From 9f809adc0a03604ae47cc05e0ff51229e2827ed6 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 7 Mar 2017 10:02:12 +0000
Subject: - Use locate_phewas for phewas files - Use logger instead of print
 statements

---
 wqflask/utility/tools.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

(limited to 'wqflask/utility/tools.py')

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index d71a9cef..4d213f4c 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -153,6 +153,9 @@ def locate(name, subdir=None):
     if subdir: sys.stderr.write(subdir)
     raise Exception("Can not locate "+name+" in "+base)
 
+def locate_phewas(name, subdir=None):
+    return locate(name,'/phewas/'+subdir)
+
 def locate_ignore_error(name, subdir=None):
     """
     Locate a static flat file in the GENENETWORK_FILES environment.
@@ -217,6 +220,7 @@ USE_REDIS          = get_setting_bool('USE_REDIS')
 USE_GN_SERVER      = get_setting_bool('USE_GN_SERVER')
 
 GENENETWORK_FILES  = get_setting('GENENETWORK_FILES')
+PHEWAS_FILES       = get_setting('GENENETWORK_FILES')+"/phewas"
 # TEMP_TRAITS        = get_setting('TEMP_TRAITS')
 
 PYLMM_COMMAND      = pylmm_command()
@@ -242,7 +246,7 @@ if os.environ.get('WQFLASK_OVERRIDES'):
                 OVERRIDES[k] = cmd
             logger.debug(OVERRIDES)
 
-assert_file(get_setting("GENENETWORK_FILES")+"/auwerx/PheWAS_pval_EMMA_norm.RData")
+assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
 assert_dir(get_setting("JS_BIODALLIANCE"))
 assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js")
 assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js")
-- 
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