From 9f27f8a499adf396da56eba4732d9e34d845ca5f Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Wed, 11 Dec 2013 18:00:23 +0100
Subject: [PATCH] Last fixes for Jinja2 (removing TAL dependency)
---
mutalyzer/templates/batch_jobs.html | 13 +-
mutalyzer/templates/menu.html | 432 ----------------------------
mutalyzer/templates/skel.html | 13 -
mutalyzer/website.py | 15 +-
requirements.txt | 1 -
5 files changed, 19 insertions(+), 455 deletions(-)
delete mode 100644 mutalyzer/templates/menu.html
delete mode 100644 mutalyzer/templates/skel.html
diff --git a/mutalyzer/templates/batch_jobs.html b/mutalyzer/templates/batch_jobs.html
index 50f771f0..829714fa 100644
--- a/mutalyzer/templates/batch_jobs.html
+++ b/mutalyzer/templates/batch_jobs.html
@@ -1,6 +1,17 @@
{% 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 %}
diff --git a/mutalyzer/templates/menu.html b/mutalyzer/templates/menu.html
deleted file mode 100644
index 82437c54..00000000
--- a/mutalyzer/templates/menu.html
+++ /dev/null
@@ -1,432 +0,0 @@
-<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 ${version}"></title>
- </head>
- <body
- style="background-image: url('static/images/background.gif');
- background-repeat: repeat-y;"
- leftmargin="0"
- topmargin="0"
- marginwidth="0"
- marginheight="0">
- <!-- Header -->
- <a id = "top" name = "top"></a>
-
- <table width="98%"
- border="0"
- cellspacing="0"
- cellpadding="0">
- <tr>
- <!-- Corner logo -->
- <td rowspan="2"
- valign="bottom"
- width="180">
- <a href="index"
- target="_top"><img
- src="static/images/mutalyzer_logo_bw.png" width="180" height="112"
- alt="Rauzy fractal" border="0" hspace="0" vspace="0"></a></td>
- <td valign="top"
- bgcolor="#FFFFFF"
- width="20"><img
- src="static/images/1x1b.gif" height="1" width="20" border="0">
- </td>
- <td align="left"
- valign="bottom"
- bgcolor="White"
- width="98%">
- <!-- Banner -->
- <center>
- <a href="index"><img
- src="static/images/mutalyzer_logo.png"
- width="90%"
- height="90"
- alt="Rauzy color fractal"
- border="0"></a>
- </center>
- </td>
- </tr>
-
- <tr>
- <td>
- </td>
- <td>
- <table width = "100%" style = "padding:0; border:0; margin:0">
- <tr>
- <td align="left">
- <a href="javascript:history.back(-1);"
- class="hornav">previous page</a>
- </td>
- <td align="right">
- <a href="index"
- class="hornav">home</a>
- <a href="about"
- class="hornav">about</a>
- <a tal:attributes = "href string:mailto:${contactEmail}"
- class="hornav">contact</a>
- <a href="#bottom" class="hornav">go to bottom</a>
- </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> </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> </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 ${version}<br>
- <small><small><small><small>
- development version
- </small></small></small></small>"></h2>
- HGVS nomenclature version
- <span tal:content = "nomenclatureVersion"></span>
- </center>
- <p>
-
- <div metal:use-macro = "sitemacros/macros/content"></div>
-
- <!-- Navigation bar -->
- <table border="0"
- cellspacing="0"
- cellpadding="0"
- width="100%"
- align="center">
- <tr>
- <td colspan="2"><img
- src="static/images/1x1b.gif"
- width="1"
- height="20"
- border="0">
- </td>
- </tr>
- <tr>
- <td bgcolor="#000000" colspan="3"><img
- src="static/images/1x1b.gif"
- width="100%"
- height="1"
- border="0"></td>
- </tr>
- <tr>
- <td align="left">
- <a href="javascript:history.back(-1);"
- class="hornav">previous page</a>
- </td>
- <td align="middle">
- <img src = "static/images/LUMC_24x24.png" align = "middle">
- © <tal tal:replace = "copyrightYears/0"></tal>-<tal tal:replace = "copyrightYears/1"></tal>
- <a href = "http://www.lumc.nl">LUMC</a>
-
-
- </td>
- <td align="right">
- <a href="#top" class="hornav">go to top</a>
- </td>
- </tr>
- <tr>
- <!--
- <td colspan="2"
- align="center">Last edited by: with /usr/bin/vim
- </td>
- -->
- </tr>
- <tr>
- <td colspan="2"><img
- src="static/images/1x1b.gif"
- width="1"
- height="10"
- border="0">
- </td>
- </tr>
- </table>
- </td>
- </tr>
- </table>
- <a id = "bottom" name = "bottom"></a>
-<div tal:condition="piwik" tal:omit-tag="">
-<!-- Piwik -->
-<script type="text/javascript" tal:content="string:
-var pkBaseURL = "${piwikBase}/";
-document.write(unescape("%3Cscript src='" + pkBaseURL + "piwik.js' type='text/javascript'%3E%3C/script%3E"));
-"></script><script type="text/javascript" tal:content="string:
-try {
-var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", ${piwikSite});
-piwikTracker.trackPageView();
-piwikTracker.enableLinkTracking();
-} catch( err ) {}
-"></script><noscript><p><img tal:attributes="src string:${piwikBase}/piwik.php?idsite=${piwikSite}" style="border:0" alt="" /></p></noscript>
-<!-- End Piwik Tracking Code -->
-</div>
- </body>
-</html>
diff --git a/mutalyzer/templates/skel.html b/mutalyzer/templates/skel.html
deleted file mode 100644
index 4057d770..00000000
--- a/mutalyzer/templates/skel.html
+++ /dev/null
@@ -1,13 +0,0 @@
-<html>
- <head>
- <title></title>
- </head>
- <body>
- <div metal:define-macro="content">
- <center>
- <h3>Skeleton</h3>
- </center>
- Your text here.
- </div>
- </body>
-</html>
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 203e39b1..4af709fe 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -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
diff --git a/requirements.txt b/requirements.txt
index 4ab10349..e2e06ca3 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -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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