From 4cf5c29a06001577054b3548a24d895cf1911e13 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 4 Mar 2021 23:05:34 +0300
Subject: Add new endpoint

"/gwa-compute/<k_filename>/loco/covariates/maf/<maf>/<token>"
---
 gn3/api/gemma.py                | 50 +++++++++++++++++++++++++++++++++++++++++
 tests/integration/test_gemma.py | 49 +++++++++++++++++++++++++++++++++++++++-
 2 files changed, 98 insertions(+), 1 deletion(-)

diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index e5a38e4..a341f62 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -154,6 +154,8 @@ values.
         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}
         _hash = get_hash_of_files([genofile, phenofile, snpsfile])
         k_output_filename = f"{_hash}-k-output.json"
@@ -309,3 +311,51 @@ def compute_gwa_with_loco_maf(k_filename, maf, token):
         return jsonify(status=128,
                        # use better message
                        message="Metadata file non-existent!")
+
+
+@gemma.route("/gwa-compute/<k_filename>/loco/covariates/maf/<maf>/<token>",
+             methods=["POST"])
+def compute_gwa_with_loco_covar(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, covarfile = [
+            os.path.join(working_dir,
+                         _dict.get(x))
+            for x in ["geno", "pheno", "snps", "covar"]]
+        if not do_paths_exist([genofile, phenofile, snpsfile, covarfile]):
+            raise FileNotFoundError
+        gemma_kwargs = {"g": genofile, "p": phenofile,
+                        "a": snpsfile, "c": covarfile,
+                        "lmm": _dict.get("lmm", 9),
+                        "maf": float(maf)}
+        _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=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 61421f2..6d2116b 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -324,7 +324,6 @@ class GemmaAPITest(unittest.TestCase):
             "geno": "genofile.txt",
             "pheno": "phenofile.txt",
             "snps": "snpfile.txt",
-            "covar": "covarfile.txt",
         }
         mock_hash.return_value = "hash"
         response = self.app.post(("/api/gemma/gwa-compute/"
@@ -349,3 +348,51 @@ class GemmaAPITest(unittest.TestCase):
             "status": "queued",
             "output_file": "hash-gwa-output.json"
         })
+
+    @mock.patch("gn3.api.gemma.queue_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")
+    @mock.patch("gn3.api.gemma.redis.Redis")
+    def test_gwa_compute_with_loco_covars(self, mock_redis,
+                                          mock_path_exist,
+                                          mock_json, mock_hash,
+                                          mock_queue_cmd):
+        """Test /gemma/gwa-compute/<k-inputfile>/loco/covariates/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",
+            "covar": "covarfile.txt",
+        }
+        mock_hash.return_value = "hash"
+        response = self.app.post(("/api/gemma/gwa-compute/"
+                                  "hash-k-output.json/loco/"
+                                  "covariates/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',
+                                           "/tmp/my-token/covarfile.txt"
+                                           ])
+        mock_queue_cmd.assert_called_once_with(
+            conn=_redis_conn,
+            email=None,
+            job_queue='GN3::job-queue',
+            cmd=("gemma-wrapper --json --loco --input "
+                 "/tmp/my-token/hash-k-output.json -- "
+                 "-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 -maf 21.0 "
+                 "-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"
+        })
-- 
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