def test_inputs_generator_secondary_files(self):
w = WorkflowBuilder("tst")
w.input("wsec", TestTypeWithSecondary, default="test.ext")
# w._add_input(Input("wsec", TestTypeWithSecondary(), value="test.ext"))
inpsdict = WdlTranslator().build_inputs_file(w, merge_resources=False)
self.assertEqual("test.ext", inpsdict.get("tst.wsec"))
self.assertEqual("test.txt", inpsdict.get("tst.wsec_txt"))
def test_two_similar_tools(self):
w = WorkflowBuilder("testTwoToolsWithSameId")
w.input("inp", str)
w.step("stp1", TestTool(testtool=w.inp))
w.step("stp2", TestToolV2(testtool=w.inp))
wf_wdl, _ = WdlTranslator.translate_workflow(w)
expected = """\
version development
import "tools/TestTranslationtool.wdl" as T
import "tools/TestTranslationtool_v0_0_2.wdl" as T2
workflow testTwoToolsWithSameId {
input {
String inp
}
call T.TestTranslationtool as stp1 {
input:
testtool=inp
}
call T2.TestTranslationtool as stp2 {
input:
testtool=inp
}
}"""
self.assertEqual(expected, wf_wdl.get_string())
def test_max_memory(self):
tool = TestTool()
resources = WdlTranslator.build_resources_input(
tool.wrapped_in_wf(), {}, max_mem=1
)
self.assertEqual(
1, resources["TestTranslationtoolWf.testtranslationtool_runtime_memory"]
)
def test_cores(self):
tool = TestTool()
resources = WdlTranslator.build_resources_input(tool.wrapped_in_wf(),
{},
is_root=True)
self.assertEqual(
2,
resources["TestTranslationtoolWf.testtranslationtool_runtime_cpu"])
def test_switch(self):
from janis_unix import Echo, Cat
w = WorkflowBuilder("switchTest")
w.input("inp", int, value=2)
w.input("inp1", str, value="Hello")
w.input("inp2", str, value="Hi there")
w.conditional(
"echoswitch",
[
(w.inp > 1, Echo(inp=w.inp1)),
(w.inp.equals(1), Echo(inp="tasy case")),
Echo(inp=w.inp2),
],
)
w.output("out", source=w.echoswitch)
_, wdl_tools = WdlTranslator.translate_workflow(w)
expected = """\
version development
import "echo_v1_0_0.wdl" as E
workflow echoswitch {
input {
Int cond_inp
String switch_case_1_inp
String? switch_case_2_inp = "tasy case"
String switch_case_3_inp
}
if ((cond_inp > 1)) {
call E.echo as switch_case_1 {
input:
inp=switch_case_1_inp
}
}
if (((cond_inp == 1) && !((cond_inp > 1)))) {
call E.echo as switch_case_2 {
input:
inp=select_first([switch_case_2_inp, "tasy case"])
}
}
if (!(((cond_inp > 1) || (cond_inp == 1)))) {
call E.echo as switch_case_3 {
input:
inp=switch_case_3_inp
}
}
output {
File out = select_first([switch_case_1.out, switch_case_2.out, switch_case_3.out])
}
}"""
echoswitch = wdl_tools["echoswitch"].get_string()
self.assertEqual(expected, echoswitch)
def test_1(self):
tool = FilenameGeneratedTool()
mapped = [
a.get_string()
for a in WdlTranslator.build_command_from_inputs(tool.inputs())
]
self.assertEqual('~{select_first([generatedInp, "~{inp}"])}',
mapped[0])
self.assertEqual(
'~{select_first([generatedInpOptional, "~{if defined(inpOptional) then inpOptional else "generated"}"])}',
mapped[1],
)
self.assertEqual(
'~{select_first([generatedFileInp, "~{basename(fileInp, ".txt")}.transformed.fnp"])}',
mapped[2],
)
self.assertEqual(
'~{select_first([generatedFileInpOptional, "~{if defined(fileInpOptional) then basename(fileInpOptional, ".txt") else "generated"}.optional.txt"])}',
mapped[3],
)
class TestWdlTranslatorOverrides(unittest.TestCase):
def setUp(self):
self.translator = WdlTranslator()
def test_stringify_workflow(self):
wdlobj = wdlgen.Workflow("wid", version="development")
self.assertEqual(
"version development\n\n\n\nworkflow wid {\n\n\n\n}",
self.translator.stringify_translated_workflow(wdlobj),
)
def test_stringify_tool(self):
wdlobj = wdlgen.Task("tid", version="development")
self.assertEqual(
"version development\n\ntask tid {\n\n\n\n\n}",
self.translator.stringify_translated_tool(wdlobj),
)
def test_stringify_inputs(self):
d = {"wid.inp1": 1}
self.assertEqual(
'{\n "wid.inp1": 1\n}', self.translator.stringify_translated_inputs(d)
)
def test_workflow_filename(self):
w = WorkflowBuilder("wid")
self.assertEqual("wid.wdl", self.translator.workflow_filename(w))
def test_tools_filename(self):
self.assertEqual(
"TestTranslationtool.wdl", self.translator.tool_filename(TestTool().id())
)
def test_inputs_filename(self):
w = WorkflowBuilder("wid")
self.assertEqual("wid-inp.json", self.translator.inputs_filename(w))
def test_resources_filename(self):
w = WorkflowBuilder("wid")
self.assertEqual("wid-resources.json", self.translator.resources_filename(w))
def test_inputs_generator_array_of_secondary_files(self):
w = WorkflowBuilder("tst")
w.input("wsec", Array(TestTypeWithSecondary()), default=["test.ext"])
inpsdict = WdlTranslator().build_inputs_file(w, merge_resources=False)
self.assertListEqual(["test.ext"], inpsdict.get("tst.wsec"))
self.assertListEqual(["test.txt"], inpsdict.get("tst.wsec_txt"))
def setUp(self):
self.translator = WdlTranslator()
def test_environment1(self):
t = WdlTranslator().translate_tool_internal(tool=TestTool())
s = t.get_string()
print(s)
