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adding filter to skip edges with deprecated node #28

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adding filter to skip edges with deprecated node #28

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4 changes: 4 additions & 0 deletions relation_engine/ontologies/obograph/parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,7 @@ def __init__(self, obo, ontology_id_prefix, graph_id=None):
raise ValueError(f'Found unprocessable node types {unknown_types}')
self._ont_prefix = ontology_id_prefix
self._property_map = self._get_property_map(obo)
self._deprecated_nodes = {}

def _get_property_map(self, obo):
ret = {}
Expand Down Expand Up @@ -196,6 +197,7 @@ def _is_valid_node(self, node, deprecated_ok=False):
if not deprecated_ok and meta.get(_OBO_DEPRECATED):
# may want some sort of special loader for loading pre-expired deprecated nodes
# needs more thought
self._deprecated_nodes[id_] = True
return False
return True

Expand Down Expand Up @@ -269,6 +271,8 @@ def get_edge_provider(self):
to = self._clean_obo_id(obj)
if not from_.startswith(self._ont_prefix) or not to.startswith(self._ont_prefix):
continue
if from_ in self._deprecated_nodes or to in self._deprecated_nodes:
continue
pred = e[_OBO_PREDICATE]
if pred in self._property_map:
pred = self._property_map[pred]
Expand Down