Minor update release of Tripal (v 0.2.1)

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Minor update release of Tripal (v 0.2.1)

Stephen Ficklin

Dear Tripal User’s Group,

 

We have just released a minor revision update for Tripal that fixes several recent bugs that some of you have reported.  Thank you to those who reported bugs!!  We apologize for the bugs….

 

You can download this new update from the CUGI website here:  http://www.genome.clemson.edu/software/tripal

 

To install this new version please follow these steps:

Note:  Fixes are backwards compatible and no Drupal style upgrade is necessary.  Just copy the new files to your site. 

 

1.         Backup your site files before proceeding.

2.       Remove the tripal modules from the sites/all/modules directory

3.       Remove the theme_tripal theme from the sites/all/themes directory.  (If you have customizations you may skip this step).

4.       Copy the tripal modules from the updated software to the sites/all/modules directory

5.       Copy the tripal_theme from the updated software to the sites/all/themes directory.  (If you have customizations you may skip this step).

 

If you have made customizations to your tripal themes you do not need to replace your theme_tripal directory as indicated in steps 3 and 5 above.  However, we have made one change to the node-chado_feature.tpl.php template that you may want to copy.   To incorporate this change without affecting your existing customizations, copy the following four lines to your template file:

 

   <?php

       # set the title of this page to be the name of the feature.

       drupal_set_title($feature->featurename); 

    ?>

 

Here is a list of fixes that have occurred:

 

1.       Previously when syncing features, the feature pages were given a title corresponding to the ‘name’ of the chado feature.  This caused several problems.   One of which is a title conflict in Drupal if two nodes have the same name.  Now, feature pages are given the ‘unique name’ plus the species name in parentheses as a Drupal node title.  We realize this may not be how everyone would like feature pages to appear, so we updated the node-chado_feature.tpl.php template file in the tripal theme to override the title with just  the feature ‘name’.   Users can customize the feature page title however they prefer in this template file.

2.       Previously, when syncing features if a feature name and unique name were different the feature would be duplicated in chado. This was a bug.   The fix described above also resolves this problem.

3.       A recent upgrade to PHP causes some pages to not appear (e.g. organism, library, analysis pages) and others to throw errors.  The problem is due to improved stringency in PHP with pass-by-reference parameters in function calls.  We fixed many of these.

 

If anyone notices other bugs please feel free to email this list.

 

Regards to all,

Stephen

 

 

 

 


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