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Diffstat (limited to 'wqflask/utility/tools.py')
| -rw-r--r-- | wqflask/utility/tools.py | 357 |
1 files changed, 0 insertions, 357 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py deleted file mode 100644 index 283b0408..00000000 --- a/wqflask/utility/tools.py +++ /dev/null @@ -1,357 +0,0 @@ -# Tools/paths finder resolves external paths from settings and/or environment -# variables - -import os -import sys -import json -import socket -from pathlib import Path - -from wqflask import app - -# Use the standard logger here to avoid a circular dependency -import logging -logger = logging.getLogger(__name__) - - -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 == "": - # ---- 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 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 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 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 assert_bin(fn): - if not valid_bin(fn): - raise Exception("ERROR: can not find binary " + fn) - return fn - - -def assert_dir(the_dir): - if not valid_path(the_dir): - raise FileNotFoundError(f"ERROR: can not find directory '{the_dir}'") - return the_dir - - -def assert_writable_dir(dir): - try: - fn = os.path.join(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 assert_file(fn): - if not valid_file(fn): - raise FileNotFoundError(f"Unable to find file '{fn}'") - return fn - - -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): - 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")) - - -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), - file=sys.stderr) - log_level = getattr(logging, LOG_LEVEL.upper()) - logging.basicConfig(level=log_level) - - logger.info(BLUE + "Mr. Mojo Risin 2" + ENDC) - keylist = list(app.config.keys()) - print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******", - file=sys.stderr) - keylist.sort() - for k in keylist: - try: - print(("%s: %s%s%s%s" % (k, BLUE, BOLD, get_setting(k), ENDC)), - file=sys.stderr) - except: - print(("%s: %s%s%s%s" % (k, GREEN, BOLD, app.config[k], ENDC)), - file=sys.stderr) - -def gn_version_repo_info(root_dir): - """retrieve the branch name and abbreviated commit hash.""" - try: - from git import Repo - repo = Repo(root_dir) - return f"{repo.head.ref.name}-{repo.head.commit.hexsha[0:9]}" - except: - return "" - -def gn_version(): - """Compute and return the version of the application.""" - hostname = socket.gethostname() - basedir = Path(__file__).absolute().parent.parent.parent - with open(Path(basedir, "etc", "VERSION"), encoding="utf8") as version_file: - version_contents = version_file.read().strip() - base_version = f"{hostname}:{basedir.name}:{version_contents}" - repo_info = gn_version_repo_info(basedir) - return f"{base_version}-{repo_info}" if bool(repo_info) else base_version - -# Cached values -GN_VERSION = 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') -AUTH_SERVER_URL = get_setting('AUTH_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") - -AUTH_SERVER_URL = get_setting("AUTH_SERVER_URL") -OAUTH2_CLIENT_ID = get_setting('OAUTH2_CLIENT_ID') -OAUTH2_CLIENT_SECRET = get_setting('OAUTH2_CLIENT_SECRET') |