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"""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/<token>"""
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/loco/<chromosomes>/<token>"""
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"
})
@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_gwa_compute(self, mock_json, mock_hash, mock_cmd,
mock_queue_cmd):
"""Test /gemma/gwa-compute/<k-inputfile>/<token>"""
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/gwa-compute/hash-k-output.json/"
"my-token"))
mock_hash.assert_called_once_with(['/tmp/my-token/genofile.txt',
'/tmp/my-token/phenofile.txt',
'/tmp/my-token/snpfile.txt'])
mock_cmd.assert_called_once_with(
gemma_cmd='gemma-wrapper',
gemma_wrapper_kwargs={
'input': '/tmp/my-token/hash-k-output.json'
},
gemma_kwargs={'g': '/tmp/my-token/genofile.txt',
'p': '/tmp/my-token/phenofile.txt',
'a': '/tmp/my-token/snpfile.txt',
'lmm': 9},
output_file='/tmp/my-token/hash-gwa-output.json')
self.assertEqual(response.get_json(), {
"unique_id": "my-unique-id",
"status": "queued",
"output_file": "hash-gwa-output.json"
})
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