def test_load_yaml():
m = MDF(handle='test')
m.files = [
'tests/samples/ctdc_model_file.yaml',
'tests/samples/ctdc_model_properties_file.yaml'
]
m.load_yaml()
def test_create_model():
m = MDF(handle='test')
m.files = [
'tests/samples/ctdc_model_file.yaml',
'tests/samples/ctdc_model_properties_file.yaml'
]
m.load_yaml()
m.create_model()
assert m.model
def test_load_yaml_url():
m = MDF(handle='ICDC')
m.files = [
'https://cbiit.github.io/icdc-model-tool/model-desc/icdc-model.yml',
'https://cbiit.github.io/icdc-model-tool/model-desc/icdc-model-props.yml'
]
m.load_yaml()
m.create_model()
assert m.model
def test_created_model():
m = MDF('tests/samples/test-model.yml', handle='test')
assert isinstance(m.model, Model)
assert set([x.handle for x in m.model.nodes.values()
]) == {'case', 'sample', 'file', 'diagnosis'}
assert set([x.triplet for x in m.model.edges.values()
]) == {('of_case', 'sample', 'case'),
('of_case', 'diagnosis', 'case'),
('of_sample', 'file', 'sample'),
('derived_from', 'file', 'file'),
('derived_from', 'sample', 'sample')}
assert set([x.handle for x in m.model.props.values()]) == {
'case_id', 'patient_id', 'sample_type', 'amount', 'md5sum',
'file_name', 'file_size', 'disease', 'days_to_sample', 'workflow_id',
'id'
}
file_ = m.model.nodes['file']
assert file_
assert file_.props
assert set([x.handle for x in file_.props.values()
]) == {'md5sum', 'file_name', 'file_size'}
assert m.model.nodes['file'].props['md5sum'].value_domain == 'regexp'
assert m.model.nodes['file'].props['md5sum'].pattern
amount = m.model.props[('sample', 'amount')]
assert amount
assert amount.value_domain == 'number'
assert amount.units == 'mg'
file_size = m.model.props[('file', 'file_size')]
assert file_size
assert file_size.units == 'Gb;Mb'
derived_from = m.model.edges[('derived_from', 'sample', 'sample')]
assert derived_from
assert len(derived_from.props.keys()) == 1
assert next(iter(derived_from.props.values())).handle == 'id'
d_f = m.model.edges_by_dst(m.model.nodes['file'])
assert d_f
assert len(d_f) == 1
assert 'workflow_id' in d_f[0].props.keys()
assert len(m.model.edges_in(m.model.nodes['case'])) == 2
assert len(m.model.edges_out(m.model.nodes['file'])) == 2
sample = m.model.nodes['sample']
sample_type = sample.props['sample_type']
assert sample_type.value_domain == 'value_set'
assert isinstance(sample_type.value_set, ValueSet)
assert set(sample_type.values) == {'tumor', 'normal'}
# try and see if the "collection" set is the same?
logging.info("...collection")
for att in coll_atts:
aset = set(getattr(a_ent, att))
bset = set(getattr(b_ent, att))
if aset != bset:
diff_.update_result(
thing,
entk,
att,
sorted(list(set(aset - bset))),
sorted(list(set(bset - aset))),
)
logging.info("done")
diff_.finalize_result()
return diff_.result
if __name__ == "__main__":
# m = hashlib.md5();
# m.update(b"Hey dude");
# print(m.hexdigest());
smp_dir = "../tests/samples"
mdl_a = MDF(os.path.join(smp_dir, "test-model-a.yml"), handle="test")
mdl_b = MDF(os.path.join(smp_dir, "test-model-b.yml"), handle="test")
result = diff_models(mdl_a.model, mdl_b.model)
print(result)
pass
mdf = {
"bento":[
"https://cbiit.github.io/bento-model/model-desc/bento_model_file.yaml",
"https://cbiit.github.io/bento-model/model-desc/bento_model_properties.yaml"
],
"icdc":[
"https://cbiit.github.io/icdc-model-tool/model-desc/icdc-model.yml",
"https://cbiit.github.io/icdc-model-tool/model-desc/icdc-model-props.yml"
],
"ctdc":[
"https://cbiit.github.io/ctdc-model/model-desc/ctdc_model_file.yaml",
"https://cbiit.github.io/ctdc-model/model-desc/ctdc_model_properties_file.yaml"
]}
print("read models")
models = { "icdc":MDF(*mdf["icdc"],handle='ICDC').model,
"ctdc":MDF(*mdf["ctdc"],handle='CTDC').model,
"bento":MDF(*mdf["bento"],handle='Bento').model}
# pulling from MDF auto-creates value set objects and their terms
# uniquify the terms within models
mdl_terms = {}
concepts = {}
put_terms = []
for mdl in models:
m = models[mdl]
mdl_terms[mdl] = {}
for v in [p.value_set for p in m.props.values() if p.value_domain=='value_set']:
def test_class():
m = MDF(handle='test')
assert isinstance(m, MDF)
with pytest.raises(ArgError, match="arg handle= must"):
MDF()