<?php
/**
* @file
* Installation of the feature module
*/
/**
* Implements hook_disable().
*
* Disable default views when module is disabled
*
* @ingroup tripal_feature
*/
function tripal_feature_disable() {
// Disable all default views provided by this module
require_once("tripal_feature.views_default.inc");
$views = tripal_feature_views_default_views();
foreach (array_keys($views) as $view_name) {
tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
}
}
/**
* Implements hook_requirements().
*
* @ingroup tripal_feature
*/
function tripal_feature_requirements($phase) {
$requirements = array();
if ($phase == 'install') {
// make sure chado is installed
if (!$GLOBALS["chado_is_installed"]) {
$requirements ['tripal_feature'] = array(
'title' => "t ripal_feature",
'value' => "ERROR: Chado must be installed before this module can be enabled",
'severity' => REQUIREMENT_ERROR,
);
}
}
return $requirements;
}
/**
* Implements hook_install().
*
* @ingroup tripal_feature
*/
function tripal_feature_install() {
// Note: the feature_property OBO that came with Chado v1.2 should not
// be automatically installed. Some of the terms are duplicates of
// others in better maintained vocabularies. New Tripal sites should
// use those.
// $obo_path = '{tripal_feature}/files/feature_property.obo';
// $obo_id = tripal_insert_obo('Chado Feature Properties', $obo_path);
// tripal_submit_obo_job(array('obo_id' => $obo_id));
// Add the materialized view.
tripal_feature_add_organism_count_mview();
// Add the custom tables.
tripal_feature_add_tripal_gff_temp_table();
tripal_feature_add_tripal_gffcds_temp_table();
tripal_feature_add_tripal_gffprotein_temp_table();
// Add the vocabularies used by the feature module.
tripal_feature_add_cvs();
// Set the default vocabularies.
tripal_set_default_cv('feature', 'type_id', 'sequence');
tripal_set_default_cv('featureprop', 'type_id', 'feature_property');
tripal_set_default_cv('feature_relationship', 'type_id', 'feature_relationship');
}
/**
* Implements hook_uninstall().
*
* @ingroup tripal_feature
*/
function tripal_feature_uninstall() {
}
function tripal_feature_add_tripal_gff_temp_table() {
$schema = array(
'table' => 'tripal_gff_temp',
'fields' => array(
'feature_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'organism_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'uniquename' => array(
'type' => 'text',
'not null' => TRUE,
),
'type_name' => array(
'type' => 'varchar',
'length' => '1024',
'not null' => TRUE,
),
),
'indexes' => array(
'tripal_gff_temp_idx0' => array('feature_id'),
'tripal_gff_temp_idx0' => array('organism_id'),
'tripal_gff_temp_idx1' => array('uniquename'),
),
'unique keys' => array(
'tripal_gff_temp_uq0' => array('feature_id'),
'tripal_gff_temp_uq1' => array('uniquename', 'organism_id', 'type_name'),
),
);
chado_create_custom_table('tripal_gff_temp', $schema, TRUE);
}
/**
*
*/
function tripal_feature_add_tripal_gffcds_temp_table($skip_recreate = TRUE) {
$schema = array(
'table' => 'tripal_gffcds_temp',
'fields' => array(
'feature_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'parent_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'phase' => array(
'type' => 'int',
'not null' => TRUE,
),
'strand' => array(
'type' => 'int',
'not null' => TRUE,
),
'fmin' => array(
'type' => 'int',
'not null' => TRUE,
),
'fmax' => array(
'type' => 'int',
'not null' => TRUE,
),
),
'indexes' => array(
'tripal_gff_temp_idx0' => array('feature_id'),
'tripal_gff_temp_idx0' => array('parent_id'),
),
);
chado_create_custom_table('tripal_gffcds_temp', $schema, $skip_recreate);
}
/**
*
*/
function tripal_feature_add_tripal_gffprotein_temp_table() {
$schema = array(
'table' => 'tripal_gffprotein_temp',
'fields' => array(
'feature_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'parent_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'fmin' => array(
'type' => 'int',
'not null' => TRUE,
),
'fmax' => array(
'type' => 'int',
'not null' => TRUE,
),
),
'indexes' => array(
'tripal_gff_temp_idx0' => array('feature_id'),
'tripal_gff_temp_idx0' => array('parent_id'),
),
'unique keys' => array(
'tripal_gff_temp_uq0' => array('feature_id'),
),
);
chado_create_custom_table('tripal_gffprotein_temp', $schema, TRUE);
}
/**
* Implementation of hook_schema().
*
* @ingroup tripal_feature
*/
function tripal_feature_schema() {
$schema['chado_feature'] = array(
'fields' => array(
'vid' => array(
'type' => 'int',
'unsigned' => TRUE,
'not null' => TRUE,
'default' => 0
),
'nid' => array(
'type' => 'int',
'unsigned' => TRUE,
'not null' => TRUE,
'default' => 0
),
'feature_id' => array(
'type' => 'int',
'not null' => TRUE,
'default' => 0
),
'sync_date' => array(
'type' => 'int',
'not null' => FALSE,
'description' => 'UNIX integer sync date/time'
),
),
'indexes' => array(
'chado_feature_idx1' => array('feature_id')
),
'unique keys' => array(
'chado_feature_uq1' => array('nid', 'vid'),
'chado_feature_uq2' => array('vid')
),
'primary key' => array('nid'),
);
return $schema;
};
/**
* Creates a materialized view that stores the type & number of features per organism
*
* @ingroup tripal_feature
*/
function tripal_feature_add_organism_count_mview() {
$view_name = 'organism_feature_count';
$comment = 'Stores the type and number of features per organism';
$schema = array(
'description' => $comment,
'table' => $view_name,
'fields' => array(
'organism_id' => array(
'size' => 'big',
'type' => 'int',
'not null' => TRUE,
),
'genus' => array(
'type' => 'varchar',
'length' => '255',
'not null' => TRUE,
),
'species' => array(
'type' => 'varchar',
'length' => '255',
'not null' => TRUE,
),
'common_name' => array(
'type' => 'varchar',
'length' => '255',
'not null' => FALSE,
),
'num_features' => array(
'type' => 'int',
'not null' => TRUE,
),
'cvterm_id' => array(
'size' => 'big',
'type' => 'int',
'not null' => TRUE,
),
'feature_type' => array(
'type' => 'varchar',
'length' => '255',
'not null' => TRUE,
),
),
'indexes' => array(
'organism_feature_count_idx1' => array('organism_id'),
'organism_feature_count_idx2' => array('cvterm_id'),
'organism_feature_count_idx3' => array('feature_type'),
),
);
$sql = "
SELECT
O.organism_id, O.genus, O.species, O.common_name,
count(F.feature_id) as num_features,
CVT.cvterm_id, CVT.name as feature_type
FROM organism O
INNER JOIN feature F ON O.Organism_id = F.organism_id
INNER JOIN cvterm CVT ON F.type_id = CVT.cvterm_id
GROUP BY
O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name
";
tripal_add_mview($view_name, 'tripal_feature', $schema, $sql, $comment);
}
/**
* Add cvs related to publications
*
* @ingroup tripal_pub
*/
function tripal_feature_add_cvs() {
// Add cv for relationship types
tripal_insert_cv(
'feature_relationship',
'Contains types of relationships between features.'
);
// The feature_property CV may already exists. It comes with Chado, but
// we need to add it just in case it doesn't get added before the feature
// module is installed. But as of Tripal v3.0 the Chado version of this
// vocabulary is no longer loaded by default.
tripal_insert_cv(
'feature_property',
'Stores properties about features'
);
// the feature type vocabulary should be the sequence ontology, and even though
// this ontology should get loaded we will create it here just so that we can
// set the default vocabulary for the feature.type_id field
tripal_insert_cv(
'sequence',
'The Sequence Ontology'
);
}