diff options
| -rw-r--r-- | gn3/api/gemma.py | 49 | ||||
| -rw-r--r-- | tests/integration/test_gemma.py | 52 |
2 files changed, 101 insertions, 0 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index acaec68..7fcf2a2 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -7,10 +7,12 @@ from flask import current_app from flask import jsonify from flask import request +from gn3.commands import compose_gemma_cmd from gn3.commands import queue_cmd from gn3.commands import run_cmd from gn3.file_utils import get_hash_of_files from gn3.file_utils import jsonfile_to_dict +from gn3.computations.gemma import do_paths_exist from gn3.computations.gemma import generate_hash_of_string from gn3.computations.gemma import generate_pheno_txt_file from gn3.computations.gemma import generate_gemma_computation_cmd @@ -252,3 +254,50 @@ def compute_gwa_with_covar(k_filename, token): return jsonify(status=128, # use better message message="Metadata file non-existent!") + + +@gemma.route("/gwa-compute/<k_filename>/loco/maf/<maf>/<token>", + methods=["POST"]) +def compute_gwa_with_loco_maf(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 = [ + 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, "lmm": _dict.get("lmm", 9), + 'maf': float(maf)} + _hash = get_hash_of_files([genofile, phenofile, snpsfile]) + _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 0c2afdc..45c9148 100644 --- a/tests/integration/test_gemma.py +++ b/tests/integration/test_gemma.py @@ -290,3 +290,55 @@ class GemmaAPITest(unittest.TestCase): "status": "queued", "output_file": "hash-gwa-output.json" }) + + # pylint: disable=R0913 + @mock.patch("gn3.api.gemma.queue_cmd") + @mock.patch("gn3.api.gemma.compose_gemma_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") + def test_gwa_compute_with_loco_only(self, mock_path_exist, + mock_json, mock_hash, + mock_cmd, + mock_queue_cmd): + """Test /gemma/gwa-compute/<k-inputfile>/loco/maf/<maf>/<token> + + """ + mock_path_exist.return_value = True + 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/" + "hash-k-output.json/loco/" + "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']) + mock_cmd.assert_called_once_with( + gemma_wrapper_cmd='gemma-wrapper', + gemma_wrapper_kwargs={ + 'loco': '--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', + 'lmm': 9, + 'maf': 21}, + gemma_args=["-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" + }) |