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