def test_load_hpo( gene_database, hpo_terms_handle, hpo_to_genes_handle, genemap_file, hpo_disease_handle, ): adapter = gene_database # GIVEN a populated database with genes but no hpo terms assert len([term for term in adapter.hpo_terms()]) == 0 genemap_handle = get_file_handle(genemap_file) # WHEN loading the disease and hpo terms load_hpo( adapter=gene_database, hpo_lines=hpo_terms_handle, hpo_gene_lines=hpo_to_genes_handle, disease_lines=genemap_handle, hpo_disease_lines=hpo_disease_handle, ) # THEN make sure that the disease terms are in the database hpo_terms_objs = adapter.hpo_terms() disease_objs = adapter.disease_terms() assert len([term for term in hpo_terms_objs]) > 0 assert len([disease for disease in disease_objs]) > 0
def real_hpo_database(request, real_gene_database, hpo_terms_handle, genemap_handle): "Returns an adapter to a database populated with hpo terms" adapter = real_gene_database load_hpo(adapter=gene_database, hpo_lines=hpo_terms_handle, disease_lines=genemap_handle, hpo_disease_lines=hpo_disease_handle) return adapter
def hpo_database(request, gene_database, hpo_terms_handle, hpo_to_genes_handle, hpo_disease_handle): "Returns an adapter to a database populated with hpo terms" adapter = gene_database load_hpo( adapter=gene_database, hpo_lines=get_file_handle(hpoterms_reduced_path), hpo_gene_lines=get_file_handle(hpo_to_genes_reduced_path), disease_lines=get_file_handle(genemap2_reduced_path), hpo_disease_lines=get_file_handle(hpo_phenotype_to_terms_reduced_path), ) return adapter
def test_load_hpo(gene_database, hpo_terms_handle, hpo_to_genes_handle, genemap_file, hpo_disease_handle): adapter = gene_database # GIVEN a populated database with genes but no hpo terms assert len([term for term in adapter.hpo_terms()]) == 0 genemap_handle = get_file_handle(genemap_file) # WHEN loading the disease and hpo terms load_hpo( adapter=gene_database, hpo_lines=hpo_terms_handle, hpo_gene_lines=hpo_to_genes_handle, disease_lines=genemap_handle, hpo_disease_lines=hpo_disease_handle, ) # THEN make sure that the disease terms are in the database hpo_terms_objs = adapter.hpo_terms() disease_objs = adapter.disease_terms() assert len([term for term in hpo_terms_objs]) > 0 assert len([disease for disease in disease_objs]) > 0