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 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_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"})