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-rw-r--r--gn3/api/gemma.py49
-rw-r--r--tests/integration/test_gemma.py52
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"
+ })