def test_skip_collection(self):
# Register original size of cache directory for comparison
cache_dir = os.path.join(os.path.expanduser('~'), ".cache",
"boutiques", "data")
original_size = 0
if os.path.exists(cache_dir):
cache_fls = os.listdir(cache_dir)
original_size = len(cache_fls)
example1_dir = os.path.join(self.get_examples_dir(), "example1")
bosh.execute(
"launch", os.path.join(example1_dir, "example1_docker.json"),
os.path.join(example1_dir,
"invocation.json"), "--skip-data-collection", "-v",
"{}:/test_mount1".format(self.get_file_path("example1_mount1")),
"-v",
"{}:/test_mount2".format(self.get_file_path("example1_mount2")))
new_size = 0
if os.path.exists(cache_dir):
cache_fls = os.listdir(cache_dir)
new_size = len(cache_fls)
self.assertEqual(new_size, original_size)
self.clean_up()
def test_directory_input_output(self):
example1_dir = self.get_examples_dir()
bosh.execute("launch",
os.path.join(example1_dir,
"dir_input.json"),
os.path.join(example1_dir,
"dir_invocation.json"))
data_collect_dict = retrieve_data_record()
public_in = data_collect_dict.get("public-invocation")
self.assertIsNotNone(public_in)
input_dir = public_in.get("input_dir")
self.assertIsNotNone(input_dir)
files = input_dir.get("files")
self.assertIsNotNone(files)
self.assertEqual(len(files), 2)
public_out = data_collect_dict.get("public-output")
self.assertIsNotNone(public_out)
output_files = public_out.get("output-files")
self.assertIsNotNone(output_files)
results = output_files.get("results")
self.assertIsNotNone(results)
files = results.get("files")
self.assertIsNotNone(files)
self.assertEqual(len(files), 2)
self.clean_up()
def test_example1_exec_docker(self):
self.clean_up()
ret = bosh.execute(
"launch", self.get_file_path("example1_docker.json"),
self.get_file_path("invocation.json"), "--skip-data-collection",
"-v",
"{}:/test_mount1".format(self.get_file_path("example1_mount1")),
"-v",
"{}:/test_mount2".format(self.get_file_path("example1_mount2")))
# Make sure stdout and stderr are not printed on the fly
# for non-streaming mode
out, err = self.capfd.readouterr()
self.assertNotIn("This is stdout", out)
self.assertNotIn("This is stderr", out)
self.assert_successful_return(ret, ["log-4-coin;plop.txt"], 2,
self.assert_reflected_output)
self.clean_up()
self.assert_successful_return(
bosh.execute(
"launch", self.get_file_path("example1_docker.json"), "-x",
self.get_file_path("invocation.json"),
"--skip-data-collection", "-v", "{}:/test_mount1".format(
self.get_file_path("example1_mount1")),
"-v", "{}:/test_mount2".format(
self.get_file_path("example1_mount2"))),
["log-4-coin;plop.txt"], 2, self.assert_reflected_output)
def test_example1_exec_docker_inv_as_json_obj(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
self.clean_up()
invocationStr = open(os.path.join(example1_dir,
"invocation.json")).read()
ret = bosh.execute("launch",
os.path.join(example1_dir, "example1_docker.json"),
invocationStr)
print(ret)
assert ("This is stdout" in ret.stdout)
assert ("This is stderr" in ret.stderr)
assert (ret.exit_code == 0)
assert (ret.error_message == "")
assert (ret.missing_files == [])
assert (len(ret.output_files) == 2)
assert (ret.output_files[0].file_name == "log-4-coin;plop.txt"
or ret.output_files[1].file_name == "log-4-coin;plop.txt")
self.clean_up()
ret = bosh.execute("launch",
os.path.join(example1_dir, "example1_docker.json"),
"-x", os.path.join(example1_dir, "invocation.json"))
print(ret)
assert ("This is stdout" in ret.stdout)
assert ("This is stderr" in ret.stderr)
assert (ret.exit_code == 0)
assert (ret.error_message == "")
assert (ret.missing_files == [])
assert (len(ret.output_files) == 2)
assert (ret.output_files[0].file_name == "log-4-coin;plop.txt"
or ret.output_files[1].file_name == "log-4-coin;plop.txt")
def test_example1_exec_docker_from_zenodo(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
self.clean_up()
ret = bosh.execute("launch", "zenodo.1472823",
os.path.join(example1_dir, "invocation.json"))
# Make sure stdout and stderr are not printed on the fly
# for non-streaming mode
out, err = self.capfd.readouterr()
assert ("This is stdout" not in out)
assert ("This is stderr" not in out)
print(ret)
assert ("This is stdout" in ret.stdout)
assert ("This is stderr" in ret.stderr)
assert (ret.exit_code == 0)
assert (ret.error_message == "")
assert (ret.missing_files == [])
assert (len(ret.output_files) == 2)
assert (ret.output_files[0].file_name == "log-4-coin;plop.txt"
or ret.output_files[1].file_name == "log-4-coin;plop.txt")
self.clean_up()
ret = bosh.execute("launch", "zenodo.1472823", "-x",
os.path.join(example1_dir, "invocation.json"))
print(ret)
assert ("This is stdout" in ret.stdout)
assert ("This is stderr" in ret.stderr)
assert (ret.exit_code == 0)
assert (ret.error_message == "")
assert (ret.missing_files == [])
assert (len(ret.output_files) == 2)
assert (ret.output_files[0].file_name == "log-4-coin;plop.txt"
or ret.output_files[1].file_name == "log-4-coin;plop.txt")
def test_data_collection(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
bosh.execute("launch",
os.path.join(example1_dir,
"example1_docker.json"),
os.path.join(example1_dir,
"invocation.json"))
data_collect_dict = retrieve_data_record()
summary = data_collect_dict.get("summary")
self.assertIsNotNone(summary)
self.assertEqual(summary.get("name"), "Example Boutiques Tool")
public_in = data_collect_dict.get("public-invocation")
self.assertIsNotNone(public_in)
self.assertEqual(public_in.get("config_num"), 4)
self.assertEqual(public_in.get("enum_input"), "val1")
file_input = public_in.get("file_input")
self.assertIsNotNone(file_input)
self.assertEqual(file_input.get("file-name"), "setup.py")
self.assertIsNotNone(file_input.get("md5sum"))
public_out = data_collect_dict.get("public-output")
self.assertIsNotNone(public_out)
self.assertEqual(public_out.get("stdout"), "This is stdout")
self.assertEqual(public_out.get("stderr"), "This is stderr")
self.assertEqual(public_out.get("exit-code"), 0)
self.assertEqual(public_out.get("error-message"), "")
output_files = public_out.get("output-files")
self.assertIsNotNone(output_files)
self.assertIsNotNone(output_files.get("logfile"))
self.assertIsNotNone(output_files.get("config_file"))
logfile = output_files.get("logfile")
self.assertEqual(logfile.get("file-name"), "log-4-coin;plop.txt")
self.clean_up()
def test_example1_exec_singularity(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
self.clean_up()
ret = bosh.execute("launch",
os.path.join(example1_dir, "example1_sing.json"),
os.path.join(example1_dir, "invocation_sing.json"))
print(ret)
assert ("This is stdout" in ret.stdout)
assert ("This is stderr" in ret.stderr)
assert (ret.exit_code == 0)
assert (ret.error_message == "")
assert (ret.missing_files == [])
assert (len(ret.output_files) == 2)
assert (ret.output_files[0].file_name == "log-4.txt"
or ret.output_files[1].file_name == "log-4.txt")
self.clean_up()
ret = bosh.execute("launch",
os.path.join(example1_dir, "example1_sing.json"),
"-x",
os.path.join(example1_dir, "invocation_sing.json"))
print(ret)
assert ("This is stdout" in ret.stdout)
assert ("This is stderr" in ret.stderr)
assert (ret.exit_code == 0)
assert (ret.error_message == "")
assert (ret.missing_files == [])
assert (len(ret.output_files) == 2)
assert (ret.output_files[0].file_name == "log-4.txt"
or ret.output_files[1].file_name == "log-4.txt")
def test_example1_crash_pull_singularity(self):
self.clean_up()
with pytest.raises(ExecutorError) as e:
bosh.execute("launch",
self.get_file_path("example1_sing_crash_pull.json"),
self.get_file_path("invocation_sing.json"),
"--skip-data-collection")
self.assertIn("Could not pull Singularity image", str(e))
def test_consistency_withAndWithout_invoc(self):
descriptor = os.path.join(
os.path.split(bfile)[0], 'schema/examples/'
'test_simulate_consistency.json')
noInvoc = bosh.execute("simulate", descriptor).stdout
wInvoc = bosh.execute("simulate", descriptor, "-i",
bosh.example(descriptor)).stdout
self.assertEqual(noInvoc, wInvoc)
def test_example1_exec_docker_json_string_invalid(self):
self.clean_up()
invocationStr = open(
self.get_file_path("invocation_invalid.json")).read()
with pytest.raises(LoadError) as e:
bosh.execute("launch", self.get_file_path("example1_docker.json"),
"-u", invocationStr, "--skip-data-collection")
self.assertIn("Cannot parse input", str(e.getrepr(style='long')))
def test_raise_error(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
invocationStr = open(
os.path.join(example1_dir, "invocation_invalid.json")).read()
with pytest.raises(LoadError) as e:
bosh.execute("launch",
os.path.join(example1_dir, "example1_docker.json"),
invocationStr, "--skip-data-collection")
self.assertIn("[ ERROR ]", str(e))
def test_example2_exec(self):
example2_dir = os.path.join(self.get_examples_dir(), "example2")
self.assertFalse(
bosh.execute("launch", os.path.join(example2_dir, "example2.json"),
os.path.join(example2_dir, "invocation.json"))[2])
self.assertFalse(
bosh.execute("launch", os.path.join(example2_dir,
"example2.json"), "-x",
os.path.join(example2_dir, "invocation.json"))[2])
def test_example1_crash_pull_singularity(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
self.clean_up()
with pytest.raises(ExecutorError) as e:
bosh.execute(
"launch",
os.path.join(example1_dir, "example1_sing_crash_pull.json"),
os.path.join(example1_dir, "invocation_sing.json"))
assert ("Could not pull Singularity image" in str(e))
def test_success_desc_from_zenodo(self):
self.assertFalse(bosh.execute("simulate",
"zenodo.1472823",
"-r", "1").exit_code)
self.assertFalse(bosh.execute("simulate",
os.path.join(self.get_examples_dir(),
"good_nooutputs.json"),
"-r", "1").exit_code)
def test_raise_error(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
invocationStr = open(
os.path.join(example1_dir, "invocation_invalid.json")).read()
with pytest.raises(ExecutorError) as e:
bosh.execute("launch",
os.path.join(example1_dir, "example1_docker.json"),
invocationStr)
assert ("[ ERROR ]" in str(e))
def test_example1_exec_docker_json_string_invalid(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
self.clean_up()
invocationStr = open(
os.path.join(example1_dir, "invocation_invalid.json")).read()
with pytest.raises(ExecutorError) as e:
bosh.execute("launch",
os.path.join(example1_dir, "example1_docker.json"),
invocationStr)
assert ("Cannot parse input" in str(e))
def test_success(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
self.assertFalse(bosh.execute("simulate",
os.path.join(example1_dir,
"example1_docker.json"
)).exit_code)
self.assertFalse(bosh.execute("simulate",
os.path.join(self.get_examples_dir(),
"good_nooutputs.json"
)).exit_code)
def test_prepare_sing_image_does_not_exist(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
# Specify the wrong path for the image
# Will try to pull it and pull will fail
with pytest.raises(ExecutorError) as e:
bosh.execute(
"prepare", os.path.join(example1_dir, "example1_sing.json"),
"--imagepath",
os.path.join(os.path.expanduser('~'),
"boutiques-example1-test.simg"))
self.assertIn("Could not pull Singularity image", str(e))
def test_read_doi_zenodo(self, mock_get):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
bosh.execute("launch", "zenodo." + str(example_boutiques_tool.id),
os.path.join(example1_dir, "invocation.json"))
data_collect_dict = retrieve_data_record()
summary = data_collect_dict.get("summary")
self.assertIsNotNone(summary)
self.assertEqual(summary.get("descriptor-doi"),
"10.5281/zenodo." + str(example_boutiques_tool.id))
self.clean_up()
def bosh_exec(self, invocation_file, mount=None):
try:
if mount is None:
boutiques.execute("launch",self.boutiques_descriptor,invocation_file, "-x")
else:
boutiques.execute("launch", self.boutiques_descriptor, invocation_file, "-v",
"{0}:{0}".format(mount), "-x")
result = 0
except SystemExit as e:
result = e.code
return (result, "Empty log, Boutiques API doesn't return it yet.\n")
def test_success_desc_as_json_obj(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
desc_json = open(os.path.join(example1_dir,
"example1_docker.json")).read()
self.assertFalse(bosh.execute("simulate",
desc_json,
"-r", "1").exit_code)
self.assertFalse(bosh.execute("simulate",
os.path.join(self.get_examples_dir(),
"good_nooutputs.json"),
"-r", "1").exit_code)
def test_example2_exec(self):
self.assert_successful_return(
bosh.execute("launch", self.get_file_path("example2.json"),
self.get_file_path("invocation.json"),
"--skip-data-collection"),
aditional_assertions=self.assert_no_output)
self.assert_successful_return(
bosh.execute("launch", self.get_file_path("example2.json"), "-x",
self.get_file_path("invocation.json"),
"--skip-data-collection"),
aditional_assertions=self.assert_no_output)
def test_prepare_sing_timeout(self, mock_mkdir, mock_sleep):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
# Specify path for image that does not exist.
# Mock that another process has the lockdir and this one
# times out while waiting.
with pytest.raises(ExecutorError) as e:
bosh.execute(
"prepare", os.path.join(example1_dir, "example1_sing.json"),
"--imagepath",
os.path.join(os.path.expanduser('~'),
"boutiques-example1-test.simg"))
self.assertIn("Unable to retrieve Singularity image", str(e))
def test_example1_crash_pull_singularity(self):
self.clean_up()
with pytest.raises(ExecutorError) as e:
bosh.execute(
"launch", self.get_file_path("example1_sing_crash_pull.json"),
self.get_file_path("invocation_sing.json"),
"--skip-data-collection", "-v", "{}:/test_mount1".format(
self.get_file_path("example1_mount1")),
"-v", "{}:/test_mount2".format(
self.get_file_path("example1_mount2")))
self.assertIn("Could not pull Singularity image",
str(e.getrepr(style='long')))
def test_example1_exec_singularity(self):
self.clean_up()
self.assert_successful_return(
bosh.execute("launch", self.get_file_path("example1_sing.json"),
self.get_file_path("invocation_sing.json"),
"--skip-data-collection"), ["log-4.txt"], 2,
self.assert_reflected_output)
self.clean_up()
self.assert_successful_return(
bosh.execute("launch", self.get_file_path("example1_sing.json"),
"-x", self.get_file_path("invocation_sing.json")),
["log-4.txt"], 2, self.assert_reflected_output)
def test_example1_exec_docker_inv_as_json_obj(self):
self.clean_up()
invocationStr = open(self.get_file_path("invocation.json")).read()
self.assert_successful_return(
bosh.execute("launch", self.get_file_path("example1_docker.json"),
invocationStr, "--skip-data-collection"),
["log-4-coin;plop.txt"], 2, self.assert_reflected_output)
self.clean_up()
self.assert_successful_return(
bosh.execute("launch", self.get_file_path("example1_docker.json"),
"-x", self.get_file_path("invocation.json"),
"--skip-data-collection"), ["log-4-coin;plop.txt"], 2,
self.assert_reflected_output)
def test_example2_exec(self):
example2_dir = os.path.join(self.get_examples_dir(), "example2")
ret = bosh.execute("launch", os.path.join(example2_dir,
"example2.json"),
os.path.join(example2_dir, "invocation.json"))
print(ret)
assert (ret.stdout == "" and ret.stderr == "" and ret.exit_code == 0
and ret.error_message == "")
ret = bosh.execute("launch", os.path.join(example2_dir,
"example2.json"), "-x",
os.path.join(example2_dir, "invocation.json"))
print(ret)
assert (ret.stdout == "" and ret.stderr == "" and ret.exit_code == 0
and ret.error_message == "")
def test_example1_exec_docker_non_utf8(self):
self.clean_up()
ret = bosh.execute("launch",
self.get_file_path("example1_docker_nonutf8.json"),
self.get_file_path("invocation.json"))
self.assert_successful_return(ret, ["log-4-coin;plop.txt"], 2,
self.assert_reflected_output_nonutf8)
self.clean_up()
self.assert_successful_return(
bosh.execute("launch",
self.get_file_path("example1_docker_nonutf8.json"),
"-x", self.get_file_path("invocation.json")),
["log-4-coin;plop.txt"], 2, self.assert_reflected_output_nonutf8)
def test_no_container(self):
self.assertFalse(bosh.execute("launch",
os.path.join(self.get_examples_dir(),
"no_container.json"),
os.path.join(self.get_examples_dir(),
"no_container_invocation."
+ "json")).exit_code)
def test_prepare_sing_specify_imagepath_basename_only(self):
example1_dir = os.path.join(self.get_examples_dir(), "example1")
ret = bosh.execute("prepare",
os.path.join(example1_dir, "example1_sing.json"),
"--imagepath", "boutiques-example1-test.simg")
self.assertIn("Local (boutiques-example1-test.simg)", ret.stdout)
self.assertNotIn("SINGULARITY_PULLFOLDER", os.environ)