diff --git a/mutalyzer/templates/base.html b/mutalyzer/templates/base.html
new file mode 100644
index 0000000000000000000000000000000000000000..f79fff29392a8c9a362dd995e5e8e1db2076d827
--- /dev/null
+++ b/mutalyzer/templates/base.html
@@ -0,0 +1,367 @@
+<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 }} — {{ 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>
+ </td>
+ <td align="right">
+ <a href="index"
+ class="hornav">home</a>
+ <a href="about"
+ class="hornav">about</a>
+ <a href="mailto:{{ contactEmail|e }}"
+ 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>
+
+{# 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> </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> </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">
+ <a href="javascript:history.back(-1);"
+ class="hornav">previous page</a>
+ </td>
+ <td align="middle">
+ <img src = "static/images/LUMC_24x24.png" align = "middle">
+ © {{ copyrightYears[0]|e }}-{{ copyrightYears[1]|e }}
+ <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>
+{% 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>
diff --git a/mutalyzer/templates/parse.html b/mutalyzer/templates/parse.html
deleted file mode 100644
index 107ad052c439110f3c66beab03869dc789d72279..0000000000000000000000000000000000000000
--- a/mutalyzer/templates/parse.html
+++ /dev/null
@@ -1,63 +0,0 @@
-<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>
- <accession number>.<version
- number>(<gene symbol>):<sequence
- type>.<variant description>
- </div><br>
- Example: AB026906.1:c.274G>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 "^" 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>
diff --git a/mutalyzer/templates/syntax_checker.html b/mutalyzer/templates/syntax_checker.html
new file mode 100644
index 0000000000000000000000000000000000000000..1052c4640afa2e2169a2bb0a8974d020059d2734
--- /dev/null
+++ b/mutalyzer/templates/syntax_checker.html
@@ -0,0 +1,55 @@
+{% 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>
+ <accession number>.<version
+ number>(<gene symbol>):<sequence
+ type>.<variant description>
+ </div><br>
+ Example: AB026906.1:c.274G>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 "^" indicates the position where the error occurred.</p>
+ {% else %}
+ <p>The syntax of this variant is OK!</p>
+ {% endif %}
+ <br>
+{% endif %}
+
+{% endblock content %}
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 138175231e88ccce507db12f60f7ac75d42c9388..01613a589c24fb4062f0f0ffad1ee9640678b3d6 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -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
diff --git a/requirements.txt b/requirements.txt
index da91f3e38069c36c2518ee045c32ef07dd44269f..4ab103492465b30593219b25d1e9575eb0e030f0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -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