From 116dfc00cab0a6830a1e846b21eeacfd9bb95896 Mon Sep 17 00:00:00 2001 From: Ismail Ugur Bayindir Date: Thu, 15 Aug 2024 14:31:50 +0100 Subject: [PATCH] Dataset IRIs are based on CxG dataset UUID (#82) * Refactor dataset_class URI logic * Add get_cxg_dataset_url method * Update assert statements * Update version to 0.2.23 --- .../graph_generator/graph_generator.py | 11 +- .../graph_generator/graph_generator_utils.py | 16 + poetry.lock | 1191 +++++++++-------- pyproject.toml | 2 +- test/graph_generator/test_graph_generator.py | 4 +- 5 files changed, 639 insertions(+), 585 deletions(-) diff --git a/pandasaurus_cxg/graph_generator/graph_generator.py b/pandasaurus_cxg/graph_generator/graph_generator.py index 34adbba..8ac11b1 100644 --- a/pandasaurus_cxg/graph_generator/graph_generator.py +++ b/pandasaurus_cxg/graph_generator/graph_generator.py @@ -22,6 +22,7 @@ colour_mapping, find_and_rotate_center_layout, generate_subgraph, + get_cxg_dataset_url, parse_citation_field_into_dict, remove_special_characters, select_node_with_property, @@ -124,15 +125,19 @@ def generate_rdf_graph(self): grouped_dict_uuid[str(uuid.uuid4())] = temp_dict # generate dataset entity and has_source property - dataset_class = URIRef(self.ns[str(uuid.uuid4())]) + uns = self.ea.enricher_manager.anndata.uns + citation_dict = {} + if citation_field_name in uns.keys(): + citation_dict = parse_citation_field_into_dict(uns[citation_field_name]) + dataset_class = URIRef(get_cxg_dataset_url(citation_dict.get("download_link").split("/")[-1].split(".")[0])) + else: + dataset_class = URIRef(self.ns[str(uuid.uuid4())]) self.graph.add((dataset_class, RDF.type, URIRef(DATASET.get("iri")))) self.graph.add((dataset_class, RDFS.label, Literal(DATASET.get("label")))) - uns = self.ea.enricher_manager.anndata.uns for key, value in uns.items(): if not isinstance(value, str): continue if key == citation_field_name: - citation_dict = parse_citation_field_into_dict(value) for citation_key, citation_value in citation_dict.items(): self.graph.add( ( diff --git a/pandasaurus_cxg/graph_generator/graph_generator_utils.py b/pandasaurus_cxg/graph_generator/graph_generator_utils.py index 511a1ad..1a2546d 100644 --- a/pandasaurus_cxg/graph_generator/graph_generator_utils.py +++ b/pandasaurus_cxg/graph_generator/graph_generator_utils.py @@ -158,3 +158,19 @@ def parse_citation_field_into_dict(value: str) -> Dict[str, str]: } ) return key_value_pairs + + +def get_cxg_dataset_url(matrix_id: str) -> str: + """ + Constructs a URL for a CellxGene dataset. + + Given a matrix ID, this function returns the corresponding URL for accessing + the dataset on the CellxGene platform. + + Args: + matrix_id: The unique identifier for the dataset matrix. + + Returns: + The full URL to access the dataset on CellxGene. + """ + return f"https://cellxgene.cziscience.com/e/{matrix_id}.cxg/" diff --git a/poetry.lock b/poetry.lock index 1b38946..90bf0a3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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len(graph_generator.graph) == 1143 + assert len(graph_generator.graph) == 1145 assert ( URIRef(CONSIST_OF.get("iri")), RDFS.label, @@ -173,7 +173,7 @@ def test_enrich_rdf_graph(graph_generator_instance_for_kidney): if str(s).startswith("http://purl.obolibrary.org/obo/CL_") ] ) - == 527 + == 529 )