From 45665f54cc941eadacd737060bbbf7829a8aa58f Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 20 Aug 2012 12:03:13 +0000
Subject: [PATCH] Javascript and template cleanup
Mainly removal of the javascript code for the menu, this is now all CSS
driven and much simplified.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@599 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/templates/base/css/style.css | 95 ++----
mutalyzer/templates/base/js/index.js | 58 ----
mutalyzer/templates/base/js/m.js | 12 -
mutalyzer/templates/base/js/menu.js | 169 ----------
mutalyzer/templates/check.html | 3 +-
mutalyzer/templates/converter.html | 7 +-
mutalyzer/templates/descriptionExtract.html | 9 +-
mutalyzer/templates/menu.html | 334 +++++---------------
mutalyzer/templates/parse.html | 21 +-
mutalyzer/templates/snp.html | 19 +-
mutalyzer/website.py | 16 +-
11 files changed, 137 insertions(+), 606 deletions(-)
delete mode 100644 mutalyzer/templates/base/js/index.js
delete mode 100644 mutalyzer/templates/base/js/m.js
delete mode 100644 mutalyzer/templates/base/js/menu.js
diff --git a/mutalyzer/templates/base/css/style.css b/mutalyzer/templates/base/css/style.css
index 1368c1bb..23e5c2b0 100644
--- a/mutalyzer/templates/base/css/style.css
+++ b/mutalyzer/templates/base/css/style.css
@@ -31,7 +31,7 @@ a:hover {
font-weight : bold;
text-decoration : none;
}
-
+
.importanttext {
border : 1px solid black;
background-color : #717B9D;
@@ -51,7 +51,7 @@ body, div, span, font, td {
.raTable tr td {
text-align : right;
border : 1px solid grey;
- padding : 0px 4px;
+ padding : 0px 4px;
}
.raTable {
border : 1px solid grey;
@@ -60,7 +60,7 @@ body, div, span, font, td {
.laTable tr td {
border : 1px solid grey;
- padding : 0px 4px;
+ padding : 0px 4px;
}
.laTable {
@@ -94,11 +94,6 @@ ul {
color: white;
}
-.bullet{
- left : -15px;
- position : absolute;
-}
-
.faculteitsonderdeel {
color : #002E65;
font-size : 18px;
@@ -165,89 +160,43 @@ ul {
padding-top : 1px;
}
-.vertnav {
- color : #C2C6D5;
- font-weight : bold;
- line-height : 18px;
- text-decoration : none;
-}
-
-.vertnav:link {
- color : #FFFFFF;
-}
-
-.vertnav:hover {
- color : #FFFFFF;
-}
-
-.vertnavactive {
- color : #FFFFFF;
- font-weight : bold;
- line-height : 18px;
- text-decoration : none;
-}
-
-.vertnavactive:hover {
- color : #FFFFFF;
- font-weight : bold;
+.menu {
line-height : 18px;
- text-decoration : none;
}
-.vertnavsub {
+.menu a {
color : #002E65;
- line-height : 18px;
text-decoration : none;
}
-.vertnavsub:visited {
- color : #002E65;
-}
-
-.vertnavsub:hover {
+.menu:hover a, .menu a:hover {
color : #FFFFFF;
}
-.vertnavsubother {
- color : #B2D6F5;
- line-height : 18px;
- text-decoration : none;
-}
-
-.vertnavsubother:visited {
- color : #92b6c5;
-}
-
-.vertnavsubother:hover {
+.menu.active a {
color : #FFFFFF;
+ font-weight: bold;
}
-.vertnavsubactive {
- color : #FFFFFF;
- font-weight : normal;
- line-height : 18px;
- text-decoration : none;
+.menu .bullet {
+ height: 22px;
+ background: url('../images/bullitdonker.gif') no-repeat top left;
}
-.vertnavsubactive:hover {
- color : #FFFFFF;
- font-weight : normal;
- line-height : 18px;
- text-decoration : none;
+.menu .bullet.sub {
+ background-image: url('../images/bullitmiddel.gif');
}
-.vertnavsubinternal {
- color : #F5D6B2;
- line-height : 18px;
- text-decoration : none;
+.menu.active .bullet, .menu:hover .bullet {
+ background-image: url('../images/bullitlicht1.gif');
}
-.vertnavsubinternal:visited {
- color : #c2b695;
+.menu.active .bullet.sub, .menu:hover .bullet.sub {
+ background-image: url('../images/bullitlicht2.gif');
}
-.vertnavsubinternal:hover {
- color : #FFFFFF;
+.menu.inactive:hover .bullet {
+ background-image: url('../images/bullitdonker.gif');
}
#content{
@@ -326,9 +275,9 @@ i {
background-image: url('../images/error.png');
}
-.thnormal {
- font-family: Arial, Helvetica, sans-serif;
- font-weight: bold;
+.thnormal {
+ font-family: Arial, Helvetica, sans-serif;
+ font-weight: bold;
color: #FFFFFF;
background-color : #002E65;
}
diff --git a/mutalyzer/templates/base/js/index.js b/mutalyzer/templates/base/js/index.js
deleted file mode 100644
index 06a6d24e..00000000
--- a/mutalyzer/templates/base/js/index.js
+++ /dev/null
@@ -1,58 +0,0 @@
-<!--
-
-// --- GET ELEMENT(LAYERREFERENCE) ---
-function getElt ()
-{
- if (document.layers)
- { var currentLayer = document.layers[getElt.arguments[0]];
- for (var i = 1; i < getElt.arguments.length && currentLayer; i++)
- { currentLayer = currentLayer.document.layers[getElt.arguments[i]];
- }
- return currentLayer;
- }
- else if (document.all)
- { var elt = eval('document.all.' + getElt.arguments[getElt.arguments.length - 1]);
- return(elt);
- }
- else if (document.getElementById)
- { var elt = document.getElementById(getElt.arguments[getElt.arguments.length - 1]);
- return(elt);
- }
-}
-
-// --- IMAGE SWAP ---
-function swapImage(imgSrc, imgID, elt)
-{
- if (document.getElementsByName)
- { var img = document.getElementsByName(imgID);
- img[0].src = imgSrc;
- }
- else
- { if (swapImage.arguments.length == 3)
- { eval("elt.document." + imgID + ".src = '" + imgSrc + "'");
- }
- else
- { eval("document." + imgID + ".src = '" + imgSrc + "'");
- }
- }
-}
-
-// --- IMAGE PRELOAD ---
-function preloadImages()
-{
- if (document.images)
- { var imgStr = preloadImages.arguments;
- if (!document.preloadArray)
- { document.preloadArray = new Array();
- }
-
- var n = document.preloadArray.length;
- for (var i = 0; i < preloadImages.arguments.length; i++)
- { document.preloadArray[n] = new Image;
- document.preloadArray[n].src = imgStr[i];
- n++;
- }
- }
-}
-
-// -->
diff --git a/mutalyzer/templates/base/js/m.js b/mutalyzer/templates/base/js/m.js
deleted file mode 100644
index 9ad5ceed..00000000
--- a/mutalyzer/templates/base/js/m.js
+++ /dev/null
@@ -1,12 +0,0 @@
-function s(p0, p1, p2)
-{
- parent.location = 'm' + 'ailto:' + p1 + '@' + p0 + '.' + p2;
- return true;
-}
-
-function ms(p0, p1, p2)
-{
- window.status = 'm'+'ail'+'to:' + p1 + '@' + p0 + '.' + p2;
- return true;
-}
-
diff --git a/mutalyzer/templates/base/js/menu.js b/mutalyzer/templates/base/js/menu.js
deleted file mode 100644
index 563bd5c4..00000000
--- a/mutalyzer/templates/base/js/menu.js
+++ /dev/null
@@ -1,169 +0,0 @@
-var a_Act;
-var a_navAct;
-var timerID;
-var timerImg;
-
-function setFont(font, hrefID) {
- document.getElementById(hrefID).className = font;
-}//setFont
-
-function setImage(imgSrc, imgID) {
- document.getElementById(imgID).src = imgSrc;
-}//setImage
-
-function setSub(state, subID) {
- var subElt = document.getElementById(subID + "_0");
- var i = 1;
-
- while (subElt) {
- subElt.style.display = state;
- subElt = document.getElementById(subID + "_" + i);
- i++;
- }//while
-}//setSub
-
-function setActive(newAct) {
- if (document.getElementById("page_" + newAct)) {
- if (newAct.match("_")) {
- setFont("vertnavsubactive", "page_" + newAct);
- setImage("base/images/bullitlicht2.gif", "b_" + newAct);
- }//if
- else {
- setFont("vertnavactive", "page_" + newAct);
- setImage("base/images/bullitlicht1.gif", "b_" + newAct);
- }//else
-
- setSub("", newAct);
- }//if
-}//setActive
-
-function setNavActive(newAct) {
- if (document.getElementById("page_" + newAct)) {
- if (newAct.match("_"))
- setImage("base/images/bullitlicht2.gif", "b_" + newAct);
- else
- setImage("base/images/bullitlicht1.gif", "b_" + newAct);
-
- setSub("", newAct);
- }//if
-}//setNavActive
-
-function setDeActive(oldAct) {
- if (document.getElementById("page_" + oldAct)) {
- setFont("vertnavsub", "page_" + oldAct);
-
- if (oldAct.match("_"))
- setImage("base/images/bullitmiddel.gif", "b_" + oldAct);
- else
- setImage("base/images/bullitdonker.gif", "b_" + oldAct);
- }//if
-}//setDeActive
-
-function alterActive(a_Alter, method) {
- var Label = a_Alter[0];
- var i;
-
- for (i = 1; i <= a_Alter.length; i++) {
- if (method)
- setActive(Label);
- else {
- setDeActive(Label);
- setSub("none", Label);
- }//else
- Label = Label + "_" + a_Alter[i];
- }//for
-}//alterActive
-
-function alterNavActive(a_Alter, method) {
- var Label = a_Alter[0];
- var i;
-
- for (i = 1; i <= a_Alter.length; i++) {
- if (method)
- setNavActive(Label);
- else
- setDeActive(Label);
- Label = Label + "_" + a_Alter[i];
- }//for
-}//alterNavActive
-
-function navPartDeAct() {
- alterNavActive(a_navAct, 0);
- alterActive(a_Act, 1);
-}//navPartDeAct
-
-function swapActive(newAct) {
- var a_newAct = newAct.split("_");
-
- alterActive(a_Act, 0);
- alterActive(a_newAct, 1);
-
- a_Act = a_newAct;
- a_navAct = a_newAct;
-}//swapActive
-
-function swapNavActive() {
- var a_newAct = timerImg.split("_");
-
- navPartDeAct();
- alterActive(a_newAct, 1);
-
- a_navAct = a_newAct;
-}//swapNavActive
-
-function navAct(imgSrc, imgID) {
- clearTimeout(timerID);
-
- timerImg = imgID;
- timerID = setTimeout("swapNavActive();", 500);
-}//navAct
-
-function navDeAct(imgSrc, imgID) {
- clearTimeout(timerID);
-
- timerID = setTimeout("navPartDeAct();", 2000);
-}//navDeAct
-
-function initActive() {
- var winLoc;
-
- winLoc = window.location.href;
- winLoc = winLoc.replace(/https?:\/\/[^\/]*\//, "");
-
- if (winLoc.match("~"))
- winLoc = winLoc.replace(/[^\/]*\//, "");
- else
- winLoc = winLoc.replace(/[^\/]*\/[^\/]*\//, "");
-
- winLoc = winLoc.replace(/\.cgi$/, "");
- winLoc = winLoc.replace(/index\.shtml/, "");
- winLoc = winLoc.replace(/\/$/, "");
- winLoc = winLoc.replace("#", "");
-
- a_Act = winLoc.split("/");
- // This is a Quick Hack (tm)
- if (a_Act[0] == '2.0' || a_Act[0] == 'mutalyzer')
- a_Act.shift();
- a_navAct = a_Act;
-
- alterActive(a_Act, 1);
-}//initActive
-
-function resetAll() {
- var a_Menu = document.getElementsByTagName("tr");
- var i;
-
- for (i = 0; i < a_Menu.length; i++)
- if (a_Menu[i].id.match("_"))
- a_Menu[i].style.display = "none";
-
- navPartDeAct();
-}//resetAll
-
-function clearForm(form, elementName) {
- for (i = 0; i < form.elements.length; i++) {
- if (form.elements[i].name == elementName) {
- form.elements[i].value = "";
- }//if
- }//for
-}//clearForm
diff --git a/mutalyzer/templates/check.html b/mutalyzer/templates/check.html
index 89da7bb0..b666ecd5 100644
--- a/mutalyzer/templates/check.html
+++ b/mutalyzer/templates/check.html
@@ -31,8 +31,7 @@
style = "width:100%"
><br>
<input type="submit" value="Submit">
- <input type="button" value="Clear field"
- onClick = "clearForm(this.form, 'name');">
+ <input type="reset" value="Clear field">
</form>
</div>
<div tal:condition = "visualisation">
diff --git a/mutalyzer/templates/converter.html b/mutalyzer/templates/converter.html
index d1bc1c4b..c238eb6f 100644
--- a/mutalyzer/templates/converter.html
+++ b/mutalyzer/templates/converter.html
@@ -30,16 +30,15 @@
</tr>
<tr>
<td><b>Variant</b></td>
- <td><input type = "text"
- name = "variant"
+ <td><input type = "text"
+ name = "variant"
tal:attributes = "value variant"
style = "width:500px"></td>
</tr>
<tr>
<td colspan="2">
<input type="submit" value="Submit">
- <input type="button" value="Clear field"
- onClick = "clearForm(this.form, 'variant');">
+ <input type="reset" value="Clear field">
</td>
</tr>
diff --git a/mutalyzer/templates/descriptionExtract.html b/mutalyzer/templates/descriptionExtract.html
index 26c5f8a8..0a3794c0 100644
--- a/mutalyzer/templates/descriptionExtract.html
+++ b/mutalyzer/templates/descriptionExtract.html
@@ -47,9 +47,7 @@
name = "referenceSeq"
tal:attributes = "value lastReferenceSeq"
style = "width:100%"
- ><br>
- <input type="button" value="Clear field"
- onClick = "clearForm(this.form, 'referenceSeq');"><br>
+ >
</div>
<br>
<div style="border: 1px solid grey; padding: 20px">
@@ -62,12 +60,11 @@
name = "variantSeq"
tal:attributes = "value lastVariantSeq"
style = "width:100%"
- ><br>
- <input type="button" value="Clear field"
- onClick = "clearForm(this.form, 'variantSeq');"><br>
+ >
</div>
<br>
<input type="submit" value="Submit">
+ <input type="reset" value="Clear fields">
</form>
</div>
<div tal:condition = "description">
diff --git a/mutalyzer/templates/menu.html b/mutalyzer/templates/menu.html
index 38544d0e..cd1665f3 100644
--- a/mutalyzer/templates/menu.html
+++ b/mutalyzer/templates/menu.html
@@ -6,16 +6,6 @@
<link rel="stylesheet"
type="text/css"
href="base/css/style.css">
- <script
- type="text/javascript"
- language="JavaScript"
- src="base/js/index.js">
- </script>
- <script
- type="text/javascript"
- language="javascript"
- src="base/js/menu.js">
- </script>
<script
type="text/javascript"
language="javascript"
@@ -36,12 +26,7 @@
leftmargin="0"
topmargin="0"
marginwidth="0"
- marginheight="0"
- onload="initActive();
- preloadImages('base/images/bullitlicht1.gif',
- 'base/images/bullitlicht2.gif',
- 'base/images/mutalyzer_logo_bw.png',
- 'base/images/mutalyzer_logo.png');">
+ marginheight="0">
<!-- Header -->
<a id = "top" name = "top"></a>
@@ -126,353 +111,186 @@
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_index">
- </td>
+ <tr tal:attributes="class active/index">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_index"
- onclick="swapActive('index');"
- href="index"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'index');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'index');"
- class="vertnavsub">Home</a>
+ <a href="index">Home</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_check">
- </td>
+ <tr tal:attributes="class active/check">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_check"
- onclick="swapActive('check');"
- href="check"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'check');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'check');"
- class="vertnavsub">Name Checker</a>
+ <a href="check">Name Checker</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_syntaxCheck">
- </td>
+ <tr tal:attributes="class active/parse">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_syntaxCheck"
- onclick="swapActive('syntaxCheck');"
- href="syntaxCheck"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'syntaxCheck');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'syntaxCheck');"
- class="vertnavsub">Syntax Checker</a>
+ <a href="syntaxCheck">Syntax Checker</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_positionConverter">
- </td>
+ <tr tal:attributes="class active/converter">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_positionConverter"
- onclick="swapActive('positionConverter');"
- href="positionConverter"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'positionConverter');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'positionConverter');"
- class="vertnavsub">Position Converter</a>
+ <a href="positionConverter">Position Converter</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_snp">
- </td>
+ <tr tal:attributes="class active/snp">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_snp"
- onclick="swapActive('snp');"
- href="snp"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'snp');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'snp');"
- class="vertnavsub">SNP Converter</a>
+ <a href="snp">SNP Converter</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_nameGenerator">
- </td>
+ <tr tal:attributes="class active/nameGenerator">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_nameGenerator"
- onclick="swapActive('nameGenerator');"
- href="nameGenerator"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'nameGenerator');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'nameGenerator');"
- class="vertnavsub">Name Generator</a>
+ <a href="nameGenerator">Name Generator</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_descriptionExtract">
- </td>
+ <tr tal:attributes="class active/descriptionExtract">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_descriptionExtract"
- onclick="swapActive('descriptionExtract');"
- href="descriptionExtract"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'descriptionExtract');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'descriptionExtract');"
- class="vertnavsub">Description Extractor</a>
+ <a href="descriptionExtract">Description Extractor</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_upload">
- </td>
+ <tr tal:attributes="class active/gbupload">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_upload"
- onclick="swapActive('upload');"
- href="upload"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'upload');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'upload');"
- class="vertnavsub">Reference File Loader</a>
+ <a href="upload">Reference File Loader</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_batch">
- </td>
+ <tr tal:attributes="class active/batch">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_batch"
- onclick="swapActive('batch');"
- href="batch"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'batch');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'batch');"
- class="vertnavsub">Batch Jobs</a>
+ <a href="batch">Batch Jobs</a>
</td>
</tr>
- <tr>
+ <tr tal:attributes="class active/batchNameChecker">
<td></td>
- <td valign="baseline" width="10">
- <img src="base/images/bullitmiddel.gif" id="b_batchNameChecker">
- </td>
+ <td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
- <a id="page_batchNameChecker"
- href="batchNameChecker"
- class="vertnavsub">Name Checker</a>
+ <a href="batchNameChecker">Name Checker</a>
</td>
</tr>
- <tr>
+ <tr tal:attributes="class active/batchSyntaxChecker">
<td></td>
- <td valign="baseline" width="10">
- <img src="base/images/bullitmiddel.gif" id="b_batchSyntaxChecker">
- </td>
+ <td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
- <a id="page_batchSyntaxChecker"
- href="batchSyntaxChecker"
- class="vertnavsub">Syntax Checker</a>
+ <a href="batchSyntaxChecker">Syntax Checker</a>
</td>
</tr>
- <tr>
+ <tr tal:attributes="class active/batchPositionConverter">
<td></td>
- <td valign="baseline" width="10">
- <img src="base/images/bullitmiddel.gif" id="b_batchPositionConverter">
- </td>
+ <td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
- <a id="page_batchPositionConverter"
- href="batchPositionConverter"
- class="vertnavsub">Position Converter</a>
+ <a href="batchPositionConverter">Position Converter</a>
</td>
</tr>
- <tr>
+ <tr tal:attributes="class active/batchSnpConverter">
<td></td>
- <td valign="baseline" width="10">
- <img src="base/images/bullitmiddel.gif" id="b_batchSnpConverter">
- </td>
+ <td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
- <a id="page_batchSnpConverter"
- href="batchSnpConverter"
- class="vertnavsub">SNP Converter</a>
+ <a href="batchSnpConverter">SNP Converter</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_webservices">
- </td>
+ <tr tal:attributes="class active/webservices">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_webservices"
- onclick="swapActive('webservices');"
- href="webservices"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'webservices');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'webservices');"
- class="vertnavsub">Webservices</a>
+ <a href="webservices">Webservices</a>
</td>
</tr>
<tr><td> </td></tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_help">
- </td>
+ <tr tal:attributes="class active/help">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_help"
- onclick="swapActive('help');"
- href="help"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'help');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'help');"
- class="vertnavsub">Help</a>
+ <a href="help">Help</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_faq">
- </td>
+ <tr tal:attributes="class active/faq">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_faq"
- onclick="swapActive('faq');"
- href="faq"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'faq');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'faq');"
- class="vertnavsub">FAQ</a>
+ <a href="faq">FAQ</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_exercise">
- </td>
+ <tr tal:attributes="class active/exercise">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_exercise"
- onclick="swapActive('exercise');"
- href="exercise"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'exercise');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'exercise');"
- class="vertnavsub">Exercise</a>
+ <a href="exercise">Exercise</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_disclaimer">
- </td>
+ <tr tal:attributes="class active/disclaimer">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_disclaimer"
- onclick="swapActive('disclaimer');"
- href="disclaimer"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'disclaimer');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'disclaimer');"
- class="vertnavsub">Disclaimer</a>
+ <a href="disclaimer">Disclaimer</a>
</td>
</tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_bugTrack">
- </td>
+ <tr class="menu">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a id="page_bugTrack"
- onclick="swapActive('bugTrack');"
- href="https://humgenprojects.lumc.nl/trac/mutalyzer"
- onmouseover="navAct('base/images/bullitlicht1.gif',
- 'bugTrack');"
- onmouseout="navDeAct('base/images/bullitdonker.gif',
- 'bugTrack');"
- class="vertnavsub">Feedback</a>
+ <a href="https://humgenprojects.lumc.nl/trac/mutalyzer">Feedback</a>
</td>
</tr>
<tr><td> </td></tr>
- <tr>
- <td valign="top" width="20">
- <img src="base/images/bullitdonker.gif" id="b_external">
- </td>
+ <tr class="menu inactive">
+ <td valign="top" width="20" class="bullet"></td>
<td colspan="3">
External Links
</td>
</tr>
- <tr>
+ <tr class="menu">
<td></td>
- <td valign="baseline" width="10">
- <img src="base/images/bullitmiddel.gif" id="b_external_hgb">
- </td>
+ <td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
- <a id="page_external_hgb"
- href="http://www.genenames.org/guidelines.html"
- class="vertnavsub">Human Gene Nomenclature</a>
+ <a href="http://www.genenames.org/guidelines.html"
+ >Human Gene Nomenclature</a>
</td>
</tr>
- <tr>
+ <tr class="menu">
<td></td>
- <td valign="baseline" width="10">
- <img src="base/images/bullitmiddel.gif" id="b_external_hgvs">
- </td>
+ <td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
- <a id="page_external_hgvs"
- href="http://www.hgvs.org/mutnomen/"
- class="vertnavsub">HGVS Variation Nomenclature</a>
+ <a href="http://www.hgvs.org/mutnomen/"
+ >HGVS Variation Nomenclature</a>
</td>
</tr>
- <tr>
+ <tr class="menu">
<td></td>
- <td valign="baseline" width="10">
- <img src="base/images/bullitmiddel.gif" id="b_external_hgvsext">
- </td>
+ <td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
- <a id="page_external_hgvsext"
- href="http://www.hgvs.org/mutnomen/HGVS_extend_PT.doc"
- class="vertnavsub">HGVS Nomenclature Extension Proposal</a>
+ <a href="http://www.hgvs.org/mutnomen/HGVS_extend_PT.doc"
+ >HGVS Nomenclature Extension Proposal</a>
</td>
</tr>
- <tr>
+ <tr class="menu">
<td></td>
- <td valign="baseline" width="10">
- <img src="base/images/bullitmiddel.gif" id="b_external_lovd">
- </td>
+ <td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
- <a id="page_external_lovd"
- onclick="swapActive('external_lovd');"
- href="http://www.lovd.nl/"
- class="vertnavsub">LOVD</a>
+ <a href="http://www.lovd.nl/">LOVD</a>
</td>
</tr>
@@ -516,7 +334,7 @@
<!-- Content -->
<table cellpadding="0" cellspacing="0" width="100%" border="0">
- <tbody onMouseover="resetAll();"><tr>
+ <tbody><tr>
<td width="0"></td>
<td width="0">
diff --git a/mutalyzer/templates/parse.html b/mutalyzer/templates/parse.html
index 9a530dec..a0d1a696 100644
--- a/mutalyzer/templates/parse.html
+++ b/mutalyzer/templates/parse.html
@@ -12,27 +12,26 @@
</center>
<div style="border: 1px solid grey; background-color: aliceblue; padding: 20px;">
<div>
- Please insert the mutation name using the
+ Please insert the mutation name using the
<span class = "helper" title =
"Human Genome Variation Society standard variant nomenclature">
<a href = "http://www.hgvs.org/mutnomen">HGVS</a> format</span>:<br>
- <Accession Number>.<version
- number>(<Gene symbol>):<sequence
+ <Accession Number>.<version
+ number>(<Gene symbol>):<sequence
type>.<mutation>
</div><br>
Example: AB026906.1:c.274G>T<br>
<br>
<form action = "" method = "post">
- <input
- type = "text"
- name = "variant"
+ <input
+ type = "text"
+ name = "variant"
tal:attributes = "value variant"
style = "width:100%"><br>
- <input
- type="submit"
+ <input
+ type="submit"
value="Submit">
- <input type="button" value="Clear field"
- onClick = "clearForm(this.form, 'variant');">
+ <input type="reset" value="Clear field">
</form>
<br>
</div>
@@ -47,7 +46,7 @@
<br>
</div>
<h4>Details of the parse error:</h4>
- <pre tal:content =
+ <pre tal:content =
"structure string:${parseError/0}<br>${parseError/1}">
</pre>
The "^" indicates the position where the error occurred.
diff --git a/mutalyzer/templates/snp.html b/mutalyzer/templates/snp.html
index 1b3c513d..9f7086c4 100644
--- a/mutalyzer/templates/snp.html
+++ b/mutalyzer/templates/snp.html
@@ -1,7 +1,7 @@
<html>
<head>
- <link rel="stylesheet"
- type="text/css"
+ <link rel="stylesheet"
+ type="text/css"
href="base/css/style.css">
<title></title>
</head>
@@ -11,7 +11,7 @@
<h3>SNP converter</h3>
</center>
<div style="border: 1px solid grey; background-color: aliceblue; padding: 20px;">
- Please insert the
+ Please insert the
<a href = "http://www.ncbi.nlm.nih.gov/projects/SNP/">dbSNP</a> rs
number below. Mutalyzer will retrieve the HGVS description of the SNP
specified on the reference sequence(s) used by dbSNP.<br>
@@ -19,17 +19,16 @@
Example: rs9919552<br>
<br>
<form action = "" method = "post">
- <input
- type = "text"
- name = "rsId"
+ <input
+ type = "text"
+ name = "rsId"
style = "width:25%"
><br>
- <input
- type="submit"
+ <input
+ type="submit"
value="Submit"
>
- <input type="button" value="Clear field"
- onClick = "clearForm(this.form, 'rsId');">
+ <input type="reset" value="Clear field">
</form>
</div>
<div tal:condition = "lastpost">
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 89ee649d..98700930 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -24,6 +24,7 @@ import os
import bz2
import web
import urllib
+from collections import defaultdict
from lxml import etree
from cStringIO import StringIO
@@ -109,7 +110,7 @@ class render_tal:
filename = name
def template(args={}, scheme='html', standalone=False,
- prevent_caching=False):
+ prevent_caching=False, page=None):
"""
Template render function.
@@ -126,6 +127,7 @@ class render_tal:
argument for template.
@return: Render of template.
"""
+ page = page or filename
file = filename
if scheme == 'html':
file += '.html'
@@ -150,6 +152,11 @@ class render_tal:
# Wrap in site layout with menu
if scheme == 'html' and not standalone:
context.addGlobal('sitemacros', template)
+ # The following three lines are a hack to get class="active"
+ # on the active menu item, working around TAL.
+ active = defaultdict(lambda: 'menu')
+ active[page] = 'menu active'
+ context.addGlobal('active', active)
templateFile = open(os.path.join(self.path, 'menu.html'), 'r')
template = simpleTAL.compileHTMLTemplate(templateFile)
templateFile.close()
@@ -1133,7 +1140,10 @@ class BatchChecker:
}
# Make sure the correct page is displayed for an entrypoint
- if not batchType:
+ if batchType:
+ page = 'batch' + batchType
+ else:
+ page = 'batch'
batchType = 'NameChecker'
if batchType in attr["batchTypes"]:
@@ -1186,7 +1196,7 @@ class BatchChecker:
attr["errors"].extend(map(util.message_info, O.getMessages()))
- return render.batch(attr)
+ return render.batch(attr, page=page)
#batch
#BatchChecker
--
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