tripal/tripal_pub/includes/pub_citation.inc

<?php
/*
 * The admin form for submitting job to create citations
*/
function tripal_pub_citation_form($form_state) {

  $form['create_all'] = array(
    '#type' => 'item',
    '#value' => t('Submit a job to create citation for the publications in chado. '),
  );
  
  $form['options'] = array(
    '#type' => 'radios',
    '#options' => 
      array('all' => 'Create citation for all publications. Replace the existing citation if it exists.', 
                'new' => 'Create citation for publication only if it does not already have one.'),
    '#default_value' => 'all'
  );
  
  $form['submit'] = array(
    '#type' => 'submit',
    '#weight' => 10,
    '#value' => t('Submit')
  );

  return $form;
}

/*
 * Submit form. Create Tripal job for citations
 */

function tripal_pub_citation_form_submit(&$form_state) {
  $options [0] = $form_state['options']['#value'];
  tripal_add_job("Create citations ($options[0])", 'tripal_pub', 'tripal_pub_create_citations', $options, $user->uid);
}

/*
 * Launch the Tripal job to generate citations
 */
function tripal_pub_create_citations ($options) {
  $skip_existing = TRUE;
  $sql = "
    SELECT cvterm_id 
    FROM {cvterm} 
    WHERE 
      name = 'Citation' AND 
      cv_id = (SELECT cv_id FROM {cv} WHERE name = 'tripal_pub')
  ";
  $citation_type_id = chado_query($sql)->fetchField();
  // Create and replace citation for all pubs
  if ($options == 'all') {
    $sql = "SELECT pub_id FROM {pub} P WHERE pub_id <> 1";
    $skip_existing = FALSE;  
  } 
  // Create citation for pubs that don't already have one
  else if ($options == 'new') {
    $sql = "
      SELECT pub_id 
      FROM {pub} P 
      WHERE 
        (SELECT value 
         FROM {pubprop} PB 
         WHERE type_id = :type_id AND P.pub_id = PB.pub_id AND rank = 0) IS NULL 
        AND  pub_id <> 1
    ";
    $skip_existing = TRUE;
  }

  $result = chado_query($sql, array(':type_id' => $citation_type_id));
  $counter_updated = 0;
  $counter_generated = 0;
  while ($pub = $result->fetchObject()) {
    $pub_arr = tripal_pub_get_publication_array($pub->pub_id, $skip_existing);
    if ($pub_arr) {
      $citation = tripal_pub_create_citation ($pub_arr);
      print $citation . "\n\n";
      // Replace if citation exists. This condition is never TRUE if $skip_existing is TRUE
      if ($pub_arr['Citation']) {
        $sql = "
          UPDATE {pubprop} SET value = :value 
          WHERE pub_id = :pub_id  AND type_id = :type_id AND rank = :rank
        ";
        chado_query($sql, array(':value' => $citation, ':pub_id' => $pub->pub_id, 
          ':type_id' => $citation_type_id, ':rank' => 0));
        $counter_updated ++;
      // Generate a new citation
      } else {
        $sql = "
          INSERT INTO {pubprop} (pub_id, type_id, value, rank) 
          VALUES (:pub_id, :type_id, :value, :rank)
        ";
        chado_query($sql, array(':pub_id' => $pub->pub_id, ':type_id' => $citation_type_id, 
          ':value' => $citation, ':rank' => 0));
        $counter_generated ++;
      }
    }
  }
  print "$counter_generated citations generated. $counter_updated citations updated.\n";
}