def test_convert(self):
cv = MIxS6Converter()
cv.core_filename = f'{INPUTS_DIR}/mixs6_core.tsv'
cv.packages_filename = f'{INPUTS_DIR}/mixs6.tsv'
cv.output_directory = OUTPUTS_DIR
self.assertTrue(True)
fn = cv.convert_and_save()
g = PythonGenerator(fn)
print(g.serialize()[0:1000])
g = JsonSchemaGenerator(fn)
print(g.serialize()[0:1000])
g = OwlSchemaGenerator(fn)
print(g.serialize()[0:1000])
def compile_model(model: str, print_python: bool = False) -> SchemaDefinition:
gen = PythonGenerator(model,
merge_imports=False,
gen_classvars=False,
gen_slots=False)
code = gen.serialize()
return code
gene sequence:
uri: dist:seq
typeof: string
description: A gene sequence
# Slots that are defined in this model extension
slots:
gene has sequence:
description: A gene pattern
domain: gene
range: gene sequence
slot_uri: dist:hasSeq
required: true
# Classes that are defined in this model extension
classes:
# The class name. For most generators, this will be transformed to CamelCase (MyGene)
my gene:
description: This is an example extension. Doesn't do a lot
is_a: gene
slots:
- gene has sequence
"""
from linkml.generators.pythongen import PythonGenerator
gen = PythonGenerator(model, log_level=ERROR)
print(gen.serialize())