[PATCH 042/100] Sanitizing locations

2 files changed, 8 insertions, 10 deletions

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 51189fa3..b8eff12a 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -1,4 +1,3 @@
-
 # Tools/paths finder resolves external paths from settings and/or environment
 # variables
 
@@ -105,9 +104,9 @@ def locate(name, subdir=None):
             print("Found: file "+lookfor+"\n")
             return lookfor
         else:
-            raise IOError("Can not locate "+lookfor)
+            raise Exception("Can not locate "+lookfor)
     if subdir: sys.stderr.write(subdir)
-    raise IOError("Can not locate "+name+" in "+base)
+    raise Exception("Can not locate "+name+" in "+base)
 
 def locate_ignore_error(name, subdir=None):
     """
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 910d0c3c..e9cfb06d 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -41,7 +41,8 @@ from wqflask.marker_regression import gemma_mapping
 #from wqflask.marker_regression import plink_mapping
 #from wqflask.marker_regression import rqtl_mapping
 
-from utility.tools import locate, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND
+from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND
+from utility.external import shell
 
 class MarkerRegression(object):
 
@@ -413,8 +414,8 @@ class MarkerRegression(object):
         write_cross     = ro.r["write.cross"]           # Map the write.cross function
         GENOtoCSVR      = ro.r["GENOtoCSVR"]            # Map the GENOtoCSVR function
 
-        genofilelocation  = webqtlConfig.HTMLPATH + "genotypes/" + self.dataset.group.name + ".geno"
-        crossfilelocation = webqtlConfig.HTMLPATH + "genotypes/" + self.dataset.group.name + ".cross"
+        genofilelocation  = locate(self.dataset.group.name + ".geno", "genotype")
+        crossfilelocation = locate(self.dataset.group.name + ".cross", "genotype")
 
         #print("Conversion of geno to cross at location:", genofilelocation, " to ", crossfilelocation)
 
@@ -860,9 +861,7 @@ class MarkerRegression(object):
                 Redis.expire(key, 60*60)
     
                 command = PYLMM_COMMAND+' --key {} --species {}'.format(key,"other")
-    
-                os.system(command)
-    
+                shell(command)
                 
                 json_results = Redis.blpop("pylmm:results:" + temp_uuid, 45*60)
                 results = json.loads(json_results[1])
@@ -941,7 +940,7 @@ class MarkerRegression(object):
             print("command is:", command)
             print("after printing command")
 
-            os.system(command)
+            shell(command)
 
             #t_stats, p_values = lmm.run(key)
             #lmm.run(key)