def test_publisher_auth(self):
example1_dir = op.join(self.get_examples_dir(), "example1")
# Bad token should fail
with self.assertRaises(ZenodoError) as e:
bosh(["publish",
op.join(example1_dir, "example1_docker.json"),
"--sandbox",
"-y", "-v", "--zenodo-token", "12345"])
self.assertTrue("Cannot authenticate to Zenodo" in str(e.exception))
# No token should fail
with self.assertRaises(ZenodoError) as e:
bosh(["publish",
op.join(example1_dir,
"example1_docker.json"),
"--sandbox", "-y", "-v"])
self.assertTrue("Cannot authenticate to Zenodo" in str(e.exception))
# Right token should work
self.assertTrue(bosh, ["publish",
op.join(example1_dir,
"example1_docker.json"),
"--sandbox", "-y", "-v",
"--zenodo-token",
"hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJ"
"i8i2hnN8r"])
# Now no token should work (config file must have been updated)
self.assertTrue(bosh, ["publish",
op.join(example1_dir,
"example1_docker.json"),
"--sandbox", "-y", "-v"])
def test_publish_nexus_no_token_fail(self, mock_dir, mock_cred):
cleanup()
setup()
with self.assertRaises(NexusError) as e:
bosh(["data", "publish", "-y", "--nexus", "--sandbox"])
self.assertIn("Cannot find Nexus credentials.", str(e.exception))
def test_publication_errors(self):
# Update an already published descriptor (wrong id)
with self.assertRaises(ZenodoError) as e:
wrong_id = bosh([
"publish", "whatever.json", "--sandbox", "-y", "-v",
"--zenodo-token", "hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJ"
"i8i2hnN8r", "--id", "this_is_a_wrong_id"
])
self.assertTrue(
"Zenodo ID must be prefixed by 'zenodo'" in str(e.exception))
# Publish a descriptor that doesn't have an author
good_desc = op.join(self.get_examples_dir(), "good.json")
temp_descriptor = tempfile.NamedTemporaryFile(suffix=".json")
shutil.copyfile(good_desc, temp_descriptor.name)
with self.assertRaises(ZenodoError) as e:
no_author = bosh([
"publish", temp_descriptor.name, "--sandbox", "-y", "-v",
"--zenodo-token", "hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJ"
"i8i2hnN8r"
])
self.assertTrue(
"Tool must have an author to be published." in str(e.exception))
# Publish a descriptor that doesn't have a container image
good_desc = op.join(self.get_examples_dir(), "no_container.json")
temp_descriptor = tempfile.NamedTemporaryFile(suffix=".json")
shutil.copyfile(good_desc, temp_descriptor.name)
with self.assertRaises(ZenodoError) as e:
no_container = bosh([
"publish", temp_descriptor.name, "--sandbox", "-y", "-v",
"--zenodo-token", "hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJ"
"i8i2hnN8r"
])
self.assertTrue("Tool must have a container image to be published." in
str(e.exception))
# Update a descriptor that doesn't have a DOI
example1_dir = op.join(self.get_examples_dir(), "example1")
example1_desc = op.join(example1_dir, "example1_docker.json")
temp_descriptor = tempfile.NamedTemporaryFile(suffix=".json")
shutil.copyfile(example1_desc, temp_descriptor.name)
# Make sure that example1.json doesn't have a DOI yet
with open(temp_descriptor.name, 'r') as fhandle:
descriptor = json.load(fhandle)
self.assertIsNone(descriptor.get('doi'))
# Try to update it
with self.assertRaises(ZenodoError) as e:
doi = bosh([
"publish", temp_descriptor.name, "--sandbox", "-y", "-v",
"--zenodo-token", "hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r", "--replace"
])
self.assertTrue("To publish an updated version of a previously "
"published descriptor, the descriptor must"
" contain a DOI" in str(e.exception))
def test_publish_bulk(self, mock_dir, mock_get, mock_post):
cleanup()
setup()
bosh(["data", "publish", "-y", "--sandbox", "--zenodo-token",
"hAaW2wSBZMskxpfigTYHcuDrCPWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r"])
self.assertEqual(len(os.listdir(os.path.join(mock_get_data_cache()))),
2)
def test_pull_missing_raises_exception(self, mock_urlretrieve):
good1 = "zenodo." + str(example_boutiques_tool.id)
good2 = "zenodo.2587160"
bad1 = "zenodo.9999990"
with self.assertRaises(ZenodoError) as e:
bosh(["pull", good1, bad1, good2])
self.assertIn(
"Descriptor \"{0}\" not found".format(bad1.split(".")[1]),
str(e.exception))
def test_invocation(self):
descriptor = os.path.join(
os.path.split(bfile)[0], "schema/examples/good.json")
invocation = os.path.join(
os.path.split(bfile)[0], "schema/examples/good_invocation.json")
self.assertFalse(
bosh(["invocation", descriptor, "-i", invocation, "-w"]))
self.assertFalse(
bosh(["invocation", descriptor, "-i", invocation, "-w"]))
def test_publish_nexus_no_organization_fail(self, mock_dir, mock_cred):
cleanup()
setup()
with self.assertRaises(NexusError) as e:
bosh(["data", "publish", "-y", "--nexus", "--sandbox",
"--nexus-token", "hAaW2wSBZMskxpfigTYHcuDrCPWr2"])
self.assertIn("Cannot find Nexus organization.",
str(e.exception))
def test_pull(self, mock_urlretrieve):
bosh(["pull", "zenodo." + str(example_boutiques_tool.id)])
cache_dir = os.path.join(os.path.expanduser('~'), ".cache",
"boutiques")
self.assertTrue(
os.path.exists(
os.path.join(
cache_dir,
"zenodo-" + str(example_boutiques_tool.id) + ".json")))
def test_publication(self, mock_get, mock_post, mock_put, mock_delete):
example1_dir = op.join(self.get_examples_dir(), "example1")
example1_desc = op.join(example1_dir, "example1_docker.json")
temp_descriptor = tempfile.NamedTemporaryFile(suffix=".json")
shutil.copyfile(example1_desc, temp_descriptor.name)
# Make sure that example1.json doesn't have a DOI yet
with open(temp_descriptor.name, 'r') as fhandle:
descriptor = json.load(fhandle)
assert (descriptor.get('doi') is None)
# Test publication of a descriptor that doesn't have a DOI
doi = bosh([
"publish", temp_descriptor.name, "--sandbox", "-y", "-v",
"--zenodo-token", "hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r"
])
assert (doi)
# Now descriptor should have a DOI
with open(temp_descriptor.name, 'r') as fhandle:
descriptor = json.load(fhandle)
assert (descriptor.get('doi') == doi)
# Test publication of a descriptor that already has a DOI
with self.assertRaises(ZenodoError) as e:
bosh([
"publish", temp_descriptor.name, "--sandbox", "-y", "-v",
"--zenodo-token", "hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r"
])
self.assertTrue("Descriptor already has a DOI" in str(e.exception))
# Test publication of an updated version of the same descriptor
example1_desc_updated = op.join(example1_dir,
"example1_docker_updated.json")
temp_descriptor_updated = tempfile.NamedTemporaryFile(suffix=".json")
shutil.copyfile(example1_desc_updated, temp_descriptor_updated.name)
with open(temp_descriptor_updated.name, 'r') as fhandle:
descriptor_updated = json.load(fhandle)
# Publish the updated version
new_doi = bosh([
"publish", temp_descriptor_updated.name, "--sandbox", "-y", "-v",
"--zenodo-token", "hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r"
])
assert (new_doi)
# Updated version of descriptor should have a new DOI
with open(temp_descriptor_updated.name, 'r') as fhandle:
descriptor_updated = json.load(fhandle)
assert (descriptor_updated.get('doi') == new_doi)
assert (descriptor_updated.get('doi') != doi)
def test_success_argparser(self):
parser = ArgumentParser(description="my tool description")
parser.add_argument('myarg1',
action="store",
help="my help 1",
type=list)
parser.add_argument('myarg2',
action="store",
help="my help 2",
type=int)
parser.add_argument("--myarg3", "-m", action="store", help="my help 3")
subparser = parser.add_subparsers(help="the choices you will make",
dest="mysubparser")
sb1 = subparser.add_parser("option1", help="the first value")
sb1.add_argument("suboption1", help="the first sub option option")
sb1.add_argument("suboption2",
help="the first sub option option",
choices=['hello', 'goodbye'],
default="hello")
sb1 = subparser.add_parser("option2", help="the second value")
sb1.add_argument("suboption1", help="the first sub option option")
sb1.add_argument("suboption3", help="the second sub option option")
sb1.add_argument("--suboptionflag1", "-s", help="the bool opt flag")
sb1.add_argument("--suboptionflag2",
"-d",
action="store_true",
help="the second sub option flag")
sb1.add_argument("--suboptlistflag",
"-l",
nargs="+",
help="listy flag")
creatorObj = bc.CreateDescriptor(parser,
execname='/path/to/myscript.py',
verbose=True,
tags={
"purpose": "testing-creator",
"foo": "bar"
})
fil = './test-created-argparse-descriptor.json'
creatorObj.save(fil)
invof = './test-created-argparse-inputs.json'
args = parser.parse_args([['val1', 'val2'], '2', 'option2', 'subval1',
'subval3', '--suboptionflag1', 't1',
'--suboptionflag2'])
invo = creatorObj.createInvocation(args)
with open(invof, 'w') as fhandle:
fhandle.write(json.dumps(invo, indent=4))
self.assertIsNone(bosh(['validate', fil]))
self.assertIsNone(bosh(['invocation', fil, '-i', invof]))
def test_publish_nexus_invalid_endpoint(self, mock_dir, mock_endpoint):
cleanup()
setup()
with self.assertRaises(NexusError) as e:
bosh(["data", "publish", "-y", "--nexus", "--sandbox",
"--nexus-token", "hAaW2wSBZMskxpfigTYHcuDrCPWr2",
"--nexus-org", "boutiques", "--nexus-project",
"test"])
self.assertIn("Cannot access Nexus endpoint",
str(e.exception))
def test_publish_nexus_invalid_token(self, mock_dir):
cleanup()
setup()
with self.assertRaises(NexusError) as e:
bosh(["data", "publish", "-y", "--nexus", "--sandbox",
"--nexus-token", "INVALIDTOKEN",
"--nexus-org", "boutiques", "--nexus-project",
"test"])
self.assertIn("Cannot authenticate to Nexus API, check "
"your access token", str(e.exception))
def test_publish_nexus_success(
self, mock_create_file, mock_fetch_project,
mock_save_inputs, mock_dir):
cleanup()
setup()
try:
bosh(["data", "publish", "-y", "--nexus", "--sandbox",
"--nexus-token", "hAaW2wSBZMskxpfigTYHcuDrCPWr2",
"--nexus-org", "test", "--nexus-project",
"test", "-v"])
except Exception as e:
self.fail("Unexpected exception raised: " + str(e))
def test_publish_single(self, mock_dir, mock_get, mock_post):
cleanup()
setup()
# Publish a record that does not exist
with self.assertRaises(ValueError) as e:
bosh(["data", "publish", "-f", "bad-filename", "--sandbox", "-y"])
self.assertIn("File bad-filename does not exist in the data cache",
str(e.exception))
# Publish a record with a correct descriptor-doi
bosh(["data", "publish", "-f", "tool1_123.json", "-y",
"--sandbox", "--zenodo-token",
"hAaW2wSBZMskxpfigTYHcuDrCPWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r"])
self.assertFalse(os.path.isfile(
os.path.join(mock_get_data_cache(), "tool1-123")))
# Publish a record without a descriptor-doi
bosh(["data", "publish", "-f", "tool2_123.json", "-y",
"--sandbox", "--zenodo-token",
"hAaW2wSBZMskxpfigTYHcuDrCPWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r"])
self.assertTrue(os.path.isfile(
os.path.join(mock_get_data_cache(), "tool2_123.json")))
self.assertTrue(os.path.isfile(
os.path.join(mock_get_data_cache(), "descriptor_tool2_123.json")))
# Publish a record without a descriptor-doi but descriptor is published
bosh(["data", "publish", "-f", "tool3_123.json", "-y",
"--sandbox", "--zenodo-token",
"hAaW2wSBZMskxpfigTYHcuDrCPWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r"])
self.assertFalse(os.path.isfile(
os.path.join(mock_get_data_cache(), "tool3-123")))
self.assertFalse(os.path.isfile(
os.path.join(mock_get_data_cache(), "descriptor-tool3-123")))
def test_publisher_auth_no_permission(self, mock_get, mock_post):
example1_dir = op.join(self.get_examples_dir(), "example1")
# Trying to update a tool published by a different
# user should inform the user that they do not
# have permission to publish an update.
with self.assertRaises(ZenodoError) as e:
bosh([
"publish",
op.join(example1_dir, "example1_docker.json"), "--sandbox",
"--id", "zenodo.12345", "-y", "-v", "--zenodo-token", "12345"
])
self.assertIn("You do not have permission to access this "
"resource.", str(e.exception))
def test_search_sorts_by_num_downloads(self, mock_get):
results = bosh(["search"])
downloads = []
for r in results:
downloads.append(r["DOWNLOADS"])
assert (all(downloads[i] >= downloads[i + 1]
for i in range(len(downloads) - 1)))
def test_publication_replace_no_id(self, mock_get, mock_post, mock_put,
mock_delete):
example1_dir = op.join(self.get_examples_dir(), "example1")
example1_desc = op.join(example1_dir, "example1_docker_with_doi.json")
temp_descriptor = tempfile.NamedTemporaryFile(suffix=".json")
shutil.copyfile(example1_desc, temp_descriptor.name)
# Make sure that descriptor has a DOI
with open(temp_descriptor.name, 'r') as fhandle:
descriptor = json.load(fhandle)
self.assertIsNotNone(descriptor.get('doi'))
old_doi = descriptor['doi']
# Publish an updated version of an already published descriptor
doi = bosh([
"publish", temp_descriptor.name, "--sandbox", "-y", "-v",
"--zenodo-token", "hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r", "--replace"
])
self.assertTrue(doi)
# Now descriptor should have a DOI which should be different
# than the old DOI
with open(temp_descriptor.name, 'r') as fhandle:
descriptor = json.load(fhandle)
self.assertNotEqual(doi, old_doi)
self.assertEqual(descriptor.get('doi'), doi)
def test_search_truncates_long_text(self, mymockget):
mymockget.side_effect = lambda *args, **kwargs:\
mock_get("boutiques", False, *args, **kwargs)
results = bosh(["search"])
for r in results:
for k, v in r.items():
self.assertLessEqual(len(str(v)), 43)
def test_search_exact_match(self, mock_get):
results = bosh(["search", "Example Tool 5", "--exact"])
print(results)
assert (len(results) > 0)
assert (any(d['TITLE'] == 'Example Tool 5' for d in results))
assert (not any(d['TITLE'] == 'foo-Example Tool 5' for d in results))
assert (not any(d['TITLE'] == 'Example Tool 5-bar' for d in results))
def test_failing_simulate(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
self.assertRaises(SystemExit, bosh, [
"exec", "simulate",
os.path.join(example1_dir, "fake.json"), "-i",
os.path.join(example1_dir, "invocation.json")
])
self.assertRaises(SystemExit, bosh, [
"exec", "simulate",
os.path.join(example1_dir, "example1.json"), "-i",
os.path.join(example1_dir, "fake.json")
])
self.assertRaises(SystemExit, bosh, [
"exec", "simulate",
os.path.join(example1_dir, "example1.json"), "-i",
os.path.join(example1_dir, "exampleTool1.py")
])
self.assertRaises(SystemExit, bosh, [
"exec", "simulate",
os.path.join(example1_dir, "example1.json"), "-r", "-2"
])
self.assertFalse(
bosh([
"exec", "simulate",
os.path.join(example1_dir, "example1.json"), "-r", "1"
]))
self.assertRaises(SystemExit, bosh, [
"exec", "simulate",
os.path.join(example1_dir, "example1.json"), "-r", "1", "-i",
os.path.join(example1_dir, "invocation.json")
])
self.assertRaises(
SystemExit, bosh,
["exec", "simulate",
os.path.join(example1_dir, "example1.json")])
def test_search_verbose(self):
results = bosh(["search", "-v"])
assert(len(results) > 0)
assert(list(results[0].keys()) == ["ID", "TITLE", "DESCRIPTION",
"AUTHOR", "VERSION", "DOI",
"SCHEMA VERSION", "CONTAINER",
"TAGS"])
def test_search_all(self, mymockget):
mymockget.side_effect = lambda *args, **kwargs:\
mock_get("", False, *args, **kwargs)
results = bosh(["search"])
self.assertGreater(len(results), 0)
self.assertEqual(list(results[0].keys()),
["ID", "TITLE", "DESCRIPTION", "DOWNLOADS"])
def test_search_exact_match(self, mymockget):
mymockget.side_effect = lambda *args, **kwargs:\
mock_get("Example Tool 5", True, *args, **kwargs)
results = bosh(["search", "Example Tool 5", "--exact"])
self.assertGreater(len(results), 0)
self.assertIn('Example Tool 5', [d['TITLE'] for d in results])
self.assertNotIn('foo-Example Tool 5', [d['TITLE'] for d in results])
self.assertNotIn('Example Tool 5-bar', [d['TITLE'] for d in results])
def test_search_sorts_by_num_downloads(self, mymockget):
mymockget.side_effect = lambda *args, **kwargs:\
mock_get("boutiques", False, *args, **kwargs)
results = bosh(["search"])
downloads = []
for r in results:
downloads.append(r["DOWNLOADS"])
self.assertEqual(sorted(downloads, reverse=True), downloads)
def test_deprecate(self, *args):
new_doi = bosh([
"deprecate", "--verbose", "--by", "zenodo.12345",
"zenodo." + str(example_boutiques_tool.id), "--zenodo-token",
"hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r"
])
self.assertTrue(new_doi)
def test_deprecate_by_inexistent(self, *args):
with self.assertRaises(DeprecateError) as e:
new_doi = bosh([
"deprecate", "--verbose", "--by", "zenodo.00000",
"zenodo." + str(example_boutiques_tool.id), "--zenodo-token",
"hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r"
])
self.assertTrue("Tool does not exist" in str(e.exception))
def test_search_verbose(self, mymockget):
mymockget.side_effect = lambda *args, **kwargs:\
mock_get("", False, *args, **kwargs)
results = bosh(["search", "-v"])
self.assertGreater(len(results), 0)
self.assertEqual(list(results[0].keys()), [
"ID", "TITLE", "DESCRIPTION", "DOWNLOADS", "AUTHOR", "VERSION",
"DOI", "SCHEMA VERSION", "CONTAINER", "TAGS"
])
def test_deprecate_previous_version(self, *args):
with self.assertRaises(DeprecateError) as e:
new_doi = bosh([
"deprecate", "--verbose", "zenodo.22222", "--zenodo-token",
"hAaW2wSBZMskxpfigTYHcuDrC"
"PWr2VeQZgBLErKbfF5RdrKhzzJi8i2hnN8r"
])
self.assertTrue(
"Tool zenodo.22222 has a newer version" in str(e.exception))
def test_publisher_auth(self, mock_get):
example1_dir = op.join(self.get_examples_dir(), "example1")
# Bad token should fail
with self.assertRaises(ZenodoError) as e:
bosh([
"publish",
op.join(example1_dir, "example1_docker.json"), "--sandbox",
"-y", "-v", "--zenodo-token", "12345"
])
self.assertIn("Cannot authenticate to Zenodo", str(e.exception))
# No token should fail
with self.assertRaises(ZenodoError) as e:
bosh([
"publish",
op.join(example1_dir, "example1_docker.json"), "--sandbox",
"-y", "-v"
])
self.assertIn("Cannot authenticate to Zenodo", str(e.exception))
def test_success_template_camel_case(self):
template = './boutiques/templates/basic.json'
fil = 'creator_output.json'
bosh(['create', fil, '--camel-case'])
self.assertIsNone(bosh(['validate', fil]))
desc = loadJson(fil)
template = loadJson(template)
# Check "_" in all instances of input indices (inputs + groups)
for inp, camelInp in zip(template['inputs'], desc['inputs']):
self.assertTrue("_" in inp['id'])
self.assertFalse("_" in camelInp['id'])
for mbrs, camelMbrs in [
(grp['members'], camelGrp['members'])
for grp, camelGrp in zip(template['groups'], desc['groups'])
]:
self.assertTrue(all([("_" in mbr) for mbr in mbrs]))
self.assertFalse(all([("_" in camelMbr)
for camelMbr in camelMbrs]))
