def test_write_valid_hierarchical_workflow(self, mocker):
mocker.patch("Pegasus.api.workflow.Workflow.write")
try:
wf = Workflow("test")
wf.add_jobs(SubWorkflow("file", False))
wf.write(file="workflow.yml", _format="yml")
except PegasusError:
pytest.fail("shouldn't have thrown PegasusError")
Pegasus.api.workflow.Workflow.write.assert_called_once_with(
file="workflow.yml", _format="yml")
def dump(obj: Workflow, fp: TextIO, _format="yml", *args, **kwargs) -> None:
"""
Serialize ``obj`` as a :py:class:`~Pegasus.api.worklfow.Workflow` formatted stream to ``fp`` (a ``.write()``-supporting file-like object).
:param obj: Workflow to serialize
:type obj: Workflow
: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 dumps(obj: Workflow, _format="yml", *args, **kwargs) -> str:
"""
Serialize ``obj`` to a :py:class:`~Pegasus.api.workflow.Workflow` formatted ``str``.
:param obj: Workflow to serialize
:type obj: Workflow
: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: Workflow serialized as a string
:rtype: str
"""
with StringIO() as s:
obj.write(s, _format=_format)
s.seek(0)
return s.read()
def test_write_hierarchical_workflow_when_catalogs_are_inlined(
self, sc, tc):
wf = Workflow("test")
wf.add_jobs(SubWorkflow("file", False))
if sc:
wf.add_site_catalog(sc)
if tc:
wf.add_transformation_catalog(tc)
with pytest.raises(PegasusError) as e:
wf.write()
assert (
"Site Catalog and Transformation Catalog must be written as a separate"
in str(e))
def test_workflow_key_ordering_on_yml_write(self):
tc = TransformationCatalog()
rc = ReplicaCatalog()
sc = SiteCatalog()
wf = Workflow("wf")
wf.add_transformation_catalog(tc)
wf.add_replica_catalog(rc)
wf.add_site_catalog(sc)
wf.add_jobs(Job("t1", _id="a"))
wf.add_env(JAVA_HOME="/java/home")
wf.add_shell_hook(EventType.START, "/bin/echo hi")
wf.add_metadata(key="value")
wf.write()
EXPECTED_FILE = Path("workflow.yml")
with EXPECTED_FILE.open() as f:
# reading in as str so ordering of keys is not disrupted
# when loaded into a dict
result = f.read()
EXPECTED_FILE.unlink()
"""
Check that wf keys have been ordered as follows (while ignoring nested keys):
- pegasus,
- name,
- hooks,
- profiles,
- metadata,
- siteCatalog,
- replicaCatalog,
- transformationCatalog,
- jobs
- jobDependencies
"""
p = re.compile(
r"pegasus: '5.0'[\w\W]+name:[\w\W]+hooks:[\w\W]+profiles:[\w\W]+metadata:[\w\W]+siteCatalog:[\w\W]+replicaCatalog:[\w\W]+transformationCatalog:[\w\W]+jobs:[\w\W]+jobDependencies:[\w\W]+"
)
assert p.match(result) is not None
def test_write_wf_catalogs_included(self):
wf = Workflow("test")
wf.add_jobs(Job("ls"))
wf.add_transformation_catalog(TransformationCatalog())
wf.add_site_catalog(SiteCatalog())
wf.add_replica_catalog(ReplicaCatalog())
wf_path = Path("workflow.yml")
with wf_path.open("w+") as f:
wf.write(f)
f.seek(0)
result = yaml.load(f)
expected = {
"pegasus":
"5.0",
"name":
"test",
"siteCatalog": {
"sites": []
},
"replicaCatalog": {
"replicas": []
},
"transformationCatalog": {
"transformations": []
},
"jobs": [{
"type": "job",
"name": "ls",
"id": "ID0000001",
"arguments": [],
"uses": [],
}],
"jobDependencies": [],
}
assert expected == result
wf_path.unlink()