diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/data_set.py | 2 | ||||
| -rw-r--r-- | wqflask/runserver.py | 12 | ||||
| -rw-r--r-- | wqflask/utility/logger.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 30 |
4 files changed, 35 insertions, 11 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 6649f8af..a4eaaa2e 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -332,7 +332,7 @@ class DatasetGroup(object): if check_plink_gemma(): marker_class = HumanMarkers else: - marker_class = Markers + marker_class = Markers if self.genofile: self.markers = marker_class(self.genofile[:-5]) diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 50805643..50f134db 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -22,11 +22,19 @@ ENDC = '\033[0m' import os app.config['SECRET_KEY'] = os.urandom(24) -from utility.tools import WEBSERVER_MODE,get_setting_int +from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting,get_setting_bool port = get_setting_int("SERVER_PORT") -logger.info("GN2 is running. Visit %shttp://localhost:%s/%s" % (BLUE,port,ENDC)) +print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]") + +if get_setting_bool("USE_GN_SERVER"): + import requests + page = requests.get(get_setting("GN_SERVER_URL")) + if page.status_code != 200: + raise Exception("API server not found!") + +print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))) werkzeug_logger = logging.getLogger('werkzeug') 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") |