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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(command_id,guess=None):
"""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 and returns the full path to
the binary command
guess = os.environ.get('HOME')+'/pylmm'
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 path "+command+"\n")
return command
else:
return None
# ---- Check whether environment exists
sys.stderr.write("Looking for "+command_id+"\n")
command = value(os.environ.get(command_id))
if not command:
# ---- Check whether setting exists in app
command = value(app.config.get(command_id))
if not command:
command = value(guess)
if not command:
raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path')
return command
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_RUN",guess))
def gemma_command(guess=None):
return valid_bin(get_setting("GEMMA_RUN",guess))
def plink_command(guess=None):
return valid_bin(get_setting("PLINK_RUN",guess))
def flat_files(subdir=None):
base = get_setting("GENENETWORK_FILES")
if subdir:
return valid_path(base+"/"+subdir)
return valid_path(base)
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):
print("Found: file "+lookfor+"\n")
return lookfor
else:
raise IOError("Can not locate "+lookfor)
if subdir: sys.stderr.write(subdir)
raise IOError("Can not locate "+name+" in "+base)
def locate_without_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):
print("Found: file "+name+"\n")
return lookfor
sys.stderr.write("WARNING: file "+name+" not found\n")
return None
def tempdir():
return valid_path(get_setting("TEMPDIR","/tmp"))
# Cached values
PYLMM_COMMAND = pylmm_command()
GEMMA_COMMAND = pylmm_command()
PLINK_COMMAND = pylmm_command()
FLAT_FILES = flat_files()
TEMPDIR = tempdir()
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