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# Tools/paths finder resolves external paths from settings and/or environment
# variables
import os
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)
def js_path(app, module=None):
"""
Find the JS module in the two paths
"""
try_gn = get_setting(app, "JS_GN_PATH") + "/" + module
if valid_path(try_gn):
return try_gn
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(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
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