def test_port_normalization():
cwl = pack("remote-cwl/wf1.cwl")
step_s1 = _find(cwl.get("steps"), "id", "s1")
step_in1 = _find(step_s1.get("in"), "id", "in1")
assert step_in1["source"] == "in1"
cwl = pack("wf2.cwl")
step_s1 = _find(cwl.get("steps"), "id", "s1")
step_in1 = _find(step_s1.get("in"), "id", "in1")
assert step_in1["source"] == "in1"
out1 = _find(cwl.get("outputs"), "id", "out1")
assert out1.get("outputSource") == "s2/out1"
def test_already_packed_graph():
"""Workflow already packed in a $graph."""
cwl = pack("workflows/scatter-wf4.cwl")
assert "inputs" not in cwl
assert "outputs" not in cwl
assert "$graph" in cwl
assert "requirements" not in cwl
def test_step_packing():
cwl = pack("remote-cwl/wf1.cwl")
s1 = _find(cwl.get("steps"), "id", "s1")
tool2 = s1.get("run")
_type = _find(tool2.get("inputs"), "id", "in1").get("type")
assert isinstance(_type, dict)
assert _type.get("type") == "array"
def test_remote_packing():
cwl = pack("https://raw.githubusercontent.com/kaushik-work/sbpack/master/tests/wf2.cwl")
s1 = _find(cwl.get("steps"), "id", "s1")
wf1 = s1.get("run")
assert wf1.get("class") == "Workflow"
tool2 = _find(wf1.get("steps"), "id", "s1").get("run")
_type = _find(tool2.get("inputs"), "id", "in1").get("type")
assert isinstance(_type, dict)
assert _type.get("type") == "array"
def test_include():
cwl = pack("remote-cwl/tool1.cwl")
assert "arguments" in cwl
assert isinstance(cwl.get("arguments"), list)
inline_js_req = _find(cwl.get("requirements"), "class", "InlineJavascriptRequirement")
include_js = inline_js_req.get("expressionLib")
assert isinstance(include_js, list)
assert "engineers walk into a" in include_js[0]
def test_local_packing_with_validation(f):
url = urllib.parse.urlparse(f)
packed_name = pathlib.Path(url.path).stem + "-packed.cwl"
cwl = pack(f)
fpacked = pathlib.Path(packed_name)
with fpacked.open("w") as fout:
fast_yaml.dump(cwl, fout)
assert cwl_is_valid(fpacked)
fpacked.unlink()
def py_pack_sb(cwl_path, profile, appid):
logging.basicConfig()
logger.setLevel(logging.INFO)
if not validate_id(appid):
print("Illegal characters in app id")
return
cwl = pack(cwl_path)
api = get_profile(profile)
cwl["sbg:revisionNotes"] = f"Uploaded using sbpack-r \nSource: {cwl_path}"
try:
app = api.apps.get(appid)
logger.debug("Creating revised app: {}".format(appid))
return api.apps.create_revision(id=appid,
raw=cwl,
revision=app.revision + 1)
except sbgerr.NotFound:
logger.debug("Creating new app: {}".format(appid))
return api.apps.install_app(id=appid, raw=cwl)
def test_remote_packing_github_soft_links():
cwl = pack("https://raw.githubusercontent.com/rabix/sbpack/master/tests/workflows/wf5.cwl")
s1 = _find(cwl.get("steps"), "id", "s1")
tool1 = s1.get("run")
assert tool1.get("class") == "CommandLineTool"
def test_step_process_id():
"""Workflow step with external "run" reference gets an "id" added."""
cwl = pack("workflows/wf2.cwl", add_ids=True)
assert cwl["id"] == "wf2.cwl"
s1 = _find(cwl.get("steps"), "id", "s1")
assert s1["run"]["id"] == "wf2.cwl@[email protected]"
def test_embedded_packing():
cwl = pack("workflows/count-lines16-wf.cwl")
def test_schema_def2():
cwl = pack("wf2.cwl")
_type = _find(cwl.get("inputs"), "id", "in2").get("type")
assert isinstance(_type, dict)
assert _type.get("type") == "enum"
def test_schema_def1():
cwl = pack("remote-cwl/tool2.cwl")
_type = _find(cwl.get("inputs"), "id", "in1").get("type")
assert isinstance(_type, dict)
assert _type.get("type") == "array"
def test_recursive_type_resolution():
cwl = pack("tools/clt1.cwl")
simple_record = _find(cwl.get("inputs"), "id", "in2").get("type")
assert simple_record.get("type") == "record"
def test_parent_type_resolution():
cwl = pack("workflows/wf6.cwl")
_type = cwl.get("steps")[0].get("run").get("inputs")[0].get("type")
assert _type.get("type") == "record"
def py_pack_file(input, output):
fast_yaml.dump(pack(input), Path(output))