From 2e45c92b78ebfd1a199b418b01c5391ef6ad82c0 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 5 Jul 2023 15:40:27 +0200 Subject: [PATCH 1/2] Update construct.py --- mira/dkg/construct.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/mira/dkg/construct.py b/mira/dkg/construct.py index e1a62dd0f..35b0c672a 100644 --- a/mira/dkg/construct.py +++ b/mira/dkg/construct.py @@ -464,7 +464,8 @@ def construct( property_values="", xref_types="", # TODO synonym_types=";".join( - synonym.type.curie for synonym in term.synonyms or [] + synonym.type.curie if synonym.type is not None else "skos:exactMatch" + for synonym in term.synonyms or [] ), ) for parent in term.parents: @@ -979,7 +980,8 @@ def get_node_info(term: pyobo.Term, type: EntityType = "class"): property_values="", xref_types="", synonym_types=";".join( - synonym.type.curie for synonym in term.synonyms or [] + synonym.type.curie if synonym.type is not None else "skos:exactMatch" + for synonym in term.synonyms or [] ), ) From e87de50e4f9cd96140385cf1278198b96ef17e65 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 5 Jul 2023 15:56:30 +0200 Subject: [PATCH 2/2] Fix predicate curie reference --- mira/dkg/construct.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/mira/dkg/construct.py b/mira/dkg/construct.py index 35b0c672a..6ea584deb 100644 --- a/mira/dkg/construct.py +++ b/mira/dkg/construct.py @@ -762,7 +762,11 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str: # intfmt=",", ) ) - edge_counter = Counter(edge.pred for edge in graph.edges) + edge_counter = Counter( + edge.predicate.curie + for edge in graph.edges + if edge.predicate is not None + ) tqdm.write( "\n" + tabulate( @@ -779,7 +783,7 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str: unstandardized_nodes.extend(node.id for node in graph.nodes if not node.reference) unstandardized_edges.extend( - edge.pred for edge in graph.edges if edge.pred.startswith("http") + edge.pred for edge in graph.edges if edge.predicate is None ) clean_edges = ( @@ -794,10 +798,10 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str: ) edges.extend( ( - edge.sub, - edge.obj, - _get_edge_name(edge.pred).lower().replace(" ", "_").replace("-", "_"), - edge.pred, + edge.subject.curie, + edge.object.curie, + _get_edge_name(edge.predicate.curie).lower().replace(" ", "_").replace("-", "_"), + edge.predicate.curie, prefix, graph_id, version or "",