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 setUp(self):
if 'pydgin_auth' in settings.INSTALLED_APPS:
from pydgin_auth.elastic_model_factory import ElasticPermissionModelFactory
from django.contrib.auth.models import Group
# create elastic models
ElasticPermissionModelFactory.create_dynamic_models()
# create the default group READ
Group.objects.get_or_create(name='READ')
def test_create_idx_type_model_permissions(self):
elastic_dict = elastic_factory.get_elastic_settings_with_user_uploads()
indexKey = 'CP_STATS_UD'
user_upload_dict = list(elastic_dict[indexKey]['idx_type'].keys())
indexName = 'CP_STATS_UD'
if len(user_upload_dict) > 1:
indexType = user_upload_dict[0]
else:
indexType = 'UD-RANDOMTMPTEST'
elastic_dict = ElasticSettings.attrs().get('IDX')
idx_type_dict = {}
idx_type_dict[indexType] = {
'label': 'testlabel',
'type': indexType
}
elastic_dict['CP_STATS_UD']['idx_type'] = idx_type_dict
indexTypeModel = indexKey.lower() + elastic_factory.PERMISSION_MODEL_NAME_TYPE_DELIMITER + indexType.lower() + \
elastic_factory.PERMISSION_MODEL_TYPE_SUFFIX
elastic_factory.create_idx_type_model_permissions(
self.user,
elastic_dict=elastic_dict,
indexKey=indexName,
indexTypeKey=indexType)
# check if model exists
db_models = elastic_factory.get_db_models(
app_label=elastic_factory.PERMISSION_MODEL_APP_NAME, existing=True)
self.assertIn(indexTypeModel, db_models,
' model exists for ' + indexType)
# check if permission exists
content_type = None
try:
content_type = ContentType.objects.get(
model=indexTypeModel.lower(),
app_label=settings.ELASTIC_PERMISSION_MODEL_APP_NAME)
except:
pass
permissions = None
perm_code_name = 'can_read_' + indexTypeModel.lower()
if content_type:
permissions = Permission.objects.filter(content_type=content_type)
self.assertIn(perm_code_name,
[perm.codename for perm in permissions],
'perm present')
# Request new instance of User
user = get_object_or_404(User, pk=self.user.id)
# Permission cache is repopulated from the database
self.assertTrue(
user.has_perm(settings.ELASTIC_PERMISSION_MODEL_APP_NAME +
'.' + perm_code_name))
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_elastic_models_pydgin(self):
'''check whether the right models are created for pydgin'''
elastic_factory.create_dynamic_models()
# check model names are created correctly
expected_models = ['disease_idx', 'gene-pathway_idx_type', 'gene-interactions_idx_type',
'marker-ic_idx_type', 'publication-publication_idx_type', 'disease-disease_idx_type']
existing_models = elastic_factory.get_db_models(existing=True)
for model in expected_models:
self.assertIn(model, existing_models, 'Model exists: ' + model)
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_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_elastic_models_pydgin(self):
'''check whether the right models are created for pydgin'''
elastic_factory.create_dynamic_models()
# check model names are created correctly
expected_models = [
'disease_idx', 'gene-pathway_idx_type',
'gene-interactions_idx_type', 'marker-ic_idx_type',
'publication-publication_idx_type', 'disease-disease_idx_type'
]
existing_models = elastic_factory.get_db_models(existing=True)
for model in expected_models:
self.assertIn(model, existing_models, 'Model exists: ' + model)
def test_create_idx_type_model_permissions(self):
elastic_settings_before = ElasticSettings.attrs().get('IDX')
user_types_before = elastic_settings_before['CP_STATS_UD']['idx_type']
self.assertEqual({}, user_types_before, 'CP_STATS_UD idx_type is empty')
idx = "cp:hg19_userdata_bed"
new_upload_file = "tmp_newly_uploaded_file"
idx_type = new_upload_file
os.system("curl -XPUT "+ElasticSettings.url()+"/"+idx+"/_mapping/"+idx_type+" -d '{\"" +
idx_type + "\":{ \"properties\" : {\"message\" : {\"type\" : \"string\", \"store\" : true } } }}'")
os.system("curl -XPUT "+ElasticSettings.url()+"/"+idx+"/"+idx_type+"/_meta -d '{\"label\": \"" +
new_upload_file + "\", \"owner\": \""+self.user.username+"\", \"uploaded\": \"" +
str(timezone.now())+"\"}'")
elastic_settings_after = elastic_factory.create_idx_type_model_permissions(self.user,
indexKey='CP_STATS_UD',
indexTypeKey='UD-'+new_upload_file.upper(), # @IgnorePep8
new_upload_file="tmp_newly_uploaded_file") # @IgnorePep8
# elastic_settings_after = elastic_factory.get_elastic_settings_with_user_uploads(elastic_settings_before)
user_types_after = elastic_settings_after['CP_STATS_UD']['idx_type']
self.assertTrue(len(user_types_after) > 0, "Has user idx_types ")
self.assertTrue('UD-TMP_NEWLY_UPLOADED_FILE' in user_types_after)
self.assertEqual(user_types_after['UD-TMP_NEWLY_UPLOADED_FILE']['type'], 'tmp_newly_uploaded_file')
def test_create_idx_type_model_permissions(self):
elastic_settings_before = ElasticSettings.attrs().get('IDX')
user_types_before = elastic_settings_before['CP_STATS_UD']['idx_type']
self.assertEqual({}, user_types_before,
'CP_STATS_UD idx_type is empty')
idx = "cp:hg19_userdata_bed"
new_upload_file = "tmp_newly_uploaded_file"
idx_type = new_upload_file
os.system(
"curl -XPUT " + ElasticSettings.url() + "/" + idx + "/_mapping/" +
idx_type + " -d '{\"" + idx_type +
"\":{ \"properties\" : {\"message\" : {\"type\" : \"string\", \"store\" : true } } }}'"
)
os.system("curl -XPUT " + ElasticSettings.url() + "/" + idx + "/" +
idx_type + "/_meta -d '{\"label\": \"" + new_upload_file +
"\", \"owner\": \"" + self.user.username +
"\", \"uploaded\": \"" + str(timezone.now()) + "\"}'")
elastic_settings_after = elastic_factory.create_idx_type_model_permissions(
self.user,
indexKey='CP_STATS_UD',
indexTypeKey='UD-' + new_upload_file.upper(), # @IgnorePep8
new_upload_file="tmp_newly_uploaded_file") # @IgnorePep8
# elastic_settings_after = elastic_factory.get_elastic_settings_with_user_uploads(elastic_settings_before)
user_types_after = elastic_settings_after['CP_STATS_UD']['idx_type']
self.assertTrue(len(user_types_after) > 0, "Has user idx_types ")
self.assertTrue('UD-TMP_NEWLY_UPLOADED_FILE' in user_types_after)
self.assertEqual(
user_types_after['UD-TMP_NEWLY_UPLOADED_FILE']['type'],
'tmp_newly_uploaded_file')
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_search_props(self):
if 'pydgin_auth' in settings.INSTALLED_APPS:
from pydgin_auth.elastic_model_factory import ElasticPermissionModelFactory
from django.contrib.contenttypes.models import ContentType
from django.contrib.auth.models import Group, User, Permission
from django.shortcuts import get_object_or_404
ElasticPermissionModelFactory.create_dynamic_models()
search_props = ElasticSettings.search_props("ALL")
idx = search_props['idx']
idx_keys = search_props['idx_keys']
idx_type = search_props['idx_type']
self.assertIn('publications', idx, 'publications found in idx')
self.assertIn('MARKER', idx_keys, 'MARKER found in idx_keys')
self.assertIn('rs_merge', idx_type, 'rs_merge found in idx_type')
# CREATE DIL group and add test_dil user to that group
dil_group, created = Group.objects.get_or_create(name='DILX')
self.assertTrue(created)
dil_user = User.objects.create_user(
username='******', email='*****@*****.**', password='******')
dil_user.groups.add(dil_group)
self.assertTrue(dil_user.groups.filter(name='DILX').exists())
# create permission for MARKER and IC
test_model_name = 'marker-ic_idx_type'
# create permissions on models and retest again to check if the idx type could be seen
content_type, created = ContentType.objects.get_or_create(
model=test_model_name, app_label="elastic",
)
# get the permission ... already created
can_read_permission = Permission.objects.get(content_type=content_type)
self.assertEqual('can_read_marker-ic_idx_type', can_read_permission.codename, "idx type permission correct")
# as soon as the permission is set for an index, the index becomes a restricted resource
idx_types_visible = ElasticSettings.search_props("ALL")["idx_type"]
self.assertFalse('immunochip' in idx_types_visible, 'immunochip idx type not visible')
# now grant permission to dil_user and check if idx type is visible
dil_group.permissions.add(can_read_permission)
dil_user = get_object_or_404(User, pk=dil_user.id)
idx_types_visible = ElasticSettings.search_props("ALL", dil_user)["idx_type"]
self.assertTrue('immunochip' in idx_types_visible, 'immunochip idx type visible now')
def test_create_idx_type_model_permissions(self):
elastic_dict = elastic_factory.get_elastic_settings_with_user_uploads()
indexKey = 'CP_STATS_UD'
user_upload_dict = list(elastic_dict[indexKey]['idx_type'].keys())
indexName = 'CP_STATS_UD'
if len(user_upload_dict) > 1:
indexType = user_upload_dict[0]
else:
indexType = 'UD-RANDOMTMPTEST'
elastic_dict = ElasticSettings.attrs().get('IDX')
idx_type_dict = {}
idx_type_dict[indexType] = {'label': 'testlabel', 'type': indexType}
elastic_dict['CP_STATS_UD']['idx_type'] = idx_type_dict
indexTypeModel = indexKey.lower() + elastic_factory.PERMISSION_MODEL_NAME_TYPE_DELIMITER + indexType.lower() + \
elastic_factory.PERMISSION_MODEL_TYPE_SUFFIX
elastic_factory.create_idx_type_model_permissions(self.user, elastic_dict=elastic_dict,
indexKey=indexName,
indexTypeKey=indexType)
# check if model exists
db_models = elastic_factory.get_db_models(app_label=elastic_factory.PERMISSION_MODEL_APP_NAME, existing=True)
self.assertIn(indexTypeModel, db_models,
' model exists for ' + indexType)
# check if permission exists
content_type = None
try:
content_type = ContentType.objects.get(model=indexTypeModel.lower(),
app_label=settings.ELASTIC_PERMISSION_MODEL_APP_NAME)
except:
pass
permissions = None
perm_code_name = 'can_read_' + indexTypeModel.lower()
if content_type:
permissions = Permission.objects.filter(content_type=content_type)
self.assertIn(perm_code_name, [perm.codename for perm in permissions], 'perm present')
# Request new instance of User
user = get_object_or_404(User, pk=self.user.id)
# Permission cache is repopulated from the database
self.assertTrue(user.has_perm(settings.ELASTIC_PERMISSION_MODEL_APP_NAME + '.' + perm_code_name))
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_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_pydgin(self):
'''check whether the right model names are created for pydgin'''
# for pydgin, returns only models for private idx and idx_types
(model_names_idx, model_names_idx_types) = elastic_factory.get_elastic_model_names()
model_names = model_names_idx + model_names_idx_types
self.assertIn('disease_idx', model_names)
self.assertIn('gene-pathway_idx_type', model_names)
self.assertIn('marker-ic_idx_type', model_names)
self.assertIn('disease-disease_idx_type', model_names)
def test_get_elastic_model_names_pydgin(self):
'''check whether the right model names are created for pydgin'''
# for pydgin, returns only models for private idx and idx_types
(model_names_idx,
model_names_idx_types) = elastic_factory.get_elastic_model_names()
model_names = model_names_idx + model_names_idx_types
self.assertIn('disease_idx', model_names)
self.assertIn('gene-pathway_idx_type', model_names)
self.assertIn('marker-ic_idx_type', model_names)
self.assertIn('disease-disease_idx_type', model_names)
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 chicpeaFileUpload(request, url):
filesDict = request.FILES
user = request.user
files = filesDict.getlist("files[]")
snpTracks = list()
idx = ElasticSettings.idx('CP_STATS_UD')
for f in files:
line = f.readlines()[0].decode()
if line.startswith("#"):
line = f.readlines()[1].decode()
parts = re.split("\t", line)
if re.match("\s", line):
parts = re.split("\s", line)
if len(parts) != 5:
logger.warn("WARNING: unexpected number of columns ("+len(parts)+"): "+line)
continue
f.seek(0)
bedFile = NamedTemporaryFile(delete=False)
bedFile.write(f.read())
bedFile.close()
idx_type = os.path.basename(bedFile.name)
snpTracks.append({"value": "ud-"+idx_type, "text": f.name})
os.system("curl -XDELETE '"+ElasticSettings.url()+"/"+idx+"/"+idx_type+"'")
call_command("index_search", indexName=idx, indexType=idx_type, indexBED=bedFile.name)
logger.debug("index_search --indexName "+idx+" --indexType "+idx_type+" --indexBED "+bedFile.name)
os.system("curl -XPUT "+ElasticSettings.url()+"/"+idx+"/"+idx_type+"/_meta -d '{\"label\": \"" + f.name +
"\", \"owner\": \""+user.username+"\", \"uploaded\": \""+str(timezone.now())+"\"}'")
bedFile.delete
elastic_factory.create_idx_type_model_permissions(user, indexKey='CP_STATS_UD',
indexTypeKey='UD-'+idx_type.upper())
context = dict()
context['userSNPTracks'] = snpTracks
return HttpResponse(json.dumps(context), content_type="application/json")
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 chicpeaFileUpload(request, url):
filesDict = request.FILES
user = request.user
files = filesDict.getlist("files[]")
snpTracks = list()
idx = ElasticSettings.idx('CP_STATS_UD')
for f in files:
line = f.readlines()[0].decode()
if line.startswith("#"):
line = f.readlines()[1].decode()
parts = re.split("\t", line)
if re.match("\s", line):
parts = re.split("\s", line)
if len(parts) != 5:
logger.warn("WARNING: unexpected number of columns ("+len(parts)+"): "+line)
continue
f.seek(0)
bedFile = NamedTemporaryFile(delete=False)
bedFile.write(f.read())
bedFile.close()
idx_type = os.path.basename(bedFile.name)
snpTracks.append({"value": "ud-"+idx_type, "text": f.name})
os.system("curl -XDELETE '"+ElasticSettings.url()+"/"+idx+"/"+idx_type+"'")
call_command("index_search", indexName=idx, indexType=idx_type, indexBED=bedFile.name)
logger.debug("index_search --indexName "+idx+" --indexType "+idx_type+" --indexBED "+bedFile.name)
os.system("curl -XPUT "+ElasticSettings.url()+"/"+idx+"/"+idx_type+"/_meta -d '{\"label\": \"" + f.name +
"\", \"owner\": \""+user.username+"\", \"uploaded\": \""+str(timezone.now())+"\"}'")
bedFile.delete
elastic_factory.create_idx_type_model_permissions(user, indexKey='CP_STATS_UD',
indexTypeKey='UD-'+idx_type.upper())
context = dict()
context['userSNPTracks'] = snpTracks
return HttpResponse(json.dumps(context), content_type="application/json")
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_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)
terms_agreed.boolean = True
terms_agreed.admin_order_field = 'is_terms_agreed'
def persons(self):
'''Returns all the users appended by , for a GROUP'''
return ', '.join(['<a href="%s">%s</a>' % (reverse('admin:auth_user_change', args=(x.id,)), x.username)
for x in self.user_set.all().order_by('username')])
persons.allow_tags = True
class UserAdmin(UserAdmin):
'''ModelAdmin Class to alter the display for Users'''
list_display = ['username', 'email', 'first_name', 'last_name', 'is_active', terms_agreed, staff, adm, roles, last]
list_filter = ['groups', 'is_staff', 'is_superuser', 'is_active']
class GroupAdmin(GroupAdmin):
'''ModelAdmin Class to alter the display for Groups'''
list_display = ['name', persons]
list_display_links = ['name']
admin.site.unregister(User)
admin.site.unregister(Group)
admin.site.register(User, UserAdmin)
admin.site.register(Group, GroupAdmin)
admin.site.register(Permission)
# call to create elastic models based on the elastic settings
ElasticPermissionModelFactory.create_dynamic_models()
def test_get_authenticated_idx_and_idx_types(self):
elastic_factory.create_dynamic_models()
# As user is none we should get back only public idx and idx_type keys
(idx_keys_auth,
idx_type_keys_auth) = get_authenticated_idx_and_idx_types(user=None)
self.assertIn('MARKER', idx_keys_auth)
self.assertIn('GENE', idx_keys_auth)
self.assertIn('PUBLICATION', idx_keys_auth)
self.assertIn('MARKER.MARKER', idx_type_keys_auth)
self.assertIn('MARKER.HISTORY', idx_type_keys_auth)
self.assertIn('GENE.GENE', idx_type_keys_auth)
# As user is not none and we have assigned the user to any group we should get back
# only public idx and idx_type keys
(idx_keys_auth,
idx_type_keys_auth) = get_authenticated_idx_and_idx_types(self.user)
self.assertIn('MARKER', idx_keys_auth)
self.assertIn('GENE', idx_keys_auth)
self.assertIn('PUBLICATION', idx_keys_auth)
self.assertIn('MARKER.MARKER', idx_type_keys_auth)
self.assertIn('MARKER.HISTORY', idx_type_keys_auth)
self.assertIn('GENE.GENE', idx_type_keys_auth)
# Create test_dil user and assign the user to DIL group
dil_group, created = Group.objects.get_or_create(name='DIL')
self.assertTrue(created)
dil_user = User.objects.create_user(username='******',
email='*****@*****.**',
password='******')
dil_user.groups.add(dil_group)
self.assertTrue(dil_user.groups.filter(name='DIL').exists())
all_groups_of_dil_user = dil_user.groups.values_list('name', flat=True)
self.assertTrue("DIL" in all_groups_of_dil_user, "Found DIL in groups")
self.assertTrue("READ" in all_groups_of_dil_user,
"Found READ in groups")
# get private idx and assign permission to dil_user
(model_names_idx,
model_names_idx_types) = elastic_factory.get_elastic_model_names(
auth_public=False)
test_idx_model = model_names_idx[0]
test_idx_type_model = model_names_idx_types[1]
self.assertTrue(test_idx_model.endswith('_idx'),
'Idx model ends with _idx')
self.assertTrue(test_idx_type_model.endswith('_idx_type'),
'Idx type model ends with _idx_type')
# create permissions on models and retest again to check if the idx could be seen
content_type_idx, created_idx = ContentType.objects.get_or_create( # @UnusedVariable
model=test_idx_model,
app_label=elastic_factory.PERMISSION_MODEL_APP_NAME,
)
content_type_idx_type, created_idx_type = ContentType.objects.get_or_create( # @UnusedVariable
model=test_idx_type_model,
app_label=elastic_factory.PERMISSION_MODEL_APP_NAME,
)
# The idx and idx_type should already exists in db, so created should be false
self.assertFalse(created_idx, test_idx_model + ' is available ')
self.assertFalse(created_idx_type,
test_idx_type_model + ' is available ')
self.assertIsNotNone(content_type_idx,
content_type_idx.name + ' is not None')
self.assertIsNotNone(content_type_idx_type,
content_type_idx_type.name + ' is not None')
# create permission and assign ...Generally we create via admin interface
can_read_permission_idx, create_permission_idx = Permission.objects.get_or_create( # @UnusedVariable
content_type=content_type_idx)
self.assertIsNotNone(
can_read_permission_idx,
' Permission is available ' + can_read_permission_idx.name)
can_read_permission_idx_type, create_permission_idx = Permission.objects.get_or_create( # @UnusedVariable
content_type=content_type_idx_type)
self.assertIsNotNone(
can_read_permission_idx_type,
' Permission is available ' + can_read_permission_idx_type.name)
# now grant access to test_dil and check if the user can see the index
# Add the permission to dil_group
dil_group.permissions.add(can_read_permission_idx)
dil_group.permissions.add(can_read_permission_idx_type)
dil_user = get_object_or_404(User, pk=dil_user.id)
available_group_perms = dil_user.get_group_permissions()
self.assertTrue('elastic.can_read_' +
test_idx_model.lower() in available_group_perms)
self.assertTrue('elastic.can_read_' +
test_idx_type_model.lower() in available_group_perms)
# Try to get the authenticated idx and idx_types keys again
(idx_keys_auth,
idx_type_keys_auth) = get_authenticated_idx_and_idx_types(dil_user)
(idx_model_name_auth,
idx_type_model_name_auth) = elastic_factory.get_elastic_model_names(
idx_keys=idx_keys_auth, idx_type_keys=idx_type_keys_auth)
self.assertTrue(test_idx_model in idx_model_name_auth)
self.assertTrue(test_idx_type_model in idx_type_model_name_auth)
self.assertIn('MARKER', idx_keys_auth)
self.assertIn('GENE', idx_keys_auth)
self.assertIn('PUBLICATION', idx_keys_auth)
self.assertIn('MARKER.MARKER', idx_type_keys_auth)
self.assertIn('MARKER.HISTORY', idx_type_keys_auth)
self.assertIn('GENE.GENE', idx_type_keys_auth)
# pass just one index key and index type and check for returned keys and types
# publication idx is public and publication.publication is private
idx_keys = ['PUBLICATION']
idx_type_keys = ['PUBLICATION.PUBLICATION']
idx_keys_auth = []
idx_type_keys_auth = []
(idx_keys_auth,
idx_type_keys_auth) = get_authenticated_idx_and_idx_types(
self.user, idx_keys=idx_keys, idx_type_keys=idx_type_keys)
self.assertIn('PUBLICATION', idx_keys_auth)
self.assertNotIn('PUBLICATION.PUBLICATION', idx_type_keys_auth)
self.assertTrue(len(idx_keys_auth) == 1, 'Got back only one idx')
# pass only one idx_keys and one idx type keys
idx_keys = ['PUBLICATION']
idx_keys_auth = []
idx_type_keys_auth = []
(idx_keys_auth,
idx_type_keys_auth) = get_authenticated_idx_and_idx_types(
self.user,
idx_keys=idx_keys,
)
self.assertIn('PUBLICATION', idx_keys_auth)
self.assertTrue(len(idx_keys_auth) == 1, 'Got back only one idx')
self.assertTrue(len(idx_type_keys_auth) == 3, 'Got back 3 idx types')
# pass only one idx type keys and idx keys
idx_type_keys = ['MARKER.MARKER', 'PUBLICATION.PUBLICATION']
idx_keys_auth = []
idx_type_keys_auth = []
(idx_keys_auth,
idx_type_keys_auth) = get_authenticated_idx_and_idx_types(
self.user,
idx_type_keys=idx_type_keys,
)
self.assertTrue(len(idx_keys_auth) == 3, 'Got back only one idx')
# as publication is private and we have passed the regular user this is right
self.assertTrue(len(idx_type_keys_auth) == 1, 'Got back 0 idx types')
def test_get_authenticated_idx_and_idx_types(self):
elastic_factory.create_dynamic_models()
# As user is none we should get back only public idx and idx_type keys
(idx_keys_auth, idx_type_keys_auth) = get_authenticated_idx_and_idx_types(user=None)
self.assertIn('MARKER', idx_keys_auth)
self.assertIn('GENE', idx_keys_auth)
self.assertIn('PUBLICATION', idx_keys_auth)
self.assertIn('MARKER.MARKER', idx_type_keys_auth)
self.assertIn('MARKER.HISTORY', idx_type_keys_auth)
self.assertIn('GENE.GENE', idx_type_keys_auth)
# As user is not none and we have assigned the user to any group we should get back
# only public idx and idx_type keys
(idx_keys_auth, idx_type_keys_auth) = get_authenticated_idx_and_idx_types(self.user)
self.assertIn('MARKER', idx_keys_auth)
self.assertIn('GENE', idx_keys_auth)
self.assertIn('PUBLICATION', idx_keys_auth)
self.assertIn('MARKER.MARKER', idx_type_keys_auth)
self.assertIn('MARKER.HISTORY', idx_type_keys_auth)
self.assertIn('GENE.GENE', idx_type_keys_auth)
# Create test_dil user and assign the user to DIL group
dil_group, created = Group.objects.get_or_create(name='DIL')
self.assertTrue(created)
dil_user = User.objects.create_user(
username='******', email='*****@*****.**', password='******')
dil_user.groups.add(dil_group)
self.assertTrue(dil_user.groups.filter(name='DIL').exists())
all_groups_of_dil_user = dil_user.groups.values_list('name', flat=True)
self.assertTrue("DIL" in all_groups_of_dil_user, "Found DIL in groups")
self.assertTrue("READ" in all_groups_of_dil_user, "Found READ in groups")
# get private idx and assign permission to dil_user
(model_names_idx, model_names_idx_types) = elastic_factory.get_elastic_model_names(auth_public=False)
test_idx_model = model_names_idx[0]
test_idx_type_model = model_names_idx_types[1]
self.assertTrue(test_idx_model.endswith('_idx'), 'Idx model ends with _idx')
self.assertTrue(test_idx_type_model.endswith('_idx_type'), 'Idx type model ends with _idx_type')
# create permissions on models and retest again to check if the idx could be seen
content_type_idx, created_idx = ContentType.objects.get_or_create( # @UnusedVariable
model=test_idx_model, app_label=elastic_factory.PERMISSION_MODEL_APP_NAME,
)
content_type_idx_type, created_idx_type = ContentType.objects.get_or_create( # @UnusedVariable
model=test_idx_type_model, app_label=elastic_factory.PERMISSION_MODEL_APP_NAME,
)
# The idx and idx_type should already exists in db, so created should be false
self.assertFalse(created_idx, test_idx_model + ' is available ')
self.assertFalse(created_idx_type, test_idx_type_model + ' is available ')
self.assertIsNotNone(content_type_idx, content_type_idx.name + ' is not None')
self.assertIsNotNone(content_type_idx_type, content_type_idx_type.name + ' is not None')
# create permission and assign ...Generally we create via admin interface
can_read_permission_idx, create_permission_idx = Permission.objects.get_or_create( # @UnusedVariable
content_type=content_type_idx)
self.assertIsNotNone(can_read_permission_idx, ' Permission is available ' + can_read_permission_idx.name)
can_read_permission_idx_type, create_permission_idx = Permission.objects.get_or_create( # @UnusedVariable
content_type=content_type_idx_type)
self.assertIsNotNone(can_read_permission_idx_type,
' Permission is available ' + can_read_permission_idx_type.name)
# now grant access to test_dil and check if the user can see the index
# Add the permission to dil_group
dil_group.permissions.add(can_read_permission_idx)
dil_group.permissions.add(can_read_permission_idx_type)
dil_user = get_object_or_404(User, pk=dil_user.id)
available_group_perms = dil_user.get_group_permissions()
self.assertTrue('elastic.can_read_' + test_idx_model.lower() in available_group_perms)
self.assertTrue('elastic.can_read_' + test_idx_type_model.lower() in available_group_perms)
# Try to get the authenticated idx and idx_types keys again
(idx_keys_auth, idx_type_keys_auth) = get_authenticated_idx_and_idx_types(dil_user)
(idx_model_name_auth, idx_type_model_name_auth) = elastic_factory.get_elastic_model_names(
idx_keys=idx_keys_auth,
idx_type_keys=idx_type_keys_auth)
self.assertTrue(test_idx_model in idx_model_name_auth)
self.assertTrue(test_idx_type_model in idx_type_model_name_auth)
self.assertIn('MARKER', idx_keys_auth)
self.assertIn('GENE', idx_keys_auth)
self.assertIn('PUBLICATION', idx_keys_auth)
self.assertIn('MARKER.MARKER', idx_type_keys_auth)
self.assertIn('MARKER.HISTORY', idx_type_keys_auth)
self.assertIn('GENE.GENE', idx_type_keys_auth)
# pass just one index key and index type and check for returned keys and types
# publication idx is public and publication.publication is private
idx_keys = ['PUBLICATION']
idx_type_keys = ['PUBLICATION.PUBLICATION']
idx_keys_auth = []
idx_type_keys_auth = []
(idx_keys_auth, idx_type_keys_auth) = get_authenticated_idx_and_idx_types(self.user,
idx_keys=idx_keys,
idx_type_keys=idx_type_keys)
self.assertIn('PUBLICATION', idx_keys_auth)
self.assertNotIn('PUBLICATION.PUBLICATION', idx_type_keys_auth)
self.assertTrue(len(idx_keys_auth) == 1, 'Got back only one idx')
# pass only one idx_keys and one idx type keys
idx_keys = ['PUBLICATION']
idx_keys_auth = []
idx_type_keys_auth = []
(idx_keys_auth, idx_type_keys_auth) = get_authenticated_idx_and_idx_types(self.user,
idx_keys=idx_keys,
)
self.assertIn('PUBLICATION', idx_keys_auth)
self.assertTrue(len(idx_keys_auth) == 1, 'Got back only one idx')
self.assertTrue(len(idx_type_keys_auth) == 3, 'Got back 3 idx types')
# pass only one idx type keys and idx keys
idx_type_keys = ['MARKER.MARKER', 'PUBLICATION.PUBLICATION']
idx_keys_auth = []
idx_type_keys_auth = []
(idx_keys_auth, idx_type_keys_auth) = get_authenticated_idx_and_idx_types(self.user,
idx_type_keys=idx_type_keys,
)
self.assertTrue(len(idx_keys_auth) == 3, 'Got back only one idx')
# as publication is private and we have passed the regular user this is right
self.assertTrue(len(idx_type_keys_auth) == 1, 'Got back 0 idx types')
