From 84790de8bcc51c00a92b71878088345cd58ccc51 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 28 May 2021 17:44:07 +0000
Subject: Fixed issue where all bool kwargs were always being passed to
 generate_rqtl_cmd and also made code check if output file already exists (so
 caching works)

---
 gn3/api/rqtl.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 0194b6f..38f4c1e 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -26,7 +26,7 @@ run the rqtl_wrapper script and return the results as JSON
 
     # Split kwargs by those with values and boolean ones that just convert to True/False
     kwargs = ["model", "method", "nperm", "scale", "control_marker"]
-    boolean_kwargs = ["addcovar", "interval"]
+    boolean_kwargs = ["addcovar", "interval", "pstrata"]
     all_kwargs = kwargs + boolean_kwargs
 
     rqtl_kwargs = {"geno": genofile, "pheno": phenofile}
@@ -41,12 +41,15 @@ run the rqtl_wrapper script and return the results as JSON
     rqtl_cmd = generate_rqtl_cmd(
         rqtl_wrapper_cmd=current_app.config.get("RQTL_WRAPPER_CMD"),
         rqtl_wrapper_kwargs=rqtl_kwargs,
-        rqtl_wrapper_bool_kwargs=boolean_kwargs
+        rqtl_wrapper_bool_kwargs=rqtl_bool_kwargs
     )
 
-    os.system(rqtl_cmd.get('rqtl_cmd'))
-
     rqtl_output = {}
+    if not os.path.isfile(os.path.join(current_app.config.get("TMPDIR"), "output", rqtl_cmd.get('output_file'))):
+        os.system(rqtl_cmd.get('rqtl_cmd'))
+
+    rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file'))
+
     rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file'))
     if int(rqtl_kwargs['nperm']) > 0:
         rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'] = process_perm_output(rqtl_cmd.get('output_file'))
-- 
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