From 9c92c4f3fb404713ecf54da8c65e856e5decfc7c Mon Sep 17 00:00:00 2001 From: ubyndr Date: Fri, 12 Jul 2024 14:39:52 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20INCATool?= =?UTF-8?q?s/pandasaurus=5Fcxg@144e986844b606db2ed562920500f6bb8a6c06c9=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../graph_generator/graph_generator.html | 28 +++++++++++-------- 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/_modules/pandasaurus_cxg/graph_generator/graph_generator.html b/_modules/pandasaurus_cxg/graph_generator/graph_generator.html index c575f89..a1fbdb6 100644 --- a/_modules/pandasaurus_cxg/graph_generator/graph_generator.html +++ b/_modules/pandasaurus_cxg/graph_generator/graph_generator.html @@ -320,6 +320,14 @@

Source code for pandasaurus_cxg.graph_generator.graph_generator

percentage_annotation_property = self.ns["percentage"] self.graph.add((percentage_annotation_property, RDF.type, OWL.AnnotationProperty)) for metadata in metadata_fields: + # Extract the ontology term ID mapping + ontology_term_id_mapping = ( + obs[[metadata, f"{metadata}_ontology_term_id"]] + .drop_duplicates() + .set_index(metadata) + .to_dict()[f"{metadata}_ontology_term_id"] + ) + for s, _, _ in self.graph.triples((None, RDF.type, URIRef(CLUSTER.get("iri")))): for a_cell_type in author_cell_types: literal = self.graph.value(subject=s, predicate=self.ns[a_cell_type]) @@ -330,19 +338,15 @@

Source code for pandasaurus_cxg.graph_generator.graph_generator

* 100 ).loc[lambda x: x != 0.0] - # Extract the ontology term ID mapping - ontology_term_id_mapping = ( - obs[[metadata, f"{metadata}_ontology_term_id"]] - .drop_duplicates() - .set_index(metadata) - .to_dict()[f"{metadata}_ontology_term_id"] - ) - for label, percentage in percentages.items(): - ontology_term_id = ontology_term_id_mapping.get(label).split(":") - annotated_target = Namespace(prefixes.get(ontology_term_id[0]))[ - ontology_term_id[-1] - ] + ontology_term_id = ontology_term_id_mapping.get(label) + if isinstance(ontology_term_id, str) and ":" in ontology_term_id: + ontology_term_id = ontology_term_id_mapping.get(label).split(":") + annotated_target = Namespace(prefixes.get(ontology_term_id[0]))[ + ontology_term_id[-1] + ] + else: + annotated_target = URIRef(self.ns[str(uuid.uuid4())]) self.graph.add((annotated_target, RDFS.label, Literal(label))) bnode_axiom = BNode() self.graph.add((bnode_axiom, RDF.type, OWL.Axiom))