def test_gene_list_count(self):
expected_sql = COUNT_QUERY
expected_params = ["hg38", "E2F4", "150", "250", "250", "150", 77]
query = GeneListQuery(schema="hg38",
custom_list_id=77,
custom_list_filter='',
custom_gene_name_type=CUSTOM_GENE_NAME_TYPE,
model_name="E2F4",
upstream="150",
downstream="250",
count=True)
sql, params = query.get_query_and_params()
self.maxDiff = None
self.assertMultiLineEqual(expected_sql, sql)
self.assertEqual(expected_params, params)
def test_gene_list_filter(self):
expected_sql = GENE_LIST_FILTER
expected_params = ["hg38", "E2F4", "150", "250", "250", "150", 45]
query = GeneListQuery(
schema="hg38",
custom_list_id=45,
custom_list_filter='',
custom_gene_name_type=CUSTOM_GENE_NAME_TYPE,
model_name="E2F4",
upstream="150",
downstream="250",
)
sql, params = query.get_query_and_params()
self.maxDiff = None
self.assertMultiLineEqual(expected_sql, sql)
self.assertEqual(expected_params, params)
def test_gene_list_filter(self):
expected_sql = GENE_LIST_FILTER
expected_params = ["hg38", "E2F4", "250", "150", "150", "250", 45]
query = GeneListQuery(
schema="hg38",
custom_list_id=45,
custom_list_filter='',
custom_gene_name_type=CUSTOM_GENE_NAME_TYPE,
model_name="E2F4",
upstream="150",
downstream="250",
)
sql, params = query.get_query_and_params()
self.maxDiff = None
self.assertMultiLineEqual(expected_sql, sql)
self.assertEqual(expected_params, params)
def test_gene_list_count(self):
expected_sql = COUNT_QUERY
expected_params = ["hg38", "E2F4", "250", "150", "150", "250", 77]
query = GeneListQuery(
schema="hg38",
custom_list_id=77,
custom_list_filter='',
custom_gene_name_type=CUSTOM_GENE_NAME_TYPE,
model_name="E2F4",
upstream="150",
downstream="250",
count=True
)
sql, params = query.get_query_and_params()
self.maxDiff = None
self.assertMultiLineEqual(expected_sql, sql)
self.assertEqual(expected_params, params)
def test_gene_list_filter_with_limit(self):
expected_sql = GENE_LIST_FILTER_WITH_LIMIT
expected_params = ["hg38", "knowngene", "E2F4", "250", "150", "150", "250", 55, "100", "200"]
query = GeneListQuery(
schema="hg38",
custom_list_id=55,
custom_list_filter='knowngene',
custom_gene_name_type=CUSTOM_GENE_NAME_TYPE,
model_name="E2F4",
upstream="150",
downstream="250",
limit="100",
offset="200",
)
sql, params = query.get_query_and_params()
self.maxDiff = None
self.assertMultiLineEqual(expected_sql, sql)
self.assertEqual(expected_params, params)
def test_gene_list_filter_with_limit(self):
expected_sql = GENE_LIST_FILTER_WITH_LIMIT
expected_params = [
"hg38", "knowngene", "E2F4", "150", "250", "250", "150", 55, "100",
"200"
]
query = GeneListQuery(
schema="hg38",
custom_list_id=55,
custom_list_filter='knowngene',
custom_gene_name_type=CUSTOM_GENE_NAME_TYPE,
model_name="E2F4",
upstream="150",
downstream="250",
limit="100",
offset="200",
)
sql, params = query.get_query_and_params()
self.maxDiff = None
self.assertMultiLineEqual(expected_sql, sql)
self.assertEqual(expected_params, params)
def gene_list_query(self, count):
custom_list_key, custom_list_filter = self.get_custom_list_fields()
limit, offset = self.get_limit_and_offset(count)
return GeneListQuery(
schema=self.genome,
custom_list_id=custom_list_key,
custom_list_filter=custom_list_filter,
custom_gene_name_type=self.args.is_custom_gene_name_search_type(),
model_name=self.args.get_model_name(),
upstream=self.args.get_upstream(),
downstream=self.args.get_downstream(),
limit=limit,
offset=offset,
count=count,
sort_by_max=self.args.get_sort_by_max(),
)
