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authorPjotr Prins2016-09-24 07:41:39 +0000
committerPjotr Prins2016-09-25 07:39:35 +0000
commite7693e53821747d294452c9bff7e8b0f38a0eb8e (patch)
treec019cd95ddf99ba1bcde1587c3d454b5b916855e /wqflask
parentae1a7f0c8bed6b1a3445a4fac26a578851715629 (diff)
downloadgenenetwork2-e7693e53821747d294452c9bff7e8b0f38a0eb8e.tar.gz
tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/webqtlConfig.py5
-rw-r--r--wqflask/utility/tools.py7
2 files changed, 8 insertions, 4 deletions
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()