diff options
| -rw-r--r-- | gn3/api/gemma.py | 41 | ||||
| -rw-r--r-- | tests/integration/test_gemma.py | 45 |
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" + }) |