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_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_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 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 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")
