# 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 gn2.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
gn2/default_settings.py or override them yourself by creating a
different settings.py file (or setting the environment).
"""
def value(command):
if command:
app_set(command_id, command)
return command
return app.config.get(command_id)
# ---- Check whether environment exists
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 == "":
raise Exception(
command_id + ' setting unknown or faulty (update default_settings.py?).')
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 gn2.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 ""
# Cached values
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")
