From be43fb87bd9ce6b6a37b3e12d7c553e4531ea322 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 17 Feb 2021 17:47:27 +0300
Subject: Add endpoint for running GEMMA

---
 gn3/api/gemma.py | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 59 insertions(+), 3 deletions(-)

(limited to 'gn3/api')

diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 1a7232d..95e71e2 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -1,9 +1,16 @@
 """Endpoints for running the gemma cmd"""
+import os
+import redis
+
 from flask import Blueprint
 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 jsonfile_to_dict
 
 gemma = Blueprint("gemma", __name__)
 
@@ -16,8 +23,57 @@ def get_version():
         run_cmd(f"{gemma_cmd} -v | head -n 1"))
 
 
+# This is basically extracted from genenetwork2
+# wqflask/wqflask/marker_regression/gemma_ampping.py
+@gemma.route("/run", methods=["POST"])
+def run_gemma():
+    """Generates a command for generating K-Values and then later, generate a GWA
+command that contains markers. These commands are queued; and the expected
+file output is returned.
 
+    """
+    data = request.get_json()
+    if not data.get("token"):
+        return jsonify(status=128, error="Please provide a token"), 400
+    app_defaults = current_app.config.get('APP_DEFAULTS')
+    metadata = os.path.join(app_defaults.get("TMPDIR"),
+                            data.get("token"),
+                            data.get("metadata", "metadata.json"))
+    if not os.path.isfile(metadata):
+        return jsonify(status=128,
+                       error=f"{metadata}: file does not exist"), 500
+    metadata = jsonfile_to_dict(metadata)
+    gemma_kwargs = {
+        "g": os.path.join(app_defaults.get("GENODIR"), "bimbam",
+                          metadata.get("genotype_file")),
+        "p": os.path.join(app_defaults.get("GENODIR"), "bimbam",
+                          metadata.get("phenotype_file")),
+        "a": os.path.join(app_defaults.get("GENODIR"), "bimbam",
+                          metadata.get("snp_file"))}
+    generate_k_cmd = compose_gemma_cmd(
+        gemma_wrapper_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"),
+        gemma_kwargs=gemma_kwargs,
+        gemma_args=["-gk", ">",
+                    os.path.join(app_defaults.get("TMPDIR"), "gn2",
+                                 f"k_output_{data.get('token')}.txt")])
+    if metadata.get("covariates"):
+        gemma_kwargs["c"] = os.path.join(app_defaults.get("GENODIR"),
+                                         "bimbam",
+                                         metadata.get("covariates"))
+    # Prevents command injection!
+    for _, value in gemma_kwargs.items():
+        if not os.path.isfile(value):
+            return jsonify(status=128, error=f"{value}: Does not exist!"), 500
 
-
-
-
+    gemma_kwargs["lmm"] = 9
+    gwa_cmd = compose_gemma_cmd(
+        gemma_wrapper_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"),
+        gemma_kwargs=gemma_kwargs,
+        gemma_args=[">",
+                    os.path.join(app_defaults.get("TMPDIR"),
+                                 "gn2",
+                                 f"gemma_output_{data.get('token')}.txt")])
+    unique_id = queue_cmd(conn=redis.Redis(), email=metadata.get("email"),
+                          cmd=f"{generate_k_cmd} && {gwa_cmd}")
+    return jsonify(unique_id=unique_id, status="queued",
+                   output_file=f"gemma_output_{data.get('token')}.txt")
-- 
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