def update_context(universe, graph):
"""Updates the context of a subgraph from the universe of all knowledge.
:param pybel.BELGraph universe: The universe of knowledge
:param pybel.BELGraph graph: A BEL graph
"""
for namespace in get_namespaces(graph):
if namespace in universe.namespace_url:
graph.namespace_url[namespace] = universe.namespace_url[namespace]
elif namespace in universe.namespace_owl:
graph.namespace_owl[namespace] = universe.namespace_owl[namespace]
elif namespace in universe.namespace_owl:
graph.namespace_pattern[namespace] = universe.namespace_pattern[namespace]
else:
log.warning('namespace: %s missing from universe', namespace)
for annotation in get_annotations(graph):
if annotation in universe.annotation_url:
graph.annotation_url[annotation] = universe.annotation_url[annotation]
elif annotation in universe.annotation_owl:
graph.annotation_owl[annotation] = universe.annotation_owl[annotation]
elif annotation in universe.annotation_owl:
graph.annotation_pattern[annotation] = universe.annotation_pattern[annotation]
else:
log.warning('annotation: %s missing from universe', annotation)
def test_namespaces_egf(self):
result = {
'HGNC': 10,
'GOBP': 1,
}
self.assertEqual(set(result), get_namespaces(egf_graph))
self.assertEqual(result, count_namespaces(egf_graph))
def get_incorrect_names(graph: BELGraph) -> Mapping[str, Set[str]]:
"""Return the dict of the sets of all incorrect names from the given namespace in the graph.
:return: The set of all incorrect names from the given namespace in the graph
"""
return {
namespace: get_incorrect_names_by_namespace(graph, namespace)
for namespace in get_namespaces(graph)
}
def test_namespaces_egf(self):
"""Test getting and counting namespaces' contents on the EGF graph."""
result = {
'HGNC': 10,
'GO': 1,
}
self.assertEqual(set(result), get_namespaces(egf_graph))
self.assertEqual(Counter(result), count_namespaces(egf_graph))
def test_namespaces_sialic(self):
"""Test getting and counting namespaces' contents on the sialic acid graph."""
result = {
'HGNC': 7,
'CHEBI': 1,
}
self.assertEqual(set(result), get_namespaces(sialic_acid_graph))
self.assertEqual(Counter(result), count_namespaces(sialic_acid_graph))
def test_namespaces_egf(self):
"""Test getting and counting namespaces' contents on the EGF graph."""
result = {
'hgnc': 15,
'go': 3,
'bel': 4,
}
self.assertEqual(set(result), get_namespaces(egf_graph))
self.assertEqual(Counter(result), count_namespaces(egf_graph))
def get_incorrect_names(graph):
"""Returns the dict of the sets of all incorrect names from the given namespace in the graph
:param pybel.BELGraph graph: A BEL graph
:return: The set of all incorrect names from the given namespace in the graph
:rtype: dict[str,set[str]]
"""
return {
namespace: get_incorrect_names_by_namespace(graph, namespace)
for namespace in get_namespaces(graph)
}
def get_names_including_errors(graph: BELGraph) -> Mapping[str, Set[str]]:
"""Get all names appearing in the graph, including erroneous names, and group in a dictionary by namespace.
Takes the names from the graph in a given namespace and the erroneous names from the same namespace and returns
them together as a unioned set
:return: The dict of the sets of all correct and incorrect names from the given namespace in the graph
"""
return {
namespace: get_names_including_errors_by_namespace(graph, namespace)
for namespace in get_namespaces(graph)
}
def get_names_including_errors(graph):
"""Takes the names from the graph in a given namespace and the erroneous names from the same namespace and returns
them together as a unioned set
:param pybel.BELGraph graph: A BEL graph
:return: The dict of the sets of all correct and incorrect names from the given namespace in the graph
:rtype: dict[str,set[str]]
"""
return {
namespace: get_names_including_errors_by_namespace(graph, namespace)
for namespace in get_namespaces(graph)
}
def test_summarize_sialic(self):
"""Test getting and counting namespaces' contents on the sialic acid graph."""
namespace_result = {
'hgnc': 8,
'chebi': 2,
'bel': 3,
}
self.assertEqual(set(namespace_result),
get_namespaces(sialic_acid_graph))
self.assertEqual(Counter(namespace_result),
count_namespaces(sialic_acid_graph))
hgnc_result = {
'CD33':
3, # once as reference, once in complex, and once as variant
'TYROBP': 1,
'SYK': 1,
'PTPN6': 1,
'PTPN11': 1,
'TREM2': 1,
}
chebi_result = {
'sialic acid': 2,
}
names = get_names(sialic_acid_graph)
self.assertEqual(set(namespace_result), set(names))
self.assertEqual(set(hgnc_result), names['hgnc'])
self.assertEqual(set(chebi_result), names['chebi'])
self.assertEqual(set(hgnc_result),
get_names_by_namespace(sialic_acid_graph, 'hgnc'))
self.assertEqual(set(chebi_result),
get_names_by_namespace(sialic_acid_graph, 'chebi'))
self.assertEqual(
hgnc_result,
dict(count_names_by_namespace(sialic_acid_graph, 'hgnc')))
self.assertEqual(
chebi_result,
dict(count_names_by_namespace(sialic_acid_graph, 'chebi')))
def test_namespaces_sialic(self):
result = {'HGNC': 7, 'CHEBI': 1}
self.assertEqual(set(result), get_namespaces(sialic_acid_graph))
self.assertEqual(result, count_namespaces(sialic_acid_graph))
