tripal/tripal_pub/tripal_pub.module

<?php

require_once "api/tripal_pub.api.inc";
require_once "theme/tripal_pub.theme.inc";
require_once "includes/tripal_pub.admin.inc";
require_once "includes/tripal_pub.pub_sync.inc";
require_once "includes/tripal_pub.chado_node.inc";
require_once "includes/tripal_pub.pub_importers.inc";
require_once "includes/tripal_pub.pub_search.inc";
require_once "includes/tripal_pub.pub_citation.inc";
require_once "includes/importers/tripal_pub.PMID.inc";
require_once "includes/importers/tripal_pub.AGL.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_css(drupal_get_path('module', 'tripal_pub') . '/theme/css/tripal_pub.css');
  drupal_add_js(drupal_get_path('module', 'tripal_pub') . '/theme/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'),
      'base' => 'chado_pub',
      'description' => t('A publication from the Chado database'),
      'title_label' => t('Article Title'),
      'body_label' => t('Abstract'),
      'has_title' => TRUE,
      'has_body' => FALSE,
  ),
  );
}

/**
 * Tripal-Publication-Menu
 *
 * Implements 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['find/publications' ]= array(
    'title' => 'Publication Search',
    'description' => ('Search for publications'),
    'page callback' => 'tripal_pub_search_page',
    'access arguments' => array('access chado_pub content'),
    'type' => MENU_CALLBACK
  );

  $items['find/publications/criteria/%/%'] = array(
    'page callback' => 'tripal_pub_search_page_update_criteria',
    'page arguments' => array(5, 6),
    'access arguments' => array('access chado_pub content'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_pub']= array(
    'title' => 'Publications',
    'description' => ('A documented provenance artefact - publications, documents, personal communication.'),
    'page callback' => 'tripal_pub_admin_pub_view',
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_NORMAL_ITEM
  );

  $items['admin/tripal/chado/tripal_pub/help']= array(
    'title' => 'Help',
    'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_pub_help'),
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );

  $items['admin/tripal/chado/tripal_pub/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Configure the Tripal publication module.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_pub_admin'),
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );

  $items['admin/tripal/chado/tripal_pub/sync'] = array(
    'title' => ' Sync',
    'description' => 'Sync publications in Chado with Drupal',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_pub_sync_form'),
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2
  );

  $items['admin/tripal/chado/tripal_pub/citation'] = array(
    'title' => 'Citations',
    'description' => 'Update publication citations',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_pub_citation_form'),
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 1
  );
  
  $items['admin/tripal/chado/tripal_pub/import_list'] = array(
    'title' => t('Importers'),
    'description' => t('List all publication importers'),
    'page callback' => 'tripal_pub_importers_list',
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 0
  );
  
  // add a second link for the importer on the data loaders page
  $items['admin/tripal/loaders/pub_import'] = array(
    'title' => 'Publications Importers',
    'description' => 'Create importers that can periodically import publications from remote online publication databases.',
    'page callback' => 'tripal_pub_importers_list',
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_NORMAL_ITEM,
  );
  
  $items['admin/tripal/chado/tripal_pub/import/new'] = array(
    'title' => t('Add an Importer'),
    'description' => t('Add a new publication importer.'),
    'page callback' => 'tripal_pub_importer_setup_page',
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_pub/import/raw/%'] = array(
    'page callback' => 'tripal_pub_get_raw_data',
    'page arguments' => array(6),
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_pub/import/edit/%'] = array(
    'page callback' => 'tripal_pub_importer_setup_page',
    'page arguments' => array(5, 6),
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );
  
  $items['admin/tripal/chado/tripal_pub/import/submit/%'] = array(
    'page callback' => 'tripal_pub_importer_submit_job',
    'page arguments' => array(6),
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_pub/import/delete/%'] = array(
    'page callback' => 'tripal_pub_importer_delete',
    'page arguments' => array(5),
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );
  $items['admin/tripal/chado/tripal_pub/import/changedb'] = array(
    'page callback' => 'tripal_pub_importer_setup_page_update_remotedb',
    'page arguments' => array(),
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_pub/import/criteria/%/%'] = array(
    'page callback' => 'tripal_pub_importer_setup_page_update_criteria',
    'page arguments' => array(5, 6),
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );

  $items['tripal_pub/chado/properties/add'] = array(
    'page callback' => 'tripal_pub_property_add',
    'access arguments' => array('edit chado_pub content'),
    'type ' => MENU_CALLBACK,
  );
  $items['tripal_pub/chado/properties/description'] = array(
    'page callback' => 'tripal_pub_property_get_description',
    'access arguments' => array('edit chado_pub content'),
    'type ' => MENU_CALLBACK,
  );
  $items['tripal_pub/chado/properties/minus/%/%'] = array(
    'page callback' => 'tripal_pub_property_delete',
    'page arguments' => array(3, 4),
    'access arguments' => array('edit chado_pub 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($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');
  
  $items = array(
    'node__chado_pub' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme",
    ),
    // node templates
    'tripal_pub_authors' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_authors',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_base' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_base',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_featuremaps' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_featuremaps',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_features' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_features',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_libraries' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_libraries',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_projects' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_projects',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_properties' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_properties',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_references' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_references',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_relationships' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_relationships',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_stocks' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_stocks',
      'path' => "$path/theme/tripal_pub",
    ),

    // instructions page for the pub module
    'tripal_pub_help' => array(
      'template' => 'tripal_pub_help',
      'arguments' =>  array(NULL),
      'path' => "$path/theme",
    ),

    // themed forms
    'tripal_pub_importer_setup_form_elements' => array(
      'render element' => 'form',
    ),
    'tripal_pub_search_setup_form_elements' => array(
      'render element' => 'form',
    ),
    
    // teaser
    'tripal_pub_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_pub_teaser',
      'path' => "$path/theme/tripal_pub",
    ),
  );

  return $items;
}

/**
 * Implements hook_help()
 * Purpose: Adds a help page to the module list
 */
function tripal_pub_help ($path, $arg) {
  if ($path == 'admin/help#tripal_pub') {
    return theme('tripal_pub_help', array());
  }
}

/**
 * Implements hook_views_api()
 * Purpose: Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_db.views.inc where all the
 *  views integration code is
 *
 * @ingroup tripal_pub
 */
function tripal_pub_views_api() {
  return array(
    'api' => 3.0,
  );
}

/**
 * Implement hook_permissions().
 */
function tripal_pub_permissions() {
  return array(
    'access chado_pub content' => array(
      'title' => t('View Publications'),
      'description' => t('Allow users to view publication pages.'),
    ),
    'create chado_pub content' => array(
      'title' => t('Create Publication'),
      'description' => t('Allow users to create new publication pages.'),
    ),
    'delete chado_pub content' => array(
      'title' => t('Delete Publication'),
      'description' => t('Allow users to delete publication pages.'),
    ),
    'edit chado_pub content' => array(
      'title' => t('Edit Publications'),
      'description' => t('Allow users to edit publication pages.'),
    ),
    'adminster tripal pub' => array(
      'title' => t('Administer Publications'),
      'description' => t('Allow users to administer all publications.'),
    ),
  );
}




/**
 *
 */
function tripal_pub_mail($key, &$message, $params) {
  $language = $message['language'];
  $variables = user_mail_tokens($params['account'], $language);
  switch($key) {
    case 'import_report':
      $headers = array(
        'MIME-Version' => '1.0',
        'Content-Type' => 'text/html; charset=UTF-8; format=flowed',
        'Content-Transfer-Encoding' => '8Bit',
        'X-Mailer' => 'Drupal'
        );
        foreach ($headers as $key => $value) {
          $message['headers'][$key] = $value;
        }
        $message['subject'] = t('Publication import from !site', $variables, $language->language);
        $message['body'][] = $params['message'];
        break;
  }
}
/**
 *
 * @ingroup tripal_feature
 */
function tripal_pub_node_view($node, $view_mode, $langcode) {
  switch ($node->type) {
    case 'chado_pub':
      // Show feature browser and counts
      if ($view_mode == 'full') {
        $node->content['tripal_pub_authors'] = array(
          '#value' => theme('tripal_pub_authors', array('node' => $node)),
        );
        $node->content['tripal_pub_base'] = array(
          '#value' => theme('tripal_pub_base', array('node' => $node)),
        );
        $node->content['tripal_pub_featuremaps'] = array(
          '#value' => theme('tripal_pub_featuremaps', array('node' => $node)),
        );
        $node->content['tripal_pub_features'] = array(
          '#value' => theme('tripal_pub_features', array('node' => $node)),
        );
        $node->content['tripal_pub_libraries'] = array(
          '#value' => theme('tripal_pub_libraries', array('node' => $node)),
        );
        $node->content['tripal_pub_projects'] = array(
          '#value' => theme('tripal_pub_projects', array('node' => $node)),
        );
        $node->content['tripal_pub_properties'] = array(
          '#value' => theme('tripal_pub_properties', array('node' => $node)),
        );
        $node->content['tripal_pub_references'] = array(
          '#value' => theme('tripal_pub_references', array('node' => $node)),
        );
        $node->content['tripal_pub_relationships'] = array(
          '#value' => theme('tripal_pub_relationships', array('node' => $node)),
        );
        $node->content['tripal_pub_stocks'] = array(
          '#value' => theme('tripal_pub_stocks', array('node' => $node)),
        );
      }
      if ($view_mode == 'teaser') {
        $node->content['tripal_pub_teaser'] = array(
          '#value' => theme('tripal_pub_teaser', array('node' => $node)),
        );
      }
      break;
  }
}
/**
 *
 * @param $node
 */
function tripal_pub_node_insert($node) {
  // we want the publications to always have a URL of http://[base url]/pub/[pub id]
  // where [pub id] is the Chado publication ID.  This will allow for easy linking
  // into the publication without needing to know the node.  Of course if you know the
  // node that will still work too (e.g. http://[base url]/node/[node id]
  // so the nodeapi function ensures that the URL path is set after insert or update
  // of the node and when the node is loaded if it hasn't yet been set.
  if ($node->type == 'chado_pub') {
    $pub_id = chado_get_id_for_node('pub', $node->nid);
    tripal_pub_set_pub_url($node, $pub_id);
  }
}
/**
 *
 * @param $node
 * @param $types
 */
function tripal_pub_node_load($nodes, $types) {

  // we want the publications to always have a URL of http://[base url]/pub/[pub id]
  // where [pub id] is the Chado publication ID.  This will allow for easy linking
  // into the publication without needing to know the node.  Of course if you know the
  // node that will still work too (e.g. http://[base url]/node/[node id]
  // so the nodeapi function ensures that the URL path is set after insert or update
  // of the node and when the node is loaded if it hasn't yet been set.
  if (count(array_intersect(array('chado_pub'), $types))) {
    foreach ($nodes as $nid => $node) {
      if ($node->type == 'chado_pub' and !property_exists($node, 'path')) {
        $pub_id = chado_get_id_for_node('pub', $node->nid);
        $path = tripal_pub_set_pub_url($node, $pub_id);
      }
    }
  }
}
/**
 *
 * @param $node
 */
function tripal_pub_node_update($node) {
  // we want the publications to always have a URL of http://[base url]/pub/[pub id]
  // where [pub id] is the Chado publication ID.  This will allow for easy linking
  // into the publication without needing to know the node.  Of course if you know the
  // node that will still work too (e.g. http://[base url]/node/[node id]
  // so the nodeapi function ensures that the URL path is set after insert or update
  // of the node and when the node is loaded if it hasn't yet been set.
  if ($node->type == 'chado_pub') {
    $pub_id = chado_get_id_for_node('pub', $node->nid);
    tripal_pub_set_pub_url($node, $pub_id);
  }
}

/**
 * Implementation of hook_form_alter()
 *
 * @param $form
 * @param $form_state
 * @param $form_id
 */
function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
  // turn of preview button for insert/updates
  if ($form_id == "chado_pub_node_form") {
    $form['actions']['preview']['#access'] = FALSE;
  }
  if ($form_id == "tripal_pub_importer_setup_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
    if (array_key_exists('values', $form_state) and $form_state['values']['action'] == 'edit') {
      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/edit/" . $form_state['values']['pub_import_id']);
    }
    if (array_key_exists('values', $form_state) and $form_state['values']['action'] == 'new') {
      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/new");
    }
    */
  }
  if ($form_id == "tripal_pub_search_form") {
    $form['#action'] = url("find/publications");
  }
  if ($form_id == "chado_pub_node_form") {
  }
}

/**
 * 
 * @param $callback
 * @param $args
 */
function tripal_pub_job_describe_args($callback, $args) {

  $new_args = array();
  if ($callback == 'tripal_pub_import_publications_by_import_id') {
    // get all of the loaders
    $qargs = array(':import_id' => $args[0]);
    $sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = :import_id ";
    $import = db_query($sql, $qargs)->fetchObject();
    
    $new_args['Importer'] = $import->name;
  }
  return $new_args;
}