<?php
/**
* @file
* Contains functions used to install/uninstall tripal_core.
*/
/**
* Implementation of hook_install().
*
* @ingroup tripal_core
*/
function tripal_core_install() {
// make the data directory for this module
$data_dir = file_directory_path() . "/tripal";
if (!file_check_directory($data_dir, FILE_CREATE_DIRECTORY)) {
$message = "Cannot create directory $data_dir. This module may not ".
"behave correctly without this directory. Please create ".
"the directory manually or fix the problem and reinstall.";
drupal_set_message(check_plain($message), 'error');
watchdog('tripal_core', $message, array(), WATCHDOG_ERROR);
}
// create the tables that manage materialized views and jobs
drupal_install_schema('tripal_core');
}
/**
* Update for Drupal 6.x, Tripal 0.4
* This update
* - adjusts the materialized view by adding status, comment and mv_schema columns
* - changes the specs of mv_table, mv_specs and indexed
* - creates the tripal_custom_tables table
*
* @ingroup tripal_feature
*/
function tripal_core_update_6000() {
// add additional columsn to the tripal_mviews table
db_add_field($ret, 'tripal_mviews', 'status', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
db_add_field($ret, 'tripal_mviews', 'comment', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
db_add_field($ret, 'tripal_mviews', 'mv_schema', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
db_change_field($ret, 'tripal_mviews', 'mv_table', 'mv_table', array('type' => 'varchar', 'length' => 128, 'not NULL' => FALSE));
db_change_field($ret, 'tripal_mviews', 'mv_specs', 'mv_specs', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
db_change_field($ret, 'tripal_mviews', 'indexed', 'indexed', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
// create the custom tables table
$ret = array();
$schema = tripal_core_custom_tables_schema();
db_create_table($ret, 'tripal_custom_tables', $schema['tripal_custom_tables']);
$ret = array(
'#finished' => 1,
);
return $ret;
}
/**
* Implementation of hook_schema().
*
* @ingroup tripal_core
*/
function tripal_core_schema() {
// get the schemas defined by this install file
$schema = tripal_core_get_schemas();
// if this module is already installed and enabled, then we want to provide
// the schemas for all of the custom tables. This will allow Views to
// see the schemas. We check if the module is installed because during
// installation we don't want to make these custom tables available as we don't
// want them created in the Drupal database. The custom tables go in the
// Chado database.
if (db_table_exists('tripal_custom_tables')) {
$sql = 'SELECT * FROM {tripal_custom_tables}';
$q = db_query($sql);
while ($custom = db_fetch_object($q)) {
$schema[$custom->table_name] = unserialize($custom->schema);
}
}
return $schema;
}
/**
* Implementation of hook_uninstall().
*
* @ingroup tripal_core
*/
function tripal_core_uninstall() {
drupal_uninstall_schema('tripal_core');
}
/**
* 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),
),
'indexes' => array(
'table_id' => array('table_id'),
),
'primary key' => array('table_id'),
);
return $schema;
}