From 55b332d6f03f20054902dabb7beeaaebef2139ac Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 25 Sep 2016 10:02:28 +0000
Subject: Make sure MAPPING_PATH exists

---
 wqflask/utility/tools.py                 |  8 +++++++-
 wqflask/wqflask/show_trait/show_trait.py | 14 +++++++-------
 2 files changed, 14 insertions(+), 8 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 907b0d6a..22779739 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -93,6 +93,10 @@ def gemma_command(guess=None):
 def plink_command(guess=None):
     return valid_bin(get_setting("PLINK_COMMAND",guess))
 
+def flat_file_exists(subdir):
+    base = get_setting("GENENETWORK_FILES")
+    return valid_path(base+"/"+subdir)
+
 def flat_files(subdir=None):
     base = get_setting("GENENETWORK_FILES")
     if subdir:
@@ -104,6 +108,7 @@ def assert_dir(dir):
         raise Exception("ERROR: can not find directory "+dir)
     return dir
 
+
 def mk_dir(dir):
     if not valid_path(dir):
         os.makedirs(dir)
@@ -187,7 +192,8 @@ LOG_BENCH          = get_setting_bool('LOG_BENCH')
 LOG_FORMAT         = "%(message)s"    # not yet in use
 USE_REDIS          = get_setting_bool('USE_REDIS')
 USE_GN_SERVER      = get_setting_bool('USE_GN_SERVER')
-GENENETWORK_FILES  = get_setting_bool('GENENETWORK_FILES')
+
+GENENETWORK_FILES  = get_setting('GENENETWORK_FILES')
 
 PYLMM_COMMAND      = pylmm_command()
 GEMMA_COMMAND      = gemma_command()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 2fd525a5..d9617c7c 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -23,7 +23,7 @@ from basicStatistics import BasicStatisticsFunctions
 
 from pprint import pformat as pf
 
-from utility.tools import flat_files
+from utility.tools import flat_files, flat_file_exists
 
 from utility.logger import getLogger
 logger = getLogger(__name__ )
@@ -162,12 +162,12 @@ class ShowTrait(object):
     def get_mapping_methods(self):
         '''Only display mapping methods when the dataset group's genotype file exists'''
         def check_plink_gemma():
-            MAPPING_PATH = flat_files("mapping")
-            if (os.path.isfile(MAPPING_PATH+"/"+self.dataset.group.name+".bed") and
-                os.path.isfile(MAPPING_PATH+"/"+self.dataset.group.name+".map")):
-                return True
-            else:
-                return False
+            if flat_file_exists("mapping"):
+                MAPPING_PATH = flat_files("mapping")+"/"
+                if (os.path.isfile(MAPPING_PATH+self.dataset.group.name+".bed") and
+                    os.path.isfile(MAPPING_PATH+self.dataset.group.name+".map")):
+                    return True
+            return False
 
         def check_pylmm_rqtl():
             if os.path.isfile(webqtlConfig.GENODIR+self.dataset.group.name+".geno") and (os.path.getsize(webqtlConfig.JSON_GENODIR+self.dataset.group.name+".json") > 0):
-- 
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