From 9e4c8f01e1a0aa49d218f7909ed5b7979ffc6fb9 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 7 Oct 2016 07:05:22 +0000
Subject: Saner handling of TMPDIR and TEMPDIR Throw error when TMPDIRs are not
 writable

---
 wqflask/base/webqtlConfig.py | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

(limited to 'wqflask/base/webqtlConfig.py')

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 6bbabdec..e5f10edf 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -8,7 +8,7 @@
 #
 #########################################
 
-from utility.tools import valid_path, mk_dir, assert_dir, flat_files, TEMPDIR
+from utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, flat_files, TEMPDIR
 
 #Debug Level
 #1 for debug, mod python will reload import each time
@@ -60,24 +60,36 @@ 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 (note that this TMPDIR is not the same directory
-# as the UNIX TMPDIR)
+# Temporary storage (note that this TMPDIR can be set as an
+# environment variable - use utility.tools.TEMPDIR when you
+# want to reach this base dir
+assert_writable_dir(TEMPDIR)
+
 TMPDIR               = mk_dir(TEMPDIR+'/gn2/')
+assert_writable_dir(TMPDIR)
+
 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/')
 
+# Make sure we have permissions to access these
+assert_writable_dir(CACHEDIR)
+assert_writable_dir(GENERATED_IMAGE_DIR)
+assert_writable_dir(GENERATED_TEXT_DIR)
+
 # Flat file directories
 GENODIR              = flat_files('genotype')+'/'
+assert_dir(GENODIR)
+
+# JSON genotypes are OBSOLETE
 JSON_GENODIR         = flat_files('genotype/json')+'/'
 if not valid_path(JSON_GENODIR):
     # fall back on old location (move the dir, FIXME)
     JSON_GENODIR = flat_files('json')
-assert_dir(GENODIR)
 
+# Are we using the following...?
 PORTADDR = "http://50.16.251.170"
-
 INFOPAGEHREF = '/dbdoc/%s.html'
 CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
 SCRIPTFILE = 'main.py'
-- 
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