From c7e661b8ff9f70955418fbc4527378904beb0cf4 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 30 Apr 2021 12:16:51 +0300 Subject: autopep8: Fix E20-E27 Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3 --- wqflask/utility/tools.py | 112 +++++++++++++++++++++++------------------------ 1 file changed, 56 insertions(+), 56 deletions(-) (limited to 'wqflask/utility/tools.py') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 65df59c3..9b751344 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -9,7 +9,7 @@ from wqflask import app # Use the standard logger here to avoid a circular dependency import logging -logger = logging.getLogger(__name__ ) +logger = logging.getLogger(__name__) OVERRIDES = {} @@ -18,7 +18,7 @@ def app_set(command_id, value): app.config.setdefault(command_id, value) return value -def get_setting(command_id,guess=None): +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 @@ -54,7 +54,7 @@ def get_setting(command_id,guess=None): # print("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": - command = OVERRIDES.get(command_id) # currently not in use + command = OVERRIDES.get(command_id) # currently not in use if command is None: # ---- Check whether setting exists in app command = value(app.config.get(command_id)) @@ -62,7 +62,7 @@ def get_setting(command_id,guess=None): command = value(guess) if command is None or command == "": # print command - raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).') + raise Exception(command_id + ' setting unknown or faulty (update default_settings.py?).') # print("Set "+command_id+"="+str(command)) return command @@ -99,13 +99,13 @@ def js_path(module=None): """ Find the JS module in the two paths """ - try_gn = get_setting("JS_GN_PATH")+"/"+module + try_gn = get_setting("JS_GN_PATH") + "/" + module if valid_path(try_gn): return try_gn - try_guix = get_setting("JS_GUIX_PATH")+"/"+module + try_guix = get_setting("JS_GUIX_PATH") + "/" + module if valid_path(try_guix): return try_guix - raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)" + raise "No JS path found for " + module + " (if not in Guix check JS_GN_PATH)" def reaper_command(guess=None): return get_setting("REAPER_COMMAND", guess) @@ -121,28 +121,28 @@ def plink_command(guess=None): def flat_file_exists(subdir): base = get_setting("GENENETWORK_FILES") - return valid_path(base+"/"+subdir) + 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 + "/" + subdir) return assert_dir(base) def assert_bin(fn): if not valid_bin(fn): - raise Exception("ERROR: can not find binary "+fn) + raise Exception("ERROR: can not find binary " + fn) return fn def assert_dir(dir): if not valid_path(dir): - raise Exception("ERROR: can not find directory "+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 = open(fn, 'w') fh.write("I am writing this text to the file\n") fh.close() os.remove(fn) @@ -152,7 +152,7 @@ def assert_writable_dir(dir): def assert_file(fn): if not valid_file(fn): - raise Exception('Unable to find file '+fn) + raise Exception('Unable to find file ' + fn) return fn def mk_dir(dir): @@ -168,19 +168,19 @@ def locate(name, subdir=None): """ base = get_setting("GENENETWORK_FILES") if subdir: - base = base+"/"+subdir + base = base + "/" + subdir if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): - logger.info("Found: file "+lookfor+"\n") + logger.info("Found: file " + lookfor + "\n") return lookfor else: - raise Exception("Can not locate "+lookfor) + raise Exception("Can not locate " + lookfor) if subdir: sys.stderr.write(subdir) - raise Exception("Can not locate "+name+" in "+base) + raise Exception("Can not locate " + name + " in " + base) def locate_phewas(name, subdir=None): - return locate(name, '/phewas/'+subdir) + return locate(name, '/phewas/' + subdir) def locate_ignore_error(name, subdir=None): """ @@ -191,13 +191,13 @@ def locate_ignore_error(name, subdir=None): """ base = get_setting("GENENETWORK_FILES") if subdir: - base = base+"/"+subdir + base = base + "/" + subdir if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): - logger.debug("Found: file "+name+"\n") + logger.debug("Found: file " + name + "\n") return lookfor - logger.info("WARNING: file "+name+" not found\n") + logger.info("WARNING: file " + name + " not found\n") return None def tempdir(): @@ -206,20 +206,20 @@ def tempdir(): """ return valid_path(get_setting("TMPDIR", "/tmp")) -BLUE = '\033[94m' +BLUE = '\033[94m' GREEN = '\033[92m' -BOLD = '\033[1m' -ENDC = '\033[0m' +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)) + 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) + logger.info(BLUE + "Mr. Mojo Risin 2" + ENDC) keylist = list(app.config.keys()) print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******") keylist.sort() @@ -231,35 +231,35 @@ def show_settings(): # Cached values -GN_VERSION = get_setting('GN_VERSION') -HOME = get_setting('HOME') -SERVER_PORT = get_setting('SERVER_PORT') -WEBSERVER_MODE = get_setting('WEBSERVER_MODE') -GN2_BASE_URL = get_setting('GN2_BASE_URL') -GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL') -GN_SERVER_URL = get_setting('GN_SERVER_URL') -SERVER_PORT = get_setting_int('SERVER_PORT') -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') -JS_GUIX_PATH = get_setting('JS_GUIX_PATH') +GN_VERSION = get_setting('GN_VERSION') +HOME = get_setting('HOME') +SERVER_PORT = get_setting('SERVER_PORT') +WEBSERVER_MODE = get_setting('WEBSERVER_MODE') +GN2_BASE_URL = get_setting('GN2_BASE_URL') +GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL') +GN_SERVER_URL = get_setting('GN_SERVER_URL') +SERVER_PORT = get_setting_int('SERVER_PORT') +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') +JS_GUIX_PATH = get_setting('JS_GUIX_PATH') assert_dir(JS_GUIX_PATH) -JS_GN_PATH = get_setting('JS_GN_PATH') +JS_GN_PATH = get_setting('JS_GN_PATH') # assert_dir(JS_GN_PATH) GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID') GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET') if GITHUB_CLIENT_ID != 'UNKNOWN' and GITHUB_CLIENT_SECRET: GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id=" + \ - GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET + GITHUB_CLIENT_ID + "&client_secret=" + GITHUB_CLIENT_SECRET GITHUB_API_URL = get_setting('GITHUB_API_URL') ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID') @@ -267,7 +267,7 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET') ORCID_AUTH_URL = None if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET: ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \ - ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" + ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST') @@ -279,28 +279,28 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT') SMTP_USERNAME = get_setting('SMTP_USERNAME') SMTP_PASSWORD = get_setting('SMTP_PASSWORD') -REAPER_COMMAND = app_set("REAPER_COMMAND", reaper_command()) -GEMMA_COMMAND = app_set("GEMMA_COMMAND", gemma_command()) +REAPER_COMMAND = app_set("REAPER_COMMAND", reaper_command()) +GEMMA_COMMAND = app_set("GEMMA_COMMAND", gemma_command()) assert(GEMMA_COMMAND is not None) -PLINK_COMMAND = app_set("PLINK_COMMAND", plink_command()) +PLINK_COMMAND = app_set("PLINK_COMMAND", plink_command()) GEMMA_WRAPPER_COMMAND = gemma_wrapper_command() -TEMPDIR = tempdir() # defaults to UNIX TMPDIR +TEMPDIR = tempdir() # defaults to UNIX TMPDIR assert_dir(TEMPDIR) # ---- Handle specific JS modules JS_GUIX_PATH = get_setting("JS_GUIX_PATH") assert_dir(JS_GUIX_PATH) -assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom') +assert_dir(JS_GUIX_PATH + '/cytoscape-panzoom') CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS # assert_dir(JS_PATH) JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher")) assert_dir(JS_TWITTER_POST_FETCHER_PATH) -assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") +assert_file(JS_TWITTER_POST_FETCHER_PATH + "/js/twitterFetcher_min.js") JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH", js_path("cytoscape")) assert_dir(JS_CYTOSCAPE_PATH) -assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js') +assert_file(JS_CYTOSCAPE_PATH + '/cytoscape.min.js') # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") -- cgit v1.2.3