From 87a3e2254bdd837e9647c42b9c4ab98e986c5e1d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 3 Mar 2021 11:51:29 +0300
Subject: Add new endpoint: "/gemma/k-compute/<token>"

* gn3/api/gemma.py (compute_k): New function.
* tests/integration/test_gemma.py (tesk_k_compute): New test case.
---
 gn3/api/gemma.py                | 41 +++++++++++++++++++++++++++++++++++++++++
 tests/integration/test_gemma.py | 27 +++++++++++++++++++++++++++
 2 files changed, 68 insertions(+)

diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index a351ab1..ec5f3f0 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -9,6 +9,8 @@ from flask import request
 
 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 generate_hash_of_string
 from gn3.computations.gemma import generate_pheno_txt_file
 from gn3.computations.gemma import generate_gemma_computation_cmd
@@ -92,3 +94,42 @@ gemma endpoints, return the status of the command
         return jsonify(status=128,
                        error="The unique id you used does not exist!"), 500
     return jsonify(status=status.decode("utf-8"))
+
+
+@gemma.route("/k-compute/<token>", methods=["POST"])
+def compute_k(token):
+    """Given a genofile, traitfile, snpsfile, and the token, compute the k-valuen
+and return <hash-of-inputs>.json with a UNIQUE-ID of the job. The genofile,
+traitfile, and snpsfile are extracted from a metadata.json file.
+
+    """
+    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=None,
+            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 e434dab..5f4e52b 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -149,3 +149,30 @@ class GemmaAPITest(unittest.TestCase):
             key="status")
         self.assertEqual(response.get_json(),
                          {"status": "test"})
+
+    @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(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("/gemma/k-compute/test-data")
+        self.assertEqual(response.get_json(), {
+            "output_file": "hash-k-output.json",
+            "status": "queued",
+            "unique_id": "my-unique-id"
+        })
-- 
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