[Gmod-tripal-devel] Tripal and Chado v1.3

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[Gmod-tripal-devel] Tripal and Chado v1.3

Stephen Ficklin-2
Hi All,

I have just committed code to the  current 7.x-2.x development branch of Tripal that supports the newest release of Chado: v1.3.    Once this is better tested we can release an official Tripal v1.2 release which will also include all of the most recent bug fixes.   However this upgrade of Chado has some important changes that may affect some sites and I'd like to solicit some help from folks how would be willing to test the upgrade on a development site.    If you would be willing to test please read a bit further, let me know and we can coordinate.


Here are some steps and things to watch for:

Download the development version from GitHub: https://github.com/tripal/tripal

After updating the code to the most recent development version you'll need to run database updates to install a new taxonomy rank vocabulary:

drush updatedb

Next, navigate to Administration -> Tripal -> Setup Tripal -> Install Chado and select the option to upgrade from v1.2 to v1.3.

Then as you test please be aware of the following:

1)  Two new fields were added to the organism table: type_id and infraspecific_name.  Both the older v1.2 and newer v1.3 tables are supported.
2)  All primary keys and foreign keys in Chado v1.3 are now of type 'bigint'.  Unfortunately, Tripal is not able to automatically convert Materialized Views and custom PL/pgSQL functions. If you have materialized views that use values from the primary of foreign key fields of Chado tables then you may have to update those views to add a size of  'big' to field definitions.  For example:

      'feature_id' => array(
        'size' => 'big',
        'type' => 'serial',
        'not null' => TRUE,
      'type_id' => array(
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,

3) If you have any custom PL/pqSQL (procedural language) functions that also refer to primary or foreign key fields then you'll need to update those as well.
4) A slew of new tables where added to link cvterms, dbxrefs, properties, etc. to base tables.  These new linking tables currently do not have template files (e.g. stock_feature, stock_library, etc.).  If you have or create template files please feel free to submit them for inclusion.

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