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 _get_interactor(self, 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": test_user_api_key, # TODO
"keep_outputs_dir": '',
}
if test_user_api_key is None:
galaxy_interactor_kwds["test_user"] = test_user
galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
return galaxy_interactor
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 build_tests(app=None,
testing_shed_tools=False,
master_api_key=None,
user_api_key=None,
name_prefix="TestForTool_",
baseclass=ToolTestCase,
create_admin=False,
user_email=None,
G=None,
contains=None):
"""
If the module level variable `toolbox` is set, generate `ToolTestCase`
classes for all of its tests and put them into this modules globals() so
they can be discovered by nose.
"""
# galaxy_interactor = None
# if app is None:
host, port, url = target_url_parts()
keep_outputs_dir = setup_keep_outdir()
galaxy_interactor_kwds = {
"galaxy_url": url,
"master_api_key": master_api_key,
"api_key": user_api_key,
"keep_outputs_dir": keep_outputs_dir,
"user_api_key_is_admin_key": True,
}
if create_admin and not user_api_key:
galaxy_interactor_kwds['test_user'] = user_email
galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
if not G:
# Push all the toolbox tests to module level
G = globals()
# Eliminate all previous tests from G.
for key, val in G.copy().items():
if key.startswith('TestForTool_'):
del G[key]
tests_summary = galaxy_interactor.get_tests_summary()
for tool_id, tool_summary in tests_summary.items():
# Create a new subclass of ToolTestCase, dynamically adding methods
# named test_tool_XXX that run each test defined in the tool config.
if contains and contains not in tool_id:
continue
name = name_prefix + tool_id.replace(' ', '_')
baseclasses = (baseclass, )
namespace = dict()
all_versions_test_count = 0
for tool_version, version_summary in tool_summary.items():
count = version_summary["count"]
for i in range(count):
test_function_name = 'test_tool_%06d' % all_versions_test_count
def make_test_method(tool_version, test_index):
def test_tool(self):
self.do_it(tool_version=tool_version, test_index=test_index)
test_tool.__name__ = test_function_name
return test_tool
test_method = make_test_method(tool_version, i)
test_method.__doc__ = "( %s ) > Test-%d" % (tool_id, all_versions_test_count + 1)
namespace[test_function_name] = test_method
namespace['tool_id'] = tool_id
namespace["galaxy_interactor"] = galaxy_interactor
namespace['master_api_key'] = master_api_key
namespace['user_api_key'] = user_api_key or galaxy_interactor.api_key
namespace['test_count'] = count
all_versions_test_count += 1
# Create new class object, with name name, derived
# from baseclasses (which should be a tuple of classes) and with namespace dict.
new_class_obj = type(str(name), baseclasses, namespace)
G[name] = new_class_obj
return G
def build_tests(app=None,
testing_shed_tools=False,
master_api_key=None,
user_api_key=None,
name_prefix="TestForTool_",
baseclass=ToolTestCase,
create_admin=False,
user_email=None,
G=None,
contains=None):
"""
If the module level variable `toolbox` is set, generate `ToolTestCase`
classes for all of its tests and put them into this modules globals() so
they can be discovered by nose.
"""
# galaxy_interactor = None
# if app is None:
host, port, url = target_url_parts()
keep_outputs_dir = setup_keep_outdir()
galaxy_interactor_kwds = {
"galaxy_url": url,
"master_api_key": master_api_key,
"api_key": user_api_key,
"keep_outputs_dir": keep_outputs_dir,
"user_api_key_is_admin_key": True,
}
if create_admin and not user_api_key:
galaxy_interactor_kwds['test_user'] = user_email
galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
if not G:
# Push all the toolbox tests to module level
G = globals()
# Eliminate all previous tests from G.
for key, val in G.copy().items():
if key.startswith('TestForTool_'):
del G[key]
tests_summary = galaxy_interactor.get_tests_summary()
for tool_id, tool_summary in tests_summary.items():
# Create a new subclass of ToolTestCase, dynamically adding methods
# named test_tool_XXX that run each test defined in the tool config.
if contains and contains not in tool_id:
continue
name = name_prefix + tool_id.replace(' ', '_')
baseclasses = (baseclass, )
namespace = dict()
all_versions_test_count = 0
for tool_version, version_summary in tool_summary.items():
count = version_summary["count"]
for i in range(count):
test_function_name = 'test_tool_%06d' % all_versions_test_count
def make_test_method(tool_version, test_index):
def test_tool(self):
self.do_it(tool_version=tool_version,
test_index=test_index)
test_tool.__name__ = test_function_name
return test_tool
test_method = make_test_method(tool_version, i)
test_method.__doc__ = "( %s ) > Test-%d" % (
tool_id, all_versions_test_count + 1)
namespace[test_function_name] = test_method
namespace['tool_id'] = tool_id
namespace["galaxy_interactor"] = galaxy_interactor
namespace['master_api_key'] = master_api_key
namespace[
'user_api_key'] = user_api_key or galaxy_interactor.api_key
namespace['test_count'] = count
all_versions_test_count += 1
# Create new class object, with name name, derived
# from baseclasses (which should be a tuple of classes) and with namespace dict.
new_class_obj = type(str(name), baseclasses, namespace)
G[name] = new_class_obj
return G
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]