def test_remote_files():
this_path = current_path / "cwl" / "misc" / "wf-remote-steps.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
# Refers to an earlier commit
hov = doc.hover(Position(13, 32))
assert "class:" in hov.contents.value
# Non existent commit
hov = doc.hover(Position(19, 32))
assert hov.contents.value == "```\n\n```"
def test_basic_JS():
path = current_path / "cwl" / "misc" / "clt1.cwl"
doc = load(doc_path=path, type_dicts=type_dicts)
hov = doc.hover(loc=Position(7, 25))
assert isinstance(hov.contents.value, str)
assert hov.contents.value.startswith("```\nA_")
hov = doc.hover(loc=Position(10, 19))
assert isinstance(hov.contents.value, str)
assert "outdirSize" in hov.contents.value
def test_port_completer():
this_path = current_path / "cwl" / "misc" / "wf-port-completer.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
cmpl = doc.completion(Position(10, 14)) # Not a list
assert "in1" in [c.label for c in cmpl]
cmpl = doc.completion(Position(23, 11)) # Is a list
assert "out1" in [c.label for c in cmpl]
cmpl = doc.completion(Position(24, 9)) # Is a list
assert "in1" in [c.label for c in cmpl]
def test_schemadef_import():
this_path = current_path / "cwl" / "misc" / "cl-schemadef-import.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 0
cmpl = doc.completion(Position(12, 21))
assert "cl-schemadef-import.cwl" in [c.label for c in cmpl]
# The completer should look for all files in the current directory
cmpl = doc.completion(Position(4, 11))
assert "./paired_end_record.yml#paired_end_options" in [
c.label for c in cmpl
]
def test_implicit_inputs():
this_path = current_path / "cwl" / "misc" / "wf-when-input.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 0
cmpl = doc.completion(Position(12, 8))
assert "new_input" in [c.label for c in cmpl]
def test_definition():
doc = load(doc_path=path, type_dicts=type_dicts)
linked_uri = pathlib.Path(current_path / "cwl" / "ebi" / "utils" /
"concatenate.cwl")
doc_def_loc = doc.definition(loc=Position(50, 20))
assert isinstance(doc_def_loc, Location)
assert doc_def_loc.uri == linked_uri.as_uri()
def test_docs_on_hover():
this_path = current_path / "cwl" / "misc" / "wf-when-input.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
hov = doc.hover(Position(10, 6))
assert "Sibling" in hov.contents.value
assert hov.contents.kind == "markdown"
def test_plain_text_include():
this_path = current_path / "cwl" / "misc" / "cl-include-text.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 0
hov = doc.hover(Position(9, 21))
assert "We hold" in hov.contents.value
def test_requirements_completion():
this_path = current_path / "cwl" / "misc" / "cl-hints-dict.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
cmpl = doc.completion(Position(12, 8))
assert "dockerLoad" in [c.label for c in cmpl]
this_path = current_path / "cwl" / "misc" / "cl-hints-list.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
cmpl = doc.completion(Position(12, 8))
assert "dockerImport" in [c.label for c in cmpl]
this_path = current_path / "cwl" / "misc" / "cl-hints-dict-start.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
cmpl = doc.completion(Position(12, 5))
assert "dockerLoad" in [c.label for c in cmpl]
def test_hints_imports():
this_path = current_path / "cwl" / "misc" / "cl-hints-import.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 1
missing_error = next(p for p in doc.problems if p.range.start.line == 4)
assert missing_error.message.startswith("Missing document:")
cmpl = doc.completion(Position(4, 20))
assert "cl-schemadef-import.cwl" in [c.label for c in cmpl]
def test_v1_1_runtime():
# No exitcode in runtime in v1.0 ever
path = current_path / "cwl" / "misc" / "clt1.cwl"
doc = load(doc_path=path, type_dicts=type_dicts)
hov = doc.hover(loc=Position(10, 19))
assert "exitCode" not in hov.contents.value
hov = doc.hover(loc=Position(17, 33))
assert "exitCode" not in hov.contents.value
# Exitcode in runtime in v1.1 when in output
path = current_path / "cwl" / "misc" / "clt2.cwl"
doc = load(doc_path=path, type_dicts=type_dicts)
hov = doc.hover(loc=Position(24, 20))
assert "exitCode" not in hov.contents.value
hov = doc.hover(loc=Position(31, 34))
assert "exitCode" in hov.contents.value
def test_requirement_sub_completion():
this_path = current_path / "cwl" / "ebi" / "workflows" / "InterProScan-v5-chunked-wf.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
cmpl = doc.completion(Position(8, 10))
assert "InlineJavascriptRequirement" in [c.label for c in cmpl]
def test_requirement_completion():
doc = load(doc_path=path, type_dicts=type_dicts)
cmpl = doc.completion(Position(8, 16))
assert "InlineJavascriptRequirement" in [c.label for c in cmpl]
def test_step_input_completion():
doc = load(doc_path=path, type_dicts=type_dicts)
cmpl = doc.completion(Position(37, 38))
assert "covariance_models" in [c.label for c in cmpl]
def test_type_completion():
doc = load(doc_path=path, type_dicts=type_dicts)
cmpl = doc.completion(Position(14, 11))
assert "string" in [c.label for c in cmpl]
def test_record_field_completion():
doc = load(doc_path=path, type_dicts=type_dicts)
cmpl = doc.completion(Position(7, 0))
assert "doc" in [c.label for c in cmpl]
