tripal/tripal_pub/tripal_pub.install

<?php
/**
 * @file
 * Installation of the publication module
 */

/**
 * Implements hook_disable().
 * Disable default views when module is disabled
 *
 * @ingroup tripal_pub
 */
function tripal_pub_disable() {

  // Disable all default views provided by this module
  require_once("tripal_pub.views_default.inc");
  $views = tripal_pub_views_default_views();
  foreach (array_keys($views) as $view_name) {
    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
  }

}

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

/**
 * Implementation of hook_install().
 *
 * @ingroup tripal_pub
 */
function tripal_pub_install() {
  global $base_path;

  // create the module's data directory
  tripal_create_files_dir('tripal_pub');

  // add loading of the the tripal pub ontology to the job queue
  $obo_path =  drupal_realpath(drupal_get_path('module', 'tripal_pub') . '/files/tpub.obo');
  $obo_id = tripal_cv_add_obo_ref('Tripal Publication', $obo_path);
  tripal_cv_submit_obo_job($obo_id);

  tripal_pub_add_cvs();
  tripal_pub_add_cvterms();

  // add the custom tables
  tripal_pub_add_custom_tables();

}

/**
 * Implementation of hook_uninstall().
 *
 * @ingroup tripal_pub
 */
function tripal_pub_uninstall() {

}

/**
 * Implements hook_enable().
 *
 * @ingroup tripal_pub
 */
function tripal_pub_enable() {
  // make sure we have our supported databases
  tripal_db_add_db('PMID', 'PubMed', 'http://www.ncbi.nlm.nih.gov/pubmed', 'http://www.ncbi.nlm.nih.gov/pubmed/', TRUE);
  tripal_db_add_db('AGL', 'USDA National Agricultural Library', 'http://agricola.nal.usda.gov/', '', TRUE);

  variable_set('tripal_pub_supported_dbs', array('PMID', 'AGL'));
}

/**
 * Implementation of hook_schema().
 *
 * @ingroup tripal_pub
 */
function tripal_pub_schema() {

  $schema['chado_pub'] = 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
      ),
      'pub_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(
      'pub_id' => array('pub_id')
    ),
    'unique keys' => array(
      'nid_vid' => array('nid', 'vid'),
      'vid' => array('vid')
    ),
    'primary key' => array('nid'),
  );

  $schema['tripal_pub_import'] = array(
    'fields' => array(
      'pub_import_id' => array(
        'type' => 'serial',
        'not null' => TRUE
      ),
      'name' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE
      ),
      'criteria' => array(
        'type' => 'text',
        'size' => 'normal',
        'not null' => TRUE,
        'description' => 'Contains a serialized PHP array containing the search criteria'
      ),
      'disabled'  => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not NULL' => TRUE,
        'default' => 0
      ),
      'do_contact'  => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not NULL' => TRUE,
        'default' => 0
      ),
    ),
    'primary key' => array('pub_import_id'),
    'indexes' => array(
      'name' => array('name')
    ),
  );

  return $schema;
}

/**
 * Add custom table related to publications
 *  - pubauthor_contact
 *
 * @ingroup tripal_pub
 */
function tripal_pub_add_custom_tables() {
  $schema = array (
    'table' => 'pubauthor_contact',
    'fields' => array (
      'pubauthor_contact_id' => array (
        'type' => 'serial',
        'not null' => true,
      ),
      'contact_id' => array (
        'type' => 'int',
        'not null' => true,
      ),
      'pubauthor_id' => array (
        'type' => 'int',
        'not null' => true,
      ),
    ),
    'primary key' => array (
      0 => 'pubauthor_contact_id',
    ),
    'unique keys' => array (
      'pubauthor_contact_c1' => array (
        0 => 'contact_id',
        1 => 'pubauthor_id',
      ),
    ),
    'foreign keys' => array (
      'contact' => array (
        'table' => 'contact',
        'columns' => array (
          'contact_id' => 'contact_id',
        ),
      ),
      'pubauthor' => array (
        'table' => 'pubauthor',
        'columns' => array (
          'pubauthor_id' => 'pubauthor_id',
        ),
      ),
    ),
  );
  chado_create_custom_table('pubauthor_contact', $schema, TRUE);
}

/**
 * Add cvs related to publications
 *
 * @ingroup tripal_pub
 */
function tripal_pub_add_cvs() {

  // Add cv for relationship types
  tripal_cv_add_cv(
    'pub_relationship_types',
    'Contains Types of relationships between publications.'
  );
}

/**
 * Add cvterms related to publications
 *
 * @ingroup tripal_pub
 */
function tripal_pub_add_cvterms() {

}

/**
 * This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
 *
 * @ingroup tripal_pub
 */
function tripal_pub_update_7200() {

  // add the new pub_relationship_types vocabulary
  // We cannot use the Tripal API calls in the 7000 update 
  // because during upgrade the tripal_core should also be disabled
  try {
    $check = db_query("SELECT cv_id FROM chado.cv WHERE name = 'pub_relationship_types'")->fetchObject();
    if (!$check->cv_id) {
      $sql = "INSERT INTO chado.cv (name, definition) VALUES (
        'pub_relationship_types',
        'Contains Types of relationships between publications.')
      ";
      db_query($sql);
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add pub_relationship_types vocabulary: '. $error);
  }
}