From 144e986844b606db2ed562920500f6bb8a6c06c9 Mon Sep 17 00:00:00 2001 From: Ismail Ugur Bayindir Date: Fri, 12 Jul 2024 15:38:50 +0100 Subject: [PATCH] Metadata percentage nodes patch for NaN values (#78) * Updated anndata version to 0.10.5 * Updated version to 0.1.21 * Add skip mechanism to add_metadata_nodes for NaN values * Use UUID URIRef for terms without a valid ontology ID --- .../graph_generator/graph_generator.py | 28 +- poetry.lock | 727 +++++++++--------- pyproject.toml | 4 +- 3 files changed, 397 insertions(+), 362 deletions(-) diff --git a/pandasaurus_cxg/graph_generator/graph_generator.py b/pandasaurus_cxg/graph_generator/graph_generator.py index 6c65edc..34adbba 100644 --- a/pandasaurus_cxg/graph_generator/graph_generator.py +++ b/pandasaurus_cxg/graph_generator/graph_generator.py @@ -237,6 +237,14 @@ def add_metadata_nodes(self, metadata_fields: List[str]): 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]) @@ -247,19 +255,15 @@ def add_metadata_nodes(self, metadata_fields: List[str]): * 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)) diff --git a/poetry.lock b/poetry.lock index 36b1baa..1b38946 100644 --- a/poetry.lock +++ b/poetry.lock @@ -28,27 +28,30 @@ files = [ [[package]] name = "anndata" -version = "0.9.2" +version = "0.10.8" description = "Annotated data." optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "anndata-0.9.2-py3-none-any.whl", hash = "sha256:badab44bf0b4d598ae49403ee634a6ffc8896d9aa21db52f0f6af98d6fe1fceb"}, - {file = "anndata-0.9.2.tar.gz", hash = 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