tripal/tripal_pub/tripal_pub.module

<?php

//require_once('cron.php');
require_once "includes/tripal_pub.admin.inc";
require_once "includes/pubmed.inc";
require_once "includes/remote_search.inc";

/**
 * @file
 *
 * The Tripal Publication module allows you to search the PubMed databse for academic articles,
 * that relate to user specified tpoic\s. As well, it allows management of publications so that
 * a user can enter specified details regarding a desired publication. This allows all of the important
 * information that is unique to a Academic Publication to be stored for access.
 */


/**
 *
 * @ingroup tripal_pub
 */
function tripal_pub_init() {
  drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/tripal_pub.js');
}


/**
 * Implementation of hook_tripal_pub_node_info().
 *
 * This node_info, is a simple node that describes the functionallity of the module.
 *
 */
function tripal_pub_node_info() {

  return array(
    'chado_pub' => array(
      'name' => t('Publication'),
      'module' => 'chado_pub',
      'description' => t('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
      'title_label' => t('Article Title'),
      'body_label' => t('Abstract'),
      'has_title' => TRUE,
      'has_body' => FALSE,
    ),
  );
}

/**
 * Tripal-Publication-Menu
 *
 * Implemets hook_menu(): Adds menu items for the tripal_pub module menu. This section
 * gives the outline for the main menu of the Tripal-Publication module
 *
 * @return
 *   An array of menu items that is visible within the Drupal Menu, returned as soon
 *   as the program is ran
 */
function tripal_pub_menu() {

  $items = array();

  $items[ 'admin/tripal/tripal_pub' ]= array(
    'title' => 'Publications',
    'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_pub_admin'),
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_NORMAL_ITEM
  );
 
  $items['admin/tripal/tripal_pub/configuration'] = array(
    'title' => 'Configuration',
    'description' => 'Configuration for this module',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_pub_configuration_form'),
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_NORMAL_ITEM  
  );

  $items['admin/tripal/tripal_pub/import_setup'] = array(
    'title' => t('Pub Loader Setup'),
    'description' => t('Finds publications using remote publication databases (e.g. PubMed).'),
    'page callback' => 'tripal_pub_remote_search_page',
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );
  
  $items['admin/tripal/tripal_pub/import_setup/criteria/%/%'] = array(
    'page callback' => 'tripal_pub_remote_search_page_update_criteria',
    'page arguments' => array(5, 6),
    'access arguments' => array('administer tripal pubs'),    
    'type ' => MENU_CALLBACK,
  );
  
  // Automatically generate checkboxes.
  $items['node/add/tripal_pub/ahah_authors'] = array(
    'title' => 'Add Additional Authors',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('author_addition_fields_ahah_callback'),
    'access callback' => TRUE,
    'type' => MENU_CALLBACK,
    'weight' => 2,
  );

  $items['tripal_pub/js/%'] = array(
    'page callback' => 'tripal_pub_js',
    'page arguments' => array(2),
    'access arguments' => array('access content'),
    'type ' => MENU_CALLBACK,
  );

  return $items;
}


/**
 * Implements hook_theme(): Register themeing functions for this module
 *
 *
 * @return
 *   An array of themeing functions to register
 *
 */
function tripal_pub_theme() {

  return array(
    'tripal_pub_author_table' => array(
      'arguments' => array('form' => NULL),
    ),
    'publication_author' => array(
      'arguments' => array('element' => NULL)
    ),
    'publication_author' => array(
      'arguments' => array('element' => NULL)
    ),
    'tripal_pub_remote_search_form' => array(
       'arguments' => array('form'),
    ),
    'tripal_pub_admin' => array(
      'template' => 'tripal_pub_admin',  
      'arguments' =>  array(NULL),  
      'path' => drupal_get_path('module', 'tripal_pub') . '/theme' 
    ),
  );
}

/**
 * Implement hook_perm().
 */
function tripal_pub_perm() {
  return array(
    'access chado_pub content',
    'create chado_pub content',
    'delete chado_pub content',
    'edit chado_pub content',
    'administer tripal pubs',
  );
}


/**
 * Implement hook_access().
 *
 * This hook allows node modules to limit access to the node types they define.
 *
 *  @param $op
 *  The operation to be performed
 *
 *  @param $node
 *  The node on which the operation is to be performed, or, if it does not yet exist, the
 *  type of node to be created
 *
 *  @param $account
 *  A user object representing the user for whom the operation is to be performed
 *
 *  @return
 *  TRUE
 *
 */
function chado_pub_access($op, $node, $account ) {
  if ($op == 'create') {
    if (!user_access('create chado_pub content', $account)) {
      return FALSE;
      }
  }

  if ($op == 'update') {
    if (!user_access('edit chado_pub content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'delete') {
    if (!user_access('delete chado_pub content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'view') {
    if (!user_access('access chado_pub content', $account)) {
      return FALSE;
    }
  }
  return NULL;
}


/**
 * Implementation of tripal_pub_form().
 *
 *
 *
 *  @parm &$node
 *    The node that is created when the database is initialized
 *
 *  @parm $form_state
 *    The state of the form, that has the user entered information that is neccessary for, setting
 *    up the database tables for the publication
 *
 *  @return $form
 *    The information that was enterd allong with
 *
 */
function chado_pub_form(&$node, $form_state) {

  $type = node_get_types('type', $node);

  // Article Title.
  $form['title'] = array(
    '#type' => 'textfield',
    '#title' => check_plain($type->title_label),
    '#default_value' => $node->title,
    '#required' => TRUE,
    '#weight' => 0,
  );

  // Abstract
  $form['abstract'] = array(
    '#title' => 'Abstract',
    '#type' => 'textarea',
    '#default_value' => isset($node->abstract) ? $node->abstract : ''
  );

  $form['pub_id'] = array(
    '#type' => 'hidden',
    '#value' => (isset($node->pub_id)) ? $node->pub_id->pub_id : NULL ,
  );

  $form['uniquename'] = array(
    '#type' => 'textfield',
    '#title' => t('Unique Name'),
    '#required' => TRUE,
    '#description' => 'A unique name/identifier for this publication. If this article exists in pubmed, entering the pubmed ID here will ensure duplicate publication pages are not created.',
    '#default_value' => isset($node->pub_id->uniquename) ? $node->pub_id->uniquename : ''
  );

  $values= array(
    'cv_id' => variable_get('tripal_pub_types_cv', NULL),
  );

  //population select list with 'cvterm' names
  $result = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), $values);

  foreach ($result as $value) {
    $newArray[$value->cvterm_id]=$value->name;     //options for the select list
  }

  $form['type_id'] = array(
    '#type' => 'select',
    '#title' => t('Publication Type'),
    '#options' => $newArray,
    '#required' => TRUE,
    '#default_value' => isset($node->pub_id->type_id) ? $node->pub_id->type_id : ''
  );

  $form['author_wrapper'] = array(
    '#tree' => FALSE,
    '#prefix' => '<div class="clear-block" id="author-wrapper">',
    '#suffix' => '</div>',
  );

  // Get number of authors
  $author_count = empty($node->authors) ? 0 : count($node->authors);

  // If a new author added, add to list and update the author count.
  if (isset($form_state['new_author'])) {

    if (!isset($node->authors)) {
      $node->authors = array();
    }

    $node->authors = array_merge($node->authors, array($form_state['new_author']));
    $author_count++;

  }

  // If a author removed, remove from list and update the author count.
  $remove_delta = -1;

  if (!empty($form_state['remove_delta'])) {

      $remove_delta = $form_state['remove_delta'] - 1;

      unset($node->authors[$remove_delta]);

      // Re-number the values.
      $node->authors = array_values($node->authors);

      $author_count--;

  }

  // Container to display existing authors.
  $form['author_wrapper']['authors'] = array(
    '#prefix' => '<div id="publication-authors">',
    '#suffix' => '</div>',
    '#theme' => 'tripal_pub_author_table',
  );

  if (!isset($node->authors)) {

    if (isset($node->new_author['new_author_name'])) {

      $node->authors = array();

      $node->authors[]['author_name'] = $node->new_author['new_author_name'];

    }

  }

  //Add the existing authors to the form.
  for ($delta = 0; $delta < $author_count; $delta++) {

      $author = isset($node->authors[$delta]['author_name']) ? $node->authors[$delta] : array();

      $form['author_wrapper']['authors'][$delta] = tripal_pub_author_display_form($delta, $author);

  }


  if (isset($form_state['values']['edit_author'])) {

      // Add new authors
      $form['author_wrapper']['edit_author'] = array(
        '#type' => 'fieldset',
        '#title' => t('Current Publication Authors'),
        '#tree' => FALSE,
      );

      // Define the form fields for the new author
      $form['author_wrapper']['edit_author']['edit_author'] = array(
        '#tree' => TRUE,
        //'#default_value'=> '',
        //'#theme' => 'author_add_author_form',
      );

      $form['author_wrapper']['edit_author']['edit_author']['delta'] = array(
        '#type' => 'hidden',
        '#value' => $form_state['values']['edit_author']['delta']
      );

      $form['author_wrapper']['edit_author']['edit_author']['edit_author_name'] = array(
        '#type' => 'publication_author',
        '#title' => t('Contributing Authors'),
        '#default_value' => array(
            'givennames' => $form_state['values']['edit_author']['author_name']['givennames'],
            'surname' => $form_state['values']['edit_author']['author_name']['surname'],
            'suffix' => $form_state['values']['edit_author']['author_name']['suffix'],
          ),
        '#weight' => 1,
      );

      // We name our button 'author_more' to avoid conflicts with other modules using
      // AHAH-enabled buttons with the id 'more'.
      $form['author_wrapper']['edit_author']['author_save'] = array(
        '#type' => 'submit',
        '#value' => t('Save Author'),
        '#weight' => 0,
        '#submit' => array('tripal_pub_edit_author_submit'),
        '#ahah' => array(
          'path' => 'tripal_pub/js/0',
          'wrapper' => 'author-wrapper',
          'method' => 'replace',
          'effect' => 'fade',
        ),
      );
  }
  else{

      // Add new authors
      $form['author_wrapper']['add_author'] = array(
        '#type' => 'fieldset',
        '#title' => t('Publication Authors'),
        '#tree' => FALSE,
      );

      // Define the form fields for the new author
      $form['author_wrapper']['add_author']['new_author'] = array(
        '#tree' => TRUE,
        //'#default_value'=> '',
        '#theme' => 'author_add_author_form',
      );

      $form['author_wrapper']['add_author']['new_author']['new_author_name'] = array(
        '#type' => 'publication_author',
        '#title' => t('Contributing Authors'),
        '#default_value' => '',
        '#weight' => 1,
      );

      // We name our button 'author_more' to avoid conflicts with other modules using
      // AHAH-enabled buttons with the id 'more'.
      $form['author_wrapper']['add_author']['author_more'] = array(
        '#type' => 'submit',
        '#value' => t('Add Author'),
        '#weight' => 0,
        '#submit' => array('tripal_pub_add_author_submit'),
        '#ahah' => array(
          'path' => 'tripal_pub/js/0',
          'wrapper' => 'author-wrapper',
          'method' => 'replace',
          'effect' => 'fade',
        ),
      );

  }

  $form['volumetitle'] = array(
    '#type' => 'textfield',
    '#title' => t('Volume Title'),
    '#description' => t('Title of part if one of a series.'),
    '#default_value' => isset($node->pub_id->volumetitle) ? $node->pub_id->volumetitle : ''
  );

  $form['volume'] = array(
    '#type' => 'textfield',
    '#title' => t('Volume'),
    '#default_value' => isset($node->pub_id->volume) ? $node->pub_id->volume : ''
  );

  $form['series_name'] = array(
    '#type' => 'textfield',
    '#title' => t('Series Name'),
    '#default_value' => isset($node->pub_id->series_name) ? $node->pub_id->series_name : ''
  );

  $form['issue'] = array(
    '#type' => 'textfield',
    '#title' => t('Issue'),
    '#default_value' => isset($node->pub_id->issue) ? $node->pub_id->issue : ''
  );

  $form['pyear'] = array(
    '#type' => 'textfield',
    '#title' => t('Publication Year'),
    '#default_value' => isset($node->pub_id->pyear) ? $node->pub_id->pyear : ''
  );

  $form['pages'] = array(
    '#type' => 'textfield',
    '#title' => t('Pages'),
    '#description' => t('Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'),
    '#default_value' => isset($node->pub_id->pages) ? $node->pub_id->pages : ''
  );

  $form['miniref'] = array(
    '#type' => 'textfield',
    '#title' => t('Mini-Ref'),
    '#required' => FALSE,
    '#default_value' => isset($node->pub_id->miniref) ? $node->pub_id->miniref : ''
  );

  $form['is_obsolete'] = array(
    '#type' => 'checkbox',
    '#title' => t('Is Obsolete?(Check for Yes)'),
    '#required' => TRUE,
    '#default_value' => isset($node->pub_id->is_obsolete) ? $node->pub_id->is_obsolete : FALSE
  );

  $form['publisher'] = array(
    '#type' => 'textfield',
    '#title' => t('Publisher Name'),
    '#required' => FALSE,
    '#default_value' => isset($node->pub_id->publisher) ? $node->pub_id->publisher : ''
  );

  $form['pubplace'] = array(
    '#type' => 'textfield',
    '#title' => t('Place of Publication'),
    '#required' => FALSE,
    '#default_value' => isset($node->pub_id->pubplace) ? $node->pub_id->pubplace  : ''
  );

  return $form;

}


/**
 * Implementation of tripal_pub_insert().
 *
 * This function inserts user entered information pertaining to the Publication instance into the
 * 'pubauthor', 'pubprop', 'chado_pub', 'pub' talble of the database.
 *
 *  @parm $node
 *    Then node which contains the information stored within the node-ID
 *
 *
 */
function chado_pub_insert($node) {

  $values =  array(
    'title' => $node->title,
    'volumetitle' => $node->volumetitle,
    'volume' => $node->volume,
    'series_name' => $node->series_name,
    'issue' => $node->issue,
    'pyear' => $node->pyear,
    'pages' => $node->pages,
    'miniref' => $node->miniref,
    'type_id' => $node->type_id,
    'is_obsolete' => $node->is_obsolete,
    'publisher' => $node->publisher,
    'pubplace' => $node->pubplace,
    'uniquename' => $node->uniquename,
    'type_id' => $node->type_id
  );

  //inserts info into chado table
  $result = tripal_core_chado_insert('pub', $values);


  if (isset($result)) {

          //inserts the row of vid,nid,project_id into the chado_pub table
          db_query("INSERT INTO {chado_pub} (nid, vid, pub_id) VALUES (%d, %d, %d)",
            $node->nid,
            $node->vid,
            $result['pub_id']
          );

          //Aquiring information for the abstract
          $abstract_info = tripal_core_chado_select('cvterm', array('cvterm_id'),
            array('name' => 'abstract', 'cv_id' => array('name' => 'tripal')
            )
          );

          //Extracting the type_id
          $type_id = $abstract_info[0]->cvterm_id;

          //setting the abstract values
          $abstract = array(
            'pub_id' => $result['pub_id'],
            'type_id' => $type_id,
            'value' => $node->abstract,
            'rank' => 1
          );

          //inserts info into chado pubpro table for abstract
          tripal_core_chado_insert('pubprop', $abstract);

          //counter for loop
          for ($i=0; $i<=sizeof($node->authors); $i++) {

              if (isset($node->authors[$i]['author_name'] )) {

                $authors = array(
                  'pub_id' => $result['pub_id'],
                  'rank' => $i,
                  'surname' => $node->authors[$i]['author_name']['surname'],
                  'givennames' => $node->authors[$i]['author_name']['givennames'],
                  'suffix' => $node->authors[$i]['author_name']['suffix'],
                );

                  //inserts info into chado pubpro table for abstract
                  tripal_core_chado_insert('pubauthor', $authors);
              }

          }


          if (!empty($node->new_author['new_author_name']['surname'])) {

              $authors = array(
                  'pub_id' => $result['pub_id'],
                  'rank' => $i+1,
                  'surname' => $node->new_author['new_author_name']['surname'],
                  'givennames' => $node->new_author['new_author_name']['givennames'],
                  'suffix' => $node->new_author['new_author_name']['suffix'],
                );

                  //inserts info into chado pubpro table for abstract
                  tripal_core_chado_insert('pubauthor', $authors);

          }


      }
      else{

        druapl_set_message('Pub_id was not set, No information has been set.');

    }

}


/**
 * Implementation of tripal_pub_delete().
 *
 * This function takes a node and if the delete button has been chosen by the user, the publication
 * and it's details will be removed.Following,given the node-ID, the instance will be deleted from
 * the 'chado_pub' table.
 *
 *  @parm $node
 *    Then node which contains the information stored within the node-ID
 *
 */
function chado_pub_delete(&$node) {

  // Matching all revision, by using the node's pub_id.
  $values =  array(
    'pub_id' => $node->pub_id->pub_id,
  );

  //deleting row in chado table
  tripal_core_chado_delete('pub', $values);

  //deleteing in drupal chado_project table
  db_query('DELETE FROM {chado_pub} WHERE nid = %d', $node->nid);

}


/*
 *
 * Implements hook_update
 *
 * The purpose of the function is to allow the module to take action when an edited node is being
 * updated. It updates any name changes to the database tables that werec reated upon registering a Publication.
 * As well, the database will be changed, so the user changed information will be saved to the database.
 *
 * @param $node
 *   The node being updated
 *
 */
function chado_pub_update($node) {


  $values =  array(
      'title' => $node->title,
      'volumetitle' => $node->volumetitle,
      'volume' => $node->volume,
      'series_name' => $node->series_name,
      'issue' => $node->issue,
      'pyear' => $node->pyear,
      'pages' => $node->pages,
      'miniref' => $node->miniref,
      'uniquename' => $node->uniquename,
      'type_id' => $node->type_id,
      'is_obsolete' => $node->is_obsolete,
      'publisher' => $node->publisher,
      'pubplace' => $node->pubplace,
      'type_id' => $node->type_id
    );

  $result = db_fetch_object(db_query('SELECT pub_id FROM {chado_pub} WHERE nid=%d AND vid=%d ', $node->nid, $node->vid));

  //extract pub_id from the chado table for update function
  $match = array( 'pub_id' => $result->pub_id );

  //$table to be updated, $match is the 'pub_id', $value are the values that are to be updated
  $update_result = tripal_core_chado_update('pub', $match, $values);

   //Aquiring information for the abstract
  $abstract_info = tripal_core_chado_select('cvterm', array('cvterm_id'),
    array('name' => 'abstract', 'cv_id' => array('name' => 'tripal')
    )
  );

  //Grabbing the type id of the old abstract
  $type_id = $abstract_info[0]->cvterm_id;

  //Aquiring information for the abstract
  $abstract = array(
    'pub_id' => $result->pub_id,
    'type_id' => $type_id,
    'value' => $node->abstract,
    'rank' => 1
  );

  //$table to be updated, $match is the 'pub_id', $value are the values that are to be updated
  tripal_core_chado_update('pubprop', array('pub_id' => $result->pub_id, 'type_id' => $type_id, 'rank' => 1), $abstract);

  //counter for loop
  for ($i=0; $i<=sizeof($node->authors); $i++) {

      if (isset($node->authors[$i]['author_name'] )) {

          //if new insert
          if (isset($node->authors[$i]['is_new'])) {

              $authors = array(
                  'pub_id' => $match['pub_id'],
                  'rank' => $i+1,
                  'surname' => $node->authors[$i]['author_name']['surname'],
                  'givennames' => $node->authors[$i]['author_name']['givennames'],
                  'suffix' => $node->authors[$i]['author_name']['suffix'],
              );

              //inserts info into chado pubpro table for abstract
              tripal_core_chado_insert('pubauthor', $authors);

          }
          else{

            //update
            //$table=pubauthor to be updated, $match=author_match is the 'pub_id', $value=author are the values that are to be updated
            tripal_core_chado_update('pubauthor', array('pub_id' => $match['pub_id'], 'rank' => $node->authors[$i]['author_name']['rank']), $node->authors[$i]['author_name']);

          }

      }

  }


}


/**
 * Implementation of tripal_pub_load().
 *
 *
 * @param $node
 *   The node that is to be accessed from the database
 *
 * @return $node
 *   The node with the information to be loaded into the database
 *
 */
function chado_pub_load($node) {

  $result = db_fetch_object(db_query('SELECT * FROM {chado_pub} WHERE nid=%d AND vid=%d ', $node->nid, $node->vid));

  $values = array(
    'pub_id' => $result->pub_id,
  );


  if (empty($result->pub_id)) {

    drupal_set_message(t("Unable to find publication"), 'error');

  }
  else{

    $node->pub = tripal_core_generate_chado_var('pub', $values);

    // add in authors
    $authors = tripal_core_chado_select(
      'pubauthor',
      array('rank', 'surname', 'givennames', 'suffix'),
      array('pub_id' => $node->pub->pub_id)
    );
    foreach ($authors as $author) {
        $node->pub->authors[$author->rank] = $author;
    }
    ksort($node->pub->authors);

  }

  return $node;

}

/**
 * Submit handler for 'Add Author' button on node form.
 */
function tripal_pub_add_author_submit($form, &$form_state) {

    $form_state['remove_delta'] = 0;

    // Set the form to rebuild and run submit handlers.
    node_form_submit_build_node($form, $form_state);

    // Make the changes we want to the form state.
    if ($form_state['values']['author_more']) {

      $new_author = array();

      $new_author['author_name'] = $form_state['values']['new_author']['new_author_name'];
      $new_author['is_new'] = TRUE;

      $form_state['new_author'] = $new_author;

    }



}


/**
 * Submit handler for 'Edit' button on node form.
 */
function tripal_pub_edit_author_submit($form, &$form_state) {

    // remember which author we're editing
    $delta = $form_state['values']['edit_author']['delta'];

    //add changes author details back
    $rank = $form_state['values']['authors'][$delta]['author_name']['rank'];
    $form_state['values']['authors'][$delta]['author_name'] = $form_state['values']['edit_author']['edit_author_name'];
    $form_state['values']['authors'][$delta]['author_name']['rank'] = $rank;

    //ensures that after they save their changes the edit fieldstate goes away
    unset($form_state['values']['edit_author']);

    // Set the form to rebuild and run submit handlers.
    node_form_submit_build_node($form, $form_state);

}


/**
 * Submit handler for 'Edit' button on node form.
 */
function tripal_pub_set_edit_author_submit($form, &$form_state) {

  $form_state['remove_delta'] = 0;

  // Make the changes we want to the form state
  $edit_author = array();

  if (preg_match('/edit_author_(\d+)/', $form_state['clicked_button']['#name'], $matches)) {


    $delta = $matches[1];

    $form_state['values']['edit_author'] = $form_state['values']['authors'][$delta];

    $form_state['values']['edit_author']['delta'] = $delta;

  }

  // Set the form to rebuild and run submit handlers.
  node_form_submit_build_node($form, $form_state);

}


/**
 * Submit handler for 'Remove' button on node form.
 */
function tripal_pub_remove_row_submit($form, &$form_state) {


  if (preg_match('/remove_author_(\d+)/', $form_state['clicked_button']['#name'], $matches)) {

    $delta = $matches[1];

    $form_state['values']['remove_author'] = $form_state['values']['authors'][$delta];

    $form_state['values']['remove_author']['delta'] = $delta;

  }

  $values =  array(
    'pub_id' => $form_state['values']['pub_id'],
    'rank' => $form_state['values']['authors'][$delta]['author_name']['rank']

    );

  //deleting row in chado table
  tripal_core_chado_delete('pubauthor', $values);


  // Set the form to rebuild and run submit handlers.
  node_form_submit_build_node($form, $form_state);

}


/*
 *
 *
 *
 */
function tripal_pub_js($delta = 0) {

    $form = tripal_pub_ajax_form_handler($delta);

    // Render the new output.
    $author_form = $form['author_wrapper']; //was ['author']

    // Prevent duplicate wrappers.
    unset($author_form['#prefix'], $author_form['#suffix']);

    $output = theme('status_messages') . drupal_render($author_form);

    // AHAH does not know about the "Remove" button.
    // This causes it not to attach AHAH behaviours to it after modifying the form.
    // So we need to tell it first.
    $javascript = drupal_add_js(NULL, NULL);

    if (isset($javascript['setting'])) {

      $output .= '<script type="text/javascript">jQuery.extend(Drupal.settings, '. drupal_to_js(call_user_func_array('array_merge_recursive', $javascript['setting'])) .');</script>';

    }

    // Final rendering callback.
    drupal_json(array('status' => TRUE, 'data' => $output));

}


/**
 * AJAX form handler.
 */
function tripal_pub_ajax_form_handler($delta=0 ) {

    // The form is generated in an include file which we need to include manually.
    include_once 'modules/node/node.pages.inc';

    $form_state = array('storage' => NULL, 'submitted' => FALSE);

    $form_build_id = filter_xss($_POST['form_build_id']);

    // Get the form from the cache.
    $form = form_get_cache($form_build_id, $form_state);

    $args = $form['#parameters'];

    $form_id = array_shift($args);

    // We need to process the form, prepare for that by setting a few internals.
    $form_state['post'] = $form['#post'] = $_POST;

    $form['#programmed'] = $form['#redirect'] = FALSE;

    // Set up our form state variable, needed for removing authors.
    $form_state['remove_delta'] = $delta;

    // Build, validate and if possible, submit the form.
    drupal_process_form($form_id, $form, $form_state);

    // If validation fails, force form submission.
    if (form_get_errors()) {

      form_execute_handlers('submit', $form, $form_state);

    }

    // This call recreates the form relying solely on the form_state that the
    // drupal_process_form set up.
    $form = drupal_rebuild_form($form_id, $form_state, $args, $form_build_id);

    return $form;
}


/*
 *
 *
 */
function theme_tripal_pub_author_table($form) {

  $rows = array();

  $headers = array(
    t('Givennames'),
    t('Surname'),
    t('Suffix'),
    '',  // Blank header title for the remove link.
  );

  foreach (element_children($form) as $key) {

    // No need to print the field title every time.
    unset(
      $form[$key]['author_name_text']['#title'],
      $form[$key]['author_name_text-2']['#title'],
      $form[$key]['author_name_text-3']['#title'],
      $form[$key]['remove_author']['#title']
    );

    // Build the table row.
    $row = array(
      'data' => array(
        array('data' => drupal_render($form[$key]['author_name']) . drupal_render($form[$key]['author_name_text']), 'class' => 'author-name'),
        array('data' => drupal_render($form[$key]['author_name']) . drupal_render($form[$key]['author_name_text-2']), 'class' => 'author-name'),
        array('data' => drupal_render($form[$key]['author_name']) . drupal_render($form[$key]['author_name_text-3']), 'class' => 'author-name'),
        array('data' => drupal_render($form[$key]['edit_author']) . drupal_render($form[$key]['remove_author']), 'class' => 'remove-author'),
      ),
    );

    // Add additional attributes to the row, such as a class for this row.
    if (isset($form[$key]['#attributes'])) {

      $row = array_merge($row, $form[$key]['#attributes']);

    }

    $rows[] = $row;

  }

  //$output = theme('table', $headers, $rows);

  $output .= drupal_render($form);

  return $output;

}

/**
 *
 * Helper function to define populated form field elements for publication node form.
 *
 */
function tripal_pub_author_display_form($delta, $author) {

  $form = array(
    '#tree' => TRUE,
  );

  // Author Name
  $form['author_name'] = array(
    '#type' => 'hidden',
    '#value' => $author,
    '#parents' => array('authors', $delta),
  );
  $form['author_name_text'] = array(
    '#type' => 'item',
    '#title' => t('Givennames'),
    '#parents' => array('authors', $delta),
    '#value' => $author['author_name']['givennames'],
  );

  $form['author_name_text-2'] = array(
    '#type' => 'item',
    '#title' => t('Surname'),
    '#parents' => array('authors', $delta),
    '#value' => $author['author_name']['surname'],
  );

  $form['author_name_text-3'] = array(
    '#type' => 'item',
    '#title' => t('Suffix'),
    '#parents' => array('authors', $delta),
    '#value' => $author['author_name']['suffix'],
  );

    // Remove button.
    $form['remove_author'] = array(
        '#type' => 'submit',
        '#name' => 'remove_author_' . $delta,
        '#value' => t('Remove'),
        '#submit' => array('tripal_pub_remove_row_submit'),
        '#parents' => array('authors', $delta, 'remove_author'),
        '#ahah' => array(
          'path' => 'tripal_pub/js/0',
          'wrapper' => 'author-wrapper',
          'method' => 'replace',
          'effect' => 'fade',
        ),
    );

      // Edit Author button
    $form['edit_author'] = array(
        '#type' => 'submit',
        '#name' => 'edit_author_' . $delta,
        '#value' => t('Edit'),
        '#submit' => array('tripal_pub_set_edit_author_submit'),
        '#parents' => array('authors', $delta, 'edit_author'),
        '#ahah' => array(
          'path' => 'tripal_pub/js/0',
          'wrapper' => 'author-wrapper',
          'method' => 'replace',
          'effect' => 'fade',
        ),
    );

  return $form;
}


/*
 * This function executes commands periodically. This is called whenever a cron run occurs. This
 * function uses the time interval that the user has entered. This Publication module, requires
 * that the program is ran in pre-determined intervals, as desired by the user. By using a time stamp
 * and comparing the current time and the time that the last time a cron was ran, this program will
 *  be ran.
 *
 *
 * @TODO: The cron function is not working correctly, not sure why the cron is not working properly.
 *
 *
 *
 */
/**
function tripal_pub_cron(){

      global $user;    //needed to make the current users details available so access of user id is available

      //Aquiring the current time
      $current_time = time();

      //Aquiring the user entered time interval
      $user_interval = variable_get('time_interval',NULL);

      //converting the user entered interval into seconds for use with unix time stamp
      $converted_interval = ($user_interval*60);

      //Accessing database for time stamp from watchdog
      $cron = db_result(db_query('select timestamp from {watchdog} where type="cron" order by timestamp desc limit 1'));

      //debugging print statement
      //print($cron);

      //taking variable value & assigning for use
      $cron_last = variable_get('cron', time());

      $updated_interval = $cron_last - $converted_interval;

      if($current_time >= $updated_interval ){

        tripal_add_job('Search & Load PubMed Publications', 'tripal_pub', 'tripal_pub_search_load_pubmed_publications', $job_args, $user->uid);

      }

}
  */




//-----------------------------------------------------------------------------
//  SECTION: Custom form Elements
//-----------------------------------------------------------------------------


/*
 * This fucnction tells the FAPI(Form-API) that this is a element that will carry a value, contains
 * arrays of callback function names. Will declare an element will create a reuseable element type.
 *
 *  @return
 *      An associative array with the name of each element type as a key and an
 *      array of attributes describingthe type as a value
 */
function tripal_pub_elements() {

      return array(
          'publication_author' => array(
               '#input' => TRUE,
               '#process' => array('expand_publication_author'),
               '#element_validate' => array('publication_author_validate'),
              ),
      );

}


/*
 *
 *
 *
 */
function expand_publication_author($element) {

    if (empty($element['#value'])) {
      $element['#value'] = array(
              'givennames' => '',
              'suffix' => '',
              'surname' => '',
            );

    }

    $element['#tree'] = TRUE;

    $parents = $element['#parents'];

    $parents[] = 'givennames';

    $element['givennames'] = array(
    '#type' => 'textfield',
              '#size' => 10,
              //'#maxlength' => TRUE,
              //'#default_value'=> $element['#value']['#given'],
              '#prefix' => 'Given Name',
    );

    if ($element['#default_value']) {

      $element['givennames']['#default_value'] = $element['#default_value']['givennames'];

    }

    $parents = $element['#parents'];

    $parents[]= 'surname';

    $element['surname'] = array(
    '#type' => 'textfield',
              '#size' => 10,
              //'#maxlength' => TRUE,
              //'#default_value'=> $element['#value']['#surname'],
              '#prefix' => 'Surname',
    );

    if ($element['#default_value']) {

      $element['surname']['#default_value'] = $element['#default_value']['surname'];

    }

    $parents = $element['#parents'];

    $parents[]= 'suffix';

    $element['suffix'] = array(
    '#type' => 'textfield',
              '#size' => 5,
              //'#maxlength' => TRUE,
              //'#default_value'=> $element['#value']['#suffix'],
              '#prefix' => 'suffix',
    );

    if ($element['#default_value']) {

      $element['suffix']['#default_value'] = $element['#default_value']['suffix'];

    }

  return $element;

}


/*
 *
 *
 *
 */
function theme_publication_author($element) {
  return theme('form_element', $element, '<div class="container-inline">' . $element['#children'] . '</div>');
}

/*
 *
 *
 *
 */
function publication_author_validate($element) {
  if ($element['#required']) {
    if (trim($element['#value']['givennames']) == '' || trim($element['#value']['suffix']) == '' || trim($element['#value']['surname']) == '' ||
      !is_string($element['#value']['givennames']) || !is_string($element['#value']['givennames']) || !is_string($element['#value']['surname'])) {
      form_error($element, t('The Author name is required.'));
    }
  }
}

/*
 * 
 */

function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
  if ($form_id == "tripal_pub_remote_search_form") {    
    // updating the form through the ahah callback sets the action of
    // the form to the ahah callback URL. We need to set it back
    // to the normal form URL
    $form['#action'] = url("admin/tripal/tripal_pub/import_setup");
  }
}