def test_write(self):
tc = TransformationCatalog()
(
tc.add_transformations(Transformation("t1")).add_transformations(
Transformation("t2")
)
)
expected = {
"pegasus": "5.0",
"transformations": [
{"name": "t1", "sites": []},
{"name": "t2", "sites": []},
],
}
expected["transformations"] = sorted(
expected["transformations"], key=lambda t: t["name"]
)
with NamedTemporaryFile("r+") as f:
tc.write(f, _format="json")
f.seek(0)
result = json.load(f)
result["transformations"] = sorted(
expected["transformations"], key=lambda t: t["name"]
)
assert "createdOn" in result["x-pegasus"]
assert result["x-pegasus"]["createdBy"] == getpass.getuser()
assert result["x-pegasus"]["apiLang"] == "python"
del result["x-pegasus"]
assert result == expected
def test_write(self):
tc = TransformationCatalog()
(tc.add_transformations(Transformation("t1")).add_transformations(
Transformation("t2")))
expected = {
"pegasus":
"5.0",
"transformations": [
{
"name": "t1",
"sites": []
},
{
"name": "t2",
"sites": []
},
],
}
expected["transformations"] = sorted(expected["transformations"],
key=lambda t: t["name"])
with NamedTemporaryFile("r+") as f:
tc.write(f, _format="json")
f.seek(0)
result = json.load(f)
result["transformations"] = sorted(expected["transformations"],
key=lambda t: t["name"])
assert result == expected
def test_example_transformation_catalog(
self, convert_yaml_schemas_to_json, load_schema, _format, loader
):
# validates the sample tc in pegasus/etc/sample-5.0-data/tc.yml
tc = TransformationCatalog()
foo = (
Transformation("foo")
.add_globus_profile(max_time=2)
.add_dagman_profile(retry=2)
.add_metadata(size=2048)
.add_sites(
TransformationSite(
"local",
"/nfs/u2/ryan/bin/foo",
True,
arch=Arch.X86_64,
os_type=OS.LINUX,
)
.add_env(JAVA_HOME="/usr/bin/java")
.add_metadata(size=2048)
)
.add_requirement("bar")
.add_shell_hook(EventType.START, "/bin/echo 'starting'")
)
bar = Transformation("bar").add_sites(
TransformationSite(
"local",
"/nfs/u2/ryan/bin/bar",
True,
arch=Arch.X86_64,
os_type=OS.LINUX,
)
)
centos_pegasus_container = Container(
"centos-pegasus",
Container.DOCKER,
"docker:///ryan/centos-pegasus:latest",
arguments="--shm-size 123",
mounts=["/Volumes/Work/lfs1:/shared-data/:ro"],
).add_env(JAVA_HOME="/usr/bin/java")
(tc.add_transformations(foo, bar).add_containers(centos_pegasus_container))
with NamedTemporaryFile(mode="r+") as f:
tc.write(f, _format=_format)
f.seek(0)
tc_json = loader(f)
tc_schema = load_schema("tc-5.0.json")
validate(instance=tc_json, schema=tc_schema)
def dumps(obj: TransformationCatalog, _format="yml", *args, **kwargs) -> str:
"""
Serialize ``obj`` to a :py:class:`~Pegasus.api.transformation_catalog.TransformationCatalog` formatted ``str``.
:param obj: TransformationCatalog to serialize
:type obj: TransformationCatalog
:param _format: format to write to if fp does not have an extension; can be one of ["yml" | "yaml" | "json"], defaults to "yml"
:type _format: str
:return: TransformationCatalog serialized as a string
:rtype: str
"""
with StringIO() as s:
obj.write(s, _format=_format)
s.seek(0)
return s.read()
def dump(obj: TransformationCatalog,
fp: TextIO,
_format="yml",
*args,
**kwargs) -> None:
"""
Serialize ``obj`` as a :py:class:`~Pegasus.api.transformation_catalog.TransformationCatalog` formatted stream to ``fp`` (a ``.write()``-supporting file-like object).
:param obj: TransformationCatalog to serialize
:type obj: TransformationCatalog
:param fp: file like object to serialize to
:type fp: TextIO
:param _format: format to write to if fp does not have an extension; can be one of ["yml" | "yaml" | "json"], defaults to "yml"
:type _format: str
:rtype: NoReturn
"""
obj.write(fp, _format=_format)
def test_transformation_catalog_ordering_on_yml_write(self):
tc = TransformationCatalog()
tc.add_transformations(Transformation("t1"))
tc.add_containers(Container("c1", Container.DOCKER, "img"))
tc.write()
EXPECTED_FILE = Path("transformations.yml")
with EXPECTED_FILE.open() as f:
result = f.read()
EXPECTED_FILE.unlink()
"""
Check that tc keys have been ordered as follows:
- pegasus
- transformations
- containers
"""
p = re.compile(
r"pegasus: '5.0'[\w\W]+transformations:[\w\W]+containers[\w\W]+")
assert p.match(result) is not None
