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-rw-r--r--gn3/api/gemma.py41
-rw-r--r--tests/integration/test_gemma.py45
2 files changed, 86 insertions, 0 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 709643d..acaec68 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -211,3 +211,44 @@ def compute_gwa(k_filename, token):
return jsonify(status=128,
# use better message
message="Metadata file non-existent!")
+
+
+@gemma.route("/gwa-compute/covars/<k_filename>/<token>", methods=["POST"])
+def compute_gwa_with_covar(k_filename, token):
+ """Compute GWA values. Covariates provided.
+
+ """
+ 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"]]
+ gemma_kwargs = {"g": genofile, "p": phenofile,
+ "a": snpsfile, "c": covarfile,
+ "lmm": _dict.get("lmm", 9)}
+ _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=generate_gemma_computation_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_WRAPPER_CMD"),
+ gemma_wrapper_kwargs={
+ "input": os.path.join(working_dir, k_filename)
+ },
+ gemma_kwargs=gemma_kwargs,
+ output_file=(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 746cfb6..0c2afdc 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -245,3 +245,48 @@ class GemmaAPITest(unittest.TestCase):
"status": "queued",
"output_file": "hash-gwa-output.json"
})
+
+ @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_with_covars(self, mock_json, mock_hash, mock_cmd,
+ mock_queue_cmd):
+ """Test /gemma/gwa-compute/covars/<k-inputfile>/<token>"""
+ 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"
+ 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/"
+ "covars/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',
+ '/tmp/my-token/covarfile.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',
+ 'c': '/tmp/my-token/covarfile.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"
+ })