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Commit 9f27f8a4 authored by Vermaat's avatar Vermaat
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Last fixes for Jinja2 (removing TAL dependency)

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mutalyzer/templates/batch_jobs.html
+ 12
− 1
View file @ 9f27f8a4
{% extends "base.html" %}
{% set active_page = "batch-jobs" %}
{% if batchType == "NameChecker" %}
{% set active_page = "batch-name-checker" %}
{% elif batchType == "SyntaxChecker" %}
{% set active_page = "batch-syntax-checker" %}
{% elif batchType == "PositionConverter" %}
{% set active_page = "batch-position-converter" %}
{% elif batchType == "SnpConverter" %}
{% set active_page = "batch-snp-converter" %}
{% else %}
{% set active_page = "batch-jobs" %}
{% endif %}
{% set page_title = "Batch {{ batchType|e }} Interface" %}
{% block content %}
......
mutalyzer/templates/menu.html deleted 100644 → 0
+ 0
− 432
View file @ 7dc49f37
<html>
<head>
<link rel="shortcut icon"
href="static/images/favicon.ico"
type="image/x-icon">
<link rel="stylesheet"
type="text/css"
href="static/css/style.css">
<script
type="text/javascript"
language="javascript"
src="static/js/interface.js">
</script>
<script
type="text/javascript"
language="javascript"
src="static/js/generator.js">
</script>
<meta http-equiv="Content-Type"
content="text/html; charset=iso-8859-1">
<title tal:content = "structure string:Mutalyzer ${version}"></title>
</head>
<body
style="background-image: url('static/images/background.gif');
background-repeat: repeat-y;"
leftmargin="0"
topmargin="0"
marginwidth="0"
marginheight="0">
<!-- Header -->
<a id = "top" name = "top"></a>
<table width="98%"
border="0"
cellspacing="0"
cellpadding="0">
<tr>
<!-- Corner logo -->
<td rowspan="2"
valign="bottom"
width="180">
<a href="index"
target="_top"><img
src="static/images/mutalyzer_logo_bw.png" width="180" height="112"
alt="Rauzy fractal" border="0" hspace="0" vspace="0"></a></td>
<td valign="top"
bgcolor="#FFFFFF"
width="20"><img
src="static/images/1x1b.gif" height="1" width="20" border="0">
</td>
<td align="left"
valign="bottom"
bgcolor="White"
width="98%">
<!-- Banner -->
<center>
<a href="index"><img
src="static/images/mutalyzer_logo.png"
width="90%"
height="90"
alt="Rauzy color fractal"
border="0"></a>
</center>
</td>
</tr>
<tr>
<td>
</td>
<td>
<table width = "100%" style = "padding:0; border:0; margin:0">
<tr>
<td align="left">
<a href="javascript:history.back(-1);"
class="hornav">previous page</a>&nbsp;&nbsp;&nbsp;
</td>
<td align="right">
<a href="index"
class="hornav">home</a>&nbsp;&nbsp;&nbsp;
<a href="about"
class="hornav">about</a>&nbsp;&nbsp;&nbsp;
<a tal:attributes = "href string:mailto:${contactEmail}"
class="hornav">contact</a>&nbsp;&nbsp;&nbsp;
<a href="#bottom" class="hornav">go to bottom</a>&nbsp;&nbsp;&nbsp;
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="3"
bgcolor="#000000"><img
src="static/images/1x1b.gif"
height="1"
border="0"></td>
</tr>
</table>
<table width="98%"
border="0"
cellspacing="0"
cellpadding="0">
<tr>
<td width="180" valign="top">
<table id="menu" width="180" border="0" cellspacing="0" cellpadding="0">
<tr>
<td valign="top" width="20">
<img src="static/images/1x1b.gif" height="19" border="0">
</td>
</tr>
<tr tal:attributes="class active/index">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="index">Home</a>
</td>
</tr>
<tr tal:attributes="class active/check">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="check">Name Checker</a>
</td>
</tr>
<tr tal:attributes="class active/parse">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="syntaxCheck">Syntax Checker</a>
</td>
</tr>
<tr tal:attributes="class active/converter">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="positionConverter">Position Converter</a>
</td>
</tr>
<tr tal:attributes="class active/snp">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="snp">SNP Converter</a>
</td>
</tr>
<tr tal:attributes="class active/nameGenerator">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="nameGenerator">Name Generator</a>
</td>
</tr>
<tr tal:attributes="class active/descriptionExtract">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="descriptionExtract">Description Extractor</a>
</td>
</tr>
<tr tal:attributes="class active/gbupload">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="upload">Reference File Loader</a>
</td>
</tr>
<tr tal:attributes="class active/batch">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="batch">Batch Jobs</a>
</td>
</tr>
<tr tal:attributes="class active/batchNameChecker">
<td></td>
<td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
<a href="batchNameChecker">Name Checker</a>
</td>
</tr>
<tr tal:attributes="class active/batchSyntaxChecker">
<td></td>
<td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
<a href="batchSyntaxChecker">Syntax Checker</a>
</td>
</tr>
<tr tal:attributes="class active/batchPositionConverter">
<td></td>
<td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
<a href="batchPositionConverter">Position Converter</a>
</td>
</tr>
<tr tal:attributes="class active/batchSnpConverter">
<td></td>
<td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
<a href="batchSnpConverter">SNP Converter</a>
</td>
</tr>
<tr tal:attributes="class active/webservices">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="webservices">Web services</a>
</td>
</tr>
<tr><td>&nbsp;</td></tr>
<tr tal:attributes="class active/help">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/MutalyzerDocumentation">Documentation</a>
</td>
</tr>
<tr tal:attributes="class active/faq">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/MutalyzerFaq">FAQ</a>
</td>
</tr>
<tr tal:attributes="class active/exercise">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/MutalyzerExercise">Exercise</a>
</td>
</tr>
<tr tal:attributes="class active/disclaimer">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/MutalyzerDisclaimer">Disclaimer</a>
</td>
</tr>
<tr class="menu">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer">Feedback</a>
</td>
</tr>
<tr><td>&nbsp;</td></tr>
<tr class="menu inactive">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
External Links
</td>
</tr>
<tr class="menu">
<td></td>
<td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
<a href="http://www.genenames.org/guidelines.html"
>Human Gene Nomenclature</a>
</td>
</tr>
<tr class="menu">
<td></td>
<td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
<a href="http://www.hgvs.org/mutnomen/"
>HGVS Variation Nomenclature</a>
</td>
</tr>
<tr class="menu">
<td></td>
<td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
<a href="http://dx.doi.org/10.1002/humu.21427"
>HGVS Nomenclature Extension Proposal</a>
</td>
</tr>
<tr class="menu">
<td></td>
<td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
<a href="http://www.lovd.nl/">LOVD</a>
</td>
</tr>
<tr>
<td width="20"><img
src="static/images/1x1b.gif"
height="10"
width="20"
border="0">
</td>
<td width="12"><img
src="static/images/1x1b.gif"
height="10"
width="10"
border="0">
</td>
<td valign="top" width="12"><img
src="static/images/1x1b.gif"
height="10"
width="10"
border="0">
</td>
<td valign="top" width="136"><img
src="static/images/1x1b.gif"
height="10"
width="136"
border="0">
</td>
</tr>
</table>
</td>
<td width="20"><img
src="static/images/1x1b.gif"
height="1"
width="20"
border="0">
</td>
<td width="98%" valign="top"><br>
<!-- Content -->
<table cellpadding="0" cellspacing="0" width="100%" border="0">
<tbody><tr>
<td width="0"></td>
<td width="0">
<center>
<h2 tal:condition = "release"
tal:content = "structure string:Mutalyzer ${version}<br>
<small><small><small><small>
released on ${releaseDate}
</small></small></small></small>"></h2>
<h2 tal:condition = "not:release"
tal:content = "structure string:Mutalyzer ${version}<br>
<small><small><small><small>
development version
</small></small></small></small>"></h2>
HGVS nomenclature version
<span tal:content = "nomenclatureVersion"></span>
</center>
<p>
<div metal:use-macro = "sitemacros/macros/content"></div>
<!-- Navigation bar -->
<table border="0"
cellspacing="0"
cellpadding="0"
width="100%"
align="center">
<tr>
<td colspan="2"><img
src="static/images/1x1b.gif"
width="1"
height="20"
border="0">
</td>
</tr>
<tr>
<td bgcolor="#000000" colspan="3"><img
src="static/images/1x1b.gif"
width="100%"
height="1"
border="0"></td>
</tr>
<tr>
<td align="left">
&nbsp;<a href="javascript:history.back(-1);"
class="hornav">previous page</a>
</td>
<td align="middle">
<img src = "static/images/LUMC_24x24.png" align = "middle">
&nbsp; &copy; <tal tal:replace = "copyrightYears/0"></tal>-<tal tal:replace = "copyrightYears/1"></tal>
<a href = "http://www.lumc.nl">LUMC</a>
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp;
</td>
<td align="right">
<a href="#top" class="hornav">go to top</a>&nbsp;&nbsp;&nbsp;&nbsp;
</td>
</tr>
<tr>
<!--
<td colspan="2"
align="center">Last edited by: with /usr/bin/vim
</td>
-->
</tr>
<tr>
<td colspan="2"><img
src="static/images/1x1b.gif"
width="1"
height="10"
border="0">
</td>
</tr>
</table>
</td>
</tr>
</table>
<a id = "bottom" name = "bottom"></a>
<div tal:condition="piwik" tal:omit-tag="">
<!-- Piwik -->
<script type="text/javascript" tal:content="string:
var pkBaseURL = &quot;${piwikBase}/&quot;;
document.write(unescape(&quot;%3Cscript src='&quot; + pkBaseURL + &quot;piwik.js' type='text/javascript'%3E%3C/script%3E&quot;));
"></script><script type="text/javascript" tal:content="string:
try {
var piwikTracker = Piwik.getTracker(pkBaseURL + &quot;piwik.php&quot;, ${piwikSite});
piwikTracker.trackPageView();
piwikTracker.enableLinkTracking();
} catch( err ) {}
"></script><noscript><p><img tal:attributes="src string:${piwikBase}/piwik.php?idsite=${piwikSite}" style="border:0" alt="" /></p></noscript>
<!-- End Piwik Tracking Code -->
</div>
</body>
</html>
mutalyzer/templates/skel.html deleted 100644 → 0
+ 0
− 13
View file @ 7dc49f37
<html>
<head>
<title></title>
</head>
<body>
<div metal:define-macro="content">
<center>
<h3>Skeleton</h3>
</center>
Your text here.
</div>
</body>
</html>
mutalyzer/website.py
+ 7
− 8
View file @ 9f27f8a4
......@@ -29,8 +29,6 @@ from web.contrib.template import render_jinja
from lxml import etree
import pkg_resources
from cStringIO import StringIO
from simpletal import simpleTALES
from simpletal import simpleTAL
from spyne.server.http import HttpBase
import mutalyzer
......@@ -191,6 +189,8 @@ render_ = render_tal(pkg_resources.resource_filename('mutalyzer', 'templates'),
})
# Jinja2 template render
# Todo: We rely on Apache to add a Content-Type header, we should actually
# set it ourselves.
render = render_jinja(pkg_resources.resource_filename('mutalyzer', 'templates'),
encoding='utf-8',
globals = {
......@@ -913,7 +913,9 @@ class Check:
output.addMessage(__file__, -1, 'INFO', 'Finished variant %s' % name)
return render.name_checker(args, prevent_caching=True)
web.header('Cache-Control', 'no-cache')
web.header('Expires', '-1')
return render.name_checker(args)
#check
#Check
......@@ -1189,10 +1191,7 @@ class BatchChecker:
}
# Make sure the correct page is displayed for an entrypoint
if batchType:
page = 'batch' + batchType
else:
page = 'batch'
if not batchType:
batchType = 'NameChecker'
if batchType in attr["batchTypes"]:
......@@ -1248,7 +1247,7 @@ class BatchChecker:
attr["errors"].extend(map(util.message_info, O.getMessages()))
return render.batch_jobs(attr, page=page)
return render.batch_jobs(attr)
#batch
#BatchChecker
......
requirements.txt
+ 0
− 1
View file @ 9f27f8a4
......@@ -20,4 +20,3 @@ WebTest==1.4.2
cssselect==0.9.1
Jinja2==2.7.1
-e git+https://github.com/mammadori/magic-python.git#egg=Magic_file_extensions
http://www.owlfish.com/software/simpleTAL/downloads/SimpleTAL-4.3.tar.gz
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