Welcome, Guest! Log In | Create Account

Share

FACT

File Release Notes and Changelog

Release Name: FACT-1.1.0

Notes:
Version 1.1.0
Essentially keeping track with the EnsEMBL API and Content changes.


Changes:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html>
<head>
<META http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
<title>FACT - flexible annotation &amp; correlation tool</title>
<link href="../style/factStyle.css" type="text/css" rel="stylesheet"/>
</head>
<body>
<div class="topmenu">
<h2>Changes since last version</h2>
</div>
<div class="pagecontent">

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-08-16T18:08:15+0200</span>
<br/>
		Message: <span><b>Last step for packaging</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-08-16T18:27:54+0200</span>
<br/>
		Message: <span><b>new FACT version 1.0.0</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-08-16T18:38:08+0200</span>
<br/>
		Message: <span><b>Changed the SQL to use EnsEMBL version 46...</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-08-16T18:42:19+0200</span>
<br/>
		Message: <span><b>corrected the archive to use EnsEMBL v.46</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-09-24T16:10:15+0200</span>
<br/>
		Message: <span><b>Added a new clean function to the daemon starter</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-09-27T20:23:45+0200</span>
<br/>
		Message: <span><b>Fixed an issue when there are no illumina IDs to be retrieved from a gene. Ensure as well that the highThroughputmethod dies properly</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-09-28T19:14:04+0200</span>
<br/>
		Message: <span><b>Corrected several interface bugs when using the admin view. Fixed the IlluminaAnnotation module to ensure that unproper character retrieved from the EnsEMBL description are removed.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-10-09T16:50:46+0200</span>
<br/>
		Message: <span><b>Added a Doc/Todo directory. Extended the install script to add the fact daemon to the default boot on gentoo.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-10-11T16:32:10+0200</span>
<br/>
		Message: <span><b>added a cron job to restart the server</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-10-11T16:45:18+0200</span>
<br/>
		Message: <span><b>end of line problem...</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-10-11T17:15:41+0200</span>
<br/>
		Message: <span><b>Corrected the sh scripts...</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-10-11T17:22:12+0200</span>
<br/>
		Message: <span><b>a final warning</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-11-23T17:34:15+0100</span>
<br/>
		Message: <span><b>Created a module to retrieve basic Entrez information using Entrez IDs</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-11-23T17:49:50+0100</span>
<br/>
		Message: <span><b>Corrected the use statements for two modules.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-11-27T14:29:24+0100</span>
<br/>
		Message: <span><b>Extracted a method to format the description properly to avoid unwanted characters in the SQL query strings</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-11-27T14:40:06+0100</span>
<br/>
		Message: <span><b>Deal with the case where no annotations are found...</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-11-27T14:45:55+0100</span>
<br/>
		Message: <span><b>Just inverted the job and admin menu for admins only.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-12-18T12:06:21+0100</span>
<br/>
		Message: <span><b>Deal with the csv delimitor programatically</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-12-18T12:31:55+0100</span>
<br/>
		Message: <span><b>Die properly when no tuples are created. It used to stay as a zombie job.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-12-18T14:06:49+0100</span>
<br/>
		Message: <span><b>Corrected a typo while passing the args for the DBD::CSV dbh creation</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-12-19T15:11:56+0100</span>
<br/>
		Message: <span><b>Removed the port argument when getting the EnsEMBL registry. They have changed the port for the version above v48 and they select the right one programatically</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-12-21T16:55:13+0100</span>
<br/>
		Message: <span><b>Implemented the high throughput upload in the one column parser to speed up things...</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2007-12-21T17:04:15+0100</span>
<br/>
		Message: <span><b>Corrected some bugs introduced while speeding up the one column import</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-01-07T15:45:03+0100</span>
<br/>
		Message: <span><b>Updated the user preferences so that a message is printed if the user update his password or email</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-01-07T16:49:59+0100</span>
<br/>
		Message: <span><b>Fixed a bug submitting the wrong parameter in the Preferences form.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-01-07T17:04:30+0100</span>
<br/>
		Message: <span><b>Forgot to close the form tag...</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-03T18:11:56+0200</span>
<br/>
		Message: <span><b>Updated the affy annotations
</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-03T18:15:11+0200</span>
<br/>
		Message: <span><b>just a tiny line got forgotten...</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-03T18:36:21+0200</span>
<br/>
		Message: <span><b>corrected minor issues</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-07T14:11:06+0200</span>
<br/>
		Message: <span><b>Just to have .txt and not .text exported files.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-08T13:23:47+0200</span>
<br/>
		Message: <span><b>Implemented the possibility to updated flatfile databases.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-08T13:26:54+0200</span>
<br/>
		Message: <span><b>Corrected a typo.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-08T13:39:54+0200</span>
<br/>
		Message: <span><b>corrected the web browser display</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-08T16:53:37+0200</span>
<br/>
		Message: <span><b>Added bioperl as a dependancy. And extended the config to have a directory to store the flatfile databases.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-09T14:09:48+0200</span>
<br/>
		Message: <span><b>Finished the implementation of the OMIM annotation tool. Testing is still required.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-09T16:05:39+0200</span>
<br/>
		Message: <span><b>corrected typos</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-09T18:40:43+0200</span>
<br/>
		Message: <span><b>Modified the update implementation to make it more genric. Added the version info for OMIM in the config</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-09T18:42:03+0200</span>
<br/>
		Message: <span><b>Ensure that all version info get displayed. Modified the updated mechanism to make it more generic.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-11T16:11:12+0200</span>
<br/>
		Message: <span><b>Corrected some issues with the flatfile update. Some modules did not work as understtod from the docu</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-11T21:04:57+0200</span>
<br/>
		Message: <span><b>Corrected some more issues with the OMIM annotation</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-11T21:08:18+0200</span>
<br/>
		Message: <span><b>Prepared the fact release 1.1.0</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-15T16:59:12+0200</span>
<br/>
		Message: <span><b>final OMIM corrections</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-22T16:18:47+0200</span>
<br/>
		Message: <span><b>Ensure that all the OMIM ID are retrieved (three different db name in EnsEMBL)  and the gene symbol as well</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-22T16:29:08+0200</span>
<br/>
		Message: <span><b>Corrected some other xref dbnames...</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-22T16:50:54+0200</span>
<br/>
		Message: <span><b>Just to escape some sql killing chars...</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-22T16:52:44+0200</span>
<br/>
		Message: <span><b>corrected a minor mistake</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-04-22T17:34:18+0200</span>
<br/>
		Message: <span><b>OMIM: corrected the alt_title and chapters content to be able to export them easily. Makes it a little less human readable.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-05-05T19:01:43+0200</span>
<br/>
		Message: <span><b>Removed a useless import.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-06-26T20:40:15+0200</span>
<br/>
		Message: <span><b>new database dump</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-06-26T20:46:41+0200</span>
<br/>
		Message: <span><b>Fixed a cmd line change of wget btw version 1.10 and 1.11</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-06-26T21:26:29+0200</span>
<br/>
		Message: <span><b>Changed the URL for the gene ontology download</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-06-26T21:52:03+0200</span>
<br/>
		Message: <span><b>another URL for downloading geneontology
</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-06-27T10:22:31+0200</span>
<br/>
		Message: <span><b>typo in the properties file</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-06-27T18:19:57+0200</span>
<br/>
		Message: <span><b>Just changed the xsl file to convert the xml change log. We are using the newest svnant jar. No more need for personalized jars.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-06-27T18:21:29+0200</span>
<br/>
		Message: <span><b>Using the new svnant jar. Deprecated the personalized jar.</b></span>
<br/>
</p>

<p>
	Author: <span style="color:#c00000">delhomme</span>
<br/>
		Date: <span style="color:#8040ff">2008-06-27T18:38:29+0200</span>
<br/>
		Message: <span><b>just convert the last change log xml file into html</b></span>
<br/>
</p>

</div>
</body>
</html>

 

About SourceForge

Find Software

Develop Software

Community

Help

Copyright © 2009 Geeknet, Inc. All rights reserved. Terms of Use