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Commit d4379004 authored by Vermaat's avatar Vermaat
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Use Jinja2 for static pages

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mutalyzer/templates/about.html
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View file @ d4379004
<html>
<head>
<title></title>
</head>
<body>
<div metal:define-macro="content">
<center>
<h3>About</h3>
</center>
Mutalyzer <span tal:content = "structure string:${version}"></span>
is designed and developed by Jeroen F.J. Laros, with the
following exceptions:
<ul>
<li>The LRG parser, as well as the Batch interfaces are written
by Gerben R. Stouten.</li>
<li>The position converter interfaces (web service and WWW) are
written by Gerard C.P. Schaafsma.</li>
<li>Current development and maintenance is done by Martijn
Vermaat.</li>
<li>Automatic extraction of variant descriptions is implemented by
Jonathan Vis.</li>
</ul>
Furthermore we would like to thank the following people for their
valuable work on previous versions that acted as a guideline for the
development of the current version:
<ul>
<li>Ernest van Ophuizen.</li>
<li>Martin Wildeman.</li>
<li>Corinne Bareil.</li>
<li>Gerben R. Stouten.</li>
</ul>
Specifications are given by Peter E.M. Taschner and Johan T. den
Dunnen.<br>
<br>
Since references to WWW-sites are not yet acknowledged as citations,
please mention
<a href="http://www.ncbi.nlm.nih.gov/pubmed/18000842">
&quot;Wildeman M et al. (2008). Improving sequence variant
descriptions in mutation databases and literature using the
Mutalyzer sequence variation nomenclature checker. Hum Mutat 29,
6-13&quot;</a> (<a href="http://dx.doi.org/10.1002/humu.20654">direct
link</a>) when referring to these pages.<br>
<br>
Project development is sponsored by
<a href="http://www.gen2phen.org" target="_blank">
<img src="static/images/gen_2_phen_logo_print.png"
width="110"
height="50"
align="middle"
border="0"
alt="Eurogentest"></a>
and
<a href="http://www.nbic.nl" target="_blank">
<img src="static/images/nbic_logo.png"
width="229"
height="50"
align="middle"
border="0"
alt="NBIC"></a>
and has been supported by
<a href="http://www.eurogentest.org" target="_blank">
<img src="static/images/Eurogentest.png"
width="110"
height="50"
align="middle"
border="0"
alt="Eurogentest"></a>
and
<a href="http://www.commit-nl.nl/" target="_blank">
<img src="static/images/commit_logo.png"
width="122"
height="50"
align="middle"
border="0"
alt="Dutch national program COMMIT"></a>
<br><br>
Some icons are copyright &copy;
<a href="http://p.yusukekamiyamane.com/">Yusuke Kamiyamane</a>.
<br>
</div>
</body>
</html>
{% extends "base.html" %}
{% set active_page = "about" %}
{% set page_title = "About Mutalyzer" %}
{% block content %}
<p>
Mutalyzer {{ version|e }} is designed and developed by Jeroen F.J. Laros, with
the following exceptions:
</p>
<ul>
<li>The LRG parser, as well as the Batch interfaces are written
by Gerben R. Stouten.</li>
<li>The position converter interfaces (web service and WWW) are
written by Gerard C.P. Schaafsma.</li>
<li>Current development and maintenance is done by Martijn
Vermaat.</li>
<li>Automatic extraction of variant descriptions is implemented by
Jonathan Vis.</li>
</ul>
<p>
Furthermore we would like to thank the following people for their
valuable work on previous versions that acted as a guideline for the
development of the current version:
</p>
<ul>
<li>Ernest van Ophuizen.</li>
<li>Martin Wildeman.</li>
<li>Corinne Bareil.</li>
<li>Gerben R. Stouten.</li>
</ul>
<p>
Specifications are given by Peter E.M. Taschner and Johan T. den
Dunnen.
</p>
<p>
Since references to WWW-sites are not yet acknowledged as citations,
please mention
<a href="http://www.ncbi.nlm.nih.gov/pubmed/18000842">
&quot;Wildeman M et al. (2008). Improving sequence variant
descriptions in mutation databases and literature using the
Mutalyzer sequence variation nomenclature checker. Hum Mutat 29,
6-13&quot;</a> (<a href="http://dx.doi.org/10.1002/humu.20654">direct
link</a>) when referring to these pages.
</p>
<p>
Project development is sponsored by
<a href="http://www.gen2phen.org" target="_blank">
<img src="static/images/gen_2_phen_logo_print.png"
width="110"
height="50"
align="middle"
border="0"
alt="Eurogentest"></a>
and
<a href="http://www.nbic.nl" target="_blank">
<img src="static/images/nbic_logo.png"
width="229"
height="50"
align="middle"
border="0"
alt="NBIC"></a>
and has been supported by
<a href="http://www.eurogentest.org" target="_blank">
<img src="static/images/Eurogentest.png"
width="110"
height="50"
align="middle"
border="0"
alt="Eurogentest"></a>
and
<a href="http://www.commit-nl.nl/" target="_blank">
<img src="static/images/commit_logo.png"
width="122"
height="50"
align="middle"
border="0"
alt="Dutch national program COMMIT"></a>
</p>
<p>
Some icons are copyright &copy;
<a href="http://p.yusukekamiyamane.com/">Yusuke Kamiyamane</a>.
</p>
{% endblock content %}
mutalyzer/templates/index.html
+ 74
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<html>
<head>
<title></title>
</head>
<body>
<div metal:define-macro="content">
<center><h3>Welcome to the Mutalyzer web site</h3></center>
<br>
{% extends "base.html" %}
The aim of this program suite is to support checks of sequence variant
nomenclature according to the
<a href="http://www.hgvs.org/mutnomen/">guidelines</a> of the
<a href="http://www.hgvs.org">Human Genome Variation Society</a>.<br>
<br>
<br>
{% set active_page = "homepage" %}
{% set page_title = "Welcome to the Mutalyzer website" %}
Different interfaces are provided to collect the information necessary
for the checks:
<ul>
<li>
The <a href = "check">Name Checker</a> takes the complete sequence
variant description as input and checks whether it is correct.
</li>
<li>
The <a href = "syntaxCheck">Syntax Checker</a> takes the complete
sequence variant description as input and checks whether the syntax
is correct.
</li>
<li>
The <a href = "positionConverter">Position Converter</a> can convert
chromosomal positions to transcript orientated positions and vice
versa.
</li>
<li>
The <a href = "snp">SNP converter</a> allows you to convert a
dbSNP rsId to HGVS notation.
</li>
<li>
The <a href = "nameGenerator">Name Generator</a> is a user friendly
interface that helps to make a valid HGVS variant description.
</li>
<li>
The <a href = "descriptionExtract">Description Extractor</a> allows
you to generate the HGVS variant description from a reference
sequence and an observed sequence.
</li>
<li>
The <a href = "upload">Reference File Loader</a> allows you to load and
use your own reference sequence.
</li>
<li>
The <a href="batch">Batch Checkers</a> are interfaces that accept a
list of inputs. These interfaces can be used for large quantities of
checks.
</li>
<li>
The <a href = "webservices">Web services</a> page provides instructions
for the web services.
</li>
</ul>
<br>
<!--
Mutalyzer <span tal:content = "structure string:${version}"></span> is
written completely in <a href="http://www.python.org">Python</a>. The
Python Scripting Language was chosen for good readability and therefore
easy maintenance.<br>
-->
GenBank sequences are retrieved from the
<a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>
(<a href="http://eutils.ncbi.nlm.nih.gov/About/disclaimer.html"
>Copyright and Disclaimers</a>).<br>
This project is sponsored by
<a href = "http://www.sun.com">SUN Microsystems</a> with server
hardware within the scope of the Academic Excellence Grant (AEG)
program (award EDUD-7832-080223-CNE).<br>
</div>
</body>
</html>
{% block content %}
<p>
The aim of this program suite is to support checks of sequence variant
nomenclature according to the
<a href="http://www.hgvs.org/mutnomen/">guidelines</a> of the
<a href="http://www.hgvs.org">Human Genome Variation Society</a>.
</p>
<p>
Different interfaces are provided to collect the information necessary
for the checks:
</p>
<ul>
<li>
The <a href = "check">Name Checker</a> takes the complete sequence
variant description as input and checks whether it is correct.
</li>
<li>
The <a href = "syntaxCheck">Syntax Checker</a> takes the complete
sequence variant description as input and checks whether the syntax
is correct.
</li>
<li>
The <a href = "positionConverter">Position Converter</a> can convert
chromosomal positions to transcript orientated positions and vice
versa.
</li>
<li>
The <a href = "snp">SNP converter</a> allows you to convert a
dbSNP rsId to HGVS notation.
</li>
<li>
The <a href = "nameGenerator">Name Generator</a> is a user friendly
interface that helps to make a valid HGVS variant description.
</li>
<li>
The <a href = "descriptionExtract">Description Extractor</a> allows
you to generate the HGVS variant description from a reference
sequence and an observed sequence.
</li>
<li>
The <a href = "upload">Reference File Loader</a> allows you to load and
use your own reference sequence.
</li>
<li>
The <a href="batch">Batch Checkers</a> are interfaces that accept a
list of inputs. These interfaces can be used for large quantities of
checks.
</li>
<li>
The <a href = "webservices">Web services</a> page provides instructions
for the web services.
</li>
</ul>
<p>
GenBank sequences are retrieved from the
<a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>
(<a href="http://eutils.ncbi.nlm.nih.gov/About/disclaimer.html"
>Copyright and Disclaimers</a>).
</p>
<p>
This project is sponsored by
<a href = "http://www.sun.com">SUN Microsystems</a> with server
hardware within the scope of the Academic Excellence Grant (AEG)
program (award EDUD-7832-080223-CNE).
</p>
{% endblock content %}
mutalyzer/templates/nameGenerator.html
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− 11
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<html>
<head>
<title></title>
</head>
<body >
<!-- Start of template -->
<div metal:define-macro="content">
<center><h3 tal:content = "structure string:Name Generator"></h3></center>
{% extends "base.html" %}
{% set active_page = "name-generator" %}
{% set page_title = "Name Generator" %}
{% block content %}
<div id="main">
<form id="mainform" onkeyup="update();" onchange="update();">
......@@ -205,6 +203,4 @@
</div>
</div>
</body>
</html>
{% endblock content %}
mutalyzer/templates/webservices.html
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− 53
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<html>
<head>
<title></title>
</head>
<body>
<div metal:define-macro="content">
<center>
<h3>Web services</h3>
</center>
<br>
Most Mutalyzer functionality is programmatically available through two
interfaces: a SOAP web service and a HTTP/RPC+JSON web service.
<br>
<h3>SOAP web service</h3>
A <a href="services/?wsdl">WSDL description</a> is available
for easy generation of client programs in many languages. See the
<a href = "soap-api">annotated API</a> for detailed documentation.
<br>
<br>
The following are some example client programs for SOAP web service. They
use the <a href="soap-api#op.checkSyntax">checkSyntax</a> method
to determine if a variant description adheres to the <span class="helper"
title="Human Genome Variation Society standard variant nomenclature">
<a href="http://www.hgvs.org/mutnomen">HGVS</a> format</span>.
<ul>
<li>Python client using the suds library:
<a href="download/client-suds.py"><tt>client-suds.py</tt></a>
<li>Python client using the soappy library:
<a href="download/client-soappy.py"><tt>client-soappy.py</tt></a>
<li>Ruby client using the Savon library:
<a href="download/client-savon.rb"><tt>client-savon.rb</tt></a>
<li>Mono client in C#:
<a href="download/client-mono.cs"><tt>client-mono.cs</tt></a>
<li>PHP client using the PHP5 SOAP extension:
<a href="download/client-php.php"><tt>client-php.php</tt></a>
</ul>
Here is an example that could be used for
<a href="download/textmining.py">text mining</a> on a
<a href="downloads/textmining_sample.txt">sample</a> input file.
<h3>HTTP/RPC+JSON web service</h3>
The HTTP/RPC+JSON web service is experimental and currently undocumented.
It can be called using HTTP GET requests on <code tal:content = "structure string:${location}${serviceJsonLocation}/method?param=value"></code> where <code>method</code> is the name of the method to be called and method parameters are expected as <code>param=value</code> query string parameters. Responses are JSON-encoded.
<br>
<br>
Example: <a tal:attributes="href string:${location}${serviceJsonLocation}/checkSyntax?variant=AB026906.1:c.274del" tal:content="structure string:checkSyntax?variant=AB026906.1:c.274del"></a>
<br>
<br>
For now, you can work from this example using the above mentioned
<a href="soap-api">annotated SOAP API</a>, since the HTTP/RPC+JSON
web service mirrors the functionality of the SOAP web service.
</div>
</body>
</html>
{% extends "base.html" %}
{% set active_page = "webservices" %}
{% set page_title = "Web Services" %}
{% block content %}
<p>
Most Mutalyzer functionality is programmatically available through two
interfaces: a SOAP web service and a HTTP/RPC+JSON web service.
</p>
<h3>SOAP web service</h3>
<p>
A <a href="services/?wsdl">WSDL description</a> is available
for easy generation of client programs in many languages. See the
<a href = "soap-api">annotated API</a> for detailed documentation.
</p>
<p>
The following are some example client programs for SOAP web service. They
use the <a href="soap-api#op.checkSyntax">checkSyntax</a> method
to determine if a variant description adheres to the <span class="helper"
title="Human Genome Variation Society standard variant nomenclature">
<a href="http://www.hgvs.org/mutnomen">HGVS</a> format</span>.
</p>
<ul>
<li>Python client using the suds library:
<a href="download/client-suds.py"><tt>client-suds.py</tt></a>
<li>Python client using the soappy library:
<a href="download/client-soappy.py"><tt>client-soappy.py</tt></a>
<li>Ruby client using the Savon library:
<a href="download/client-savon.rb"><tt>client-savon.rb</tt></a>
<li>Mono client in C#:
<a href="download/client-mono.cs"><tt>client-mono.cs</tt></a>
<li>PHP client using the PHP5 SOAP extension:
<a href="download/client-php.php"><tt>client-php.php</tt></a>
</ul>
<p>
Here is an example that could be used for
<a href="download/textmining.py">text mining</a> on a
<a href="downloads/textmining_sample.txt">sample</a> input file.
</p>
<h3>HTTP/RPC+JSON web service</h3>
<p>
The HTTP/RPC+JSON web service is experimental and currently undocumented.
It can be called using HTTP GET requests on
<code>{{ location|e }}{{ serviceJsonLocation|e }}/method?param=value</code>
where <code>method</code> is the name of the method to be called and method
parameters are expected as <code>param=value</code> query string
parameters. Responses are JSON-encoded.
</p>
<p>
Example: <a href="{{ location|e }}{{ serviceJsonLocation|e }}/checkSyntax?variant=AB026906.1:c.274del">checkSyntax?variant=AB026906.1:c.274del</a>
</p>
<p>
For now, you can work from this example using the above mentioned
<a href="soap-api">annotated SOAP API</a>, since the HTTP/RPC+JSON
web service mirrors the functionality of the SOAP web service.
</p>
{% endblock content %}
mutalyzer/website.py
+ 3
− 3
View file @ d4379004
......@@ -134,8 +134,6 @@ class render_tal:
context.addGlobal('interactive', not standalone)
context.addGlobal('location', web.ctx.homedomain + web.ctx.homepath)
for name, value in self.globals.items():
context.addGlobal(name, value)
......@@ -1596,6 +1594,8 @@ class Static:
if not page:
page = 'index'
return getattr(render_, page)()
args = {'location': web.ctx.homedomain + web.ctx.homepath}
return getattr(render, page)(args)
#GET
#Static
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