def test_aquery_ensembl_multi(df_query_ensembl_hsapiens_gene_chrom_1,
df_query_ensembl_hsapiens_gene_chrom_2,
df_query_ensembl_hsapiens_gene_chrom_3):
"""Test the async query results for multiple queries run in a loop for
the hsapiens_gene_ensembl dataset."""
expect1 = (df_query_ensembl_hsapiens_gene_chrom_1.reset_index(drop=True))
expect2 = (df_query_ensembl_hsapiens_gene_chrom_2.reset_index(drop=True))
expect3 = (df_query_ensembl_hsapiens_gene_chrom_3.reset_index(drop=True))
loop = asyncio.get_event_loop()
tasks = [
aquery(attributes=["ensembl_gene_id", "external_gene_name"],
filters={"chromosome_name": "1"},
dataset="hsapiens_gene_ensembl"),
aquery(attributes=["ensembl_gene_id", "external_gene_name"],
filters={"chromosome_name": "2"},
dataset="hsapiens_gene_ensembl"),
aquery(attributes=["ensembl_gene_id", "external_gene_name"],
filters={"chromosome_name": "3"},
dataset="hsapiens_gene_ensembl")
]
result1, result2, result3 = loop.run_until_complete(asyncio.gather(*tasks))
assert_frame_equal(result1, expect1)
assert_frame_equal(result2, expect2)
assert_frame_equal(result3, expect3)
def test_aquery_ensembl(df_query_ensembl_hsapiens_gene_chrom_2):
"""Test the async query results for the hsapiens_gene_ensembl dataset."""
expect = (df_query_ensembl_hsapiens_gene_chrom_2.reset_index(drop=True))
loop = asyncio.get_event_loop()
result = loop.run_until_complete(
aquery(attributes=["ensembl_gene_id", "external_gene_name"],
filters={"chromosome_name": "2"},
dataset="hsapiens_gene_ensembl")).reset_index(drop=True)
assert_frame_equal(result, expect)
def test_aquery_save(df_query_ensembl_hsapiens_gene_chrom_2):
"""Test the saved async query results for the default dataset
(hsapiens_gene_ensembl)."""
expect = (df_query_ensembl_hsapiens_gene_chrom_2.reset_index(drop=True))
loop = asyncio.get_event_loop()
result = loop.run_until_complete( # noqa
aquery(attributes=["ensembl_gene_id", "external_gene_name"],
filters={"chromosome_name": "2"},
save=True))
saved = (pd.read_csv("apybiomart_aquery.csv").replace(
pd.np.nan, "").reset_index(drop=True))
try:
assert_frame_equal(saved, expect)
finally:
os.remove("apybiomart_aquery.csv")