def wf3():
wf = Workflow("test")
wf.add_jobs(Job("ls"))
wf.add_site_catalog(SiteCatalog())
wf.add_transformation_catalog(TransformationCatalog())
wf.add_replica_catalog(ReplicaCatalog())
return wf
def test_job_id_assignment_by_workflow(self):
wf = Workflow("wf")
j1 = Job("t1", _id="a")
j2 = Job("t2")
j3 = Job("t3", _id="b")
j4 = Job("t4")
j5 = Job("t5")
wf.add_jobs(j1, j2, j3, j4, j5)
assert j2._id == "ID0000001"
assert j4._id == "ID0000002"
assert j5._id == "ID0000003"
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 test_add_duplicate_parent_dependency(self):
wf = Workflow("wf")
job = Job("t", _id="job")
parent = Job("t", _id="parent")
wf.add_jobs(job, parent)
with pytest.raises(DuplicateError) as e:
wf.add_dependency(job, parents=[parent, parent])
assert (
"A dependency already exists between parent id: parent and job id: job"
in str(e))
def test_add_duplicate_child_dependency(self):
wf = Workflow("wf")
job = Job("t", _id="job")
child = Job("t", _id="child")
wf.add_jobs(job, child)
with pytest.raises(DuplicateError) as e:
wf.add_dependency(job, children=[child, child])
assert (
"A dependency already exists between job id: job and child id: child"
in str(e))
def test_infer_dependencies_when_job_uses_stdin_stdout_and_stderr(self):
wf = Workflow("wf")
j1 = Job("t1", _id="j1").add_outputs(File("f1"))
j2 = Job("t1",
_id="j2").set_stdin(*j1.get_outputs()).set_stdout(File("f2"))
j3 = Job("t1", _id="j3").add_inputs(*j2.get_outputs())
wf.add_jobs(j1, j2, j3)
# manually call _infer_dependencies() as it is only called when
# wf.write() is called
wf._infer_dependencies()
assert wf.dependencies["j1"] == _JobDependency("j1", {"j2"})
assert wf.dependencies["j2"] == _JobDependency("j2", {"j3"})
def test_add_dependency_parents(self):
wf = Workflow("wf")
job = Job("t", _id="job")
parents = [
Job("t", _id="parent1"),
Job("t", _id="parent2"),
Job("t", _id="parent3"),
]
wf.add_jobs(job, *parents)
wf.add_dependency(job, parents=[parents[0]])
wf.add_dependency(job, parents=parents[1:])
for parent in parents:
assert wf.dependencies[parent._id] == _JobDependency(
parent._id, {job._id})
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_add_dependency_children(self):
wf = Workflow("wf")
job = Job("t", _id="job")
children = [
Job("t", _id="child1"),
Job("t", _id="child2"),
Job("t", _id="child3"),
]
wf.add_jobs(job, *children)
wf.add_dependency(job, children=[children[0]])
assert wf.dependencies[job._id] == _JobDependency(
job._id, {children[0]._id})
wf.add_dependency(job, children=children[1:])
assert wf.dependencies[job._id] == _JobDependency(
job._id, {child._id
for child in children})
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()
def wf():
wf = Workflow("wf")
j1 = (Job("t1", _id="a").add_outputs(File("f1"), File("f2")).add_args(
File("do-nothing"), "-n", 1,
1.1).set_stdin("stdin").set_stdout("stdout").set_stderr("stderr"))
j2 = (Job("t1", _id="b").add_inputs(File("f1"), File("f2")).add_checkpoint(
File("checkpoint")))
j3 = SubWorkflow("subworkflow.dag", True,
_id="c").add_args("--sites", "condorpool")
j4 = SubWorkflow(File("subworkflow.dax"), False, _id="d")
wf.add_jobs(j1, j2, j3, j4)
wf._infer_dependencies()
wf.add_env(JAVA_HOME="/java/home")
wf.add_shell_hook(EventType.START, "/bin/echo hi")
wf.add_metadata(key="value")
return wf
def test_add_dependency_parents_and_children(self):
wf = Workflow("wf")
job = Job("t", _id="job")
parents = [Job("t", _id="parent1"), Job("t", _id="parent2")]
children = [Job("t", _id="child1"), Job("t", _id="child2")]
wf.add_jobs(*parents, *children)
# add nothing
wf.add_dependency(job)
assert len(wf.dependencies) == 0
wf.add_dependency(job, parents=parents, children=children)
for parent in parents:
assert wf.dependencies[parent._id] == _JobDependency(
parent._id, {job._id})
assert wf.dependencies[job._id] == _JobDependency(
job._id, {child._id
for child in children})
def test_infer_dependencies_fork_join_wf(self):
wf = Workflow("wf")
f1 = File("f1")
f2 = File("f2")
f3 = File("f3")
f4 = File("f4")
fork = Job("t1", _id="fork").add_outputs(f1, f2)
work1 = Job("t1", _id="work1").add_inputs(f1).add_outputs(f3)
work2 = Job("t1", _id="work2").add_inputs(f2).add_outputs(f4)
join = Job("t1", _id="join").add_inputs(f3, f4)
wf.add_jobs(fork, work1, work2, join)
# manually call _infer_dependencies() as it is only called when
# wf.write() is called
wf._infer_dependencies()
assert wf.dependencies["fork"] == _JobDependency(
"fork", {"work1", "work2"})
assert wf.dependencies["work1"] == _JobDependency("work1", {"join"})
assert wf.dependencies["work2"] == _JobDependency("work2", {"join"})
def test_get_job(self):
wf = Workflow("wf")
j1 = Job("t1", _id="j1")
wf.add_jobs(j1)
assert j1 == wf.get_job("j1")
def test_add_job(self, job):
wf = Workflow("wf")
wf.add_jobs(job)
assert job == wf.get_job("job")
def _to_wf(d: dict) -> Workflow:
"""Convert dict to Workflow
:param d: Workflow represented as a dict
:type d: dict
:raises PegasusError: encountered error parsing
:return: a Workflow object based on d
:rtype: Workflow
"""
try:
#
wf = Workflow(d["name"], infer_dependencies=False)
# add rc
if "replicaCatalog" in d:
wf.replica_catalog = _to_rc(d["replicaCatalog"])
# add tc
if "transformationCatalog" in d:
wf.transformation_catalog = _to_tc(d["transformationCatalog"])
# add sc
if "siteCatalog" in d:
wf.site_catalog = _to_sc(d["siteCatalog"])
# add jobs
for j in d["jobs"]:
# create appropriate job based on type
if j["type"] == "job":
job = Job(
j["name"],
_id=j["id"],
node_label=j.get("nodeLabel"),
namespace=j.get("namespace"),
version=j.get("version"),
)
elif j["type"] in {"pegasusWorkflow", "condorWorkflow"}:
f = File(j["file"])
is_planned = False if j["type"] == "pegasusWorkflow" else True
job = SubWorkflow(
f, is_planned, _id=j["id"], node_label=j.get("nodeLabel")
)
else:
raise ValueError
# add args
args = list()
for a in j["arguments"]:
args.append(a)
job.args = args
# add uses
uses = set()
for u in j["uses"]:
f = File(u["lfn"], size=u.get("size"))
try:
f.metadata = u["metadata"]
except KeyError:
pass
uses.add(
_Use(
f,
getattr(_LinkType, u["type"].upper()),
stage_out=u.get("stageOut"),
register_replica=u.get("registerReplica"),
bypass_staging=u.get("bypass"),
)
)
job.uses = uses
# set stdin
if "stdin" in j:
for u in job.uses:
if u.file.lfn == j["stdin"]:
job.stdin = u.file
break
# set stdout
if "stdout" in j:
for u in job.uses:
if u.file.lfn == j["stdout"]:
job.stdout = u.file
break
# set stderr
if "stderr" in j:
for u in job.uses:
if u.file.lfn == j["stderr"]:
job.stderr = u.file
break
# add profiles
if j.get("profiles"):
job.profiles = defaultdict(dict, j.get("profiles"))
# add metadata
if j.get("metadata"):
job.metadata = j.get("metadata")
# add hooks
if j.get("hooks"):
job.hooks = defaultdict(list, j.get("hooks"))
# add job to wf
wf.add_jobs(job)
# add dependencies
if d.get("jobDependencies"):
dependencies = defaultdict(_JobDependency)
for item in d.get("jobDependencies"):
dependencies[item["id"]] = _JobDependency(
item["id"], {child for child in item["children"]}
)
wf.dependencies = dependencies
# add profiles
if d.get("profiles"):
wf.profiles = defaultdict(dict, d.get("profiles"))
# add metadata
if d.get("metadata"):
wf.metadata = d.get("metadata")
# add hooks
if d.get("hooks"):
wf.hooks = defaultdict(list, d.get("hooks"))
return wf
except (KeyError, ValueError):
raise PegasusError("error parsing {}".format(d))
def test_add_duplicate_job(self):
wf = Workflow("wf")
with pytest.raises(DuplicateError):
wf.add_jobs(Job("t1", _id="j1"), Job("t2", _id="j1"))