tripal/tripal_cv/tripal_cv.install

<?php

/**
 * @file
 * Contains functions executed only on install/uninstall of this module
 */

/**
 * Implementation of hook_requirements().
 */
function tripal_cv_requirements($phase) {
  $requirements = array();
  if ($phase == 'install') {
    // make sure chado is installed
    if (!tripal_core_is_chado_installed()) {
      $requirements ['tripal_cv'] = array(
        'title' => "tripal_cv",
        'value' => "ERROR: Chado most be installed before this module can be enabled",
        'severity' => REQUIREMENT_ERROR,
      );
    }
  }
  return $requirements;
}
/**
 * Implementation of hook_install().
 *
 * @ingroup tripal_cv
 */
function tripal_cv_install() {

  // create the module's data directory
  tripal_create_moddir('tripal_cv');
    
  // add the cv_root_mview 
  tripal_cv_add_cv_root_mview();
  
  // create the tables that correlate OBO files/references with a chado CV
  tripal_cv_add_obo_defaults();
}
/**
 * Implementation of hook_uninstall().
 *
 * @ingroup tripal_cv
 */
function tripal_cv_uninstall() {
  // remove the materialized view
  if ($mview = tripal_mviews_get_mview_id('cv_root_mview')) {
    tripal_mviews_action('delete', $mview);
  }
}

/**
 * Implementation of hook_schema().
 *
 * @ingroup tripal_cv
 */
function tripal_cv_schema() {
  
  $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(
      'tripal_cv_obo_idx1' => array('obo_id'),
    ),
    'primary key' => array('obo_id'),
  );

  return $schema;
}

/**
 * 
 * @ingroup tripal_cv
 */
function tripal_cv_add_cv_root_mview() {
  $mv_name = 'cv_root_mview';
  $comment = 'A list of the root terms for all controlled vocabularies. This is needed for viewing CV trees';
  $schema = array(
    'table' => $mv_name,
    'description' => $comment,
    'fields' => array(
      'name' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ),
      'cvterm_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'cv_id' => array(
        'type' => 'int',
        'not null' => TRUE, 
      ),
      'cv_name' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'cv_root_mview_indx1' => array('cvterm_id'),
      'cv_root_mview_indx2' => array('cv_id'),
    ),
  );
  
  $sql = "
    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 CV on CV.cv_id = CVT.cv_id
    WHERE CVTR.object_id not in
      (SELECT subject_id FROM cvterm_relationship)
  ";
  
  // Create the MView
  tripal_add_mview($mv_name, 'tripal_cv', $schema, $sql, $comment);
}


/**
 * 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 (:name, :path)", array(':name' => $o[0], ':path' => $o[1]));
  }
}