"""Integration tests for gemma API endpoints""" import os import unittest from dataclasses import dataclass from typing import Callable from unittest import mock from gn3.app import create_app @dataclass class MockRedis: """Mock the Redis Module""" redis: Callable hget: Callable class GemmaAPITest(unittest.TestCase): """Test cases for the Gemma API""" def setUp(self): self.app = create_app({ "GENODIR": os.path.abspath( os.path.join(os.path.dirname(__file__), "test_data/")), "REDIS_JOB_QUEUE": "GN3::job-queue", "GEMMA_WRAPPER_CMD": "gemma-wrapper"}).test_client() @mock.patch("gn3.api.gemma.run_cmd") def test_get_version(self, mock_run_cmd): """Test that the correct response is returned""" mock_run_cmd.return_value = {"status": 0, "output": "v1.9"} response = self.app.get("/api/gemma/version", follow_redirects=True) self.assertEqual(response.get_json(), {"status": 0, "output": "v1.9"}) self.assertEqual(response.status_code, 200) @mock.patch("gn3.api.gemma.redis.Redis") @mock.patch("gn3.api.gemma.queue_cmd") @mock.patch("gn3.api.gemma.generate_gemma_computation_cmd") def test_run_gemma_no_loco(self, mock_gemma_computation_cmd, mock_queue_cmd, mock_redis): """Test that gemma composes the command correctly without loco""" _redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock.MagicMock()) mock_redis.return_value = _redis_conn mock_gemma_computation_cmd.side_effect = [ ("gemma-wrapper --json -- " "-g genofile.txt -p " "test.txt -a genofile_snps.txt " "-gk > /tmp/gn2/" "bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"), ("gemma-wrapper --json --input /tmp/gn2/" "bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt -- " "-a genofile_snps.txt -lmm 9 " "-g genofile.txt -p " "test.txt -a genofile_snps.txt " "-gk > /tmp/gn2/" "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt") ] mock_queue_cmd.return_value = "my-unique-id" response = self.app.post("/api/gemma/k-gwa-computation", json={ "trait_filename": "BXD.txt", "geno_filename": "BXD_geno", "values": ["X", "N/A", "X"], "dataset_groupname": "BXD", "trait_name": "Height", "email": "me@me.com", "dataset_name": "BXD" }) mock_queue_cmd.assert_has_calls( [mock.call(conn=_redis_conn, email="me@me.com", job_queue="GN3::job-queue", cmd=("gemma-wrapper --json -- -g " "genofile.txt -p test.txt " "-a genofile_snps.txt -gk > " "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt " "&& gemma-wrapper --json --input " "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt" " -- -a genofile_snps.txt -lmm 9 -g " "genofile.txt -p test.txt " "-a genofile_snps.txt " "-gk > " "/tmp/gn2/" "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))] ) # mock_pheno_txt_file.return_value = "/tmp/gn2/BXD_6OBEPW." self.assertEqual( response.get_json(), {"unique_id": 'my-unique-id', "status": "queued", "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"}) @mock.patch("gn3.api.gemma.redis.Redis") @mock.patch("gn3.api.gemma.queue_cmd") def test_run_gemma_with_loco(self, mock_queue_cmd, mock_redis): """Test that gemma composes the command correctly with loco""" _redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock.MagicMock()) mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" response = self.app.post("/api/gemma/k-gwa-computation", json={ "trait_filename": os.path.abspath(os.path.join( os.path.dirname(__file__), "test_data/" )), "geno_filename": "BXD_geno.txt.gz", "values": ["X", "N/A", "X"], "dataset_groupname": "BXD", "trait_name": "Height", "email": "me@me.com", "dataset_name": "BXD", "loco": "1,2,3,4,5,6" }) mock_queue_cmd.called_with( conn=_redis_conn, email="me@me.com", job_queue="GN3::job-queue", cmd=("gemma-wrapper --json -- -g " "genofile.txt -p test.txt " "-a genofile_snps.txt -gk > " "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt " "&& gemma-wrapper --json --input " "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt" " -- -a genofile_snps.txt -lmm 9 -g " "genofile.txt -p test.txt " "-a genofile_snps.txt " "-gk > " "/tmp/gn2/" "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt")) self.assertEqual( response.get_json(), {"unique_id": 'my-unique-id', "status": "queued", "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"}) @mock.patch("gn3.api.gemma.redis.Redis") def test_check_cmd_status(self, mock_redis): """Test that you can check the status of a given command""" mock_hget = mock.MagicMock() mock_hget.return_value = b"test" _redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock_hget) mock_redis.return_value = _redis_conn response = self.app.get(("/api/gemma/status/" "cmd%3A%3A2021-02-1217-3224-3224-1234"), follow_redirects=True) mock_hget.assert_called_once_with( name="cmd::2021-02-1217-3224-3224-1234", key="status") self.assertEqual(response.get_json(), {"status": "test"}) @mock.patch("gn3.api.gemma.queue_cmd") @mock.patch("gn3.api.gemma.generate_gemma_computation_cmd") @mock.patch("gn3.api.gemma.get_hash_of_files") @mock.patch("gn3.api.gemma.jsonfile_to_dict") def test_k_compute(self, mock_json, mock_hash, mock_cmd, mock_queue_cmd): """Test /gemma/k-compute/""" mock_queue_cmd.return_value = "my-unique-id" mock_json.return_value = { "geno": "genofile.txt", "pheno": "phenofile.txt", "snps": "snpfile.txt", } mock_hash.return_value = "hash" mock_cmd.return_value = ("gemma-wrapper --json -- " "-debug -g " "genotype_name.txt " "-p traitfilename.txt " "-a genotype_snps.txt " "-gk > k_output_filename.json") response = self.app.post("/api/gemma/k-compute/test-data") self.assertEqual(response.get_json(), { "output_file": "hash-k-output.json", "status": "queued", "unique_id": "my-unique-id" }) @mock.patch("gn3.api.gemma.queue_cmd") @mock.patch("gn3.api.gemma.generate_gemma_computation_cmd") @mock.patch("gn3.api.gemma.get_hash_of_files") @mock.patch("gn3.api.gemma.jsonfile_to_dict") def test_k_compute_loco(self, mock_json, mock_hash, mock_cmd, mock_queue_cmd): """Test /gemma/k-compute/""" mock_queue_cmd.return_value = "my-unique-id" mock_json.return_value = { "geno": "genofile.txt", "pheno": "phenofile.txt", "snps": "snpfile.txt", } mock_hash.return_value = "hash" mock_cmd.return_value = ("gemma-wrapper --json -- " "-debug -g " "genotype_name.txt " "-p traitfilename.txt " "-a genotype_snps.txt " "-gk > k_output_filename.json") response = self.app.post(("/api/gemma/k-compute/loco/" "1%2C2%2C3%2C4%2C5%2C6/test-data")) self.assertEqual(response.get_json(), { "output_file": "hash-k-output.json", "status": "queued", "unique_id": "my-unique-id" })