def test_cleanup(self):
''' Cleanup objects created by tests. '''
# Delete all of the objects in the test workspace.
wsClient = Workspace(self._config["workspace_url"], token=self._token)
listObjectsParams = dict()
listObjectsParams['workspaces'] = [ self._config['test_ws'] ]
objectList = wsClient.list_objects(listObjectsParams)
deleteList = list()
for object in objectList:
deleteList.append( { 'wsid': object[6], 'objid': object[0], 'ver': object[4] })
wsClient.delete_objects(deleteList)
objectList = wsClient.list_objects(listObjectsParams)
for object in objectList:
print 'After delete Object %s %s' %(object[1], object[4])
def test_cleanup(self):
''' Cleanup objects created by tests. '''
# Delete all of the objects in the test workspace.
wsClient = Workspace(self._config["workspace_url"], token=self._token)
listObjectsParams = dict()
listObjectsParams['workspaces'] = [self._config['test_ws']]
objectList = wsClient.list_objects(listObjectsParams)
deleteList = list()
for object in objectList:
deleteList.append({
'wsid': object[6],
'objid': object[0],
'ver': object[4]
})
wsClient.delete_objects(deleteList)
objectList = wsClient.list_objects(listObjectsParams)
for object in objectList:
print 'After delete Object %s %s' % (object[1], object[4])
def setUp(cls):
token = environ.get('KB_AUTH_TOKEN', None)
if token is None:
sys.stderr.write(
"Error: Unable to run tests without authentication token!\n")
sys.exit(1)
token_file = open('ltest/script_test/token.txt', 'w')
token_file.write(token)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('CoExpression'):
cls.cfg[nameval[0]] = nameval[1]
auth_service_url = cls.cfg.get(
'auth-service-url',
"https://kbase.us/services/authorization/Sessions/Login")
ws_url = cls.cfg['ws_url']
auth_service_url_allow_insecure = cls.cfg[
'auth-service-url-allow-insecure']
auth_client = _KBaseAuth(auth_service_url)
user_id = auth_client.get_user(token)
ws = Workspace(
url=ws_url,
token=token,
auth_svc=auth_service_url,
trust_all_ssl_certificates=auth_service_url_allow_insecure)
# update input data in reverse order of references
ordered_file_list = [
INPUT_META_DATA_DIR + '/test_diff_p_distribution_input_ref2.json',
INPUT_META_DATA_DIR + '/test_diff_p_distribution_input_ref1.json',
INPUT_META_DATA_DIR + '/test_diff_p_distribution_input.json',
INPUT_META_DATA_DIR + '/test_view_heatmap_input_ref1.json',
INPUT_META_DATA_DIR + '/test_view_heatmap_input.json',
INPUT_META_DATA_DIR + '/test_coex_clust_input.json',
INPUT_META_DATA_DIR + '/test_filter_genes_input.json'
]
for filename in ordered_file_list:
with open(filename, 'r') as infile:
input_meta_data = json.load(infile)
# create workspace that is local to the user if it does not exist
workspace_name_t = Template(
str(input_meta_data['params'][0]['workspace_name']))
workspace_name = workspace_name_t.substitute(user_id=user_id)
print('workspace_name: ' + workspace_name)
try:
ws_info = ws.get_workspace_info({'workspace': workspace_name})
print("workspace already exists: " + str(ws_info))
except:
ws_info = ws.create_workspace({
'workspace':
workspace_name,
'description':
'Workspace for ' + str(input_meta_data['method'])
})
print("Created new workspace: " + str(ws_info))
print('reading input file: ' + filename)
object_name = str(input_meta_data['params'][0]['object_name'])
print('object_name: ' + object_name)
input_data_filename = INPUT_DATA_DIR + '/' + object_name + '.json'
print('input data filename: ' + input_data_filename)
with open(input_data_filename, 'r') as infile:
input_data = json.load(infile)
# update workspace name in input data
input_data_str = json.dumps(input_data)
input_data_t = Template(input_data_str)
input_data_str = input_data_t.substitute(
workspace_name=workspace_name)
input_data = json.loads(input_data_str)
print('type: ' + input_data[0]['info'][2])
#upload data (no effect if data already exists in workspace)
print('uploading input data to workspace')
ws.save_objects({
'workspace':
workspace_name,
'objects': [{
'type': input_data[0]['info'][2],
'data': input_data[0]['data'],
'name': object_name
}]
})
print('ws objects: ' +
str(ws.list_objects({'workspaces': [workspace_name]})))
def setUp(cls):
token = environ.get('KB_AUTH_TOKEN', None)
if token is None:
sys.stderr.write("Error: Unable to run tests without authentication token!\n")
sys.exit(1)
token_file = open('ltest/script_test/token.txt', 'w')
token_file.write(token)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('CoExpression'):
cls.cfg[nameval[0]] = nameval[1]
auth_service_url = cls.cfg.get('auth-service-url',
"https://kbase.us/services/authorization/Sessions/Login")
ws_url = cls.cfg['ws_url']
auth_service_url_allow_insecure = cls.cfg['auth-service-url-allow-insecure']
auth_client = _KBaseAuth(auth_service_url)
user_id = auth_client.get_user(token)
ws = Workspace(url=ws_url, token=token, auth_svc=auth_service_url,
trust_all_ssl_certificates=auth_service_url_allow_insecure)
# update input data in reverse order of references
ordered_file_list = [INPUT_META_DATA_DIR+'/test_diff_p_distribution_input_ref2.json',
INPUT_META_DATA_DIR+'/test_diff_p_distribution_input_ref1.json',
INPUT_META_DATA_DIR+'/test_diff_p_distribution_input.json',
INPUT_META_DATA_DIR+'/test_view_heatmap_input_ref1.json',
INPUT_META_DATA_DIR+'/test_view_heatmap_input.json',
INPUT_META_DATA_DIR+'/test_coex_clust_input.json',
INPUT_META_DATA_DIR+'/test_filter_genes_input.json']
for filename in ordered_file_list:
with open(filename, 'r') as infile:
input_meta_data = json.load(infile)
# create workspace that is local to the user if it does not exist
workspace_name_t = Template(str(input_meta_data['params'][0]['workspace_name']))
workspace_name = workspace_name_t.substitute(user_id=user_id)
print('workspace_name: ' + workspace_name)
try:
ws_info = ws.get_workspace_info({'workspace': workspace_name})
print("workspace already exists: " + str(ws_info))
except:
ws_info = ws.create_workspace(
{'workspace': workspace_name, 'description': 'Workspace for ' + str(input_meta_data['method'])})
print("Created new workspace: " + str(ws_info))
print('reading input file: '+filename)
object_name = str(input_meta_data['params'][0]['object_name'])
print('object_name: '+object_name)
input_data_filename = INPUT_DATA_DIR + '/' + object_name + '.json'
print('input data filename: ' + input_data_filename)
with open(input_data_filename, 'r') as infile:
input_data = json.load(infile)
# update workspace name in input data
input_data_str = json.dumps(input_data)
input_data_t = Template(input_data_str)
input_data_str = input_data_t.substitute(workspace_name=workspace_name)
input_data = json.loads(input_data_str)
print('type: '+input_data[0]['info'][2])
#upload data (no effect if data already exists in workspace)
print('uploading input data to workspace')
ws.save_objects(
{'workspace': workspace_name, 'objects': [{'type': input_data[0]['info'][2],
'data': input_data[0]['data'],
'name': object_name}]})
print('ws objects: ' + str(ws.list_objects({'workspaces': [workspace_name]})))
