tripal/tripal_organism/includes/tripal_organism.admin.inc

<?php
/**
 * @file
 * Administration of organisms
 */

/**
 * Admin launchpad
 *
 * @ingroup tripal_organism
 */
function tripal_organism_admin_organism_view() {
  $output = '';

  // set the breadcrumb
  $breadcrumb = array();
  $breadcrumb[] = l('Home', '<front>');
  $breadcrumb[] = l('Administration', 'admin');
  $breadcrumb[] = l('Tripal', 'admin/tripal');
  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
  $breadcrumb[] = l('Organisms', 'admin/tripal/chado/tripal_organism');
  drupal_set_breadcrumb($breadcrumb);

  // Add the view
  $view = views_embed_view('tripal_organism_admin_organisms','default');
  if (isset($view)) {
    $output .= $view;
  }
  else {
    $output .= '<p>The Organism module uses primarily views to provide an '
      . 'administrative interface. Currently one or more views needed for this '
      . 'administrative interface are disabled. <strong>Click each of the following links to '
      . 'enable the pertinent views</strong>:</p>';
    $output .= '<ul>';
      $output .= '<li>'.l('Organisms View', 'admin/tripal/chado/tripal_organism/views/organisms/enable').'</li>';
    $output .= '</ul>';
  }

  return $output;
}

/**
 * Administrative settings for chado_orgnism
 *
 * @ingroup tripal_organism
 */
function tripal_organism_admin() {

  $form = array();

  $form['nothing'] = array(
    '#markup' => t('There are currently no settings to configure.')
  );

  return system_settings_form($form);
}


/**
 * Validate the organism settings form
 *
 * @ingroup tripal_organism
 */
function tripal_organism_admin_validate($form, &$form_state) {
  global $user;  // we need access to the user info
  $job_args = array();

  // -------------------------------------
  // Submit the Reindex Job if selected
  if ($form_state['values']['op'] == t('Reindex Features')) {
    $organisms = $form_state['values']['re-organisms'];
    foreach ($organisms as $organism_id) {
      if ($organism_id and preg_match("/^\d+$/i" , $organism_id)) {
        // get the organism info
        $sql = "SELECT * FROM {organism} WHERE organism_id = :organism_id";
        $organism = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
        $job_args[0] = $organism_id;
        tripal_add_job("Reindex features for organism: $organism->genus " .
         "$organism->species", 'tripal_organism' ,
         'tripal_organism_reindex_features', $job_args, $user->uid);
      }
    }
  }

  // -------------------------------------
  // Submit the taxonomy Job if selected
  if ($form_state['values']['op'] == t('Set Feature Taxonomy')) {
    $organisms = $form_state['values']['tx-organisms'];
    foreach ($organisms as $organism_id) {
      if ($organism_id and preg_match("/^\d+$/i", $organism_id)) {
        // get the organism info
        $sql = "SELECT * FROM {organism} WHERE organism_id = :organism_id";
        $organism = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
        $job_args[0] = $organism_id;
        tripal_add_job("Set taxonomy for features in organism: " .
          "$organism->genus $organism->species" , 'tripal_organism',
          'tripal_organism_taxonify_features', $job_args, $user->uid);
      }
    }
  }
}

/**
 * Add a job to reindex the features associated with an organism for drupal search
 *
 * @param $organism_id
 *  The organism_id of the organism to re-index features of
 * @param $job_id
 *  (optional) specify a tripal job_id to create
 *
 * @ingroup tripal_organism
 */
function tripal_organism_reindex_features($organism_id = NULL, $job_id = NULL) {
  $i = 0;

  if (!$organism_id) {
    return;
  }

  $sql = "
    SELECT *
    FROM {feature}
    WHERE organism_id = :organism_id
    ORDER BY feature_id";
  $results = chado_query($sql, array(':organism_id' => $organism_id));

  // load into ids array
  $count = 0;
  $ids = array();
  foreach ($results as $id) {
    $ids[$count] = $id->feature_id;
    $count++;
  }

  $interval = intval($count * 0.01);
  foreach ($ids as $feature_id) {
    // update the job status every 1% features
    if ($job_id and $i % $interval == 0) {
      tripal_set_job_progress($job_id , intval(($i/$count)*100));
    }
    $i++;
  }
}

/**
 * Add a tripal job to add drupal taxonomy to organisms
 *
 * @param $organism_id
 *  The organism_id of the organism to add taxonomy to
 * @param $job_id
 *  (optional) specify a tripal job_id to create
 *
 * @ingroup tripal_organism
 */
function tripal_organism_taxonify_features($organism_id = NULL, $job_id = NULL) {
  $i = 0;

  if (!$organism_id) {
    return;
  }

  $sql = "
    SELECT *
    FROM {feature}
    WHERE organism_id = :organism_id
    ORDER BY feature_id
  ";
  $results = chado_query($sql, array(':organism_id' => $organism_id));

  // load into ids array
  $count = 0;
  $ids = array();
  foreach ($results as $id) {
    $ids[$count] = $id->feature_id;
    $count++;
  }

  // make sure our vocabularies are set before proceeding
  tripal_feature_set_vocabulary();

  // use this SQL for getting the nodes
  $nsql = "SELECT * FROM {chado_feature} CF " .
          "  INNER JOIN {node} N ON N.nid = CF.nid " .
          "WHERE feature_id = :feature_id";

  // iterate through the features and set the taxonomy
  $interval = intval($count * 0.01);
  foreach ($ids as $feature_id) {
    // update the job status every 1% features
    if ($job_id and $i % $interval == 0) {
      tripal_set_job_progress($job_id, intval(($i/$count)*100));
    }
    $node = db_query($nsql, array(':feature_id' => $feature_id))->fetchObject();
    tripal_feature_set_taxonomy($node, $feature_id);
    $i++;
  }
}