def test_namespace_entry(self):
model = NamespaceEntry(name='entry',
namespace=Namespace(keyword='test'))
expected = {NAMESPACE: 'test', NAME: 'entry'}
self.assertEqual(model.to_json(), expected)
expected['id'] = model.id = 1
self.assertEqual(model.to_json(include_id=True), expected)
expected[IDENTIFIER] = model.identifier = 'test:00001'
self.assertEqual(model.to_json(include_id=True), expected)
def test_drop_namespace(self):
keyword, url = n(), n()
namespace = Namespace(keyword=keyword, url=url)
self.manager.session.add(namespace)
n_entries = 5
for _ in range(n_entries):
entry = NamespaceEntry(name=n(), namespace=namespace)
self.manager.session.add(entry)
self.manager.session.commit()
self.assertEqual(1,
self.manager.count_namespaces(),
msg='Should have one namespace')
self.assertEqual(n_entries,
self.manager.count_namespace_entries(),
msg='Should have {} entries'.format(n_entries))
self.manager.drop_namespace_by_url(url)
self.assertEqual(0,
self.manager.count_namespaces(),
msg='Should have no namespaces')
self.assertEqual(0,
self.manager.count_namespace_entries(),
msg='Entries should have been dropped')
def _create_namespace_entry_from_model(
self, model: Pathway, namespace: Namespace) -> NamespaceEntry:
"""Create a namespace entry from the model."""
return NamespaceEntry(encoding='B',
name=model.name,
identifier=model.wikipathways_id,
namespace=namespace)
def _create_namespace_entry_from_model(self, model: FlyGene, namespace: Namespace) -> NamespaceEntry:
return NamespaceEntry(
encoding='GRP',
name=model.symbol,
identifier=model.flybase_id,
namespace=namespace,
)
def _create_namespace_entry_from_model(self, model: Drug, namespace: Namespace) -> NamespaceEntry:
return NamespaceEntry(
encoding='A',
name=model.name,
identifier=model.drugbank_id,
namespace=namespace,
)
def _create_namespace_entry_from_model(self, gene: Gene, namespace: Namespace) -> NamespaceEntry:
return NamespaceEntry(
encoding=gene.bel_encoding,
name=gene.name,
identifier=gene.entrez_id,
namespace=namespace,
)
def _create_namespace_entry_from_model(
self, model: Antibody, namespace: Namespace) -> NamespaceEntry:
return NamespaceEntry(
namespace=namespace,
identifier=model.antibodyregistry_id,
name=model.name,
encoding='A',
)
def _create_namespace_entry_from_model(
self, term: Term, namespace: Namespace) -> NamespaceEntry:
return NamespaceEntry(
name=term.name,
identifier=term.go_id,
encoding=term.bel_encoding,
namespace=namespace,
)
def _create_namespace_entry_from_model(
self, model: Homologene, namespace: Namespace) -> NamespaceEntry:
return NamespaceEntry(
namespace=namespace,
name=model.homologene_id,
identifier=model.homologene_id,
encoding=model.bel_encoding,
)
def _create_namespace_entry_from_model(
self, sequence: Sequence, namespace: Namespace) -> NamespaceEntry:
return NamespaceEntry(
name=sequence.name,
identifier=sequence.mirbase_id,
encoding='GM',
namespace=namespace,
)
def _create_namespace_entry_from_model(
self, model: Enzyme, namespace: Namespace) -> NamespaceEntry:
return NamespaceEntry(
namespace=namespace,
name=model.expasy_id,
identifier=model.expasy_id,
encoding='GRP',
)
def _create_namespace_entry_from_model(
self, model: CompathPathwayMixin,
namespace: Namespace) -> NamespaceEntry:
"""Create a namespace entry from the model."""
return NamespaceEntry(encoding='B',
name=model.name,
identifier=model.identifier,
namespace=namespace)
def _create_namespace_entry_from_model(
self, descriptor: Descriptor,
namespace: Namespace) -> NamespaceEntry:
return NamespaceEntry(
namespace=namespace,
name=descriptor.name,
identifier=descriptor.descriptor_ui,
encoding=descriptor.bel_encoding,
)
def _create_namespace_entry_from_model(self,
model: Model,
namespace=None):
"""Create a namespace entry."""
return NamespaceEntry(
name=model.name,
identifier=model.test_id,
namespace=namespace,
)
def _create_namespace_entry_from_model(
self, mouse_gene: MouseGene,
namespace: Namespace) -> NamespaceEntry:
return NamespaceEntry(
encoding=mouse_gene.bel_encoding,
name=mouse_gene.symbol,
identifier=mouse_gene.mgi_id,
namespace=namespace,
)
def _create_namespace_entry_from_model(
self, chemical: Chemical, namespace: Namespace) -> NamespaceEntry:
"""Create a namespace entry from a chemical model."""
if chemical.name:
return NamespaceEntry(
encoding=chemical.bel_encoding,
name=chemical.name,
identifier=chemical.chebi_id,
namespace=namespace,
)
def make_dummy_namespaces(manager, graph, namespaces):
"""
:param pybel.manager.Manager manager:
:param pybel.BELGraph graph:
:param dict[str,iter[str]] namespaces:
"""
for keyword, names in namespaces.items():
url = n()
graph.namespace_url[keyword] = url
namespace = Namespace(keyword=keyword, url=url)
manager.session.add(namespace)
manager.namespace_model[url] = namespace
for name in names:
entry = manager.namespace_object_cache[url][
entry.name] = NamespaceEntry(name=name, namespace=namespace)
manager.session.add(entry)
manager.session.commit()
def _create_namespace_entry_from_model(
self, gene: RatGene, namespace: Namespace) -> NamespaceEntry:
return NamespaceEntry(encoding=gene.bel_encoding,
name=gene.symbol,
identifier=gene.rgd_id,
namespace=namespace)
