diff options
| -rw-r--r-- | gn3/api/gemma.py | 53 | ||||
| -rw-r--r-- | tests/integration/test_gemma.py | 54 |
2 files changed, 107 insertions, 0 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index d141e18..372ef82 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -452,3 +452,56 @@ covars; lmm defaults to 9! status=128, # use better message message="Metadata file non-existent!") + + +@gemma.route("/k-gwa-compute/loco/<chromosomes>/maf/<maf>/<token>", + methods=["POST"]) +def compute_k_gwa_with_loco_only(chromosomes, maf, token): + """k-gwa-compute; Loco no 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 = [ + 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} + 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["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 2055829..fdc061d 100644 --- a/tests/integration/test_gemma.py +++ b/tests/integration/test_gemma.py @@ -507,3 +507,57 @@ 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_only(self, mock_redis, mock_path_exist, + mock_json, mock_hash, + mock_queue_cmd): + """Test /gemma/k-gwa-compute/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", + } + mock_hash.return_value = "hash" + response = self.app.post( + "/api/gemma/k-gwa-compute/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' + ]), + ]) + 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 -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" + }) |