From 05b32e8642bb44037800673a3b65b810542ef5c2 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Wed, 11 Dec 2013 11:59:59 +0100
Subject: [PATCH] Use Jinja2 for reference loader
---
mutalyzer/templates/gbupload.html | 193 ---------------------
mutalyzer/templates/reference_loader.html | 200 ++++++++++++++++++++++
mutalyzer/website.py | 4 +-
3 files changed, 202 insertions(+), 195 deletions(-)
delete mode 100644 mutalyzer/templates/gbupload.html
create mode 100644 mutalyzer/templates/reference_loader.html
diff --git a/mutalyzer/templates/gbupload.html b/mutalyzer/templates/gbupload.html
deleted file mode 100644
index f47270af..00000000
--- a/mutalyzer/templates/gbupload.html
+++ /dev/null
@@ -1,193 +0,0 @@
-<html>
- <head>
- <title></title>
- </head>
- <body>
- <div metal:define-macro="content">
- <script>
- var oldLoad = window.onload;
- window.onload=function(){
- if (oldLoad) oldLoad();
- updateVisibility();
- }
- </script>
- <center><h3>Reference File Loader</h3></center>
- The Reference File Loader allows you to use your own reference
- sequence when no appropriate RefSeq, GenBank or LRG file is available.
- <br>
- Please select one of the options below to upload or retrieve your reference
- sequence (maximum size is <span tal:content = "maxSize"></span> megabytes):
- <br>
- <br>
- <form name='invoer' enctype="multipart/form-data"
- action="" method="post">
- <table border="0" cellpadding="0" cellspacing="0">
- <tr valign="top">
- <th width="100" style="text-align: left; padding-left : 70px">Options</th>
- <td>
- <input type="radio" name="invoermethode" value='file' checked
- onClick="updateVisibility();">
- The reference sequence file is a local file<br>
- <input type="radio" name="invoermethode" value='url'
- onClick="updateVisibility();">
- The reference sequence file can be found at the following URL<br>
- <input type="radio" name="invoermethode" value='gene'
- onClick="updateVisibility();">
- Retrieve part of the reference genome for a (HGNC) gene symbol<br>
- <input type="radio" name="invoermethode" value='chr'
- onClick="updateVisibility();">
- Retrieve a range of a chromosome by accession number<br>
- <input type="radio" name="invoermethode" value='chrname'
- onClick="updateVisibility();">
- Retrieve a range of a chromosome by name<br>
- </td>
- </tr>
- <tr height="20px"></tr>
- <tr valign="top">
- <th width="100" style="text-align : left; padding-left : 70px">Input
- </th>
- <td>
- <span id="file_label">
- <i>Please select the GenBank file in plain text format</i><br>
- <input type='file' name="bestandsveld"><br>
- </span>
- <span id="url_label">
- <i>Please enter the URL of the GenBank file in plain text
- (including http://)</i>
- <br>
- <input type='text' name="urlveld"><br>
- </span>
- <span id="gene_label">
- <i>Please enter the Gene symbol and organism name without spaces
- and specify the length of the flanking sequences</i>
- <br>
- <b>Note:</b> This uses
- the <a href="http://www.ncbi.nlm.nih.gov/sites/gquery">NCBI
- Entrez</a> search engine and is therefore based on the current
- Entrez assembly for the given organism (GRCh37/hg19 for human).
- <table>
- <tr>
- <td>Gene symbol</td>
- <td><input type='text' name="genesymbol"></td>
- </tr>
- <tr>
- <td>Organism name</td>
- <td><input type='text' name="organism"></td>
- </tr>
- <tr>
- <td>Number of 5' flanking nucleotides</td>
- <td><input type='text' name="fiveutr" value="5000"></td>
- </tr>
- <tr><td>Number of 3' flanking nucleotides</td>
- <td><input type='text' name="threeutr" value="2000"></td>
- </tr>
- </table>
- </span>
- <span id="range_label">
- <i>Please enter the accession number of the chromosome or contig
- and specify the range</i><br>
- <table>
- <tr>
- <td>Chromosome accession number</td>
- <td><input type='text' name="chracc"></td>
- </tr>
- <tr>
- <td>Start position</td>
- <td><input type='text' name="start"></td>
- </tr>
- <tr>
- <td>Stop position</td>
- <td><input type='text' name="stop"></td>
- </tr>
- <tr>
- <td>Orientation</td>
- <td>
- <select name="orientation">
- <option value="1">Forward</option>
- <option value="2">Reverse</option>
- </select>
- </td>
- </tr>
- </table>
- </span>
- <span id="chrname_label">
- <i>Please enter the name of the chromosome
- and specify the range</i><br>
- <table>
- <tr>
- <td>Assembly</td>
- <td>
- <select name="chrnameassembly">
- <option
- selected="selected"
- tal:content = "selected_assembly"
- tal:attributes = "value selected_assembly">
- </option>
- <option tal:repeat = "i unselected_assemblies"
- tal:content = "i"
- tal:attributes = "value i">
- </option>
- </select>
- </td>
- </tr>
- <tr>
- <td>Chromosome name</td>
- <td><input type='text' name="chrname"></td>
- </tr>
- <tr>
- <td>Start position</td>
- <td><input type='text' name="chrnamestart"></td>
- </tr>
- <tr>
- <td>Stop position</td>
- <td><input type='text' name="chrnamestop"></td>
- </tr>
- <tr>
- <td>Orientation</td>
- <td>
- <select name="chrnameorientation">
- <option value="1">Forward</option>
- <option value="2">Reverse</option>
- </select>
- </td>
- </tr>
- </table>
- </span>
- <input type='hidden' name="method" value="gbupload">
- <input type='hidden' name="client" value="human">
- <input type='hidden' name="location" value="file">
- <input type='hidden' name="bestandsnaam"
- value="">
- </td>
- </tr>
- <tr height="20px"></tr>
- <tr>
- <td></td>
- <td>
- <input type="submit" value="Submit">
- <a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/ReferenceLoader">Help</a>
- </td>
- </tr>
- </table>
- </form><br>
-
- <div tal:condition = "errors">
- <b>Error output:</b><br>
- <pre><div tal:repeat = "i errors"
- tal:replace = "structure string:${i}<br>">
- </div></pre>
- </div>
- <div tal:condition = "UD">
- <b>Output:</b><br>
- <br>
- Your reference sequence was loaded successfully.<br>
- You now can use mutalyzer with the following accession number as
- reference: <b tal:content = "UD"></b><br>
- <a tal:attributes = "href string:Reference/${UD}.gb">
- Download this reference sequence.
- </a>
- </div>
- <br>
- </div>
- </body>
-</html>
diff --git a/mutalyzer/templates/reference_loader.html b/mutalyzer/templates/reference_loader.html
new file mode 100644
index 00000000..21565761
--- /dev/null
+++ b/mutalyzer/templates/reference_loader.html
@@ -0,0 +1,200 @@
+{% extends "base.html" %}
+
+{% set active_page = "reference-loader" %}
+{% set page_title = "Reference File Loader" %}
+
+{% block content %}
+
+<script>
+var oldLoad = window.onload;
+window.onload=function(){
+ if (oldLoad) oldLoad();
+ updateVisibility();
+}
+</script>
+
+<p>
+The Reference File Loader allows you to use your own reference
+sequence when no appropriate RefSeq, GenBank or LRG file is available.
+</p>
+<p>
+Please select one of the options below to upload or retrieve your reference
+sequence (maximum size is {{ maxSize|e }} megabytes):
+</p>
+
+<form name='invoer' enctype="multipart/form-data"
+ action="" method="post">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <th width="100" style="text-align: left; padding-left : 70px">Options</th>
+ <td>
+ <input type="radio" name="invoermethode" value='file' checked
+ onClick="updateVisibility();">
+ The reference sequence file is a local file<br>
+ <input type="radio" name="invoermethode" value='url'
+ onClick="updateVisibility();">
+ The reference sequence file can be found at the following URL<br>
+ <input type="radio" name="invoermethode" value='gene'
+ onClick="updateVisibility();">
+ Retrieve part of the reference genome for a (HGNC) gene symbol<br>
+ <input type="radio" name="invoermethode" value='chr'
+ onClick="updateVisibility();">
+ Retrieve a range of a chromosome by accession number<br>
+ <input type="radio" name="invoermethode" value='chrname'
+ onClick="updateVisibility();">
+ Retrieve a range of a chromosome by name<br>
+ </td>
+ </tr>
+ <tr height="20px"></tr>
+ <tr valign="top">
+ <th width="100" style="text-align : left; padding-left : 70px">Input
+ </th>
+ <td>
+ <span id="file_label">
+ <i>Please select the GenBank file in plain text format</i><br>
+ <input type='file' name="bestandsveld"><br>
+ </span>
+ <span id="url_label">
+ <i>Please enter the URL of the GenBank file in plain text
+ (including http://)</i>
+ <br>
+ <input type='text' name="urlveld"><br>
+ </span>
+ <span id="gene_label">
+ <i>Please enter the Gene symbol and organism name without spaces
+ and specify the length of the flanking sequences</i>
+ <br>
+ <b>Note:</b> This uses
+ the <a href="http://www.ncbi.nlm.nih.gov/sites/gquery">NCBI
+ Entrez</a> search engine and is therefore based on the current
+ Entrez assembly for the given organism (GRCh37/hg19 for human).
+ <table>
+ <tr>
+ <td>Gene symbol</td>
+ <td><input type='text' name="genesymbol"></td>
+ </tr>
+ <tr>
+ <td>Organism name</td>
+ <td><input type='text' name="organism"></td>
+ </tr>
+ <tr>
+ <td>Number of 5' flanking nucleotides</td>
+ <td><input type='text' name="fiveutr" value="5000"></td>
+ </tr>
+ <tr><td>Number of 3' flanking nucleotides</td>
+ <td><input type='text' name="threeutr" value="2000"></td>
+ </tr>
+ </table>
+ </span>
+ <span id="range_label">
+ <i>Please enter the accession number of the chromosome or contig
+ and specify the range</i><br>
+ <table>
+ <tr>
+ <td>Chromosome accession number</td>
+ <td><input type='text' name="chracc"></td>
+ </tr>
+ <tr>
+ <td>Start position</td>
+ <td><input type='text' name="start"></td>
+ </tr>
+ <tr>
+ <td>Stop position</td>
+ <td><input type='text' name="stop"></td>
+ </tr>
+ <tr>
+ <td>Orientation</td>
+ <td>
+ <select name="orientation">
+ <option value="1">Forward</option>
+ <option value="2">Reverse</option>
+ </select>
+ </td>
+ </tr>
+ </table>
+ </span>
+ <span id="chrname_label">
+ <i>Please enter the name of the chromosome
+ and specify the range</i><br>
+ <table>
+ <tr>
+ <td>Assembly</td>
+ <td>
+ <select name="chrnameassembly">
+ <option
+ selected="selected"
+ value="{{ selected_assembly|e }}">{{ selected_assembly|e }}</option>
+ {% for i in unselected_assemblies %}
+ <option value="{{ i|e }}">{{ i|e }}</option>
+ {% endfor %}
+ </select>
+ </td>
+ </tr>
+ <tr>
+ <td>Chromosome name</td>
+ <td><input type='text' name="chrname"></td>
+ </tr>
+ <tr>
+ <td>Start position</td>
+ <td><input type='text' name="chrnamestart"></td>
+ </tr>
+ <tr>
+ <td>Stop position</td>
+ <td><input type='text' name="chrnamestop"></td>
+ </tr>
+ <tr>
+ <td>Orientation</td>
+ <td>
+ <select name="chrnameorientation">
+ <option value="1">Forward</option>
+ <option value="2">Reverse</option>
+ </select>
+ </td>
+ </tr>
+ </table>
+ </span>
+ <input type='hidden' name="method" value="gbupload">
+ <input type='hidden' name="client" value="human">
+ <input type='hidden' name="location" value="file">
+ <input type='hidden' name="bestandsnaam"
+ value="">
+ </td>
+ </tr>
+ <tr height="20px"></tr>
+ <tr>
+ <td></td>
+ <td>
+ <input type="submit" value="Submit">
+ <a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/ReferenceLoader">Help</a>
+ </td>
+ </tr>
+ </table>
+</form>
+
+{% if errors %}
+ <p>
+ <b>Error output:</b>
+ </p>
+
+ <pre>
+ {% for i in errors %}
+ {{ i|e }}<br>
+ {% endfor %}
+ </pre>
+{% endif %}
+
+{% if UD %}
+ <p>
+ <b>Output:</b>
+ </p>
+ <p>
+ Your reference sequence was loaded successfully.<br>
+ You now can use mutalyzer with the following accession number as
+ reference: <b>{{ UD|e }}</b>
+ </p>
+ <p>
+ <a href="Reference/{{ UD|e }}.gb">Download this reference sequence.</a>
+ </p>
+{% endif %}
+
+{% endblock content %}
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index c58f979d..a784717d 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -1355,7 +1355,7 @@ class Uploader:
'maxSize' : float(maxUploadSize) / 1048576,
'errors' : errors
}
- return render_.gbupload(args)
+ return render.reference_loader(args)
#GET
def POST(self):
@@ -1522,7 +1522,7 @@ 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.reference_loader(args)
#POST
#Uploader
--
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