def test_gene_list_too_big(self):
with self.assertRaises(ClientException) as cm:
save_custom_file(db=FakeDB(),
user_info=None,
type=GENE_LIST_TYPE,
content=make_too_big())
self.assertEqual(ErrorType.UPLOADED_DATA_TOO_BIG,
cm.exception.error_type)
self.assertEqual(400, cm.exception.status_code)
def test_custom_range_list_range_sum_too_big(self):
db = create_db_connection(TestWithPostgres.config.dbconfig)
try:
custom_list_key = save_custom_file(db, 'john', RANGE_TYPE, "1 1000 30001001")
self.fail("Should have raised ValueError exception.")
except ValueError as err:
self.assertEqual(str(err), MAX_RANGE_ERROR_STR)
def test_custom_range_list_range_sum_too_big(self):
db = create_db_connection(TestWithPostgres.config.dbconfig)
try:
custom_list_key = save_custom_file(db, 'john', RANGE_TYPE, "1 1000 30001001")
self.fail("Should have raised ValueError exception.")
except ValueError as err:
self.assertEqual(str(err), MAX_RANGE_ERROR_STR)
def create_custom_file():
user_info = "Addr:{} Browser:{} Platform:{} Agent:{}".format(
request.remote_addr, request.user_agent.browser,
request.user_agent.platform, request.user_agent.string)
json_data = request.get_json()
key = save_custom_file(get_db(), user_info, json_data.get('type'),
json_data.get('content'))
return make_json_response({'key': key})
def create_custom_file():
user_info = "Addr:{} Browser:{} Platform:{} Agent:{}".format(
request.remote_addr,
request.user_agent.browser,
request.user_agent.platform,
request.user_agent.string)
json_data = request.get_json()
key = save_custom_file(get_db(), user_info, json_data.get('type'), json_data.get('content'))
return make_json_response({'key': key})
def test_custom_range_list(self):
db = create_db_connection(TestWithPostgres.config.dbconfig)
custom_list_key = save_custom_file(db, 'john', RANGE_TYPE, "chr1 11873 11895")
params = {
SearchArgs.GENE_LIST: CUSTOM_RANGES_LIST,
SearchArgs.CUSTOM_LIST_DATA: custom_list_key,
SearchArgs.MODEL: "E2F1_0001(JS)",
SearchArgs.UPSTREAM: "100",
SearchArgs.DOWNSTREAM: "100",
SearchArgs.PAGE: "1",
SearchArgs.PER_PAGE: "10",
}
predictions, search_args, search_warning = get_predictions_with_guess(db, TestWithPostgres.config, "hg19", params)
self.assertEqual(len(predictions), 1)
self.assertEqual(0.4, float(predictions[0]['max']))
def test_custom_gene_list_with_lc_results(self):
db = create_db_connection(TestWithPostgres.config.dbconfig)
custom_list_key = save_custom_file(db, 'john', GENE_LIST_TYPE, "ddx11l1")
params = {
SearchArgs.GENE_LIST: CUSTOM_GENE_LIST,
SearchArgs.CUSTOM_LIST_DATA: custom_list_key,
SearchArgs.CUSTOM_GENE_SEARCH_TYPE: CUSTOM_GENE_NAME_TYPE,
SearchArgs.MODEL: "E2F1_0001(JS)",
SearchArgs.UPSTREAM: "100",
SearchArgs.DOWNSTREAM: "100",
SearchArgs.PAGE: "1",
SearchArgs.PER_PAGE: "10",
}
predictions, search_args, search_warning = get_predictions_with_guess(db, TestWithPostgres.config, "hg19", params)
self.assertEqual(len(predictions), 1)
def test_custom_range_list(self):
db = create_db_connection(TestWithPostgres.config.dbconfig)
custom_list_key = save_custom_file(db, 'john', RANGE_TYPE, "chr1 11873 11895")
params = {
SearchArgs.GENE_LIST: CUSTOM_RANGES_LIST,
SearchArgs.CUSTOM_LIST_DATA: custom_list_key,
SearchArgs.MODEL: "E2F1_0001(JS)",
SearchArgs.UPSTREAM: "100",
SearchArgs.DOWNSTREAM: "100",
SearchArgs.PAGE: "1",
SearchArgs.PER_PAGE: "10",
}
predictions, search_args, search_warning = get_predictions_with_guess(db, TestWithPostgres.config, "hg19", params)
self.assertEqual(len(predictions), 1)
self.assertEqual(0.4, float(predictions[0]['max']))
def test_custom_gene_list_with_lc_results(self):
db = create_db_connection(TestWithPostgres.config.dbconfig)
custom_list_key = save_custom_file(db, 'john', GENE_LIST_TYPE, "ddx11l1")
params = {
SearchArgs.GENE_LIST: CUSTOM_GENE_LIST,
SearchArgs.CUSTOM_LIST_DATA: custom_list_key,
SearchArgs.CUSTOM_GENE_SEARCH_TYPE: CUSTOM_GENE_NAME_TYPE,
SearchArgs.MODEL: "E2F1_0001(JS)",
SearchArgs.UPSTREAM: "100",
SearchArgs.DOWNSTREAM: "100",
SearchArgs.PAGE: "1",
SearchArgs.PER_PAGE: "10",
}
predictions, search_args, search_warning = get_predictions_with_guess(db, TestWithPostgres.config, "hg19", params)
self.assertEqual(len(predictions), 1)
def test_custom_range_list_bad_range(self):
db = create_db_connection(TestWithPostgres.config.dbconfig)
custom_list_key = save_custom_file(db, 'john', RANGE_TYPE, "chr1 91873 91883")
params = {
SearchArgs.GENE_LIST: CUSTOM_RANGES_LIST,
SearchArgs.CUSTOM_LIST_DATA: custom_list_key,
SearchArgs.MODEL: "E2F1_0001(JS)",
SearchArgs.UPSTREAM: "100",
SearchArgs.DOWNSTREAM: "100",
SearchArgs.PAGE: "1",
SearchArgs.PER_PAGE: "10",
}
predictions, search_args, search_warning = get_predictions_with_guess(db, TestWithPostgres.config, "hg19", params)
self.assertEqual(len(predictions), 1)
# we always return a record for range requests just with empty data for the matches
self.assertEqual('None', predictions[0]['max'])
def test_custom_range_list_bad_range(self):
db = create_db_connection(TestWithPostgres.config.dbconfig)
custom_list_key = save_custom_file(db, 'john', RANGE_TYPE, "chr1 91873 91883")
params = {
SearchArgs.GENE_LIST: CUSTOM_RANGES_LIST,
SearchArgs.CUSTOM_LIST_DATA: custom_list_key,
SearchArgs.MODEL: "E2F1_0001(JS)",
SearchArgs.UPSTREAM: "100",
SearchArgs.DOWNSTREAM: "100",
SearchArgs.PAGE: "1",
SearchArgs.PER_PAGE: "10",
}
predictions, search_args, search_warning = get_predictions_with_guess(db, TestWithPostgres.config, "hg19", params)
self.assertEqual(len(predictions), 1)
# we always return a record for range requests just with empty data for the matches
self.assertEqual('None', predictions[0]['max'])
def test_custom_gene_list_id_results(self):
"""
These two splice variants belong to the same gene so they should list together in a single prediction.
"""
db = create_db_connection(TestWithPostgres.config.dbconfig)
custom_list_key = save_custom_file(db, 'john', GENE_LIST_TYPE, "uc001aaa.3\nuc010nxr.1")
params = {
SearchArgs.GENE_LIST: CUSTOM_GENE_LIST,
SearchArgs.CUSTOM_LIST_DATA: custom_list_key,
SearchArgs.CUSTOM_GENE_SEARCH_TYPE: CUSTOM_ID_TYPE,
SearchArgs.MODEL: "E2F1_0001(JS)",
SearchArgs.UPSTREAM: "100",
SearchArgs.DOWNSTREAM: "100",
SearchArgs.PAGE: "1",
SearchArgs.PER_PAGE: "10",
}
predictions, search_args, search_warning = get_predictions_with_guess(db, TestWithPostgres.config, "hg19", params)
self.assertEqual(len(predictions), 1)
first_pred_name = predictions[0]['name']
first_pred_name_parts = first_pred_name.split("; ")
self.assertEqual(len(first_pred_name_parts), 2)
self.assertIn("uc001aaa.3", first_pred_name_parts)
self.assertIn("uc010nxr.1", first_pred_name_parts)
def test_custom_gene_list_id_results(self):
"""
These two splice variants belong to the same gene so they should list together in a single prediction.
"""
db = create_db_connection(TestWithPostgres.config.dbconfig)
custom_list_key = save_custom_file(db, 'john', GENE_LIST_TYPE, "uc001aaa.3\nuc010nxr.1")
params = {
SearchArgs.GENE_LIST: CUSTOM_GENE_LIST,
SearchArgs.CUSTOM_LIST_DATA: custom_list_key,
SearchArgs.CUSTOM_GENE_SEARCH_TYPE: CUSTOM_ID_TYPE,
SearchArgs.MODEL: "E2F1_0001(JS)",
SearchArgs.UPSTREAM: "100",
SearchArgs.DOWNSTREAM: "100",
SearchArgs.PAGE: "1",
SearchArgs.PER_PAGE: "10",
}
predictions, search_args, search_warning = get_predictions_with_guess(db, TestWithPostgres.config, "hg19", params)
self.assertEqual(len(predictions), 1)
first_pred_name = predictions[0]['name']
first_pred_name_parts = first_pred_name.split("; ")
self.assertEqual(len(first_pred_name_parts), 2)
self.assertIn("uc001aaa.3", first_pred_name_parts)
self.assertIn("uc010nxr.1", first_pred_name_parts)
def test_custom_range_list_range_as_big_as_possible(self):
db = create_db_connection(TestWithPostgres.config.dbconfig)
custom_list_key = save_custom_file(db, 'john', RANGE_TYPE, "1 1000 30001000")
def test_gene_list_good_size(self):
save_custom_file(db=FakeDB(),
user_info=None,
type=GENE_LIST_TYPE,
content="WASH7P\nELK1\nNETS2")
def test_custom_range_list_range_as_big_as_possible(self):
db = create_db_connection(TestWithPostgres.config.dbconfig)
custom_list_key = save_custom_file(db, 'john', RANGE_TYPE, "1 1000 30001000")
def test_range_list_good_size(self):
save_custom_file(db=FakeDB(),
user_info=None,
type=RANGE_TYPE,
content="chr1 100 200\nchr2 200 300")