From 0a8754a582f057bd335441eab15da3f629df9ad7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 17 May 2021 23:56:10 +0000
Subject: Fixed variety of issues detected by pylint

---
 gn3/api/rqtl.py          | 13 ++++++-------
 gn3/computations/rqtl.py | 50 ++++++++++++++++++++++++------------------------
 2 files changed, 31 insertions(+), 32 deletions(-)

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 82cf34f..7756310 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -1,5 +1,4 @@
-import os
-
+"""Endpoints for running the rqtl cmd"""
 from flask import Blueprint
 from flask import current_app
 from flask import jsonify
@@ -12,8 +11,10 @@ rqtl = Blueprint("rqtl", __name__)
 
 @rqtl.route("/compute", methods=["POST"])
 def compute():
-    working_dir = os.path.join(current_app.config.get("TMPDIR"))
+    """Given at least a geno_file and pheno_file, generate and
+run the rqtl_wrapper script and return the results as JSON
 
+    """
     genofile = request.form['geno_file']
     phenofile = request.form['pheno_file']
 
@@ -28,10 +29,8 @@ def compute():
             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
+        rqtl_wrapper_cmd=current_app.config.get("RQTL_WRAPPER_CMD"),
+        rqtl_wrapper_kwargs=rqtl_kwargs
     )
 
     return jsonify(results)
-
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 087a99f..0e8cd1f 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,25 +1,25 @@
-"""Procedures related rqtl computations"""
-import os
-
-from typing import Dict
-from gn3.commands import compose_rqtl_cmd
-from gn3.fs_helpers import get_hash_of_files
-
-def generate_rqtl_cmd(rqtl_wrapper_cmd: str,
-                      output_dir: str,
-                      rqtl_wrapper_kwargs: Dict) -> Dict:
-
-    _hash = get_hash_of_files(
-        [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p", "addcovar",
-                                                    "model", "method",
-                                                    "interval", "nperm",
-                                                    "scale", "control"]])
-
-    _output_filename = f"{_hash}-output.json"
-    return {
-        "output_file":
-        _output_filename,
-        "rqtl_cmd":
-        compose_rqtl_cmd(rqtl_wrapper_cmd=rqtl_wrapper_cmd,
-                         rqtl_wrapper_kwargs=rqtl_wrapper_kwargs)
-    }
\ No newline at end of file
+"""Procedures related rqtl computations"""
+
+from typing import Dict
+from gn3.commands import compose_rqtl_cmd
+from gn3.fs_helpers import get_hash_of_files
+
+def generate_rqtl_cmd(rqtl_wrapper_cmd: str,
+                      rqtl_wrapper_kwargs: Dict) -> Dict:
+    """Given the base rqtl_wrapper command and
+dict of keyword arguments, return the full rqtl_wrapper command and an
+output filename generated from a hash of the genotype and phenotype files
+
+    """
+
+    _hash = get_hash_of_files(
+        [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p"]])
+
+    _output_filename = f"{_hash}-output.json"
+    return {
+        "output_file":
+        _output_filename,
+        "rqtl_cmd":
+        compose_rqtl_cmd(rqtl_wrapper_cmd=rqtl_wrapper_cmd,
+                         rqtl_wrapper_kwargs=rqtl_wrapper_kwargs)
+    }
-- 
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