Merge https://github.com/genenetwork/genenetwork2

2 files changed, 85 insertions, 16 deletions

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
new file mode 100644
index 00000000..760ded7c
--- /dev/null
+++ b/wqflask/utility/tools.py
@@ -0,0 +1,84 @@
+# 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
+
+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
+
+    guess = os.environ.get('HOME')+'/plink'
+    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
+
+    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
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 4d7981d9..f842dde0 100755
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -43,6 +43,7 @@ ParInfo ={
 'BXH':['BHF1', 'HBF1',  'C57BL/6J', 'C3H/HeJ'],
 'AKXD':['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
 'BXD':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+'C57BL-6JxC57BL-6NJF2':['', '', 'C57BL/6J', 'C57BL/6NJ'],
 'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
 'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
 'BHHBF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
@@ -880,22 +881,6 @@ def cmpGenoPos(A,B):
     except:
         return 0
 
-#XZhou: Must use "BINARY" to enable case sensitive comparison.
-def authUser(name,password,db, encrypt=None):
-    try:
-        if encrypt:
-            query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY \'%s\'' % (name,password)
-        else:
-            query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY SHA(\'%s\')' % (name,password)
-        db.execute(query)
-        records = db.fetchone()
-        if not records:
-            raise ValueError
-        return records#(privilege,id,name,password,grpName)
-    except:
-        return (None, None, None, None, None)
-
-
 def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
     access_to_confidential_phenotype_trait = 0
     if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']: