diff options
Diffstat (limited to 'wqflask/utility/tools.py')
| -rw-r--r-- | wqflask/utility/tools.py | 129 |
1 files changed, 97 insertions, 32 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index c28c617a..75bddb24 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -13,6 +13,11 @@ logger = logging.getLogger(__name__ ) OVERRIDES = {} +def app_set(command_id, value): + """Set application wide value""" + app.config.setdefault(command_id,value) + return value + 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 @@ -40,15 +45,16 @@ def get_setting(command_id,guess=None): def value(command): if command: # sys.stderr.write("Found "+command+"\n") + app_set(command_id,command) return command else: return None # ---- Check whether environment exists - logger.debug("Looking for "+command_id+"\n") + # print("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": - command = OVERRIDES.get(command_id) + 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)) @@ -57,7 +63,7 @@ def get_setting(command_id,guess=None): 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)) + # print("Set "+command_id+"="+str(command)) return command def get_setting_bool(id): @@ -89,14 +95,29 @@ def valid_path(dir): return dir return None -def pylmm_command(guess=None): - return valid_bin(get_setting("PYLMM_COMMAND",guess)) +def js_path(module=None): + """ + Find the JS module in the two paths + """ + try_gn = get_setting("JS_GN_PATH")+"/"+module + if valid_path(try_gn): + return try_gn + 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)" + +def reaper_command(guess=None): + return get_setting("REAPER_COMMAND",guess) def gemma_command(guess=None): - return valid_bin(get_setting("GEMMA_COMMAND",guess)) + return assert_bin(get_setting("GEMMA_COMMAND",guess)) + +def gemma_wrapper_command(guess=None): + return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND",guess)) def plink_command(guess=None): - return valid_bin(get_setting("PLINK_COMMAND",guess)) + return assert_bin(get_setting("PLINK_COMMAND",guess)) def flat_file_exists(subdir): base = get_setting("GENENETWORK_FILES") @@ -108,6 +129,11 @@ def flat_files(subdir=None): 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) + return fn + def assert_dir(dir): if not valid_path(dir): raise Exception("ERROR: can not find directory "+dir) @@ -121,9 +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) @@ -148,6 +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. @@ -186,7 +220,7 @@ def show_settings(): logger.info(OVERRIDES) logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC) - print "runserver.py: ****** Webserver configuration ******" + print "runserver.py: ****** Webserver configuration - k,v pairs from app.config ******" keylist = app.config.keys() keylist.sort() for k in keylist: @@ -201,38 +235,69 @@ GN_VERSION = get_setting('GN_VERSION') HOME = get_setting('HOME') WEBSERVER_MODE = get_setting('WEBSERVER_MODE') 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_SQLALCHEMY = get_setting_bool('LOG_SQLALCHEMY') +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') -TEMP_TRAITS = get_setting('TEMP_TRAITS') - -PYLMM_COMMAND = pylmm_command() -GEMMA_COMMAND = gemma_command() -GEMMA_RESULTS_PATH = get_setting('GEMMA_RESULTS_PATH') -PLINK_COMMAND = plink_command() +JS_GUIX_PATH = get_setting('JS_GUIX_PATH') +assert_dir(JS_GUIX_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_API_URL = get_setting('GITHUB_API_URL') + +ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID') +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 + ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') + +ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST') +ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT') +import utility.elasticsearch_tools as es +es.test_elasticsearch_connection() + +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()) +assert(GEMMA_COMMAND is not None) +PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command()) +GEMMA_WRAPPER_COMMAND = gemma_wrapper_command() 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') + +CSS_PATH = "UNKNOWN" +# 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") + +JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape")) +assert_dir(JS_CYTOSCAPE_PATH) +assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js') -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("TWITTER_POST_FETCHER_JS_PATH")) +# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") |