blob: 27522187eceff23f44f8f91a273b06bc7cf630bf (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
|
# Default settings file defines a single Flask process for the Python
# webserver running in developer mode with limited console
# output. Copy this file and run it from ./bin/genenetwork2 configfile
#
# Note: these settings are fetched in ./wqflask/utilities/tools.py
# which has support for overriding them through environment variables,
# e.g.
#
# env LOG_SQL=True USE_REDIS=False ./bin/genenetwork2
# env LOG_LEVEL=DEBUG ./bin/genenetwork2 ~/gn2_settings.py
#
# Typically you need to set GN2_PROFILE too.
#
# Note also that in the near future we will additionally fetch
# settings from a JSON file
#
# Note: values for False and 0 have to be strings here - otherwise
# Flask won't pick them up
#
# For GNU Guix deployment also check the paths in
#
# ~/.guix-profile/lib/python3.8/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py
import os
import sys
GN_VERSION = open("../etc/VERSION", "r").read()
GN_SERVER_URL = "http://localhost:8880/" # REST API server
# ---- MySQL
SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
SQL_ALCHEMY_POOL_RECYCLE = 3600
GN_SERVER_URL = "http://localhost:8880/" # REST API server
GN2_BASE_URL = "http://genenetwork.org/" # to pick up REST API
GN2_BRANCH_URL = GN2_BASE_URL
# ---- Flask configuration (see website)
TRAP_BAD_REQUEST_ERRORS = True
SECURITY_CONFIRMABLE = True
SECURITY_TRACKABLE = True
SECURITY_REGISTERABLE = True
SECURITY_RECOVERABLE = True
SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org"
SECURITY_POST_LOGIN_VIEW = "/thank_you"
# ---- SERVER_PORT needs an override before firing up the server
SERVER_PORT = os.environ['SERVER_PORT']
if isinstance(SERVER_PORT, str):
SERVER_PORT = int(SERVER_PORT) # don't do this for other settings!
else:
SERVER_PORT = 5003
SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
GITHUB_CLIENT_ID = "UNKNOWN"
GITHUB_CLIENT_SECRET = "UNKNOWN"
GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize"
GITHUB_API_URL = "https://api.github.com/user"
ORCID_CLIENT_ID = "UNKNOWN"
ORCID_CLIENT_SECRET = "UNKNOWN"
ORCID_AUTH_URL = "https://orcid.org/oauth/authorize"
ORCID_TOKEN_URL = "https://orcid.org/oauth/token"
ELASTICSEARCH_HOST = "localhost"
ELASTICSEARCH_PORT = '9200'
SMTP_CONNECT = "localhost"
SMTP_USERNAME = "UNKNOWN"
SMTP_PASSWORD = "UNKNOWN"
# ---- Behavioural settings (defaults) note that logger and log levels can
# be overridden at the module level and with enviroment settings
WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD)
WEBSERVER_BRANDING = None # Set the branding (nyi)
WEBSERVER_DEPLOY = None # Deployment specifics (nyi)
WEBSERVER_URL = "http://localhost:"+str(SERVER_PORT)+"/" # external URL
LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
LOG_LEVEL_DEBUG = '0' # logger.debugf log level (0-5, 5 = show all)
LOG_SQL = 'False' # Log SQL/backend and GN_SERVER calls
LOG_SQL_ALCHEMY = 'False'
LOG_BENCH = True # Log bench marks
USE_REDIS = True # REDIS caching (note that redis will be phased out)
USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls
HOME = os.environ['HOME']
# ---- Default locations
GENENETWORK_FILES = HOME+"/genotype_files" # base dir for all static data files
# ---- Path overrides for Genenetwork - the defaults are normally
# picked up from Guix or in the HOME directory
# TMPDIR is normally picked up from the environment
# PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files (unused)
# ---- Local path to JS libraries - for development modules (only)
JS_GN_PATH = os.environ['HOME']+"/genenetwork/javascript"
# ---- GN2 Executables (overwrite for testing only)
# PLINK_COMMAND = str.strip(os.popen("which plink2").read())
# GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
REAPER_COMMAND = os.environ['GN2_PROFILE'] + "/bin/qtlreaper"
# GEMMA_WRAPPER_COMMAND = str.strip(os.popen("which gemma-wrapper").read())
|
