diff options
Diffstat (limited to 'wqflask/utility/tools.py')
| -rw-r--r-- | wqflask/utility/tools.py | 364 |
1 files changed, 121 insertions, 243 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 894bef76..feb1a674 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -1,267 +1,145 @@ # Tools/paths finder resolves external paths from settings and/or environment # variables - import os -import sys -import json - -from wqflask import app from .configuration import ( mk_dir, + tempdir, valid_bin, valid_file, valid_path, assert_bin, assert_dir, assert_file, + get_setting, + get_setting_int, + get_setting_bool, assert_writable_dir) -# Use the standard logger here to avoid a circular dependency -import logging -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 - 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") - app_set(command_id, command) - return command - else: - return app.config.get(command_id) - - # ---- Check whether environment exists - # 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 - 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?).') - # print("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 js_path(module=None): +def js_path(app, module=None): """ Find the JS module in the two paths """ - try_gn = get_setting("JS_GN_PATH") + "/" + module + try_gn = get_setting(app, "JS_GN_PATH") + "/" + module if valid_path(try_gn): return try_gn - try_guix = get_setting("JS_GUIX_PATH") + "/" + module + try_guix = get_setting(app, "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 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 assert_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 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): - 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_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. - - 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): - return lookfor - return None - - -def tempdir(): - """ - Get UNIX TMPDIR by default - """ - return valid_path(get_setting("TMPDIR", "/tmp")) - - -# 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') -GN_PROXY_URL = get_setting('GN_PROXY_URL') -GN3_LOCAL_URL = get_setting('GN3_LOCAL_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') -REDIS_URL = get_setting('REDIS_URL') -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') -# assert_dir(JS_GN_PATH) - -GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID') -GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET') -GITHUB_AUTH_URL = "" -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 + \ - "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" - ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') - - -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 = 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") - -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(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") - -OAUTH2_CLIENT_ID = get_setting('OAUTH2_CLIENT_ID') -OAUTH2_CLIENT_SECRET = get_setting('OAUTH2_CLIENT_SECRET') +def reaper_command(app, guess=None): + return get_setting(app, "REAPER_COMMAND", guess) + +def gemma_command(app, guess=None): + return assert_bin(get_setting(app, "GEMMA_COMMAND", guess)) + +def gemma_wrapper_command(app, guess=None): + return assert_bin(get_setting(app, "GEMMA_WRAPPER_COMMAND", guess)) + +def plink_command(app, guess=None): + return assert_bin(get_setting(app, "PLINK_COMMAND", guess)) + +def set_mandatory_settings(app): + """Set up the mandatory settings.""" + ## Setup profile dependent settings: Remove these eventually ## + GN2_PROFILE = get_setting(app, "GN2_PROFILE", os.environ.get("GN2_PROFILE")) + app.config["GN2_PROFILE"] = GN2_PROFILE + app.config["JS_GUIX_PATH"] = get_setting( + app, + "JS_GUIX_PATH", + f"{GN2_PROFILE}/share/genenetwork2/javascript") + app.config["REAPER_COMMAND"] = reaper_command(app) + app.config["GEMMA_COMMAND"] = gemma_command(app, f"{GN2_PROFILE}/bin/gemma") + assert(app.config["GEMMA_COMMAND"] is not None) + app.config["PLINK_COMMAND"] = plink_command( + app, f"{GN2_PROFILE}/bin/plink2") + app.config["GEMMA_WRAPPER_COMMAND"] = gemma_wrapper_command( + app, f"{GN2_PROFILE}/bin/gemma-wrapper") + app.config["GUIX_GENENETWORK_FILES"] = get_setting( + app, + "GUIX_GENENETWORK_FILES", + f"{GN2_PROFILE}/share/genenetwork2") + assert_dir(app.config["JS_GUIX_PATH"]) + ## END: Setup profile dependent settings: Remove these eventually ## + + # Cached values + app.config["GN_VERSION"] = get_setting(app, 'GN_VERSION') + app.config["HOME"] = get_setting(app, 'HOME') + app.config["SERVER_PORT"] = get_setting_int(app, 'SERVER_PORT') + app.config["WEBSERVER_MODE"] = get_setting(app, 'WEBSERVER_MODE') + app.config["GN2_BASE_URL"] = get_setting(app, 'GN2_BASE_URL') + app.config["GN2_BRANCH_URL"] = get_setting(app, 'GN2_BRANCH_URL') + app.config["GN_SERVER_URL"] = get_setting(app, 'GN_SERVER_URL') + app.config["GN_PROXY_URL"] = get_setting(app, 'GN_PROXY_URL') + app.config["GN3_LOCAL_URL"] = get_setting(app, 'GN3_LOCAL_URL') + app.config["SQL_URI"] = get_setting(app, 'SQL_URI') + app.config["LOG_LEVEL"] = get_setting(app, 'LOG_LEVEL') + app.config["LOG_LEVEL_DEBUG"] = get_setting_int(app, 'LOG_LEVEL_DEBUG') + app.config["LOG_SQL"] = get_setting_bool(app, 'LOG_SQL') + app.config["LOG_SQL_ALCHEMY"] = get_setting_bool(app, 'LOG_SQL_ALCHEMY') + app.config["LOG_BENCH"] = get_setting_bool(app, 'LOG_BENCH') + app.config["LOG_FORMAT"] = "%(message)s" # not yet in use + app.config["USE_REDIS"] = get_setting_bool(app, 'USE_REDIS') + app.config["REDIS_URL"] = get_setting(app, 'REDIS_URL') + app.config["USE_GN_SERVER"] = get_setting_bool(app, 'USE_GN_SERVER') + + app.config["GENENETWORK_FILES"] = get_setting(app, 'GENENETWORK_FILES') + app.config["JS_GN_PATH"] = get_setting(app, 'JS_GN_PATH') + # assert_dir(JS_GN_PATH) + + app.config["GITHUB_CLIENT_ID"] = get_setting(app, 'GITHUB_CLIENT_ID') + app.config["GITHUB_CLIENT_SECRET"] = get_setting(app, 'GITHUB_CLIENT_SECRET') + app.config["GITHUB_AUTH_URL"] = get_setting(app, "GITHUB_AUTH_URL") + if app.config["GITHUB_CLIENT_ID"] != 'UNKNOWN' and app.config["GITHUB_CLIENT_SECRET"]: + app.config["GITHUB_AUTH_URL"] = ( + "https://github.com/login/oauth/authorize?" + f"client_id={GITHUB_CLIENT_ID}" + f"&client_secret={GITHUB_CLIENT_SECRET}") + app.config["GITHUB_API_URL"] = get_setting(app, 'GITHUB_API_URL') + + app.config["ORCID_CLIENT_ID"] = get_setting(app, 'ORCID_CLIENT_ID') + app.config["ORCID_CLIENT_SECRET"] = get_setting(app, 'ORCID_CLIENT_SECRET') + app.config["ORCID_AUTH_URL"] = get_setting(app, "ORCID_AUTH_URL") + if app.config["ORCID_CLIENT_ID"] != 'UNKNOWN' and app.config["ORCID_CLIENT_SECRET"]: + app.config["ORCID_AUTH_URL"] = ( + "https://orcid.org/oauth/authorize?response_type=code" + f"&scope=/authenticate&show_login=true&client_id={ORCID_CLIENT_ID}" + f"&client_secret={ORCID_CLIENT_SECRET}" + f"&redirect_uri={GN2_BRANCH_URL}n/login/orcid_oauth2") + app.config["ORCID_TOKEN_URL"] = get_setting(app, 'ORCID_TOKEN_URL') + + + app.config["SMTP_CONNECT"] = get_setting(app, 'SMTP_CONNECT') + app.config["SMTP_USERNAME"] = get_setting(app, 'SMTP_USERNAME') + app.config["SMTP_PASSWORD"] = get_setting(app, 'SMTP_PASSWORD') + + app.config["TEMPDIR"] = tempdir(app) # defaults to UNIX TMPDIR + assert_dir(app.config["TEMPDIR"]) + + # ---- Handle specific JS modules + app.config["JS_GUIX_PATH"] = get_setting(app, "JS_GUIX_PATH") + assert_dir(app.config["JS_GUIX_PATH"]) + assert_dir(app.config["JS_GUIX_PATH"] + '/cytoscape-panzoom') + + app.config["CSS_PATH"] = get_setting(app, "JS_GUIX_PATH") # The CSS is bundled together with the JS + # assert_dir(JS_PATH) + + app.config["JS_TWITTER_POST_FETCHER_PATH"] = get_setting( + app, + "JS_TWITTER_POST_FETCHER_PATH", + js_path(app, "javascript-twitter-post-fetcher")) + assert_dir(app.config["JS_TWITTER_POST_FETCHER_PATH"]) + assert_file(app.config["JS_TWITTER_POST_FETCHER_PATH"] + "/js/twitterFetcher_min.js") + + app.config["JS_CYTOSCAPE_PATH"] = get_setting( + app, "JS_CYTOSCAPE_PATH", js_path(app, "cytoscape")) + assert_dir(app.config["JS_CYTOSCAPE_PATH"]) + assert_file(app.config["JS_CYTOSCAPE_PATH"] + '/cytoscape.min.js') + + # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") + + app.config["OAUTH2_CLIENT_ID"] = get_setting(app, 'OAUTH2_CLIENT_ID') + app.config["OAUTH2_CLIENT_SECRET"] = get_setting(app, 'OAUTH2_CLIENT_SECRET') + return app |