diff --git a/pandasaurus_cxg/graph_generator/graph_generator.py b/pandasaurus_cxg/graph_generator/graph_generator.py index 4aa6599..71888c9 100644 --- a/pandasaurus_cxg/graph_generator/graph_generator.py +++ b/pandasaurus_cxg/graph_generator/graph_generator.py @@ -6,6 +6,7 @@ import matplotlib.pyplot as plt import networkx as nx import pandas as pd +from pandasaurus.graph.graph_generator import GraphGenerator as graphgen from rdflib import OWL, RDF, RDFS, BNode, Graph, Literal, Namespace, URIRef from rdflib.plugins.sparql import prepareQuery @@ -162,6 +163,9 @@ def generate_rdf_graph(self): for s, _, _ in self.graph.triples((None, predicate, Literal(iv))): self.graph.add((resource, subcluster, s)) + # transitive reduction step + self.graph = graphgen.apply_transitive_reduction(self.graph, [subcluster.toPython()]) + def enrich_rdf_graph(self): """ Enrich RDF graph with enriched DataFrame from AnndataEnricher diff --git a/poetry.lock b/poetry.lock index 142e4f8..d3bab94 100644 --- 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"0.1.8" description = "Ontology enrichment tool for CxG standard AnnData files." authors = ["Ugur Bayindir "] license = "http://www.apache.org/licenses/LICENSE-2.0" diff --git a/test/graph_generator/test_graph_generator.py b/test/graph_generator/test_graph_generator.py index ac4f312..cf572fc 100644 --- a/test/graph_generator/test_graph_generator.py +++ b/test/graph_generator/test_graph_generator.py @@ -54,7 +54,9 @@ def graph_generator_instance_for_kidney(enrichment_analyzer_instance_for_kidney_ return GraphGenerator(ea) -def test_graph_generator_init_missing_enrichment_process(enrichment_analyzer_instance_for_immune_data): +def test_graph_generator_init_missing_enrichment_process( + enrichment_analyzer_instance_for_immune_data, +): ea = enrichment_analyzer_instance_for_immune_data ea.co_annotation_report() @@ -72,7 +74,9 @@ def test_graph_generator_init_missing_enrichment_process(enrichment_analyzer_ins assert exception.args[0] == expected_message -def test_graph_generator_init_missing_analysis_process(enrichment_analyzer_instance_for_immune_data): +def test_graph_generator_init_missing_analysis_process( + enrichment_analyzer_instance_for_immune_data, +): ea = enrichment_analyzer_instance_for_immune_data ea.enricher_manager.simple_enrichment() @@ -119,7 +123,7 @@ def test_graph_generator_init_with_valid_input(enrichment_analyzer_instance_for_ def test_generate_rdf_graph(graph_generator_instance_for_kidney): graph_generator = graph_generator_instance_for_kidney graph_generator.generate_rdf_graph() - assert len(graph_generator.graph) == 441 + assert len(graph_generator.graph) == 433 assert ( len([[s, p, o] for s, p, o in graph_generator.graph.triples((None, RDF.type, None))]) == 95 ) @@ -135,7 +139,7 @@ def test_generate_rdf_graph(graph_generator_instance_for_kidney): ) ] ) - == 85 + == 77 ) assert ( len( @@ -161,11 +165,11 @@ def test_enrich_rdf_graph(graph_generator_instance_for_kidney): graph_generator = graph_generator_instance_for_kidney graph_generator.generate_rdf_graph() - assert len(graph_generator.graph) == 441 + assert len(graph_generator.graph) == 433 graph_generator.enrich_rdf_graph() - assert len(graph_generator.graph) == 1024 + assert len(graph_generator.graph) == 903 assert ( URIRef(CONSIST_OF.get("iri")), RDFS.label, @@ -182,7 +186,7 @@ def test_enrich_rdf_graph(graph_generator_instance_for_kidney): if str(s).startswith("http://purl.obolibrary.org/obo/CL_") ] ) - == 530 + == 417 ) diff --git a/test/test_anndata_enricher.py b/test/test_anndata_enricher.py index bfb2f20..a88e833 100644 --- a/test/test_anndata_enricher.py +++ b/test/test_anndata_enricher.py @@ -39,7 +39,15 @@ def slim_data(): ] -def test_init_defaults(sample_immune_data, slim_data): +def test_init_defaults(mocker, sample_immune_data, slim_data): + iterable_slim_data = slim_data + mocker.patch.object( + SlimManager, + "get_slim_list", + side_effect=[ + iter(iterable_slim_data), + ], + ) # Test initialization with default values enricher = AnndataEnricher(sample_immune_data)