def check_rule_with_data(rule_path, data_path):
r = load_yamldown(rule_path)
schema = os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../metadata/rules.schema.yaml")
validate(r, schema)
if not rule.sparql_from(r):
raise Exception("No SPARQL impl for rule {}".format(rule_path))
g = rdflib.graph.ConjunctiveGraph()
test_data_graph = g.parse(data_path, format="ttl", publicID="http://geneontology.org/rules/test")
test_data_graph.add((term.URIRef("http://model.geneontology.org/rules/test"), term.URIRef("http://model.geneontology.org/graphType"), term.URIRef("http://model.geneontology.org/gafCam")))
test_data_graph.add((term.URIRef("http://model.geneontology.org/rules/test"), term.URIRef("http://www.w3.org/2000/01/rdf-schema#"), term.Literal("test_graph.ttl")))
results = g.query(rule.sparql_from(r))
return results
def check_rule_with_data(rule_path, data_path):
r = load_yamldown(rule_path)
schema = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"../../../metadata/rules.schema.yml")
validate(r, schema)
if not rule.sparql_from(r):
raise Exception("No SPARQL impl for rule {}".format(rule_path))
g = rdflib.graph.ConjunctiveGraph()
test_data_graph = g.parse(data_path,
format="ttl",
publicID="http://geneontology.org/rules/test")
test_data_graph.add((term.URIRef("http://geneontology.org/rules/test"),
term.URIRef("http://geneontology.org/graphType"),
term.URIRef("http://geneontology.org/gafCam")))
results = g.query(rule.sparql_from(r))
return results
def group(endpoint, rules_dir, schema, verbose, out) -> None:
gorules_paths = glob.glob(os.path.join(rules_directory(path=rules_dir), "gorule-*.md"))
rules = [load_yamldown(path) for path in gorules_paths if rule.sparql_from(load_yamldown(path))]
s = schema if schema else SCHEMA
results = []
for r in rules:
validate(r, s)
result = rule.test_rule(r, endpoint)
results.append(result)
click.echo(result.short_summary())
if result.returned and verbose:
click.echo(result.verbose_readable())
if out:
json.dump(rule.generate_results_json(results), out, indent=4)
def test(ctx, endpoint, rule_path, verbose, schema, out):
r = load_yamldown(rule_path)
s = schema if schema else SCHEMA
validate(r, s)
if not rule.sparql_from(r):
raise click.ClickException("No SPARQL implementation for this rule.")
result = rule.test_rule(r, endpoint)
click.echo(result.short_summary())
if result.returned and verbose:
click.echo(result.verbose_readable())
if out:
json.dump(result.jsonify(), out, indent=4)
if result.passing in ["Warn", "Fail"]:
ctx.exit(1)