[PATCH 023/100] WIP fixing all paths

1 files changed, 36 insertions, 46 deletions

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 0db195df..c3c9b292 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -9,22 +9,22 @@ import os
 import sys
 from wqflask import app
 
-def get_setting(id,default,guess,find_path):
+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 an returns the full path e.g.
+    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',default,guess,get_valid_path)
+      get_setting('PYLMM_PATH',guess)
 
     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+.
+    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 default and finally the guess (which is
-    $HOME/repo). A valid path is returned. If none is resolved an
-    exception is thrown.
+    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
@@ -33,46 +33,36 @@ def get_setting(id,default,guess,find_path):
     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
+    def valid(command):
+        if command:
+            sys.stderr.write("Found value "+command+"\n")
+            return command
         else:
-            None
+            return None
+    
+    # ---- Check whether environment exists
+    sys.stderr.write("Looking for "+command_id+"\n")
+    command = valid(os.environ.get(command_id))
+    if not command:
+        # ---- Check whether setting exists in app
+        command = valid(app.config.get(command_id))
+        if not command:
+            command = valid(guess)
+            if not command:
+                raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path')
+    return command
 
-    path = get_setting(id1,default,guess,find_path)
-    binary = path+'/'+command
-    sys.stderr.write("Found "+binary+"\n")
-    return path,binary
+def pylmm_command(guess=None):
+    return get_setting("PYLMM_RUN",guess)
 
-def pylmm_command(default=None):
-    return find_command('pylmm_gn2/lmm.py',"PYLMM_PATH",default,'/pylmm2')
+def gemma_command(guess=None):
+    return get_setting("GEMMA_RUN",guess)
 
-def gemma_command(default=None):
-    return find_command('gemma',"GEMMA_PATH",default,'/gemma')
+def plink_command(guess=None):
+    return get_setting("PLINK_RUN",guess)
 
-def plink_command(default=None):
-    return find_command('plink2',"PLINK_PATH",default,'/plink')
+def flat_files(subdir=None):
+    base = get_setting("GENENETWORK_FILES")
+    if subdir:
+        return base+"/"+subdir
+    return base