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-rw-r--r--gn3/api/gemma.py50
-rw-r--r--tests/integration/test_gemma.py49
2 files changed, 98 insertions, 1 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index e5a38e4..a341f62 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -154,6 +154,8 @@ values.
genofile, phenofile, snpsfile = [os.path.join(working_dir,
_dict.get(x))
for x in ["geno", "pheno", "snps"]]
+ if not do_paths_exist([genofile, phenofile, snpsfile]):
+ raise FileNotFoundError
gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
_hash = get_hash_of_files([genofile, phenofile, snpsfile])
k_output_filename = f"{_hash}-k-output.json"
@@ -309,3 +311,51 @@ def compute_gwa_with_loco_maf(k_filename, maf, token):
return jsonify(status=128,
# use better message
message="Metadata file non-existent!")
+
+
+@gemma.route("/gwa-compute/<k_filename>/loco/covariates/maf/<maf>/<token>",
+ methods=["POST"])
+def compute_gwa_with_loco_covar(k_filename, maf, token):
+ """Compute GWA values. No Covariates provided. Only loco and maf vals given.
+
+ """
+ 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, covarfile]):
+ raise FileNotFoundError
+ gemma_kwargs = {"g": genofile, "p": phenofile,
+ "a": snpsfile, "c": covarfile,
+ "lmm": _dict.get("lmm", 9),
+ "maf": float(maf)}
+ _hash = get_hash_of_files([genofile, phenofile, snpsfile, covarfile])
+ _output_filename = f"{_hash}-gwa-output.json"
+ 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=compose_gemma_cmd(
+ gemma_wrapper_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ gemma_wrapper_kwargs={
+ "loco": ("--input "
+ f"{os.path.join(working_dir, k_filename)}")
+ },
+ gemma_kwargs=gemma_kwargs,
+ gemma_args=["-gk", ">",
+ (f"{current_app.config.get('TMPDIR')}/"
+ f"{token}/{_output_filename}")])),
+ status="queued",
+ output_file=_output_filename)
+ # 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 61421f2..6d2116b 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -324,7 +324,6 @@ class GemmaAPITest(unittest.TestCase):
"geno": "genofile.txt",
"pheno": "phenofile.txt",
"snps": "snpfile.txt",
- "covar": "covarfile.txt",
}
mock_hash.return_value = "hash"
response = self.app.post(("/api/gemma/gwa-compute/"
@@ -349,3 +348,51 @@ class GemmaAPITest(unittest.TestCase):
"status": "queued",
"output_file": "hash-gwa-output.json"
})
+
+ @mock.patch("gn3.api.gemma.queue_cmd")
+ @mock.patch("gn3.api.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_gwa_compute_with_loco_covars(self, mock_redis,
+ mock_path_exist,
+ mock_json, mock_hash,
+ mock_queue_cmd):
+ """Test /gemma/gwa-compute/<k-inputfile>/loco/covariates/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/gwa-compute/"
+ "hash-k-output.json/loco/"
+ "covariates/maf/21/my-token"))
+ mock_hash.assert_called_once_with(['/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 "
+ "/tmp/my-token/hash-k-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 "
+ "-lmm 9 -maf 21.0 "
+ "-gk > /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"
+ })