# Tools/paths finder resolves external paths from settings and/or environment # variables 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 path points to an expected directory and returns the full path to the binary command guess = os.environ.get('HOME')+'/pylmm' valid_path(get_setting('PYLMM_PATH',guess)) first tries the environment variable in +id+, next gets the Flask app setting for the same +id+ and finally does an educated +guess+. In all, the environment overrides the others, next is the flask setting, then the guess. A valid path to the binary command is returned. If none is resolved an exception is thrown. Note that we do not use the system path. This is on purpose because it will mess up controlled (reproducible) deployment. The proper way is to either use the GNU Guix defaults as listed in etc/default_settings.py or override them yourself by creating a different settings.py file (or setting the environment). """ def value(command): if command: # sys.stderr.write("Found "+command+"\n") return command else: return None # ---- Check whether environment exists logger.debug("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": command = OVERRIDES.get(command_id) if command is None: # ---- 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 def get_setting_bool(id): v = get_setting(id) if v not in [0,False,'False','FALSE',None]: return True return False def get_setting_int(id): v = get_setting(id) if isinstance(v, str): return int(v) if v is None: return 0 return v def valid_bin(bin): if os.path.islink(bin) or valid_file(bin): return bin return None def valid_file(fn): if os.path.isfile(fn): return fn return None def valid_path(dir): if os.path.isdir(dir): return dir return None def pylmm_command(guess=None): return valid_bin(get_setting("PYLMM_COMMAND",guess)) def gemma_command(guess=None): return valid_bin(get_setting("GEMMA_COMMAND",guess)) 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: return assert_dir(base+"/"+subdir) return assert_dir(base) def assert_dir(dir): if not valid_path(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) return assert_dir(dir) def locate(name, subdir=None): """ Locate a static flat file in the GENENETWORK_FILES environment. This function throws an error when the file is not found. """ base = get_setting("GENENETWORK_FILES") if subdir: base = base+"/"+subdir if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): logger.info("Found: file "+lookfor+"\n") return lookfor else: raise Exception("Can not locate "+lookfor) if subdir: sys.stderr.write(subdir) raise Exception("Can not locate "+name+" in "+base) def locate_ignore_error(name, subdir=None): """ Locate a static flat file in the GENENETWORK_FILES environment. This function does not throw an error when the file is not found but returns None. """ base = get_setting("GENENETWORK_FILES") if subdir: base = base+"/"+subdir if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): logger.debug("Found: file "+name+"\n") return lookfor logger.info("WARNING: file "+name+" not found\n") return None def tempdir(): """ Get UNIX TMPDIR by default """ return valid_path(get_setting("TMPDIR","/tmp")) BLUE = '\033[94m' GREEN = '\033[92m' BOLD = '\033[1m' ENDC = '\033[0m' def show_settings(): from utility.tools import LOG_LEVEL print("Set global log level to "+BLUE+LOG_LEVEL+ENDC) 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: ****** 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)) except: 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') LOG_LEVEL = get_setting('LOG_LEVEL') LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG') LOG_SQL = get_setting_bool('LOG_SQL') LOG_SQL_ALCHEMY = get_setting_bool('LOG_SQL_ALCHEMY') 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('GENENETWORK_FILES') GUIX_JS_PATH = get_setting('GUIX_JS_PATH') assert_dir(GUIX_JS_PATH) PYLMM_COMMAND = pylmm_command() GEMMA_COMMAND = gemma_command() PLINK_COMMAND = plink_command() TEMPDIR = tempdir() # defaults to UNIX TMPDIR TWITTER_POST_FETCHER_JS_PATH = GUIX_JS_PATH + "/Twitter-Post-Fetcher" assert_dir(TWITTER_POST_FETCHER_JS_PATH) 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)