def test_mass_wf_load():
type_dicts = load_type_dicts()
for wf_dir in [
"ebi/workflows", "mgi/subworkflows", "mgi/pipelines", "cwl-v1.2"
]:
path = current_path / "cwl" / wf_dir
for fname in path.glob("*.cwl"):
_ = load(doc_path=fname, type_dicts=type_dicts)
def test_ebi_wf_cmsearch_multimodel():
path = current_path / "cwl" / "ebi" / "workflows" / "cmsearch-multimodel-wf.cwl"
doc = load(doc_path=path, type_dicts=load_type_dicts())
step_symbols = next((symb for symb in doc.symbols if symb.name == "steps"),
None)
assert isinstance(step_symbols.children, list)
cmsearch_symbol = next(
(symb for symb in step_symbols.children if symb.name == "cmsearch"),
None)
assert cmsearch_symbol.range.start.line == 33
def test_connections():
path = current_path / "cwl" / "misc" / "wf-port-completer.cwl"
doc = load(doc_path=path, type_dicts=load_type_dicts())
assert len(doc.problems) == 0
def test_troublesome_tool_load():
type_dicts = load_type_dicts()
path = current_path / "cwl" / "misc"
for fname in path.glob("*.cwl"):
_ = load(doc_path=fname, type_dicts=type_dicts)
def test_mass_tool_load():
type_dicts = load_type_dicts()
for wf_dir in ["ebi/tools", "mgi/tools"]:
path = current_path / "cwl" / wf_dir
for fname in path.glob("*.cwl"):
_ = load(doc_path=fname, type_dicts=type_dicts)
# Copyright (c) 2019 Seven Bridges. See LICENSE
import pathlib
from lib import load, load_type_dicts
from benten.langserver.lspobjects import Position, Location
current_path = pathlib.Path(__file__).parent
schema_path = pathlib.Path(current_path, "../benten/000.package.data/")
type_dicts = load_type_dicts()
path = current_path / "cwl" / "ebi" / "workflows" / "cmsearch-multimodel-wf.cwl"
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_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]
def test_type_completion():