def test_loadGenome(self):
''' Load a test Genome object into the test workspace. '''
# Create the test workspace.
wsClient = Workspace(self._config["workspace_url"], token=self._token)
try:
# See if the workspace exists.
wsInfo = wsClient.get_workspace_info( { "workspace": self._config["test_ws"] } )
except WorkspaceServerError as e:
# Hopefully this means the workspace does not exist. (It could also mean someone messed up setting up the URLs)
traceback.print_exc(file=sys.stderr)
wsInfo = wsClient.create_workspace( { "workspace": self._config["test_ws"] } )
# We also need to put in a mapping and a biochemistry object somewhere.
# To do this, I just create a "dependency workspace" and pull them from there.
try:
# See if the workspace exists.
wsInfo = wsClient.get_workspace_info( { "workspace": self._config["dependency_ws"] } )
except WorkspaceServerError as e:
# Hopefully this means the workspace does not exist. (It could also mean someone messed up setting up the URLs)
# traceback.print_exc(file=sys.stderr)
depWsInfo = wsClient.create_workspace( { "workspace": self._config["dependency_ws"] } )
# Load the mapping and biochemistry objects
testContigSet = json.load(open(self._config['contigset_file'], 'r'))
contigSetSaveData = dict()
contigSetSaveData['type'] = 'KBaseGenomes.ContigSet'
contigSetSaveData['name'] = self._config['contigsetid']
contigSetSaveData['data'] = testContigSet
testGenome = json.load(open(self._config["genome_file"], "r"))
genomeSaveData = dict()
genomeSaveData['type'] = 'KBaseGenomes.Genome'
genomeSaveData['name'] = self._config['genomeid']
genomeSaveData['data'] = testGenome
wsClient.save_objects( { 'workspace': self._config['test_ws'], 'objects': [ genomeSaveData, contigSetSaveData ] } )
def upload_narrative(nar_file, auth_token, user_id, url=ci_ws, set_public=False):
"""
Uploads a Narrative from a downloaded object file.
This file needs to be in JSON format, and it expects all
data and info that is usually returned by the Workspace.get_objects
method.
Returns a dict of three elements:
ws: the id of the workspace that was created
obj: the id of the narrative object
ref: the above two joined together into an object ref (for convenience)
"""
# read the file
f = open(nar_file, "r")
nar = json.loads(f.read())
f.close()
# do some setup.
current_nar_metadata = ws_metadata
current_nar_metadata["narrative_nice_name"] = nar["data"]["metadata"]["name"]
ws_client = Workspace(url=url, token=auth_token)
# create the new workspace for the narrative
ws_info = ws_client.create_workspace(
{
"workspace": "{}:{}".format(user_id, str(time.time()).replace(".", "")),
"meta": current_nar_metadata,
"globalread": "r" if set_public else "n",
}
)
ws_id = ws_info[0]
# setup and save the narrative object
nar["info"][10]
ws_save_obj = {
"type": "KBaseNarrative.Narrative",
"data": nar["data"],
"name": nar["info"][1],
"meta": nar["info"][10],
"provenance": [
{
"script": "upload_narrative_test.py",
"description": "Temporary Narrative uploaded for automated testing",
}
],
}
obj_info = ws_client.save_objects({"id": ws_id, "objects": [ws_save_obj]})
# tweak the workspace's metadata to properly present its narrative
ws_client.alter_workspace_metadata(
{"wsi": {"id": ws_id}, "new": {"narrative": obj_info[0][0]}}
)
return {
"ws": ws_info[0],
"obj": obj_info[0][0],
"refstr": "{}/{}".format(ws_info[0], obj_info[0][0]),
"ref": NarrativeRef({"wsid": ws_info[0], "objid": obj_info[0][0]}),
}
def test_loadGenome(self):
''' Load a test Genome object into the test workspace. '''
# Create the test workspace.
wsClient = Workspace(self._config["workspace_url"], token=self._token)
try:
# See if the workspace exists.
wsInfo = wsClient.get_workspace_info(
{"workspace": self._config["test_ws"]})
except WorkspaceServerError as e:
# Hopefully this means the workspace does not exist. (It could also mean someone messed up setting up the URLs)
traceback.print_exc(file=sys.stderr)
wsInfo = wsClient.create_workspace(
{"workspace": self._config["test_ws"]})
# We also need to put in a mapping and a biochemistry object somewhere.
# To do this, I just create a "dependency workspace" and pull them from there.
try:
# See if the workspace exists.
wsInfo = wsClient.get_workspace_info(
{"workspace": self._config["dependency_ws"]})
except WorkspaceServerError as e:
# Hopefully this means the workspace does not exist. (It could also mean someone messed up setting up the URLs)
# traceback.print_exc(file=sys.stderr)
depWsInfo = wsClient.create_workspace(
{"workspace": self._config["dependency_ws"]})
# Load the mapping and biochemistry objects
testContigSet = json.load(open(self._config['contigset_file'], 'r'))
contigSetSaveData = dict()
contigSetSaveData['type'] = 'KBaseGenomes.ContigSet'
contigSetSaveData['name'] = self._config['contigsetid']
contigSetSaveData['data'] = testContigSet
testGenome = json.load(open(self._config["genome_file"], "r"))
genomeSaveData = dict()
genomeSaveData['type'] = 'KBaseGenomes.Genome'
genomeSaveData['name'] = self._config['genomeid']
genomeSaveData['data'] = testGenome
wsClient.save_objects({
'workspace': self._config['test_ws'],
'objects': [genomeSaveData, contigSetSaveData]
})
def upload_narrative(nar_file, auth_token, user_id, url=ci_ws, set_public=False):
"""
Uploads a Narrative from a downloaded object file.
This file needs to be in JSON format, and it expects all
data and info that is usually returned by the Workspace.get_objects
method.
Returns a dict of three elements:
ws: the id of the workspace that was created
obj: the id of the narrative object
ref: the above two joined together into an object ref (for convenience)
"""
# read the file
f = open(nar_file, 'r')
nar = json.loads(f.read())
f.close()
# do some setup.
current_nar_metadata = ws_metadata
current_nar_metadata['narrative_nice_name'] = nar['data']['metadata']['name']
ws_client = Workspace(url=url, token=auth_token)
# create the new workspace for the narrative
ws_info = ws_client.create_workspace({
'workspace': '{}:{}'.format(user_id, str(time.time()).replace('.', '')),
'meta': current_nar_metadata,
'globalread': 'r' if set_public else 'n'
})
ws_id = ws_info[0]
# setup and save the narrative object
metadata = nar['info'][10]
ws_save_obj = {
'type': 'KBaseNarrative.Narrative',
'data': nar['data'],
'name': nar['info'][1],
'meta': nar['info'][10],
'provenance': [{
'script': 'upload_narrative_test.py',
'description': 'Temporary Narrative uploaded for automated testing'
}]
}
obj_info = ws_client.save_objects({'id': ws_id,
'objects': [ws_save_obj]})
# tweak the workspace's metadata to properly present its narrative
ws_client.alter_workspace_metadata({'wsi': {'id': ws_id}, 'new': {'narrative': obj_info[0][0]}})
return {
'ws': ws_info[0],
'obj': obj_info[0][0],
'refstr': '{}/{}'.format(ws_info[0], obj_info[0][0]),
'ref': NarrativeRef({'wsid': ws_info[0], 'objid': obj_info[0][0]})
}
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]})))
