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Commit 364e017a authored by Vermaat's avatar Vermaat
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Use Jinja2 for syntax checker page

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mutalyzer/templates/base.html 0 → 100644
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View file @ 364e017a
<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>Mutalyzer {{ version|e }} &mdash; {{ page_title|e }}</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 href="mailto:{{ contactEmail|e }}"
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>
{# Fields are: url, id, caption, subnav #}
{% set navigation_menu = [
('index', 'homepage', 'Home', False),
('check', 'name-checker', 'Name Checker', False),
('syntaxCheck', 'syntax-checker', 'Syntax Checker', False),
('positionConverter', 'position-converter', 'Position Converter', False),
('snp', 'snp-converter', 'SNP Converter', False),
('nameGenerator', 'name-generator', 'Name Generator', False),
('descriptionExtract', 'description-extractor', 'Description Extractor', False),
('upload', 'reference-loader', 'Reference File Loader', False),
('batch', 'batch-jobs', 'Batch Jobs', False),
('batchNameChecker', 'batch-name-checker', 'Name Checker', True),
('batchSyntaxChecker', 'batch-syntax-checker', 'Syntax Checker', True),
('batchPositionConverter', 'batch-position-converter', 'Position Converter', True),
('batchSnpConverter', 'batch-snp-converter', 'SNP Converter', True),
('webservices', 'webservices', 'Web Services', False)
] -%}
{% set active_page = active_page|default('home') -%}
{% for url, id, caption, subnav in navigation_menu %}
<tr class="menu{% if id == active_page %} active{% endif %}">
{% if subnav %}
<td></td>
<td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
<a href="{{ url|e }}">{{ caption|e }}</a>
</td>
{% else %}
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
<a href="{{ url|e }}">{{ caption|e }}</a>
</td>
{% endif %}
</tr>
{% endfor %}
<tr><td>&nbsp;</td></tr>
<tr class="menu">
<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 class="menu">
<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 class="menu">
<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 class="menu">
<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>Mutalyzer {{ version|e }}<br>
<small><small><small><small>
{% if release %}
released on {{ releaseDate|e }}
{% else %}
development version
{% endif %}
</small></small></small></small>
</h2>
HGVS nomenclature version
<span>{{ nomenclatureVersion|e }}</span>
</center>
<p>
<h3><center>{{ page_title|e }}</center></h3>
{% block content %}{% endblock %}
<!-- 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; {{ copyrightYears[0]|e }}-{{ copyrightYears[1]|e }}
<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>
{% if piwik %}
<!-- Piwik -->
<script type="text/javascript">
var pkBaseURL = "{{ piwikBase|e }}/";
document.write(unescape("%3Cscript src='" + pkBaseURL + "piwik.js' type='text/javascript'%3E%3C/script%3E"));
</script><script type="text/javascript">
try {
var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", {{ piwikSite|e }});
piwikTracker.trackPageView();
piwikTracker.enableLinkTracking();
} catch( err ) {}
</script><noscript><p><img src="{{ piwikBase|e }}/piwik.php?idsite={{ piwikSite|e }}" style="border:0" alt="" /></p></noscript>
<!-- End Piwik Tracking Code -->
{% endif %}
</body>
</html>
mutalyzer/templates/parse.html deleted 100644 → 0
+ 0
− 63
View file @ c03cbccf
<html>
<head>
<link rel="stylesheet"
type="text/css"
href="static/css/style.css">
<title></title>
</head>
<body>
<div metal:define-macro="content">
<center>
<h3>Variant syntax checker</h3>
</center>
<div style="border: 1px solid grey; background-color: aliceblue; padding: 20px;">
<div>
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>
&lt;accession number&gt;.&lt;version
number&gt;(&lt;gene symbol&gt;):&lt;sequence
type&gt;.&lt;variant description&gt;
</div><br>
Example: AB026906.1:c.274G&gt;T<br>
<br>
<form action = "" method = "post">
<input
type = "text"
name = "variant"
tal:attributes = "value variant"
style = "width:100%"><br>
<input
type="submit"
value="Submit">
<input type="button" value="Clear field"
onclick="clearField(this.form, 'variant');">
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/SyntaxChecker">Help</a>
</form>
<br>
</div>
<br>
<div tal:condition = "variant">
<h3>Variant syntax checker results:</h3>
<div tal:condition = "parseError">
<div class="messages">
<p tal:repeat = "m messages" tal:content = "m/description"
tal:attributes = "class m/class; title string:${m/level} (origin: ${m/origin})"></p>
<p tal:content = "summary"></p>
<br>
</div>
<h4>Details of the parse error:</h4>
<pre tal:content =
"structure string:${parseError/0}<br>${parseError/1}">
</pre>
The &quot;^&quot; indicates the position where the error occurred.
</div>
<div tal:condition = "not:parseError">
The syntax of this variant is OK!
</div>
<br>
</div>
</div>
</body>
</html>
mutalyzer/templates/syntax_checker.html 0 → 100644
+ 55
− 0
View file @ 364e017a
{% extends "base.html" %}
{% set active_page = "syntax-checker" %}
{% set page_title = "Variant syntax checker" %}
{% block content %}
<div style="border: 1px solid grey; background-color: aliceblue; padding: 20px;">
<div>
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>
&lt;accession number&gt;.&lt;version
number&gt;(&lt;gene symbol&gt;):&lt;sequence
type&gt;.&lt;variant description&gt;
</div><br>
Example: AB026906.1:c.274G&gt;T<br>
<br>
<form action = "" method = "post">
<input
type = "text"
name = "variant"
value = "{{ variant|e }}"
style = "width:100%"><br>
<input
type="submit"
value="Submit">
<input type="button" value="Clear field"
onclick="clearField(this.form, 'variant');">
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/SyntaxChecker">Help</a>
</form>
<br>
</div>
<br>
{% if variant %}
<h3>Variant syntax checker results:</h3>
{% if parseError %}
<div class="messages">
{% for m in messages %}
<p class="{{ m.class|e }}" title="{{ m.level|e }} (origin: {{ m.origin|e }})">{{ m.description|e }}</p>
{% endfor %}
<p>{{ summary|e }}</p>
<br>
</div>
<h4>Details of the parse error:</h4>
<pre>{{- parseError[0]|e }}<br>{{- parseError[1]|e }}</pre>
<p>The &quot;^&quot; indicates the position where the error occurred.</p>
{% else %}
<p>The syntax of this variant is OK!</p>
{% endif %}
<br>
{% endif %}
{% endblock content %}
mutalyzer/website.py
+ 32
− 15
View file @ 364e017a
......@@ -24,6 +24,7 @@ import bz2
import web
import urllib
from collections import defaultdict
from web.contrib.template import render_jinja
from lxml import etree
import pkg_resources
......@@ -176,7 +177,7 @@ class render_tal:
# TAL template render
render = render_tal(pkg_resources.resource_filename('mutalyzer', 'templates'),
render_ = render_tal(pkg_resources.resource_filename('mutalyzer', 'templates'),
globals = {
'version' : mutalyzer.__version__,
'nomenclatureVersion' : mutalyzer.NOMENCLATURE_VERSION,
......@@ -191,6 +192,22 @@ render = render_tal(pkg_resources.resource_filename('mutalyzer', 'templates'),
'piwikSite' : config.get('piwikSite')
})
# Jinja2 template render
render = render_jinja(pkg_resources.resource_filename('mutalyzer', 'templates'),
encoding='utf-8',
globals = {
'version' : mutalyzer.__version__,
'nomenclatureVersion' : mutalyzer.NOMENCLATURE_VERSION,
'releaseDate' : mutalyzer.__date__,
'release' : mutalyzer.RELEASE,
'copyrightYears' : mutalyzer.COPYRIGHT_YEARS,
'contactEmail' : config.get('email'),
'serviceSoapLocation' : SERVICE_SOAP_LOCATION,
'serviceJsonLocation' : SERVICE_JSON_LOCATION,
'piwik' : config.get('piwik'),
'piwikBase' : config.get('piwikBase'),
'piwikSite' : config.get('piwikSite')})
# web.py application
app = web.application(urls, globals(), autoreload = False)
......@@ -424,7 +441,7 @@ class SyntaxCheck:
"parseError" : None,
"debug" : ""
}
return render.parse(args)
return render.syntax_checker(args)
#GET
def POST(self):
......@@ -468,7 +485,7 @@ class SyntaxCheck:
output.addMessage(__file__, -1, 'INFO',
'Finished request syntaxCheck(%s)' % i.variant)
return render.parse(args)
return render.syntax_checker(args)
#POST
#SyntaxCheck
......@@ -531,7 +548,7 @@ class Snp:
'lastpost' : rs_id
}
return render.snp(args)
return render_.snp(args)
#snp
#Snp
......@@ -637,7 +654,7 @@ class PositionConverter:
'Finished request positionConverter(%s, %s)' % (build,
variant))
return render.converter(attr)
return render_.converter(attr)
#position_converter
#PositionConverter
......@@ -801,7 +818,7 @@ class Check:
the site layout and include the HTML form.
"""
if not name:
return render.check(dict(name=None), standalone=standalone)
return render_.check(dict(name=None), standalone=standalone)
output = Output(__file__)
output.addMessage(__file__, -1, 'INFO', 'Received variant %s from %s'
......@@ -904,7 +921,7 @@ class Check:
output.addMessage(__file__, -1, 'INFO', 'Finished variant %s' % name)
return render.check(args, standalone=standalone, prevent_caching=True)
return render_.check(args, standalone=standalone, prevent_caching=True)
#check
#Check
......@@ -953,7 +970,7 @@ class DescriptionExtractor:
}
if not (referenceSeq and variantSeq):
return render.descriptionExtract(args)
return render_.descriptionExtract(args)
output.addMessage(__file__, -1, 'INFO',
"Received Description Extract request from %s" % IP)
......@@ -990,7 +1007,7 @@ class DescriptionExtractor:
output.addMessage(__file__, -1, 'INFO',
"Finished Description Extract request")
return render.descriptionExtract(args)
return render_.descriptionExtract(args)
#descriptionExtract
#DescriptionExtract
......@@ -1101,7 +1118,7 @@ class BatchProgress:
web.header('Content-Type', 'text/plain')
return ret
return render.progress(attr)
return render_.progress(attr)
#GET
#BatchProgress
......@@ -1245,7 +1262,7 @@ class BatchChecker:
attr["errors"].extend(map(util.message_info, O.getMessages()))
return render.batch(attr, page=page)
return render_.batch(attr, page=page)
#batch
#BatchChecker
......@@ -1341,7 +1358,7 @@ class Uploader:
'maxSize' : float(maxUploadSize) / 1048576,
'errors' : errors
}
return render.gbupload(args)
return render_.gbupload(args)
#GET
def POST(self):
......@@ -1508,7 +1525,7 @@ class Uploader:
i.fiveutr, i.threeutr, i.chracc, i.start, i.stop, i.orientation,
i.chrnameassembly, i.chrname, i.chrnamestart, i.chrnamestop, i.chrnameorientation))
return render.gbupload(args)
return render_.gbupload(args)
#POST
#Uploader
......@@ -1567,7 +1584,7 @@ class Static:
"""
Render a TAL template as HTML.
@kwarg page: Page name to render. A TAL template with this name must
@kwarg page: Page name to render_. A TAL template with this name must
exist. Special case is a page of None, having the same
effect as 'index'.
@type page: string
......@@ -1579,6 +1596,6 @@ class Static:
if not page:
page = 'index'
return getattr(render, page)()
return getattr(render_, page)()
#GET
#Static
requirements.txt
+ 1
− 0
View file @ 364e017a
......@@ -18,5 +18,6 @@ xlrd==0.9.2
WebOb==1.1.1
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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