From e7693e53821747d294452c9bff7e8b0f38a0eb8e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 24 Sep 2016 07:41:39 +0000
Subject: tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2

---
 etc/default_settings.py      | 13 ++++++++-----
 wqflask/base/webqtlConfig.py |  5 +++--
 wqflask/utility/tools.py     |  7 +++++--
 3 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/etc/default_settings.py b/etc/default_settings.py
index df734f7c..9dddd0ad 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -22,7 +22,7 @@ SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s'
 SQLALCHEMY_POOL_RECYCLE = 3600
 GN_SERVER_URL = "http://localhost:8880/"
 
-# Flask configuration (see website)
+# ---- Flask configuration (see website)
 TRAP_BAD_REQUEST_ERRORS = True
 SECURITY_CONFIRMABLE = True
 SECURITY_TRACKABLE = True
@@ -34,8 +34,8 @@ SECURITY_POST_LOGIN_VIEW = "/thank_you"
 SERVER_PORT = 5003
 SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
 
-# Behavioural settings (defaults) note that logger and log levels can
-# be overridden at the module level and with enviroment settings
+# ---- Behavioural settings (defaults) note that logger and log levels can
+#      be overridden at the module level and with enviroment settings
 WEBSERVER_MODE  = 'DEV'     # Python webserver mode (DEBUG|DEV|PROD)
 WEBSERVER_BRANDING = None   # Set the branding (nyi)
 WEBSERVER_DEPLOY = None     # Deployment specifics (nyi)
@@ -49,10 +49,13 @@ LOG_BENCH       = True      # Log bench marks
 USE_REDIS       = True      # REDIS caching (note that redis will be phased out)
 USE_GN_SERVER   = 'False'   # Use GN_SERVER SQL calls
 
-# Path overrides for Genenetwork
+# ---- Path overrides for Genenetwork
+# TMPDIR is normally picked up from the environment
 HOME=os.environ['HOME']
 LOGFILE = HOME+"/genenetwork2.log"
-GENENETWORK_FILES = HOME+"/gn2_data"
+GENENETWORK_FILES = HOME+"/gn2_data"  # base dir for all static data files
+
+# ---- GN2 Executables
 PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read())
 PLINK_COMMAND = str.strip(os.popen("which plink2").read())
 GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 8c67a6fd..6bbabdec 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -60,9 +60,10 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp
 #   HTMLPATH is replaced by GENODIR
 #   IMGDIR is replaced by GENERATED_IMAGE_DIR
 
-# Temporary storage:
+# Temporary storage (note that this TMPDIR is not the same directory
+# as the UNIX TMPDIR)
 TMPDIR               = mk_dir(TEMPDIR+'/gn2/')
-CACHEDIR             = mk_dir(TEMPDIR+'/cache/')
+CACHEDIR             = mk_dir(TMPDIR+'/cache/')
 # We can no longer write into the git tree:
 GENERATED_IMAGE_DIR  = mk_dir(TMPDIR+'/generated/')
 GENERATED_TEXT_DIR   = mk_dir(TMPDIR+'/generated_text/')
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 2c8cc5c5..907b0d6a 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -147,7 +147,10 @@ def locate_ignore_error(name, subdir=None):
     return None
 
 def tempdir():
-    return valid_path(get_setting("TEMPDIR","/tmp"))
+    """
+    Get UNIX TMPDIR by default
+    """
+    return valid_path(get_setting("TMPDIR","/tmp"))
 
 BLUE  = '\033[94m'
 GREEN = '\033[92m'
@@ -184,9 +187,9 @@ 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')
 
 PYLMM_COMMAND      = pylmm_command()
 GEMMA_COMMAND      = gemma_command()
 PLINK_COMMAND      = plink_command()
-FLAT_FILES         = flat_files()
 TEMPDIR            = tempdir()
-- 
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