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_get_idx_and_idx_type_keys_pydgin(self):
'''create idx and idxtype keys for chicp'''
elastic_factory.create_dynamic_models()
# get all private idx and keys
(idx_keys, idx_type_keys) = elastic_factory.get_idx_and_idx_type_keys(
auth_public=False)
# private idx keys
self.assertIn('DISEASE', idx_keys)
# public idx keys
self.assertNotIn('GENE', idx_keys)
self.assertNotIn('MARKER', idx_keys)
self.assertNotIn('PUBLICATION', idx_keys)
# private idx type keys
self.assertIn('DISEASE.DISEASE', idx_type_keys)
self.assertIn('GENE.PATHWAY', idx_type_keys)
self.assertIn('GENE.INTERACTIONS', idx_type_keys)
self.assertIn('PUBLICATION.PUBLICATION', idx_type_keys)
# public idx type keys
self.assertNotIn('GENE.GENE', idx_type_keys)
self.assertNotIn('MARKER.MARKER', idx_type_keys)
# get all public idx and keys
(idx_keys, idx_type_keys) = elastic_factory.get_idx_and_idx_type_keys(
auth_public=True)
# private idx key
self.assertNotIn('DISEASE', idx_keys)
# public idx key
self.assertIn('MARKER', idx_keys)
self.assertIn('PUBLICATION', idx_keys)
self.assertIn('GENE', idx_keys)
# private idx type keys
self.assertNotIn('DISEASE.DISEASE', idx_type_keys)
self.assertNotIn('GENE.PATHWAY', idx_type_keys)
self.assertNotIn('GENE.INTERACTIONS', idx_type_keys)
self.assertNotIn('PUBLICATION.PUBLICATION', idx_type_keys)
# public idx type keys
self.assertIn('GENE.GENE', idx_type_keys)
self.assertIn('MARKER.MARKER', idx_type_keys)
self.assertIn('MARKER.MARKER', idx_type_keys)
self.assertIn('MARKER.MARKER', idx_type_keys)
def test_get_idx_and_idx_type_keys_pydgin(self):
'''create idx and idxtype keys for chicp'''
elastic_factory.create_dynamic_models()
# get all private idx and keys
(idx_keys, idx_type_keys) = elastic_factory.get_idx_and_idx_type_keys(auth_public=False)
# private idx keys
self.assertIn('DISEASE', idx_keys)
# public idx keys
self.assertNotIn('GENE', idx_keys)
self.assertNotIn('MARKER', idx_keys)
self.assertNotIn('PUBLICATION', idx_keys)
# private idx type keys
self.assertIn('DISEASE.DISEASE', idx_type_keys)
self.assertIn('GENE.PATHWAY', idx_type_keys)
self.assertIn('GENE.INTERACTIONS', idx_type_keys)
self.assertIn('PUBLICATION.PUBLICATION', idx_type_keys)
# public idx type keys
self.assertNotIn('GENE.GENE', idx_type_keys)
self.assertNotIn('MARKER.MARKER', idx_type_keys)
# get all public idx and keys
(idx_keys, idx_type_keys) = elastic_factory.get_idx_and_idx_type_keys(auth_public=True)
# private idx key
self.assertNotIn('DISEASE', idx_keys)
# public idx key
self.assertIn('MARKER', idx_keys)
self.assertIn('PUBLICATION', idx_keys)
self.assertIn('GENE', idx_keys)
# private idx type keys
self.assertNotIn('DISEASE.DISEASE', idx_type_keys)
self.assertNotIn('GENE.PATHWAY', idx_type_keys)
self.assertNotIn('GENE.INTERACTIONS', idx_type_keys)
self.assertNotIn('PUBLICATION.PUBLICATION', idx_type_keys)
# public idx type keys
self.assertIn('GENE.GENE', idx_type_keys)
self.assertIn('MARKER.MARKER', idx_type_keys)
self.assertIn('MARKER.MARKER', idx_type_keys)
self.assertIn('MARKER.MARKER', idx_type_keys)
def test_get_idx_and_idx_type_keys_cp(self):
'''create idx and idxtype keys for chicp'''
elastic_factory.create_dynamic_models()
# usually you can get the IDX dict via ElasticSettings.attrs().get('IDX')
(idx_keys, idx_type_keys) = elastic_factory.get_idx_and_idx_type_keys(
auth_public=False)
# private idx
self.assertIn('TARGET_MIFSUD', idx_keys)
self.assertIn('CP_STATS_UD', idx_keys)
# private idx types
self.assertIn('CP_STATS_IC.IC-MS_IMSGC', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-JIA_HINKS_UK', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-NAR_FARACO', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-BARRETT', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-ANDERSON', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-STAHL', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-OKADA', idx_type_keys)
# public idx
(idx_keys, idx_type_keys) = elastic_factory.get_idx_and_idx_type_keys(
auth_public=True)
# public idx
self.assertIn('CP_STATS_IC', idx_keys)
self.assertIn('CP_STATS_GWAS', idx_keys)
self.assertIn('TARGET_MARTIN', idx_keys)
self.assertIn('TARGET_CHICAGO', idx_keys)
# public idx and idx_type
self.assertIn('CP_STATS_IC.IC-T1D_ONENGUT', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-ATD_COOPER', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-CEL_TRYNKA', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-RA_EYRE', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-PBC_LIU', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-COOPER', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-DUBOIS', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-FRANKE', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-IMSGC', idx_type_keys)
def test_get_idx_and_idx_type_keys_cp(self):
'''create idx and idxtype keys for chicp'''
elastic_factory.create_dynamic_models()
# usually you can get the IDX dict via ElasticSettings.attrs().get('IDX')
(idx_keys, idx_type_keys) = elastic_factory.get_idx_and_idx_type_keys(auth_public=False)
# private idx
self.assertIn('TARGET_MIFSUD', idx_keys)
self.assertIn('CP_STATS_UD', idx_keys)
# private idx types
self.assertIn('CP_STATS_IC.IC-MS_IMSGC', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-JIA_HINKS_UK', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-NAR_FARACO', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-BARRETT', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-ANDERSON', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-STAHL', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-OKADA', idx_type_keys)
# public idx
(idx_keys, idx_type_keys) = elastic_factory.get_idx_and_idx_type_keys(auth_public=True)
# public idx
self.assertIn('CP_STATS_IC', idx_keys)
self.assertIn('CP_STATS_GWAS', idx_keys)
self.assertIn('TARGET_MARTIN', idx_keys)
self.assertIn('TARGET_CHICAGO', idx_keys)
# public idx and idx_type
self.assertIn('CP_STATS_IC.IC-T1D_ONENGUT', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-ATD_COOPER', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-CEL_TRYNKA', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-RA_EYRE', idx_type_keys)
self.assertIn('CP_STATS_IC.IC-PBC_LIU', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-COOPER', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-DUBOIS', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-FRANKE', idx_type_keys)
self.assertIn('CP_STATS_GWAS.GWAS-IMSGC', idx_type_keys)
def test_get_elastic_model_names_chicp(self):
'''check whether the right model names are created for chicp'''
elastic_factory.create_dynamic_models()
(idx_keys, idx_type_keys) = elastic_factory.get_idx_and_idx_type_keys(auth_public=False)
(model_names_idx, model_names_idx_types) = elastic_factory.get_elastic_model_names(
idx_keys=idx_keys,
idx_type_keys=idx_type_keys)
self.assertIn('target_mifsud_idx', model_names_idx)
self.assertIn('cp_stats_ic-ic-ms_imsgc_idx_type', model_names_idx_types)
self.assertIn('cp_stats_ic-ic-nar_faraco_idx_type', model_names_idx_types)
self.assertIn('cp_stats_gwas-gwas-okada_idx_type', model_names_idx_types)
self.assertIn('cp_stats_gwas-gwas-stahl_idx_type', model_names_idx_types)
def test_get_elastic_model_names_chicp(self):
'''check whether the right model names are created for chicp'''
elastic_factory.create_dynamic_models()
(idx_keys, idx_type_keys) = elastic_factory.get_idx_and_idx_type_keys(
auth_public=False)
(model_names_idx,
model_names_idx_types) = elastic_factory.get_elastic_model_names(
idx_keys=idx_keys, idx_type_keys=idx_type_keys)
self.assertIn('target_mifsud_idx', model_names_idx)
self.assertIn('cp_stats_ic-ic-ms_imsgc_idx_type',
model_names_idx_types)
self.assertIn('cp_stats_ic-ic-nar_faraco_idx_type',
model_names_idx_types)
self.assertIn('cp_stats_gwas-gwas-okada_idx_type',
model_names_idx_types)
self.assertIn('cp_stats_gwas-gwas-stahl_idx_type',
model_names_idx_types)
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)
