[Gmod-tripal] External Chado support with Tripal v3.3

[Tapia, A. C. <and...@uk...>]

Hi,

I am currently experimenting with setting up a Tripal site, and I wanted to know if it is still possible to use an external Chado database with Tripal v3.3.

I tried adding the following code to my settings.php file (as suggested in https://sourceforge.net/p/gmod/mailman/message/34332841/).

$databases['chado']['default'] = array(
    'driver' => 'pgsql',
    'database' => 'gmod-chado',
    'username' => 'chado',
    'password' => '*******',
    'host' => 'localhost',
    'prefix' => '',
);

Although it seems that Tripal recognizes that Chado is installed when the above code is in settings.php, Tripal still warns that Drupal and Chado need to be prepared, and running the "Prepare Chado" job gives an error like the one below.

Job execution failed: PDOException: SQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "db" does not exist                                                                      [error]
LINE 1: SELECT * FROM db WHERE name = 'NCIT'
                      ^ in /var/www/html/includes/database/database.inc:2227
Stack trace:
#0 /var/www/html/includes/database/database.inc(2227): PDOStatement->execute(Array)
#1 /var/www/html/includes/database/pgsql/database.inc(111): DatabaseStatementBase->execute(Array, Array)
#2 /var/www/html/includes/database/database.inc(2406): DatabaseConnection_pgsql->query('SELECT * FROM {...', Array, Array)
#3 /var/www/html/sites/all/modules/tripal/tripal_chado/api/tripal_chado.query.api.inc(1808): db_query('SELECT * FROM {...', Array)
#4 /var/www/html/sites/all/modules/tripal/tripal_chado/api/tripal_chado.query.api.inc(1612): chado_query('SELECT * FROM {...', Array)
#5 /var/www/html/sites/all/modules/tripal/tripal_chado/api/modules/tripal_chado.db.api.inc(376): chado_select_record('db', Array, Array)
#6 /var/www/html/sites/all/modules/tripal/tripal_chado/includes/setup/tripal_chado.setup.inc(78): chado_insert_db(Array)
#7 /var/www/html/sites/all/modules/tripal/tripal_chado/includes/setup/tripal_chado.setup.inc(235): tripal_chado_load_ontologies()
#8 /var/www/html/sites/all/modules/tripal/tripal/includes/TripalJob.inc(341): tripal_chado_prepare_chado(Object(TripalJob))
#9 /var/www/html/sites/all/modules/tripal/tripal/api/tripal.jobs.api.inc(419): TripalJob->run()
#10 /var/www/html/sites/all/modules/tripal/tripal/tripal.drush.inc(236): tripal_launch_job(0, '34', -1, 0)
#11 /root/.composer/vendor/drush/drush/includes/command.inc(361): drush_tripal_trp_run_jobs()
#12 /root/.composer/vendor/drush/drush/includes/command.inc(212): _drush_invoke_hooks(Array, Array)
#13 /root/.composer/vendor/drush/drush/includes/command.inc(180): drush_command()
#14 /root/.composer/vendor/drush/drush/lib/Drush/Boot/BaseBoot.php(64): drush_dispatch(Array)
#15 /root/.composer/vendor/drush/drush/drush.php(70): Drush\Boot\BaseBoot->bootstrap_and_dispatch()
#16 /root/.composer/vendor/drush/drush/drush.php(11): drush_main()
#17 {main}

Likewise, attempting to load an OBO file gives this sort of error.

SQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "cv" does not exist
LINE 1: SELECT * FROM cv CV
                      ^
[site http://default] [TRIPAL ERROR] [TRIPAL_JOB] SQLSTATE[42P01]: Undefined table: 7 ERROR:  relation "cv" does not existLINE 1: SELECT * FROM cv CV


Are external Chado databases still supported, or could this just be a problem with my configuration?

Thanks,

Andrew Tapia