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.
your site files before proceeding.
the tripal modules from the sites/all/modules directory
the theme_tripal theme from the sites/all/themes directory. (If you have
customizations you may skip this step).
the tripal modules from the updated software to the sites/all/modules directory
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:
# set the title of this
page to be the name of the feature.
Here is a list of fixes that have occurred:
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.
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.
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