From 7ed84670c0d13de38b578a4e4177b2529ff3fb40 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 17 May 2021 21:54:42 +0000
Subject: Read in kwargs fromrequest and pass the command, tmpdir, and kwargs
 to generate_rqtl_cmd which returns the actual command and output path

---
 gn3/api/rqtl.py | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 8dd4bb7..82cf34f 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -2,8 +2,12 @@ import os
 
 from flask import Blueprint
 from flask import current_app
+from flask import jsonify
 from flask import request
 
+from gn3.computations.rqtl import generate_rqtl_cmd
+from gn3.computations.gemma import do_paths_exist
+
 rqtl = Blueprint("rqtl", __name__)
 
 @rqtl.route("/compute", methods=["POST"])
@@ -16,4 +20,18 @@ def compute():
     if not do_paths_exist([genofile, phenofile]):
         raise FileNotFoundError
 
-    return current_app.config.get("RQTL_WRAPPER_CMD")
\ No newline at end of file
+    kwarg_list = ["addcovar", "model", "method", "interval", "nperm", "scale", "control_marker"]
+
+    rqtl_kwargs = {"geno": genofile, "pheno": phenofile}
+    for kwarg in kwarg_list:
+        if kwarg in request.form:
+            rqtl_kwargs[kwarg] = request.form[kwarg]
+
+    results = generate_rqtl_cmd(
+        rqtl_wrapper_cmd = current_app.config.get("RQTL_WRAPPER_CMD"),
+        output_dir = current_app.config.get('TMPDIR'),
+        rqtl_wrapper_kwargs = rqtl_kwargs
+    )
+
+    return jsonify(results)
+
-- 
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