From 7ab86429219a2ed5ad7b94f0ce9667dd4c38c56d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 13 May 2021 10:58:19 +0300
Subject: Add end-point for running an rQTL program

* gn3/api/general.py (run_r_qtl): New function.
* gn3/settings.py: New variable.
---
 gn3/api/general.py | 14 ++++++++++++++
 gn3/settings.py    |  1 +
 2 files changed, 15 insertions(+)

diff --git a/gn3/api/general.py b/gn3/api/general.py
index a9a8da2..cebb2e3 100644
--- a/gn3/api/general.py
+++ b/gn3/api/general.py
@@ -6,6 +6,7 @@ from flask import jsonify
 from flask import request
 
 from gn3.fs_helpers import extract_uploaded_file
+from gn3.commands import run_cmd
 
 
 general = Blueprint("general", __name__)
@@ -50,3 +51,16 @@ TTL is set in the metadata file. If none is provided, the default is 1 week.
     if results.get("status") > 0:
         status = 500
     return jsonify(results), status
+
+
+@general.route("/qtl/run/<geno_filestr>/<pheno_filestr>",
+               methods=["POST"],
+               strict_slashes=False)
+def run_r_qtl(geno_filestr, pheno_filestr):
+    """Run r_qtl command using the written rqtl_wrapper program
+
+    """
+    rqtl_wrapper = current_app.config["RQTL_WRAPPER"]
+    cmd = (f"Rscript {rqtl_wrapper} "
+           f"{geno_filestr} {pheno_filestr}")
+    return jsonify(run_cmd(cmd)), 201
diff --git a/gn3/settings.py b/gn3/settings.py
index 7b3ffb7..2057ce1 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -10,6 +10,7 @@ CACHEDIR = ""
 REDIS_URI = "redis://localhost:6379/0"
 REDIS_JOB_QUEUE = "GN3::job-queue"
 TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir())
+RQTL_WRAPPER = "rqtl_wrapper.R"
 
 # SQL confs
 SQL_URI = os.environ.get("SQL_URI", "mysql://webqtlout:webqtlout@localhost/db_webqtl")
-- 
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