Removed zach_settings.py from git tracking

Changed mysql password as a result of it being up on git before

5 files changed, 60 insertions, 48 deletions

diff --git a/misc/notes.txt b/misc/notes.txt
index 976573a6..cdd353ea 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -11,6 +11,9 @@ git add -A
 Get the default path being used when a command is typed:
 which _______
 
+Change default path python looks at when importing
+export PYTHONPATH="/home/zas1024/gene/wqflask"
+
 Get the paths checked when a user types a command:
 echo $PATH
 
@@ -67,7 +70,11 @@ Deactivate virtual environment:
 deactivate (just type deactivate)
 
 To set WQFLASK_SETTINGS environment variable:
-export WQFLASK_SETTINGS=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located)
+export WQFLASK_SETTINGS=~/zach_settings.py (or wherever file is located)
+
+zach_settings.py is the local config file with the DB_URI
+default_settings.py is the config file with the configuration information that would apply
+to any running instance of GeneNetwork
 
 To change screen environment variable (if man not working or to get color, for example):
 export TERM=screen
@@ -84,6 +91,13 @@ python runserver.py
 
 ===========================================
 
+Update user password:
+use mysql;
+UPDATE user SET password=PASSWORD('whatever') WHERE user='webqtl';
+FLUSH PRIVILEGES;
+
+===========================================
+
 Redis things
 
 Restart redis server:
diff --git a/wqflask/cfg/default_settings.py b/wqflask/cfg/default_settings.py
index 1811ccfd..53b5a96e 100644
--- a/wqflask/cfg/default_settings.py
+++ b/wqflask/cfg/default_settings.py
@@ -3,3 +3,6 @@ LOGFILE = """/tmp/flask_gn_log"""
 #This is needed because Flask turns key errors into a
 #400 bad request response with no exception/log 
 TRAP_BAD_REQUEST_ERRORS = True
+
+#SECURITY_CONFIRMABLE = True
+SECURITY_TRACKABLE = True
\ No newline at end of file
diff --git a/wqflask/cfg/zach_settings.py b/wqflask/cfg/zach_settings.py
deleted file mode 100644
index 1970bd9c..00000000
--- a/wqflask/cfg/zach_settings.py
+++ /dev/null
@@ -1,5 +0,0 @@
-LOGFILE = """/tmp/flask_gn_log"""
-
-TRAP_BAD_REQUEST_ERRORS = True
-
-DB_URI = """mysql://webqtl:f2ZypIflRM@gn.cazhbciu2y1i.us-east-1.rds.amazonaws.com/db_webqtl"""
diff --git a/wqflask/wqflask/my_pylmm/pylmmKinship.py b/wqflask/wqflask/my_pylmm/pylmmKinship.py
index 403e739d..db1449a4 100644
--- a/wqflask/wqflask/my_pylmm/pylmmKinship.py
+++ b/wqflask/wqflask/my_pylmm/pylmmKinship.py
@@ -122,7 +122,7 @@ np.savetxt(outFile,K)
 if options.saveEig:
     if options.verbose:
         sys.stderr.write("Obtaining Eigendecomposition\n")
-    Kva,Kve = linalg.eigh(K)
+    Kva, Kve = linalg.eigh(K)
     if options.verbose:
         sys.stderr.write("Saving eigendecomposition to %s.[kva | kve]\n" % outFile)
     np.savetxt(outFile+".kva",Kva)
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 590f5789..71c12941 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -26,49 +26,49 @@
     <!-- Navbar
     ================================================== -->
     <div class="navbar navbar-inverse navbar-fixed-top">
-      <div class="navbar-inner">
-        <div class="container">
-          <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-          </button>
-          <a class="brand" href="/">GeneNetwork</a>
-          <div class="nav-collapse collapse">
-            <ul class="nav">
-              <li class="active">
-                <a href="/">Home</a>
-              </li>
-              <li class="dropdown">
-                <a id="drop1" href="#" role="button" class="dropdown-toggle" data-toggle="dropdown">
-                    Search <b class="caret"></b>
-                </a>
-                    <ul class="dropdown-menu" role="menu" aria-labelledby="drop1">
-                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=tissueCorrelation">Tissue Corrleation</a></li>
-                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=snpBrowser">SNP Browser</a></li>
-                        <li class="divider"></li>
-                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=geneWiki">Gene Wiki</a></li>
+        <div class="navbar-inner">
+            <div class="container">
+                <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
+                    <span class="icon-bar"></span>
+                    <span class="icon-bar"></span>
+                    <span class="icon-bar"></span>
+                </button>
+                <a class="brand" href="/">GeneNetwork</a>
+                <div class="nav-collapse collapse">
+                    <ul class="nav">
+                        <li class="active">
+                            <a href="/">Home</a>
+                        </li>
+                        <li class="dropdown">
+                        <a id="drop1" href="#" role="button" class="dropdown-toggle" data-toggle="dropdown">
+                            Search <b class="caret"></b>
+                        </a>
+                            <ul class="dropdown-menu" role="menu" aria-labelledby="drop1">
+                                <li><a tabindex="-1" href="/webqtl/main.py?FormID=tissueCorrelation">Tissue Corrleation</a></li>
+                                <li><a tabindex="-1" href="/webqtl/main.py?FormID=snpBrowser">SNP Browser</a></li>
+                                <li class="divider"></li>
+                                <li><a tabindex="-1" href="/webqtl/main.py?FormID=geneWiki">Gene Wiki</a></li>
+                            </ul>
+                        </li>
+                        <li class="">
+                            <a href="#">Help</a>
+                        </li>
+                        <li class="">
+                            <a href="/whats_new">News</a>
+                        </li>
+                        <li class="">
+                            <a href="./reference.html">References</a>
+                        </li>
+                        <li class="">
+                            <a href="./policies">Policies</a>
+                        </li>
+                        <li class="">
+                            <a href="./links">Links</a>
+                        </li>
                     </ul>
-              </li>
-              <li class="">
-                <a href="#">Help</a>
-              </li>
-              <li class="">
-                <a href="/whats_new">News</a>
-              </li>
-              <li class="">
-                <a href="./reference.html">References</a>
-              </li>
-              <li class="">
-                <a href="./policies">Policies</a>
-              </li>
-              <li class="">
-                <a href="./links">Links</a>
-              </li>
-            </ul>
-          </div>
+                </div>
+            </div>
         </div>
-      </div>
     </div>
 
     {% block content %}{% endblock %}