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# Tools/paths finder resolves external paths from settings and/or environment
# variables
#
# Currently supported:
#
# PYLMM_PATH finds the root of the git repository of the pylmm_gn2 tool
import os
import sys
from wqflask import app
def get_setting(id,default,guess,find_path):
"""Resolve a setting from the environment or the global settings in
app.config, with get_valid_path is a function checking whether the
path points to an expected directory an returns the full path e.g.
guess = os.environ.get('HOME')+'/pylmm'
get_setting('PYLMM_PATH',default,guess,get_valid_path)
first tries the environment variable in +id+, next gets the Flask
app setting for the same +id+, next tries the path passed in with
+default+ and finally does an educated +guess+.
In all, the environment overrides the others, next is the flask
setting, then the default and finally the guess (which is
$HOME/repo). A valid path 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).
"""
# ---- Check whether environment exists
path = find_path(os.environ.get(id))
# ---- Check whether setting exists
setting = app.config.get(id)
if not path:
path = find_path(setting)
# ---- Check whether default exists
if not path:
path = find_path(default)
# ---- Guess directory
if not path:
guess = os.environ.get('HOME')+guess
if not setting:
setting = guess
path = find_path(guess)
if not path:
raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the path')
return path
def find_command(command,id1,default,guess):
def find_path(path):
"""Test for a valid repository"""
if path:
sys.stderr.write("Trying "+id1+" in "+path+"\n")
binary = str.split(command)[0]
if path and os.path.isfile(path+'/'+binary):
return path
else:
None
path = get_setting(id1,default,guess,find_path)
binary = path+'/'+command
sys.stderr.write("Found "+binary+"\n")
return path,binary
def pylmm_command(default=None):
return find_command('pylmm_gn2/lmm.py',"PYLMM_PATH",default,'/pylmm2')
def gemma_command(default=None):
return find_command('gemma',"GEMMA_PATH",default,'/gemma')
def plink_command(default=None):
return find_command('plink2',"PLINK_PATH",default,'/plink')
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