def test_get_expressions(self):
test_cwl_yaml = yaml.round_trip_load(TEST_CWL)
schema = process.get_schema("v1.0")[1].names["CommandLineTool"]
exprs = get_expressions(test_cwl_yaml, schema)
self.assertEqual(len(exprs), 1)
def test_get_expressions():
test_cwl_yaml = yaml.round_trip_load(TEST_CWL)
schema = process.get_schema("v1.0")[1].names["CommandLineTool"]
exprs = validate_js.get_expressions(test_cwl_yaml, schema)
assert len(exprs) == 1
def test_validate_js_expressions(self, print_js_hint_messages):
test_cwl_yaml = yaml.round_trip_load(TEST_CWL)
schema = process.get_schema("v1.0")[1].names["CommandLineTool"]
validate_js_expressions(test_cwl_yaml, schema)
assert print_js_hint_messages.call_args is not None
assert len(print_js_hint_messages.call_args[0]) > 0
def test_validate_js_expressions(mocker):
test_cwl_yaml = yaml.round_trip_load(TEST_CWL)
schema = process.get_schema("v1.0")[1].names["CommandLineTool"]
mocker.patch("cwltool.validate_js.print_js_hint_messages")
validate_js.validate_js_expressions(test_cwl_yaml, schema)
assert validate_js.print_js_hint_messages.call_args is not None
assert len(validate_js.print_js_hint_messages.call_args[0]) > 0
def test_get_expressions() -> None:
test_cwl_yaml = yaml.main.round_trip_load(TEST_CWL)
schema = process.get_schema("v1.0")[1]
assert isinstance(schema, Names)
clt_schema = schema.names["CommandLineTool"]
exprs = validate_js.get_expressions(test_cwl_yaml, clt_schema)
assert len(exprs) == 1
def parse_workflow(cwlpath):
(document_loader, avsc_names, schema_metadata) = process.get_schema()
fileuri = "file://" + cwlpath
workflowobj = document_loader.fetch(fileuri)
# If strict is true, names are required everywhere (among other requirements)
strict = False
# This updates from draft2 to draft3
workflowobj = update.update(workflowobj, document_loader, fileuri)
document_loader.idx.clear()
processobj, metadata = schema.load_and_validate(document_loader, avsc_names, workflowobj, strict)
return processobj
def test_validate_js_expressions(mocker: Any) -> None:
test_cwl_yaml = yaml.main.round_trip_load(TEST_CWL)
schema = process.get_schema("v1.0")[1]
assert isinstance(schema, Names)
clt_schema = schema.names["CommandLineTool"]
mocker.patch("cwltool.validate_js._logger")
# mocker.patch("cwltool.validate_js.print_js_hint_messages")
validate_js.validate_js_expressions(test_cwl_yaml, clt_schema)
validate_js._logger.warning.assert_called_with(
" JSHINT: (function(){return ((kjdbfkjd));})()\n JSHINT: ^\n JSHINT: W117: 'kjdbfkjd' is not defined."
) # type: ignore
def load_nocheck(upstream):
loading_context, workflowobj, uri = cwltool.load_tool.fetch_document(
upstream)
(sch_document_loader, avsc_names) = \
get_schema(workflowobj["cwlVersion"])[:2]
cp = sch_document_loader.ctx.copy()
cp["upstream"] = {"@type": "@id"}
sch_document_loader = schema_salad.ref_resolver.Loader(cp)
document, metadata = sch_document_loader.resolve_all(workflowobj,
uri,
checklinks=False)
return document, loading_context
def validate_js_expressions_strict(tool: dict):
"""
Run cwltool function to validate JS in an app
:param tool: CWL dict
"""
data = ruamel.yaml.load(ruamel.yaml.dump(tool),
ruamel.yaml.RoundTripLoader)
schema = get_schema(tool['cwlVersion'])[1].names[tool['class']]
add_lc_filename(data, data.get('label', 'input_document'))
jshint_options = {
"includewarnings": [
"W117", # <VARIABLE> not defined
"W104",
"W119" # using ES6 features
],
"strict": "implied",
"esversion": 5
}
validate_js_expressions(data, schema, jshint_options)