tripal/tripal_cv/tripal_cv.install

<?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]
    );
  }

}