type_keys_auth:
idx_type_keys_auth.append(idx)
return (idx_keys_auth, idx_type_keys_auth)
