def test__parse_path(self):
manager = KBaseWSManager()
cases = [
("123", NarrativeRef({
"wsid": "123",
"objid": None,
"ver": None
})),
("ws.123", NarrativeRef({
"wsid": "123",
"objid": None,
"ver": None
})),
(
"ws.123.obj.456",
NarrativeRef({
"wsid": "123",
"objid": "456",
"ver": None
}),
),
(
"ws.123.obj.456.ver.7",
NarrativeRef({
"wsid": "123",
"objid": "456",
"ver": "7"
}),
),
]
for c in cases:
self.assertEqual(c[1], manager._parse_path(c[0]))
def test_ref_init_fail(self):
with self.assertRaises(ValueError) as e:
NarrativeRef({"wsid": "x", "objid": None, "ver": None})
self.assertIn("A numerical Workspace id is required for a Narrative ref, not x", str(e.exception))
with self.assertRaises(ValueError) as e:
NarrativeRef({"wsid": 678, "objid": "x", "ver": None})
self.assertIn("objid must be numerical, not x", str(e.exception))
with self.assertRaises(ValueError) as e:
NarrativeRef({"wsid": 678, "objid": 1, "ver": "x"})
self.assertIn("If ver is present in the ref, it must be numerical, not x", str(e.exception))
def str_to_ref(s):
""" Takes a ref string, returns a NarrativeRef object """
vals = s.split("/")
ref = {"wsid": vals[0], "objid": vals[1]}
if len(vals) == 3:
ref["ver"] = vals[2]
return NarrativeRef(ref)
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 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 _parse_path(self, path):
"""
From the URL path for a Narrative, returns a NarrativeRef
if the path isn't parseable, this raises a 404 with the invalid path.
"""
path = path.strip("/")
m = self.path_regex.match(path)
if m is None:
raise HTTPError(404, "Invalid Narrative path {}".format(path))
try:
return NarrativeRef(
dict(wsid=m.group("wsid"), objid=m.group("objid"), ver=m.group("ver"))
)
except RuntimeError as e:
raise HTTPError(500, str(e))
except WorkspaceError as e:
raise HTTPError(e.http_code, e.message)
def test_no_ws_perm(self):
with self.assertRaises(WorkspaceError) as e:
NarrativeRef({"wsid": 789, "objid": None, "ver": None})
self.assertEqual(403, e.exception.http_code)
self.assertIn("You do not have access to this workspace", e.exception.message)
def test_no_objid_fail(self):
with self.assertRaises(RuntimeError) as e:
NarrativeRef({"wsid": 678, "objid": None, "ver": None})
self.assertIn("Couldn't find Narrative object id in Workspace metadata", str(e.exception))
def test_ok(self):
ref = NarrativeRef({"wsid": 123, "objid": 456, "ver": 7})
self.assertEqual(ref.wsid, 123)
self.assertEqual(ref.objid, 456)
self.assertEqual(ref.ver, 7)
def test_no_objid_ok(self):
ref = NarrativeRef({"wsid": 123, "objid": None, "ver": None})
self.assertEqual(ref.wsid, 123)
self.assertEqual(ref.objid, 1)
self.assertIsNone(ref.ver)