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-rw-r--r--misc/notes.txt16
-rw-r--r--wqflask/cfg/default_settings.py3
-rw-r--r--wqflask/cfg/zach_settings.py5
-rw-r--r--wqflask/wqflask/my_pylmm/pylmmKinship.py2
-rw-r--r--wqflask/wqflask/templates/base.html82
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 %}