Merge pull request #39 from pjotrp/master

Refactoring finding tools such as pylmm

INSTALL.md

@@ -82,8 +82,8 @@ Next update the setting.py file to point at the tree
 
 GN2 can locate PYLMM through PYLMM_PATH in setting.py (or in ENV)
 
-    PYLMM_PATH = '/home/test/opensource/python/pylmm_gn2/pylmm_gn2'
+    PYLMM_PATH = '/home/test/opensource/python/pylmm_gn2'
 
 ## Other information
 
-Check also the ./misc/ directory for settings
+Check also the ./misc/ directory for settings

wqflask/utility/tools.py

@@ -0,0 +1,51 @@
+# 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
+    """
+    # ---- 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):
+    """
+    Return the path to the repository and the python command to call
+    """
+    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
+        else:
+            None
+
+    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

wqflask/wqflask/marker_regression/marker_regression.py

@@ -25,7 +25,6 @@
 Redis = Redis()
 
 from flask import Flask, g
-from wqflask import app
 
 from base.trait import GeneralTrait
 from base import data_set
@@ -36,23 +35,13 @@
 #from wqflask.marker_regression import plink_mapping
 from wqflask.marker_regression import gemma_mapping
 #from wqflask.marker_regression import rqtl_mapping
-from wqflask.my_pylmm.data import prep_data
-# from wqflask.my_pylmm.pyLMM import lmm
-# from wqflask.my_pylmm.pyLMM import input
 from utility import helper_functions
 from utility import Plot, Bunch
 from utility import temp_data
-
 from utility.benchmark import Bench
+from utility.tools import pylmm_command
 
-import os
-if os.environ.get('PYLMM_PATH') is None:
-    PYLMM_PATH=app.config.get('PYLMM_PATH')
-    if PYLMM_PATH is None:
-        PYLMM_PATH=os.environ['HOME']+'/gene/wqflask/wqflask/my_pylmm/pyLMM'
-if not os.path.isfile(PYLMM_PATH+'/lmm.py'):
-    raise Exception('PYLMM_PATH '+PYLMM_PATH+' unknown or faulty')
-PYLMM_COMMAND= 'python '+PYLMM_PATH+'/lmm.py'
+PYLMM_PATH,PYLMM_COMMAND = pylmm_command()
 
 class MarkerRegression(object):