From 837ce8b9c779b1da6e4390220ccd353b289c1fca Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 20 Dec 2017 09:11:31 -0600
Subject: Bring in some earlier work - mostly documentation and startup
handling
---
wqflask/utility/logger.py | 2 +-
wqflask/utility/tools.py | 27 +++++++++++++++++++++------
2 files changed, 22 insertions(+), 7 deletions(-)
(limited to 'wqflask/utility')
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index bacb0aa4..128706df 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -72,7 +72,7 @@ LOG_LEVEL_DEBUG (NYI).
def warning(self,*args):
"""Call logging.warning for multiple args"""
self.collect(self.logger.warning,*args)
- self.logger.warning(self.collect(*args))
+ # self.logger.warning(self.collect(*args))
def error(self,*args):
"""Call logging.error for multiple args"""
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index c5685cdd..63b7149c 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -147,9 +147,14 @@ def assert_writable_dir(dir):
fh.close()
os.remove(fn)
except IOError:
- raise Exception('Unable to write test.txt to directory ' + dir )
+ raise Exception('Unable to write test.txt to directory ' + dir)
return dir
+def assert_file(fn):
+ if not valid_file(fn):
+ raise Exception('Unable to find file '+fn)
+ return fn
+
def mk_dir(dir):
if not valid_path(dir):
os.makedirs(dir)
@@ -174,6 +179,9 @@ def locate(name, subdir=None):
if subdir: sys.stderr.write(subdir)
raise Exception("Can not locate "+name+" in "+base)
+def locate_phewas(name, subdir=None):
+ return locate(name,'/phewas/'+subdir)
+
def locate_ignore_error(name, subdir=None):
"""
Locate a static flat file in the GENENETWORK_FILES environment.
@@ -243,11 +251,11 @@ JS_GUIX_PATH = get_setting('JS_GUIX_PATH')
JS_GN_PATH = get_setting('JS_GN_PATH')
# assert_dir(JS_GN_PATH)
-PYLMM_COMMAND = pylmm_command()
-GEMMA_COMMAND = gemma_command()
-GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
-PLINK_COMMAND = plink_command()
-TEMPDIR = tempdir() # defaults to UNIX TMPDIR
+PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command())
+GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command())
+PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command())
+TEMPDIR = tempdir() # defaults to UNIX TMPDIR
+assert_dir(TEMPDIR)
# ---- Handle specific JS modules
JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher"))
@@ -267,3 +275,10 @@ if os.environ.get('WQFLASK_OVERRIDES'):
else:
OVERRIDES[k] = cmd
logger.debug(OVERRIDES)
+
+assert_file(PHEWAS_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")
+assert_dir(get_setting("JS_TWITTER_POST_FETCHER"))
+assert_file(get_setting("JS_TWITTER_POST_FETCHER")+"/js/twitterFetcher_min.js")
--
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