diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 22 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 12 |
2 files changed, 28 insertions, 6 deletions
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' diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 23d6fb62..5105ba42 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -113,6 +113,16 @@ def assert_dir(dir): raise Exception("ERROR: can not find directory "+dir) return dir +def assert_writable_dir(dir): + try: + fn = dir + "/test.txt" + fh = open( fn, 'w' ) + fh.write("I am writing this text to the file\n") + fh.close() + os.remove(fn) + except IOError: + raise Exception('Unable to write to directory ' + dir ) + return dir def mk_dir(dir): if not valid_path(dir): @@ -205,7 +215,7 @@ GENENETWORK_FILES = get_setting('GENENETWORK_FILES') PYLMM_COMMAND = pylmm_command() GEMMA_COMMAND = gemma_command() PLINK_COMMAND = plink_command() -TEMPDIR = tempdir() +TEMPDIR = tempdir() # defaults to UNIX TMPDIR from six import string_types |