diff options
| -rw-r--r-- | gn3/api/gemma.py | 38 | ||||
| -rw-r--r-- | tests/integration/test_gemma.py | 28 |
2 files changed, 66 insertions, 0 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index ec5f3f0..e5a1a72 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -133,3 +133,41 @@ traitfile, and snpsfile are extracted from a metadata.json file. return jsonify(status=128, # use better message message="Metadata file non-existent!") + + +@gemma.route("/k-compute/loco/<chromosomes>/<token>", methods=["POST"]) +def compute_k_loco(chromosomes, token): + """Similar to 'compute_k' with the extra option of using loco given chromosome +values. + + """ + 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"]] + gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} + _hash = get_hash_of_files([genofile, phenofile, snpsfile]) + k_output_filename = f"{_hash}-k-output.json" + k_computation_cmd = generate_gemma_computation_cmd( + gemma_cmd=current_app.config.get("GEMMA_WRAPPER_CMD"), + gemma_wrapper_kwargs={"loco": f"--input {chromosomes}"}, + gemma_kwargs=gemma_kwargs, + output_file=(f"{current_app.config.get('TMPDIR')}/" + f"{token}/{k_output_filename}")) + 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"{k_computation_cmd}"), + status="queued", + output_file=k_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 18e3fb0..3e64987 100644 --- a/tests/integration/test_gemma.py +++ b/tests/integration/test_gemma.py @@ -176,3 +176,31 @@ class GemmaAPITest(unittest.TestCase): "status": "queued", "unique_id": "my-unique-id" }) + + @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_k_compute_loco(self, mock_json, mock_hash, mock_cmd, + mock_queue_cmd): + """Test /gemma/k-compute/<token>""" + 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" + 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/k-compute/loco/" + "1%2C2%2C3%2C4%2C5%2C6/test-data")) + self.assertEqual(response.get_json(), { + "output_file": "hash-k-output.json", + "status": "queued", + "unique_id": "my-unique-id" + }) |