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authorBonfaceKilz2021-03-08 15:21:34 +0300
committerBonfaceKilz2021-03-08 21:09:58 +0300
commitc4449fe7eacc0dedf2d7456bd790d0c0f9ef6210 (patch)
tree68e48f485f6cb03848a4974adf7b24728c03f5c1
parentcb1adaceb074f2d2d7a0d903808a1853092e127f (diff)
downloadgenenetwork3-c4449fe7eacc0dedf2d7456bd790d0c0f9ef6210.tar.gz
Add "/k-gwa-compute/covars/loco/<chromosomes>/maf/<maf>/<token>"
Reviewed-by: BonfaceKilz <me@bonfacemunyoki.com>
-rw-r--r--gn3/api/gemma.py54
-rw-r--r--tests/integration/test_gemma.py56
2 files changed, 110 insertions, 0 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 372ef82..ed698d3 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -505,3 +505,57 @@ def compute_k_gwa_with_loco_only(chromosomes, maf, token):
status=128,
# use better message
message="Metadata file non-existent!")
+
+
+@gemma.route("/k-gwa-compute/covars/loco/<chromosomes>/maf/<maf>/<token>",
+ methods=["POST"])
+def compute_k_gwa_with_loco_and_cavar(chromosomes, maf, token):
+ """k-gwa-compute; Loco with covars; lmm defaults to 9!
+
+ """
+ working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
+ _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
+ try:
+ genofile, phenofile, snpsfile, covarfile = [
+ os.path.join(working_dir, _dict.get(x))
+ for x in ["geno", "pheno", "snps", "covar"]
+ ]
+ if not do_paths_exist([genofile, phenofile, snpsfile]):
+ raise FileNotFoundError
+ gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
+ gemma_k_cmd = generate_gemma_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs,
+ chromosomes=chromosomes)
+ gemma_kwargs["c"] = covarfile
+ gemma_kwargs["maf"] = float(maf)
+ gemma_kwargs["lmm"] = _dict.get("lmm", 9)
+ gemma_gwa_cmd = generate_gemma_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs,
+ gemma_wrapper_kwargs={
+ "loco":
+ ("--input "
+ f"{os.path.join(working_dir, gemma_k_cmd.get('output_file'))}"
+ )
+ })
+ return jsonify(unique_id=queue_cmd(
+ conn=redis.Redis(),
+ email=(request.get_json() or {}).get('email'),
+ job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
+ cmd=(f"{gemma_k_cmd.get('gemma_cmd')} && "
+ f"{gemma_gwa_cmd.get('gemma_cmd')}")),
+ status="queued",
+ output_file=gemma_gwa_cmd.get("output_file"))
+ # pylint: disable=W0703
+ except Exception:
+ return jsonify(
+ status=128,
+ # use better message
+ message="Metadata file non-existent!")
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index fdc061d..bfce37a 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -561,3 +561,59 @@ class GemmaAPITest(unittest.TestCase):
"status": "queued",
"output_file": "hash-output.json"
})
+
+ @mock.patch("gn3.api.gemma.queue_cmd")
+ @mock.patch("gn3.computations.gemma.get_hash_of_files")
+ @mock.patch("gn3.api.gemma.jsonfile_to_dict")
+ @mock.patch("gn3.api.gemma.do_paths_exist")
+ @mock.patch("gn3.api.gemma.redis.Redis")
+ def test_k_gwa_compute_with_loco_and_covar(self, mock_redis,
+ mock_path_exist, mock_json,
+ mock_hash, mock_queue_cmd):
+ """Test /k-gwa-compute/covars/loco/<chromosomes>/maf/<maf>/<token>
+
+ """
+ mock_path_exist.return_value, _redis_conn = True, mock.MagicMock()
+ mock_redis.return_value = _redis_conn
+ mock_queue_cmd.return_value = "my-unique-id"
+ mock_json.return_value = {
+ "geno": "genofile.txt",
+ "pheno": "phenofile.txt",
+ "snps": "snpfile.txt",
+ "covar": "covarfile.txt",
+ }
+ mock_hash.return_value = "hash"
+ response = self.app.post(("/api/gemma/k-gwa-compute/covars/"
+ "loco/1%2C2%2C3%2C4/maf/9/my-token"))
+ mock_hash.assert_has_calls([
+ mock.call([
+ '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt',
+ '/tmp/my-token/snpfile.txt'
+ ]),
+ mock.call([
+ '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt',
+ '/tmp/my-token/snpfile.txt', '/tmp/my-token/covarfile.txt'
+ ]),
+ ])
+ mock_queue_cmd.assert_called_once_with(
+ conn=_redis_conn,
+ email=None,
+ job_queue='GN3::job-queue',
+ cmd=("gemma-wrapper --json --loco --input 1,2,3,4 -- "
+ "-g /tmp/my-token/genofile.txt "
+ "-p /tmp/my-token/phenofile.txt "
+ "-a /tmp/my-token/snpfile.txt "
+ "-gk > /tmp/my-token/hash-+O9bus-output.json "
+ "&& gemma-wrapper --json --loco "
+ "--input /tmp/my-token/hash-+O9bus-output.json -- "
+ "-g /tmp/my-token/genofile.txt "
+ "-p /tmp/my-token/phenofile.txt "
+ "-a /tmp/my-token/snpfile.txt "
+ "-c /tmp/my-token/covarfile.txt -maf 9.0 -lmm 9 "
+ "-gk > /tmp/my-token/hash-output.json"))
+ self.assertEqual(
+ response.get_json(), {
+ "unique_id": "my-unique-id",
+ "status": "queued",
+ "output_file": "hash-output.json"
+ })