Bugs Fixes for Tripal version 6.x-0.1b

Below are solutions to a few bugs that exist in the 6.x-0.1b version of Tripal. Fixes for these bugs will be available on the next release of Tripal.

Syncing an Organism
For syncing organism the job properly completes but the organisms are not synced. This occurs when the ./sites/default/files/tripal/tripal_organism/images does not exist. Also the directory must be writeable by the web user. Creating the directory and setting the permissions will allow for proper syncing of organisms.

Editing a Feature
When editing a feature the feature type select box only shows 'EST' and 'contig'. This is a bug which has been fixed in CVS but not in the release. We will release a bug fix in the near future to resolve this.

Organism Theme
If Clean URLs are enabled and a picture is uploaded for an organism, the picture will not show. This is due to a typo in the node-chado_organism.tpl.php template in the theme_tripal directory. Edit the template and change the line from this:

<img src=<?php print "sites/default/files/tripal/tripal_organism/images/".$node->genus."_".$node->species.".jpg"?>>

to this:

<img src=<?php print file_create_url(file_directory_path() . "/tripal/tripal_organism/images/".$node->genus."_".$node->species.".jpg")?>>

Organism CSS
When a picture is present on the organism page a large swath of white space appears between the top of the page and the content. This is caused by an incorrect comment at the tripal.css file in the theme_tripal directory. To resolve this change this text:

//
// Copyright 2009 Clemson University
//

to this:

/*
Copyright 2009 Clemson University
*/