From 7ad6aca76c84b0a246fecada8011035d23c8342c Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 5 Mar 2017 12:39:04 +0000
Subject: Settings: make sure paths exist when starting server

---
 etc/default_settings.py  | 1 +
 wqflask/utility/tools.py | 5 ++++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/etc/default_settings.py b/etc/default_settings.py
index 08eae024..97792fed 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -67,6 +67,7 @@ HOME=os.environ['HOME']
 LOGFILE = HOME+"/genenetwork2.log"
 GENENETWORK_FILES = HOME+"/gn2_data"  # base dir for all static data files
 LOCAL_PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files
+GEMMA_RESULTS_PATH = HOME+"/tmp/gemma_results"
 
 # ---- GN2 Executables
 # Paths to invoked binaries
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 82ef136f..d71a9cef 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -217,13 +217,15 @@ USE_REDIS          = get_setting_bool('USE_REDIS')
 USE_GN_SERVER      = get_setting_bool('USE_GN_SERVER')
 
 GENENETWORK_FILES  = get_setting('GENENETWORK_FILES')
-TEMP_TRAITS        = get_setting('TEMP_TRAITS')
+# TEMP_TRAITS        = get_setting('TEMP_TRAITS')
 
 PYLMM_COMMAND      = pylmm_command()
 GEMMA_COMMAND      = gemma_command()
 GEMMA_RESULTS_PATH = get_setting('GEMMA_RESULTS_PATH')
+assert_dir(GEMMA_RESULTS_PATH)
 PLINK_COMMAND      = plink_command()
 TEMPDIR            = tempdir() # defaults to UNIX TMPDIR
+assert_dir(TEMPDIR)
 
 from six import string_types
 
@@ -240,6 +242,7 @@ 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_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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