[PATCH 018/100] Find external tools: refactored code to work with GNU Guix

3 files changed, 56 insertions, 52 deletions

diff --git a/etc/default_settings.py b/etc/default_settings.py
index 0c7d7bad..929bd687 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -1,3 +1,5 @@
+import os
+
 LOGFILE = "/var/log/genenetwork/wqflask.log"
 
 # This is needed because Flask turns key errors into a
@@ -20,5 +22,7 @@ SERVER_PORT = 5003
 SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
 
 # Path overrides for Genenetwork
-# PYLMM_PATH = 'UNUSED'
-
+HOME=os.environ.get('HOME')
+PYLMM_PATH = HOME+"/izip/git/opensource/python/pylmm_gn2/"
+PLINK_PATH = HOME+"/.guix-profile/bin"
+GEMMA_PATH = HOME+"/.guix-profile/bin"
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index b8a41f60..0db195df 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -9,76 +9,70 @@ 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(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 = get_valid_path(os.environ.get(id))
+    path = find_path(os.environ.get(id))
     # ---- Check whether setting exists
     setting = app.config.get(id)
     if not path:
-        path = get_valid_path(setting)
+        path = find_path(setting)
     # ---- Check whether default exists
     if not path:
-        path = get_valid_path(default)
+        path = find_path(default)
     # ---- Guess directory
     if not path:
+        guess = os.environ.get('HOME')+guess
         if not setting:
             setting = guess
-        path = get_valid_path(guess)
+        path = find_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')
-
+        raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the path')
     return path
 
-def pylmm_command(default=None):
-    """
-    Return the path to the repository and the python command to call
-    """
-    def get_valid_path(path):
+def find_command(command,id1,default,guess):
+    def find_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'):
+            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
 
-    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):
-    """
-    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 PLINK_PATH in "+path+"\n")
-        if path and os.path.isfile(path+'/plink'):
-            return path
-        else:
-            None
+    path = get_setting(id1,default,guess,find_path)
+    binary = path+'/'+command
+    sys.stderr.write("Found "+binary+"\n")
+    return path,binary
 
-    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 pylmm_command(default=None):
+    return find_command('pylmm_gn2/lmm.py',"PYLMM_PATH",default,'/pylmm2')
 
 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
+    return find_command('gemma',"GEMMA_PATH",default,'/gemma')
 
-    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
+def plink_command(default=None):
+    return find_command('plink2',"PLINK_PATH",default,'/plink')
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index af320f65..a657510d 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -42,9 +42,15 @@ from wqflask.marker_regression import gemma_mapping
 #from wqflask.marker_regression import plink_mapping
 #from wqflask.marker_regression import rqtl_mapping
 
+# Check for valid binary paths of pylmm, plink, rqtl etc. This code
+# runs at startup, so a missing binary will balk before running the
+# service
+
+GEMMA_PATH,GEMMA_COMMAND = gemma_command()
 PYLMM_PATH,PYLMM_COMMAND = pylmm_command()
 PLINK_PATH,PLINK_COMMAND = plink_command()
-GEMMA_PATH,GEMMA_COMMAND = gemma_command()
+# RQTL_PATH,RQTL_COMMAND   = rqtl_command()
+
 
 class MarkerRegression(object):