tripal/tripal_library/tripal_library.install

<?php
/**
 * @file
 * @todo Add file header description
 */

/**
 * Implementation of hook_install().
 *
 * @ingroup tripal_library
 */
function tripal_library_install() {
  // create the module's data directory
  tripal_create_moddir('tripal_library');

  // create the tables that correlate drupal nodes with chado
  // features, librarys, etc....
  drupal_install_schema('tripal_library');

  // Add the materialized view needed to count the features for the library
  // Create the MView
  tripal_add_mview('library_feature_count', 'tripal_library',
    'library_feature_count',
    'library_id integer, name character varying(255), '.
    '  num_features integer, feature_type character varying(255)',
    'library_id',
    'SELECT '.
    '   L.library_id, '.
    '   L.name, '.
    '    count(F.feature_id) as num_features, '.
    '    CVT.name as feature_type '.
    'FROM Library L '.
    '    INNER JOIN Library_Feature LF  ON LF.library_id = L.library_id '.
    '    INNER JOIN Feature F           ON LF.feature_id = F.feature_id '.
    '    INNER JOIN Cvterm CVT          ON F.type_id = CVT.cvterm_id '.
    'GROUP BY L.library_id, L.name, CVT.name',
    ''
  );
  
  // Add cvterms
  tripal_library_add_cvterms();
}

/**
 * Implementation of hook_schema().
 *
 * @ingroup tripal_library
 */
function tripal_library_schema() {
  $schema = tripal_library_get_schemas();
  return $schema;
}

/**
 * Implementation of hook_uninstall().
 *
 * @ingroup tripal_library
 */
function tripal_library_uninstall() {
  drupal_uninstall_schema('tripal_library');

  // remove the materialized view
  $sql = "SELECT * FROM {tripal_mviews} ".
        "WHERE name = 'library_feature_count'";

  if (db_table_exists('tripal_mviews')) {
    $mview = db_fetch_object(db_query($sql));
    if ($mview) {
      tripal_mviews_action('delete', $mview->mview_id);
    }
  }

  // Get the list of nodes to remove
  $sql_lib_id = "SELECT nid, vid ".
               "FROM {node} ".
               "WHERE type='chado_library'";
  $result = db_query($sql_lib_id);
  while ($node = db_fetch_object($result)) {
    node_delete($node->nid);
  }
}

/**
 * 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_library
 */
function tripal_library_get_schemas() {
  $schema = array();
  $schema['chado_library'] = 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
      ),
    'library_id' => array(
      'type' => 'int',
      'not null' => TRUE,
      'default' => 0
      )
      ),
    'indexes' => array(
      'library_id' => array('library_id')
      ),
    'unique keys' => array(
      'nid_vid' => array('nid', 'vid'),
      'vid' => array('vid')
      ),
    'primary key' => array('nid'),
  );
  return $schema;
}
/**
 * Implementation of hook_requirements(). 
 */
function tripal_library_requirements($phase) {
  $requirements = array();
  if ($phase == 'install') {
    // make sure chado is installed
    if (!tripal_core_is_chado_installed()) {
      $requirements ['tripal_library'] = array(
        'title' => "tripal_library",
        'value' => "ERROR: Chado most be installed before this module can be enabled",
        'severity' => REQUIREMENT_ERROR,
      );
    }
  }
  return $requirements;
}

/*
 * 
 */
function tripal_library_add_cvterms() {
  
  // Insert cvterm 'library_description' into cvterm table of chado
  // database. This CV term is used to keep track of the library
  // description in the libraryprop table.
  tripal_cv_add_cvterm(array('name' => 'library_description', 'def' => 'Description of a library'), 
    'tripal', 0, 1, 'tripal');
  
  // add cvterms for the map unit types
  tripal_cv_add_cvterm(array('name' => 'cdna_library','def' => 'cDNA library'), 
    'tripal_library_types', 0, 1, 'tripal');
  tripal_cv_add_cvterm(array('name' => 'bac_library','def' => 'Bacterial Artifical Chromsome (BAC) library'), 
    'tripal_library_types', 0, 1, 'tripal');
  tripal_cv_add_cvterm(array('name' => 'fosmid_library','def' => 'Fosmid library'), 
    'tripal_library_types', 0, 1, 'tripal');   
  tripal_cv_add_cvterm(array('name' => 'cosmid_library','def' => 'Cosmid library'), 
    'tripal_library_types', 0, 1, 'tripal');
  tripal_cv_add_cvterm(array('name' => 'yac_library','def' => 'Yeast Artificial Chromosome (YAC) library'), 
    'tripal_library_types', 0, 1, 'tripal');
  tripal_cv_add_cvterm(array('name' => 'genomic_library','def' => 'Genomic Library'), 
    'tripal_library_types', 0, 1, 'tripal');
}

/**
 *  Update for Drupal 6.x, Tripal 1.0
 *  This update
 *   - adds the library types
 *
 * @ingroup tripal_library
 */
function tripal_library_update_6000() {
  // add in the missing library typ cv terms
  tripal_library_add_cvterms();
  return $ret;
}