diff options
Diffstat (limited to 'wqflask/utility')
| -rw-r--r-- | wqflask/utility/helper_functions.py | 12 | ||||
| -rw-r--r-- | wqflask/utility/logger.py | 22 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 48 |
3 files changed, 64 insertions, 18 deletions
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 149ee553..377f6b26 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -5,19 +5,21 @@ from base import data_set from base.species import TheSpecies from wqflask import user_manager +import logging +logger = logging.getLogger(__name__ ) def get_species_dataset_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" self.dataset = data_set.create_dataset(start_vars['dataset']) - print("After creating dataset") + logger.debug("After creating dataset") self.species = TheSpecies(dataset=self.dataset) - print("After creating species") + logger.debug("After creating species") self.this_trait = GeneralTrait(dataset=self.dataset, name=start_vars['trait_id'], cellid=None, get_qtl_info=True) - print("After creating trait") + logger.debug("After creating trait") #if read_genotype: #self.dataset.group.read_genotype_file() @@ -27,7 +29,7 @@ def get_species_dataset_trait(self, start_vars): def get_trait_db_obs(self, trait_db_list): if isinstance(trait_db_list, basestring): trait_db_list = trait_db_list.split(",") - + self.trait_list = [] for trait in trait_db_list: data, _separator, hmac = trait.rpartition(':') @@ -38,4 +40,4 @@ def get_trait_db_obs(self, trait_db_list): trait_ob = GeneralTrait(dataset=dataset_ob, name=trait_name, cellid=None) - self.trait_list.append((trait_ob, dataset_ob))
\ No newline at end of file + self.trait_list.append((trait_ob, dataset_ob)) diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index ddc0ea82..bacb0aa4 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -31,6 +31,7 @@ import string from inspect import isfunction from pprint import pformat as pf from inspect import stack +import datetime from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL, LOG_FORMAT @@ -49,11 +50,20 @@ class GNLogger: self.logger.setLevel(value) def debug(self,*args): + """Call logging.debug for multiple args. Use (lazy) debugf and +level=num to filter on LOG_LEVEL_DEBUG. + + """ + self.collect(self.logger.debug,*args) + + def debug20(self,*args): """Call logging.debug for multiple args. Use level=num to filter on LOG_LEVEL_DEBUG (NYI). """ - self.collect(self.logger.debug,*args) + if level <= LOG_LEVEL_DEBUG: + if self.logger.getEffectiveLevel() < 20: + self.collect(self.logger.debug,*args) def info(self,*args): """Call logging.info for multiple args""" @@ -66,7 +76,10 @@ LOG_LEVEL_DEBUG (NYI). def error(self,*args): """Call logging.error for multiple args""" - self.collect(self.logger.error,*args) + now = datetime.datetime.utcnow() + time_str = now.strftime('%H:%M:%S UTC %Y%m%d') + l = [time_str]+list(args) + self.collect(self.logger.error,*l) def infof(self,*args): """Call logging.info for multiple args lazily""" @@ -75,7 +88,10 @@ LOG_LEVEL_DEBUG (NYI). self.collectf(self.logger.debug,*args) def debugf(self,level=0,*args): - """Call logging.debug for multiple args lazily""" + """Call logging.debug for multiple args lazily and handle + LOG_LEVEL_DEBUG correctly + + """ # only evaluate function when logging if level <= LOG_LEVEL_DEBUG: if self.logger.getEffectiveLevel() < 20: diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 907b0d6a..23d6fb62 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -3,6 +3,7 @@ import os import sys +import json from wqflask import app @@ -10,6 +11,8 @@ from wqflask import app import logging logger = logging.getLogger(__name__ ) +OVERRIDES = {} + def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in app.config, with valid_path is a function checking whether the @@ -45,13 +48,15 @@ def get_setting(command_id,guess=None): logger.debug("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": - # ---- Check whether setting exists in app - command = value(app.config.get(command_id)) + command = OVERRIDES.get(command_id) if command is None: - command = value(guess) - if command is None or command == "": - print command - raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).') + # ---- Check whether setting exists in app + command = value(app.config.get(command_id)) + if command is None: + command = value(guess) + 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)) return command @@ -93,6 +98,10 @@ def gemma_command(guess=None): def plink_command(guess=None): return valid_bin(get_setting("PLINK_COMMAND",guess)) +def flat_file_exists(subdir): + base = get_setting("GENENETWORK_FILES") + return valid_path(base+"/"+subdir) + def flat_files(subdir=None): base = get_setting("GENENETWORK_FILES") if subdir: @@ -104,6 +113,7 @@ def assert_dir(dir): raise Exception("ERROR: can not find directory "+dir) return dir + def mk_dir(dir): if not valid_path(dir): os.makedirs(dir) @@ -164,18 +174,20 @@ def show_settings(): log_level = getattr(logging, LOG_LEVEL.upper()) logging.basicConfig(level=log_level) + logger.info(OVERRIDES) logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC) - print "runserver.py: ****** The webserver has the following configuration ******" + print "runserver.py: ****** Webserver configuration ******" keylist = app.config.keys() keylist.sort() for k in keylist: try: - print("%s %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC)) + print("%s: %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC)) except: - print("%s %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC)) + print("%s: %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC)) # Cached values +HOME = get_setting('HOME') WEBSERVER_MODE = get_setting('WEBSERVER_MODE') GN_SERVER_URL = get_setting('GN_SERVER_URL') SQL_URI = get_setting('SQL_URI') @@ -187,9 +199,25 @@ LOG_BENCH = get_setting_bool('LOG_BENCH') LOG_FORMAT = "%(message)s" # not yet in use USE_REDIS = get_setting_bool('USE_REDIS') USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') -GENENETWORK_FILES = get_setting_bool('GENENETWORK_FILES') + +GENENETWORK_FILES = get_setting('GENENETWORK_FILES') PYLMM_COMMAND = pylmm_command() GEMMA_COMMAND = gemma_command() PLINK_COMMAND = plink_command() TEMPDIR = tempdir() + +from six import string_types + +if os.environ.get('WQFLASK_OVERRIDES'): + jsonfn = get_setting('WQFLASK_OVERRIDES') + logger.error("WQFLASK_OVERRIDES: %s" % jsonfn) + with open(jsonfn) as data_file: + overrides = json.load(data_file) + for k in overrides: + cmd = overrides[k] + if isinstance(cmd, string_types): + OVERRIDES[k] = eval(cmd) + else: + OVERRIDES[k] = cmd + logger.debug(OVERRIDES) |