def load_entities(self):
# To potentially save time, sanity check if entities already exist
r1 = fapi.get_entity(self.project, self.workspace, "sample_set",
"SS-TP")
r2 = fapi.get_entity(self.project, self.workspace, "participant_set",
"PARTICIP_SET_2")
if r1.status_code == 200 and r2.status_code == 200:
return
if r1.status_code not in [404, 200
] or r2.status_code not in [404, 200]:
raise RuntimeError("while checking for sample_set/participant_set")
print("\n\tLoading data entities for tests ...", file=sys.stderr)
args = ("entity_import", "-p", self.project, "-w", self.workspace)
datapath = os.path.join("firecloud", "tests")
call_func(*(args + ("-f", os.path.join(datapath, "participants.tsv"))))
call_func(
*(args +
("-f", os.path.join(datapath, "particip_set_members.tsv"))))
call_func(*(args + ("-f", os.path.join(datapath, "particip_set.tsv"))))
call_func(*(args + ("-f", os.path.join(datapath, "samples.tsv"))))
call_func(*(args +
("-f", os.path.join(datapath, "sset_membership.tsv"))))
call_func(*(args + ("-f", os.path.join(datapath, "sset.tsv"))))
call_func(*(args + ("-f", os.path.join(datapath, "pairs.tsv"))))
call_func(*(args +
("-f", os.path.join(datapath, "pairset_membership.tsv"))))
call_func(*(args + ("-f", os.path.join(datapath, "pairset_attr.tsv"))))
print("\t... done loading data ...", file=sys.stderr)
def load_entities(self):
# To potentially save time, check if entities already exist
r = fapi.get_entity(self.project, self.workspace, "sample_set",
"SS-NT")
if r.status_code == 200:
return
if r.status_code != 404:
raise RuntimeError("while determining if SS-NT sample_set exists")
call_func("entity_import", "-p", self.project, "-w", self.workspace,
"-f", os.path.join("firecloud", "tests", "participants.tsv"))
call_func("entity_import", "-p", self.project, "-w", self.workspace,
"-f", os.path.join("firecloud", "tests", "samples.tsv"))
call_func("entity_import", "-p", self.project, "-w", self.workspace,
"-f",
os.path.join("firecloud", "tests", "sset_membership.tsv"))
call_func("entity_import", "-p", self.project, "-w", self.workspace,
"-f", os.path.join("firecloud", "tests", "sset.tsv"))
call_func("entity_import", "-p", self.project, "-w", self.workspace,
"-f", os.path.join("firecloud", "tests", "pairs.tsv"))
call_func("entity_import", "-p", self.project, "-w", self.workspace,
"-f",
os.path.join("firecloud", "tests", "pairset_membership.tsv"))
call_func("entity_import", "-p", self.project, "-w", self.workspace,
"-f", os.path.join("firecloud", "tests", "pairset_attr.tsv"))
def get_entity(self, etype, entity_id):
"""Return entity in this workspace.
Args:
etype (str): Entity type
entity_id (str): Entity name/unique id
"""
r = fapi.get_entity(self.namespace, self.name, etype,
entity_id, self.api_url)
fapi._check_response_code(r, 200)
dresp = r.json()
return Entity(etype, entity_id, dresp['attributes'])