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
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
|
# Tools/paths finder resolves external paths from settings and/or environment
# variables
import os
import sys
from wqflask import app
# Use the standard logger here to avoid a circular dependency
import logging
logger = logging.getLogger(__name__ )
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")
return command
else:
return None
# ---- Check whether environment exists
logger.debug("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?).')
logger.debug("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 pylmm_command(guess=None):
return valid_bin(get_setting("PYLMM_COMMAND",guess))
def gemma_command(guess=None):
return valid_bin(get_setting("GEMMA_COMMAND",guess))
def plink_command(guess=None):
return valid_bin(get_setting("PLINK_COMMAND",guess))
def flat_files(subdir=None):
base = get_setting("GENENETWORK_FILES")
if subdir:
return assert_dir(base+"/"+subdir)
return assert_dir(base)
def assert_dir(dir):
if not valid_path(dir):
raise Exception("ERROR: can not find directory "+dir)
return dir
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):
logger.info("Found: file "+lookfor+"\n")
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_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):
logger.debug("Found: file "+name+"\n")
return lookfor
logger.info("WARNING: file "+name+" not found\n")
return None
def tempdir():
return valid_path(get_setting("TEMPDIR","/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)
log_level = getattr(logging, LOG_LEVEL.upper())
logging.basicConfig(level=log_level)
logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
print "runserver.py: ****** The webserver has the following configuration ******"
keylist = app.config.keys()
keylist.sort()
for k in keylist:
try:
print("%s %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC))
except:
print("%s %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC))
# Cached values
WEBSERVER_MODE = get_setting('WEBSERVER_MODE')
GN_SERVER_URL = get_setting('GN_SERVER_URL')
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_SQLALCHEMY = get_setting_bool('LOG_SQLALCHEMY')
LOG_BENCH = get_setting_bool('LOG_BENCH')
LOG_FORMAT = "%(message)s" # not yet in use
USE_REDIS = get_setting_bool('USE_REDIS')
USE_GN_SERVER = get_setting_bool('USE_GN_SERVER')
PYLMM_COMMAND = pylmm_command()
GEMMA_COMMAND = gemma_command()
PLINK_COMMAND = plink_command()
FLAT_FILES = flat_files()
TEMPDIR = tempdir()
|
