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authorzsloan2016-05-17 16:03:05 +0000
committerzsloan2016-05-17 16:03:05 +0000
commit0d590051ce073a169295382e5adac34cc803e5ac (patch)
tree76bea6f1f69288a498e9f13d20b638b942ab0a0c /wqflask/utility/tools.py
parentf6cee1731772c3482b0afd4c77472d69e747c655 (diff)
parent04afa563e6d53fe2a91ac2e6eb4af2f2fa5d5c3b (diff)
downloadgenenetwork2-0d590051ce073a169295382e5adac34cc803e5ac.tar.gz
Merge branch 'staging' of github.com:genenetwork/genenetwork2
Diffstat (limited to 'wqflask/utility/tools.py')
-rw-r--r--wqflask/utility/tools.py189
1 files changed, 121 insertions, 68 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index b8a41f60..dd8c4a1e 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -1,84 +1,137 @@
# 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,get_valid_path):
- """
- Resolve a setting from the environment or the global settings in app.config
+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
- path = get_valid_path(os.environ.get(id))
- # ---- Check whether setting exists
- setting = app.config.get(id)
- if not path:
- path = get_valid_path(setting)
- # ---- Check whether default exists
- if not path:
- path = get_valid_path(default)
- # ---- Guess directory
- if not path:
- if not setting:
- setting = guess
- path = get_valid_path(guess)
- if not path:
- raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the root of the git repository')
-
- return path
-
-def pylmm_command(default=None):
+ 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_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):
"""
- Return the path to the repository and the python command to call
+ Locate a static flat file in the GENENETWORK_FILES environment.
+
+ This function throws an error when the file is not found.
"""
- def get_valid_path(path):
- """Test for a valid repository"""
- if path:
- sys.stderr.write("Trying PYLMM_PATH in "+path+"\n")
- if path and os.path.isfile(path+'/pylmm_gn2/lmm.py'):
- return path
+ 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:
- None
+ raise Exception("Can not locate "+lookfor)
+ if subdir: sys.stderr.write(subdir)
+ raise Exception("Can not locate "+name+" in "+base)
- guess = os.environ.get('HOME')+'/pylmm_gn2'
- path = get_setting('PYLMM_PATH',default,guess,get_valid_path)
- pylmm_command = 'python '+path+'/pylmm_gn2/lmm.py'
- return path,pylmm_command
-
-def plink_command(default=None):
+def locate_ignore_error(name, subdir=None):
"""
- Return the path to the repository and the python command to call
+ 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.
"""
- def get_valid_path(path):
- """Test for a valid repository"""
- if path:
- sys.stderr.write("Trying PLINK_PATH in "+path+"\n")
- if path and os.path.isfile(path+'/plink'):
- return path
- else:
- None
-
- guess = os.environ.get('HOME')+'/plink_gemma'
- path = get_setting('PLINK_PATH',default,guess,get_valid_path)
- plink_command = path+'/plink'
- return path,plink_command
-
-def gemma_command(default=None):
- def get_valid_path(path):
- """Test for a valid repository"""
- if path:
- sys.stderr.write("Trying PLINK_PATH in "+path+"\n")
- if path and os.path.isfile(path+'/plink'):
- return path
- else:
- 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"))
- guess = os.environ.get('HOME')+'/plink'
- path = get_setting('PLINK_PATH',default,guess,get_valid_path)
- gemma_command = path+'/gemma'
- return path, gemma_command \ No newline at end of file
+
+# Cached values
+PYLMM_COMMAND = pylmm_command()
+GEMMA_COMMAND = gemma_command()
+PLINK_COMMAND = plink_command()
+FLAT_FILES = flat_files()
+TEMPDIR = tempdir()