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-rwxr-xr-xwqflask/wqflask/correlation/show_corr_results.py1
-rwxr-xr-xwqflask/wqflask/correlation_matrix/show_corr_matrix.py1
-rwxr-xr-xwqflask/wqflask/dataSharing/SharingInfoPage.py4
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py1
-rwxr-xr-xwqflask/wqflask/static/packages/bootstrap/css/docs.css13
-rwxr-xr-xwqflask/wqflask/templates/base.html15
-rwxr-xr-xwqflask/wqflask/templates/index_page.html66
7 files changed, 39 insertions, 62 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index ade2d242..aa37c29e 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -45,7 +45,6 @@ from utility.THCell import THCell
from utility.TDCell import TDCell
from base.trait import GeneralTrait
from base import data_set
-from base.templatePage import templatePage
from utility import webqtlUtil, helper_functions, corr_result_helpers
from dbFunction import webqtlDatabaseFunction
import utility.webqtlUtil #this is for parallel computing only.
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index d734117e..e1df5b24 100755
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -48,7 +48,6 @@ from utility.THCell import THCell
from utility.TDCell import TDCell
from base.trait import GeneralTrait
from base import data_set
-from base.templatePage import templatePage
from utility import webqtlUtil, helper_functions, corr_result_helpers
from dbFunction import webqtlDatabaseFunction
import utility.webqtlUtil #this is for parallel computing only.
diff --git a/wqflask/wqflask/dataSharing/SharingInfoPage.py b/wqflask/wqflask/dataSharing/SharingInfoPage.py
index 7ad44440..c32eec50 100755
--- a/wqflask/wqflask/dataSharing/SharingInfoPage.py
+++ b/wqflask/wqflask/dataSharing/SharingInfoPage.py
@@ -32,7 +32,6 @@ import urlparse
import flask
-from base.templatePage import templatePage
from base import webqtlConfig
from dbFunction import webqtlDatabaseFunction
import SharingBody
@@ -42,10 +41,9 @@ import SharingInfo
#########################################
# Sharing Info Page
#########################################
-class SharingInfoPage(templatePage):
+class SharingInfoPage():
def __init__(self, fd):
- templatePage.__init__(self, fd)
self.redirect_url = None # Set if you want a redirect
print("fd is:", pf(fd.__dict__))
# Todo: Need a [0] in line below????d
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 11fd2644..929f5abb 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -19,7 +19,6 @@ from utility import webqtlUtil, Plot, Bunch, helper_functions
from base.trait import GeneralTrait
from base import data_set
from dbFunction import webqtlDatabaseFunction
-from base.templatePage import templatePage
from basicStatistics import BasicStatisticsFunctions
from pprint import pformat as pf
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/docs.css b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
index b95c44ed..2d6a713c 100755
--- a/wqflask/wqflask/static/packages/bootstrap/css/docs.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
@@ -25,25 +25,28 @@ h3 code {
/* Tweak navbar brand link to be super sleek
-------------------------------------------------- */
-
+/*
body > .navbar {
font-size: 12px;
font-weight: bold;
}
+*/
/* Change the docs' brand */
-body > .navbar .brand {
- padding-right: 0;
- padding-left: 0;
+
+body > .navbar .navbar-brand {
+ padding-right: 20px;
+ padding-left: 20px;
margin-left: 20px;
float: left;
font-weight: bold;
- color: #336699;
+ color: #ffffff;
text-shadow: 0 1px 0 rgba(255,255,255,.1), 0 0 30px rgba(255,255,255,.125);
-webkit-transition: all .2s linear;
-moz-transition: all .2s linear;
transition: all .2s linear;
}
+
body > .navbar .brand:hover {
text-decoration: none;
text-shadow: 0 1px 0 rgba(255,255,255,.1), 0 0 30px rgba(255,255,255,.4);
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 3d4e6d28..462a59a2 100755
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -74,6 +74,13 @@
<a href="/">Search</a>
</li>
<li class="">
+ <a href="/collections/list">Collections
+ {% if g.user_session.user_ob %}
+ <span class="badge badge-info">{{ g.user_session.user_ob.display_num_collections() }}</span>
+ {% endif %}
+ </a>
+ </li>
+ <li class="">
<a href="/help">Help</a>
</li>
<li class="">
@@ -92,14 +99,6 @@
<a href="/environments">Environments</a>
</li>
<li class="">
- <a href="/collections/list">Collections
- {% if g.user_session.user_ob %}
- <span class="badge badge-info">{{ g.user_session.user_ob.display_num_collections() }}</span>
- {% endif %}
- </a>
- </li>
-
- <li class="">
{% if g.user_session.logged_in %}
<a id="login_out" title="Signed in as {{ g.user_session.user_ob.name_and_org }}." href="/n/logout">Sign out</a>
{% else %}
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 538a6799..ba017bfb 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -29,19 +29,19 @@
<div class="form-group">
<label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label>
- <div class="col-xs-10 controls">
+ <div class="col-xs-10 controls input-append" style="padding-right: 0px;">
<div class="col-xs-8">
<select name="species" id="species" class="form-control selectpicker span3" style="width: 280px !important;"></select>
</div>
<div class="col-xs-4">
- <input id="make_default" class="btn btn-default form-control" value="Make Default">
+ <input id="make_default" class="btn btn-primary form-control" value="Make Default">
</div>
</div>
</div>
<div class="form-group">
<label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label>
- <div class="col-xs-4 controls input-append">
+ <div class="col-xs-10 controls input-append">
<div class="col-xs-8">
<select name="group" id="group" class="form-control selectpicker span3" style="width: 280px !important;"></select>
<i class="icon-question-sign"></i>
@@ -51,7 +51,7 @@
<div class="form-group">
<label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label>
- <div class="col-xs-4 controls">
+ <div class="col-xs-10 controls">
<div class="col-xs-8">
<select name="type" id="type" class="form-control selectpicker span3" style="width: 280px !important;"></select>
</div>
@@ -60,7 +60,7 @@
<div class="form-group">
<label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label>
- <div class="col-xs-4 controls input-append">
+ <div class="col-xs-10 controls input-append">
<div class="col-xs-8">
<select name="dataset" id="dataset" class="form-control selectpicker span5" style="width: 450px !important;"></select>
<i class="icon-question-sign"></i>
@@ -86,15 +86,15 @@
<!-- GET ANY HELP -->
<div class="form-group">
- <label for="tfor" class="col-xs-1 control-label" style="width: 65px !important;"></label>
+ <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
<div class="col-xs-10 controls">
- <div class="col-xs-10">
- <p>Enter terms, genes, ID numbers in the
- <b>Search</b> field<br>
- Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
- synap*)<br>
- Use <b>quotes</b> for terms such as <i>"tyrosine
- kinase"</i></p>
+ <div class="col-xs-2 controls" style="width: 100px !important;">
+ <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
+ </div>
+ <div class="col-xs-9 controls">
+ Enter terms, genes, ID numbers in the <b>Search</b> field
+ Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*)
+ Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>
</div>
</div>
</div>
@@ -103,10 +103,6 @@
<!-- SEARCH, MAKE DEFAULT -->
<div class="form-group">
-
- <div class="col-xs-3 controls" style="width: 100px !important;">
- <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
- </div>
</div>
<input type="hidden" name="FormID" value="searchResult" class="form-control">
@@ -159,7 +155,7 @@
</ul>
</section>
</div>
- <div style="padding-left:120px" class="col-xs-6" style="width: 600px !important;">
+ <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;">
<!--
<section id="tour-info">
<div class="page-header">
@@ -207,32 +203,16 @@
<li>GeneNetwork Source Code at <a href="https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
</ul>
- <h3>Mirror and development sites</h3>
- <ul>
- <li><a href="http://www.genenetwork.org/" target="_blank">
- Main GN site</a> at UTHSC</li>
-
- <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank">
- Australia</a> at the UWA</li>
+ <h3>GN1 Mirror and development sites</h3>
- <li><a href="http://gn.genetics.ucla.edu/" target="_blank">
- California</a> at UCLA</li>
-
- <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">
- Germany</a> at the HZI</li>
-
- <li><a href="https://genenetwork.hubrecht.eu/" target="_blank">
- Netherlands</a> at the Hubrecht
- (development)</li>
-
- <li><a href="http://genenetwork.memphis.edu/" target="_blank">
- Memphis</a> at the U of M</li>
-
- <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank">
- Singapore</a> at the NUS</li>
-
- <li><a href="http://genenetwork.epfl.ch/" target="_blank">
- Switzerland</a> at the EPFL</li>
+ <ul>
+ <li><a href="http://www.genenetwork.org/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Main GN1 site at UTHSC</a> (main site)</li>
+ <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Australia at the UWA</a></li>
+ <li><a href="http://gn.genetics.ucla.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li>
+ <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li>
+ <li><a href="http://genenetwork.memphis.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li>
+ <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</a></li>
+ <li><a href="http://genenetwork.epfl.ch/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li>
</ul>
</section>