<?php /** * @file * Contains functions executed only on install/uninstall of this module */ /** * Implementation of hook_install(). * * @ingroup tripal_cv */ function tripal_cv_install() { // create the module's data directory tripal_create_moddir('tripal_cv'); // Add the materialized view needed to keep track of the // $previous_db = tripal_db_set_active('chado'); if (db_table_exists('cv_root_mview')) { $sql = "DROP TABLE cv_root_mview"; db_query($sql); } tripal_db_set_active($previous_db); // Create the MView tripal_add_mview( // view name 'cv_root_mview', // module name 'tripal_cv', // table name 'cv_root_mview', // table schema 'name character varying(1024), cvterm_id integer, cv_id integer, cv_name character varying(255)', // indexed columns 'cvterm_id, cv_id', // SQL statement that populates the view 'SELECT DISTINCT CVT.name,CVT.cvterm_id, CV.cv_id, CV.name FROM {cvterm_relationship} CVTR INNER JOIN cvterm CVT on CVTR.object_id = CVT.cvterm_id INNER JOIN CV on CV.cv_id = CVT.cv_id WHERE CVTR.object_id not in (SELECT subject_id FROM {cvterm_relationship}) ', // special index '' ); // create the tables that correlate OBO files/references with a chado CV drupal_install_schema('tripal_cv'); tripal_cv_add_obo_defaults(); } /** * This update adds the new tripal_obo table. This is an upgrade from * Tripal version 0.2 * * @ingroup tripal_cv */ function tripal_cv_update_6000() { drupal_install_schema('tripal_cv'); tripal_cv_add_obo_defaults(); $ret = array( '#finished' => 1, ); return $ret; } /** * Implementation of hook_uninstall(). * * @ingroup tripal_cv */ function tripal_cv_uninstall() { // remove the materialized view $mview = tripal_mviews_get_mview_id('cv_root_mview'); if ($mview) { tripal_mviews_action('delete', $mview); } drupal_uninstall_schema('tripal_cv'); } /** * Implementation of hook_schema(). * * @ingroup tripal_cv */ function tripal_cv_schema() { $schema = tripal_cv_get_schemas(); return $schema; } /** * 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_cv */ function tripal_cv_get_schemas() { $schema = array(); $schema['tripal_cv_obo'] = array( 'fields' => array( 'obo_id' => array('type' => 'serial', 'unsigned' => TRUE, 'not null' => TRUE), 'name' => array('type' => 'varchar', 'length' => 255), 'path' => array('type' => 'varchar', 'length' => 1024), ), 'indexes' => array( 'obo_id' => array('obo_id'), ), 'primary key' => array('obo_id'), ); return $schema; } /** * Add's defaults to the tripal_cv_obo table * * @ingroup tripal_cv */ function tripal_cv_add_obo_defaults() { // insert commonly used ontologies into the tables $ontologies = array( array('Chado Feature Properties', drupal_get_path('module', 'tripal_cv') . '/feature_property.obo'), array('Relationship Ontology', 'http://www.obofoundry.org/ro/ro.obo'), array('Sequence Ontology', 'http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo'), array('Gene Ontology', 'http://www.geneontology.org/ontology/gene_ontology.obo'), array('Cell Ontology', 'http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cell.obo?rev=HEAD'), array('Plant Structure Ontology', 'http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co'), array('Plant Growth and Development Stages Ontology', 'http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_temporal.obo?view=co') ); foreach ($ontologies as $o) { db_query( "INSERT INTO {tripal_cv_obo} (name,path) VALUES ('%s','%s')", $o[0], $o[1] ); } }