def test():
wdl_namespace = wdl.loads(wdl_code)
wf = wdl_namespace.workflows[0]
engine = Engine(wdl_run)
engine.submit(Workflow(wf), {"inp": "README.md"}, "test")
engine.run_all()
assert engine.get("test").state == Job.FINISHED
assert engine.jobs.vars["test.my_task.output"].endswith("output.txt")
def test_scatter_upstream_downstream():
wdl_namespace = wdl.loads("""
task t1 {
File i
String pattern
command { grep '${pattern}' ${i} > "filtered" }
output { File filtered = "filtered" }
}
task t2 {
File i
Array[String] s = ["a", "b", "c"]
command {
cat ${i} > out_file
echo -e "${sep="\\n" s}" >> out_file
}
output { Array[String] strings = read_lines("out_file") }
}
task t3 {
String x
command {echo ${x}}
output { String y = read_string(stdout()) }
}
workflow w {
call t1
call t2 {
input: i=t1.filtered
}
scatter(x in t2.strings) {
call t3 {
input: strings=x
}
}
}
""")
call_t1 = wdl_namespace.resolve('w.t1')
call_t2 = wdl_namespace.resolve('w.t2')
call_t3 = wdl_namespace.resolve('w.t3')
scatter = wdl_namespace.resolve('w._s7')
assert call_t2.task.declarations[1].wdl_string() == 'Array[String] s = ["a", "b", "c"]'
assert call_t1.name == 't1'
assert call_t2.name == 't2'
assert call_t3.name == 't3'
assert scatter.name == '_s7'
assert call_t1.upstream() == set()
assert call_t2.upstream() == set([call_t1])
assert call_t3.upstream() == set([call_t2, scatter])
assert scatter.upstream() == set([call_t2])
assert call_t1.downstream() == set([call_t2])
assert call_t2.downstream() == set([call_t3, scatter])
assert call_t3.downstream() == set()
assert scatter.downstream() == set([call_t3])
def test_fqn_and_upstream():
wdl_namespace = wdl.loads("""
task t1 {
Int i
Int j
String foo = "bar"
command { echo ${i+1} }
output { Int o = read_int(stdout()) }
}
workflow w {
call t1
call t1 as x {input: i=t1.o+10}
call t1 as y {input: i=10+x.o, j=t1.o}
}
""")
call_t1 = wdl_namespace.resolve('w.t1')
call_x = wdl_namespace.resolve('w.x')
call_y = wdl_namespace.resolve('w.y')
assert call_t1.name == 't1'
assert call_x.name == 'x'
assert call_y.name == 'y'
assert call_t1.upstream() == set()
assert call_x.upstream() == set([call_t1])
assert call_y.upstream() == set([call_t1, call_x])
assert call_t1.downstream() == set([call_x, call_y])
assert call_x.downstream() == set([call_y])
assert call_y.downstream() == set()
decl_i = wdl_namespace.resolve('w.t1.i')
decl_i2 = wdl_namespace.resolve('w.t1.i')
decl_j = wdl_namespace.resolve('w.x.j')
decl_j2 = wdl_namespace.resolve('w.x.j')
decl_foo = wdl_namespace.resolve('w.y.foo')
assert decl_i.name == 'i'
assert decl_i.type == WdlIntegerType()
assert decl_i.expression == None
assert decl_i2.name == 'i'
assert decl_i2.type == WdlIntegerType()
assert decl_i2.expression == None
assert decl_j.name == 'j'
assert decl_j.type == WdlIntegerType()
assert decl_j.expression == None
assert decl_j2.name == 'j'
assert decl_j2.type == WdlIntegerType()
assert decl_j2.expression == None
assert decl_foo.name == 'foo'
assert decl_foo.type == WdlStringType()
assert decl_foo.expression.wdl_string() == '"bar"'
def test_beyond_scatter_upstream_downstream():
wdl_namespace = wdl.loads("""
task t1 {
File i
String pattern
command { grep '${pattern}' ${i} > "filtered" }
output { File filtered = "filtered" }
}
task t2 {
File i
Array[String] s = ["a", "b", "c"]
command {
cat ${i} > out_file
echo -e "${sep="\\n" s}" >> out_file
}
output { Array[String] strings = read_lines("out_file") }
}
task t3 {
String x
command {echo ${x}}
output { String y = read_string(stdout()) }
}
workflow w {
call t1
call t2 {
input: i=t1.filtered
}
Array[String] s = ["a", "b", "c"]
scatter(n in s) {
call t3 {
input: x=t2.strings
}
}
}
""")
call_t1 = wdl_namespace.resolve('w.t1')
call_t2 = wdl_namespace.resolve('w.t2')
call_t3 = wdl_namespace.resolve('w.t3')
scatter = call_t3.parent
assert call_t3.upstream() == set([call_t2, scatter])
