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authorzsloan2018-01-24 20:14:06 +0000
committerzsloan2018-01-24 20:14:06 +0000
commit4634cf87761980a1682473211259698b7be720e4 (patch)
tree7168293e7cf674a4250ea84080bd83112552ae93 /wqflask/utility
parent623cdd2cfafc3d2dd45bc1adf460c9f3c5120e7a (diff)
parent56065c9f994c9247eaa17e5216d44d0e5e733aa2 (diff)
downloadgenenetwork2-4634cf87761980a1682473211259698b7be720e4.tar.gz
Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing
Diffstat (limited to 'wqflask/utility')
-rw-r--r--wqflask/utility/logger.py2
-rw-r--r--wqflask/utility/tools.py30
2 files changed, 24 insertions, 8 deletions
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..57f97a81 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -105,7 +105,7 @@ def js_path(module=None):
try_guix = get_setting("JS_GUIX_PATH")+"/"+module
if valid_path(try_guix):
return try_guix
- raise "No JS path found for "+module+" (check JS_GN_PATH)"
+ raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)"
def pylmm_command(guess=None):
return assert_bin(get_setting("PYLMM_COMMAND",guess))
@@ -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.
@@ -239,15 +247,16 @@ USE_GN_SERVER = get_setting_bool('USE_GN_SERVER')
GENENETWORK_FILES = get_setting('GENENETWORK_FILES')
JS_GUIX_PATH = get_setting('JS_GUIX_PATH')
-# assert_dir(JS_GUIX_PATH) - don't enforce right now
+assert_dir(JS_GUIX_PATH)
JS_GN_PATH = get_setting('JS_GN_PATH')
# assert_dir(JS_GN_PATH)
-PYLMM_COMMAND = pylmm_command()
-GEMMA_COMMAND = gemma_command()
+PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command())
+GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command())
+PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command())
GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
-PLINK_COMMAND = plink_command()
-TEMPDIR = tempdir() # defaults to UNIX TMPDIR
+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 +276,10 @@ 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(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")