diff options
Diffstat (limited to 'wqflask/utility')
| -rw-r--r-- | wqflask/utility/helper_functions.py | 24 | ||||
| -rw-r--r-- | wqflask/utility/logger.py | 22 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 70 |
3 files changed, 92 insertions, 24 deletions
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 15f60765..377f6b26 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -4,18 +4,22 @@ from base.trait import GeneralTrait 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() @@ -23,15 +27,17 @@ 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 i, trait_db in enumerate(trait_db_list): - if i == (len(trait_db_list) - 1): - break - trait_name, dataset_name = trait_db.split(":") - #print("dataset_name:", dataset_name) + for trait in trait_db_list: + data, _separator, hmac = trait.rpartition(':') + data = data.strip() + assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?" + trait_name, dataset_name = data.split(":") dataset_ob = data_set.create_dataset(dataset_name) 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 bb8241f5..77cb6ac5 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -3,12 +3,16 @@ import os import sys +import json + from wqflask import app # Use the standard logger here to avoid a circular dependency 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 @@ -44,13 +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 @@ -92,6 +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: @@ -103,6 +113,17 @@ def assert_dir(dir): raise Exception("ERROR: can not find directory "+dir) return dir +def assert_writable_dir(dir): + try: + fn = dir + "/test.txt" + fh = open( fn, 'w' ) + fh.write("I am writing this text to the file\n") + fh.close() + os.remove(fn) + except IOError: + raise Exception('Unable to write test.txt to directory ' + dir ) + return dir + def mk_dir(dir): if not valid_path(dir): os.makedirs(dir) @@ -146,7 +167,10 @@ def locate_ignore_error(name, subdir=None): return None def tempdir(): - return valid_path(get_setting("TEMPDIR","/tmp")) + """ + Get UNIX TMPDIR by default + """ + return valid_path(get_setting("TMPDIR","/tmp")) BLUE = '\033[94m' GREEN = '\033[92m' @@ -160,18 +184,21 @@ 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 +GN_VERSION = get_setting('GN_VERSION') +HOME = get_setting('HOME') WEBSERVER_MODE = get_setting('WEBSERVER_MODE') GN_SERVER_URL = get_setting('GN_SERVER_URL') SQL_URI = get_setting('SQL_URI') @@ -184,8 +211,27 @@ 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('GENENETWORK_FILES') + PYLMM_COMMAND = pylmm_command() GEMMA_COMMAND = gemma_command() PLINK_COMMAND = plink_command() -FLAT_FILES = flat_files() -TEMPDIR = tempdir() +TEMPDIR = tempdir() # defaults to UNIX TMPDIR + +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) + +assert_dir(get_setting("JS_BIODALLIANCE")) +assert_dir(get_setting("JS_TWITTER_POST_FETCHER")) |