def run_test(index, test_id):
def register(job_data):
tool_test_results.append({
'id': test_id,
'has_data': True,
'data': job_data,
})
try:
if log:
log.info("Executing test '%s'", test_id)
verify_tool(
tool_id,
galaxy_interactor,
test_index=index,
tool_version=tool_version,
register_job_data=register,
quiet=True,
test_history=test_history,
)
tests_passed.append(test_id)
if log:
log.info("Test '%s' passed", test_id)
except Exception as e:
if log:
log.warning("Test '%s' failed", test_id, exc_info=True)
test_exceptions.append((test_id, e))
def do_it(self, tool_id=None, tool_version=None, test_index=0, resource_parameters={}):
"""
Run through a tool test case.
"""
if tool_id is None:
tool_id = self.tool_id
assert tool_id
verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)
def do_it(self, tool_id=None, tool_version=None, test_index=0, resource_parameters={}):
"""
Run through a tool test case.
"""
if tool_id is None:
tool_id = self.tool_id
assert tool_id
verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)
def run_tool_test(self, tool_id, index=0, resource_parameters={}):
host, port, url = target_url_parts()
galaxy_interactor_kwds = {
"galaxy_url": url,
"master_api_key": get_master_api_key(),
"api_key": get_user_api_key(),
"keep_outputs_dir": None,
}
galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
verify_tool(tool_id=tool_id,
test_index=index,
galaxy_interactor=galaxy_interactor,
resource_parameters=resource_parameters)
def _test_tool(self, tool, test_user, test_user_api_key):
if test_user_api_key is None:
whoami = self.gi.make_get_request(self.gi.url + "/whoami").json()
if whoami is not None:
test_user_api_key = self.gi.key
galaxy_interactor_kwds = {
"galaxy_url": re.sub('/api', '', self.gi.url),
"master_api_key": self.gi.key,
"api_key": None, # TODO
"keep_outputs_dir": '',
}
if test_user_api_key is None:
galaxy_interactor_kwds["test_user"] = test_user
galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
tool_id = tool["id"]
tool_version = tool["version"]
tool_test_dicts = galaxy_interactor.get_tool_tests(
tool_id, tool_version=tool_version)
test_indices = list(range(len(tool_test_dicts)))
tool_test_results = []
tests_passed = []
test_exceptions = []
for test_index in test_indices:
test_id = tool_id + "-" + str(test_index)
def register(job_data):
tool_test_results.append({
'id': test_id,
'has_data': True,
'data': job_data,
})
try:
verify_tool(tool_id,
galaxy_interactor,
test_index=test_index,
tool_version=tool_version,
register_job_data=register,
quiet=True)
tests_passed.append(test_id)
except Exception as e:
test_exceptions.append((test_id, e))
Results = namedtuple(
"Results",
["tool_test_results", "tests_passed", "test_exceptions"])
return Results(tool_test_results=tool_test_results,
tests_passed=tests_passed,
test_exceptions=test_exceptions)
def run_tool_test(self, tool_id, index=0, resource_parameters={}):
host, port, url = target_url_parts()
galaxy_interactor_kwds = {
"galaxy_url": url,
"master_api_key": get_master_api_key(),
"api_key": get_user_api_key(),
"keep_outputs_dir": None,
}
galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
verify_tool(
tool_id=tool_id,
test_index=index,
galaxy_interactor=galaxy_interactor,
resource_parameters=resource_parameters
)
def _run_test_case(self, test_case):
if hasattr(test_case, "job_path"):
# Simple file-based job path.
return super(GalaxyEngine, self)._run_test_case(test_case)
else:
with self.ensure_runnables_served([test_case.runnable]) as config:
galaxy_interactor_kwds = {
"galaxy_url": config.galaxy_url,
"master_api_key": config.master_api_key,
"api_key": config.user_api_key,
"keep_outputs_dir": "", # TODO: this...
}
tool_id = test_case.tool_id
test_index = test_case.test_index
tool_version = test_case.tool_version
galaxy_interactor = interactor.GalaxyInteractorApi(
**galaxy_interactor_kwds)
test_results = []
def _register_job_data(job_data):
test_results.append({
'id': tool_id + "-" + str(test_index),
'has_data': True,
'data': job_data,
})
verbose = self._ctx.verbose
try:
if verbose:
# TODO: this is pretty hacky, it'd be better to send a stream
# and capture the output information somehow.
interactor.VERBOSE_GALAXY_ERRORS = True
interactor.verify_tool(
tool_id,
galaxy_interactor,
test_index=test_index,
tool_version=tool_version,
register_job_data=_register_job_data,
quiet=not verbose,
)
except Exception:
pass
return test_results[0]
def _run_test_case(self, test_case):
if hasattr(test_case, "job_path"):
# Simple file-based job path.
return super(GalaxyEngine, self)._run_test_case(test_case)
else:
with self.ensure_runnables_served([test_case.runnable]) as config:
galaxy_interactor_kwds = {
"galaxy_url": config.galaxy_url,
"master_api_key": config.master_api_key,
"api_key": config.user_api_key,
"keep_outputs_dir": "", # TODO: this...
}
tool_id = test_case.tool_id
test_index = test_case.test_index
tool_version = test_case.tool_version
galaxy_interactor = interactor.GalaxyInteractorApi(**galaxy_interactor_kwds)
test_results = []
def _register_job_data(job_data):
test_results.append({
'id': tool_id + "-" + str(test_index),
'has_data': True,
'data': job_data,
})
verbose = self._ctx.verbose
try:
if verbose:
# TODO: this is pretty hacky, it'd be better to send a stream
# and capture the output information somehow.
interactor.VERBOSE_GALAXY_ERRORS = True
interactor.verify_tool(
tool_id,
galaxy_interactor,
test_index=test_index,
tool_version=tool_version,
register_job_data=_register_job_data,
quiet=not verbose,
)
except Exception:
pass
return test_results[0]
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
args = _arg_parser().parse_args(argv)
galaxy_interactor_kwds = {
"galaxy_url": args.galaxy_url,
"master_api_key": args.admin_key,
"api_key": args.key,
"keep_outputs_dir": args.output,
}
tool_id = args.tool_id
tool_version = args.tool_version
galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
raw_test_index = args.test_index
if raw_test_index == ALL_TESTS:
tool_test_dicts = galaxy_interactor.get_tool_tests(
tool_id, tool_version=tool_version)
test_indices = list(range(len(tool_test_dicts)))
else:
test_indices = [int(raw_test_index)]
test_results = []
if args.append:
with open(args.output_json, "r") as f:
previous_results = json.load(f)
test_results = previous_results["tests"]
exceptions = []
verbose = args.verbose
for test_index in test_indices:
if tool_version:
tool_id_and_version = "%s/%s" % (tool_id, tool_version)
else:
tool_id_and_version = tool_id
test_identifier = "tool %s test # %d" % (tool_id_and_version,
test_index)
def register(job_data):
test_results.append({
'id': tool_id + "-" + str(test_index),
'has_data': True,
'data': job_data,
})
try:
verify_tool(tool_id,
galaxy_interactor,
test_index=test_index,
tool_version=tool_version,
register_job_data=register,
quiet=not verbose,
force_path_paste=args.force_path_paste)
if verbose:
print("%s passed" % test_identifier)
except Exception as e:
if verbose:
print("%s failed, %s" % (test_identifier, e))
exceptions.append(e)
report_obj = {
'version': '0.1',
'tests': test_results,
}
output_json = args.output_json
if output_json:
if args.output_json == "-":
assert not args.append
print(json.dumps(report_obj))
else:
with open(args.output_json, "w") as f:
json.dump(report_obj, f)
if exceptions:
raise exceptions[0]
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
args = _arg_parser().parse_args(argv)
galaxy_interactor_kwds = {
"galaxy_url": args.galaxy_url,
"master_api_key": args.admin_key,
"api_key": args.key,
"keep_outputs_dir": args.output,
}
tool_id = args.tool_id
tool_version = args.tool_version
galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
raw_test_index = args.test_index
if raw_test_index == ALL_TESTS:
tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version)
test_indices = list(range(len(tool_test_dicts)))
else:
test_indices = [int(raw_test_index)]
test_results = []
if args.append:
with open(args.output_json, "r") as f:
previous_results = json.load(f)
test_results = previous_results["tests"]
exceptions = []
verbose = args.verbose
for test_index in test_indices:
if tool_version:
tool_id_and_version = "%s/%s" % (tool_id, tool_version)
else:
tool_id_and_version = tool_id
test_identifier = "tool %s test # %d" % (tool_id_and_version, test_index)
def register(job_data):
test_results.append({
'id': tool_id + "-" + str(test_index),
'has_data': True,
'data': job_data,
})
try:
verify_tool(
tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version,
register_job_data=register, quiet=not verbose
)
if verbose:
print("%s passed" % test_identifier)
except Exception as e:
if verbose:
print("%s failed, %s" % (test_identifier, e))
exceptions.append(e)
report_obj = {
'version': '0.1',
'tests': test_results,
}
output_json = args.output_json
if output_json:
if args.output_json == "-":
assert not args.append
print(json.dumps(report_obj))
else:
with open(args.output_json, "w") as f:
json.dump(report_obj, f)
if exceptions:
raise exceptions[0]