diff options
Diffstat (limited to 'wqflask/utility')
| -rw-r--r-- | wqflask/utility/logger.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 35 |
2 files changed, 25 insertions, 12 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..d3113302 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -16,7 +16,7 @@ OVERRIDES = {} def app_set(command_id, value): """Set application wide value""" app.config.setdefault(command_id,value) - value + return value def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in @@ -51,7 +51,7 @@ def get_setting(command_id,guess=None): return None # ---- Check whether environment exists - logger.debug("Looking for "+command_id+"\n") + # print("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": command = OVERRIDES.get(command_id) @@ -63,7 +63,7 @@ def get_setting(command_id,guess=None): if command is None or command == "": # print command raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).') - logger.debug("Set "+command_id+"="+str(command)) + # print("Set "+command_id+"="+str(command)) return command def get_setting_bool(id): @@ -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 +247,17 @@ 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()) +assert(GEMMA_COMMAND is not None) +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")) @@ -257,7 +267,7 @@ from six import string_types if os.environ.get('WQFLASK_OVERRIDES'): jsonfn = get_setting('WQFLASK_OVERRIDES') - logger.error("WQFLASK_OVERRIDES: %s" % jsonfn) + logger.info("WQFLASK_OVERRIDES: %s" % jsonfn) with open(jsonfn) as data_file: overrides = json.load(data_file) for k in overrides: @@ -267,3 +277,6 @@ if os.environ.get('WQFLASK_OVERRIDES'): else: OVERRIDES[k] = cmd logger.debug(OVERRIDES) + +# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") +assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") |