diff --git a/mutalyzer/templates/about.html b/mutalyzer/templates/about.html
index 8f880555a21bb14ccd6f609bb34d377532223765..dcf17b906f8f753bc0f17f5f37bc9e5eac7b77d9 100644
--- a/mutalyzer/templates/about.html
+++ b/mutalyzer/templates/about.html
@@ -1,82 +1,93 @@
-<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">
- "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"</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 ©
- <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">
+ "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"</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 ©
+<a href="http://p.yusukekamiyamane.com/">Yusuke Kamiyamane</a>.
+</p>
+
+{% endblock content %}
diff --git a/mutalyzer/templates/index.html b/mutalyzer/templates/index.html
index e248df27f794f3269674fa02828b014ba3a111c2..15246e76a7dc69aabe13487544a0ee5fa17275b4 100644
--- a/mutalyzer/templates/index.html
+++ b/mutalyzer/templates/index.html
@@ -1,78 +1,76 @@
-<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 %}
diff --git a/mutalyzer/templates/nameGenerator.html b/mutalyzer/templates/nameGenerator.html
index 9e7befe78f5dc9179df5395475deb15666199de4..90716289fb909c4a439faf314758784b8d232461 100644
--- a/mutalyzer/templates/nameGenerator.html
+++ b/mutalyzer/templates/nameGenerator.html
@@ -1,11 +1,9 @@
-<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 %}
diff --git a/mutalyzer/templates/webservices.html b/mutalyzer/templates/webservices.html
index b6aa91ef738ae2e5b04821aafec9b8dddad14042..c1f65448ef14f0a30551d86cde211a3b72f81d79 100644
--- a/mutalyzer/templates/webservices.html
+++ b/mutalyzer/templates/webservices.html
@@ -1,53 +1,69 @@
-<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 %}
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 01613a589c24fb4062f0f0ffad1ee9640678b3d6..53e65cfdf4488bd08a00b2a76474a061a9966871 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -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