table_name] = unserialize($custom->schema); } } return $schema; } /** * Implementation of hook_uninstall(). * * @ingroup tripal_core */ function tripal_core_uninstall() { // drop the foreign key between tripal_custom_tables and tripal_mviews // so that Drupal can then drop the tables db_query(' ALTER TABLE {tripal_custom_tables} DROP CONSTRAINT IF EXISTS tripal_custom_tables_fk1 CASCADE '); } /** * This function simply defines all tables needed for the module to work * correctly. By putting the table definitions in a separate function we * can easily provide the entire list for hook_install or individual * tables for an update. * * @ingroup tripal_core */ function tripal_core_get_schemas() { $schema = array(); // get all the various schema parts and join them together $temp = tripal_core_jobs_schema(); foreach ($temp as $table => $arr) { $schema[$table] = $arr; } $temp = tripal_core_mviews_schema(); foreach ($temp as $table => $arr) { $schema[$table] = $arr; } $temp = tripal_core_custom_tables_schema(); foreach ($temp as $table => $arr) { $schema[$table] = $arr; } return $schema; } /** * Describes the Tripal Materialized View (tripal_mviews) table * This table keeps track of all materialized views created by Tripal and stored in chado * * @ingroup tripal_core */ function tripal_core_mviews_schema() { $schema = array(); $schema['tripal_mviews'] = array( 'fields' => array( 'mview_id' => array( 'type' => 'serial', 'unsigned' => TRUE, 'not NULL' => TRUE ), 'name' => array( 'type' => 'varchar', 'length' => 255, 'not NULL' => TRUE ), 'modulename' => array( 'type' => 'varchar', 'length' => 50, 'not NULL' => TRUE, 'description' => 'The module name that provides the callback for this job' ), 'mv_table' => array( 'type' => 'varchar', 'length' => 128, 'not NULL' => FALSE ), 'mv_specs' => array( 'type' => 'text', 'size' => 'normal', 'not NULL' => FALSE ), 'mv_schema' => array( 'type' => 'text', 'size' => 'normal', 'not NULL' => FALSE ), 'indexed' => array( 'type' => 'text', 'size' => 'normal', 'not NULL' => FALSE ), 'query' => array( 'type' => 'text', 'size' => 'normal', 'not NULL' => TRUE ), 'special_index' => array( 'type' => 'text', 'size' => 'normal', 'not NULL' => FALSE ), 'last_update' => array( 'type' => 'int', 'not NULL' => FALSE, 'description' => 'UNIX integer time' ), 'status' => array( 'type' => 'text', 'size' => 'normal', 'not NULL' => FALSE ), 'comment' => array( 'type' => 'text', 'size' => 'normal', 'not NULL' => FALSE ), ), 'indexes' => array( 'mview_id' => array('mview_id') ), 'unique keys' => array( 'mv_table' => array('mv_table'), 'mv_name' => array('name'), ), 'primary key' => array('mview_id'), ); return $schema; } /** * Describes the Tripal Jobs (tripal_jobs) table * This table keeps track of all tripal jobs including their current status and is used * by tripal_launch_jobs to determine which jobs need to be run * * @ingroup tripal_core */ function tripal_core_jobs_schema() { $schema = array(); $schema['tripal_jobs'] = array( 'fields' => array( 'job_id' => array( 'type' => 'serial', 'unsigned' => TRUE, 'not NULL' => TRUE ), 'uid' => array( 'type' => 'int', 'unsigned' => TRUE, 'not NULL' => TRUE, 'description' => 'The Drupal userid of the submitee' ), 'job_name' => array( 'type' => 'varchar', 'length' => 255, 'not NULL' => TRUE ), 'modulename' => array( 'type' => 'varchar', 'length' => 50, 'not NULL' => TRUE, 'description' => 'The module name that provides the callback for this job' ), 'callback' => array( 'type' => 'varchar', 'length' => 255, 'not NULL' => TRUE ), 'arguments' => array( 'type' => 'text', 'size' => 'normal', 'not NULL' => FALSE ), 'progress' => array( 'type' => 'int', 'unsigned' => TRUE, 'default' => 0, 'not NULL' => FALSE, 'description' => 'a value from 0 to 100 indicating percent complete' ), 'status' => array( 'type' => 'varchar', 'length' => 50, 'not NULL' => TRUE ), 'submit_date' => array( 'type' => 'int', 'not NULL' => TRUE, 'description' => 'UNIX integer submit time' ), 'start_time' => array( 'type' => 'int', 'not NULL' => FALSE, 'description' => 'UNIX integer start time' ), 'end_time' => array( 'type' => 'int', 'not NULL' => FALSE, 'description' => 'UNIX integer end time' ), 'error_msg' => array( 'type' => 'text', 'size' => 'normal', 'not NULL' => FALSE ), 'pid' => array( 'type' => 'int', 'unsigned' => TRUE, 'not NULL' => FALSE, 'description' => 'The process id for the job' ), 'priority' => array( 'type' => 'int', 'unsigned' => TRUE, 'not NULL' => TRUE, 'default' => '0', 'description' => 'The job priority' ), 'mlock' => array( 'type' => 'int', 'unsigned' => TRUE, 'not NULL' => FALSE, 'description' => 'If set to 1 then all jobs for the module are held until this one finishes' ), 'lock' => array( 'type' => 'int', 'unsigned' => TRUE, 'not NULL' => FALSE, 'description' => 'If set to 1 then all jobs are held until this one finishes' ), ), 'indexes' => array( 'job_id' => array('job_id'), 'job_name' => array('job_name') ), 'primary key' => array('job_id'), ); return $schema; } /** * Describes the Tripal Custom Tables (tripal_custom_tables) table * This keeps track of tables created by Tripal and stored in chado that may or may not * also be materialized views. * * @ingroup tripal_core */ function tripal_core_custom_tables_schema() { $schema = array(); $schema['tripal_custom_tables'] = array( 'fields' => array( 'table_id' => array( 'type' => 'serial', 'unsigned' => TRUE, 'not NULL' => TRUE ), 'table_name' => array( 'type' => 'varchar', 'length' => 255, 'not NULL' => TRUE ), 'schema' => array( 'type' => 'text', 'not NULL' => TRUE ), 'mview_id' => array( 'type' => 'int', 'not NULL' => FALSE ) ), 'indexes' => array( 'table_id' => array('table_id'), ), 'primary key' => array('table_id'), 'foreign keys' => array( 'tripal_mviews' => array( 'table' => 'tripal_mviews', 'columns' => array( 'mview_id' => 'mview_id' ), ), ), ); return $schema; } /** * Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table * */ function tripal_core_update_7200() { // add an mview column to the tripal_custom_tables table so we // can associate which of the custom tables are also mviews if (!db_field_exists('tripal_custom_tables', 'mview_id')) { $spec = array( 'type' => 'int', 'not NULL' => FALSE ); $keys = array( 'foreign keys' => array( 'tripal_mviews' => array( 'table' => 'tripal_mviews', 'columns' => array( 'mview_id' => 'mview_id' ), ), ), ); db_add_field('tripal_custom_tables', 'mview_id', $spec, $keys); // the foreign key specification doesn't really add one to the // Drupal schema, it is just used internally, but we want one db_query(' ALTER TABLE {tripal_custom_tables} ADD CONSTRAINT tripal_custom_tables_fk1 FOREIGN KEY (mview_id) REFERENCES {tripal_mviews} (mview_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED '); } // now link the materialized view to it's custom table entry $mviews = db_select('tripal_mviews', 'tmv') ->fields('tmv', array('mview_id', 'mv_table')) ->execute(); foreach ($mviews as $mview) { db_update('tripal_custom_tables') ->fields(array( 'mview_id' => $mview->mview_id )) ->condition('table_name', $mview->mv_table) ->execute(); } }