islandora_chem_sp.module

<?php

/**
 * @file
 *
 * Provides the functionality to process and view chemical structure files.
 */
define('ISLANDORA_CHEM_SP_MODS_FORM_NAME', 'Islandora Chem MODS Form');
define('ISLANDORA_CHEM_SP_MADS_FORM_NAME', 'Islandora Chem MADS Form');

/**
 * Declare the objects that are required by this solution pack
 * @return type 
 */
function islandora_chem_sp_required_fedora_objects() {

  $module_path = drupal_get_path('module', 'islandora_chem_sp');

  // Put the form in the database
  module_load_include('inc', 'xml_form_builder', 'XMLFormDatabase');
  if (!XMLFormDatabase::Exists(ISLANDORA_CHEM_SP_MODS_FORM_NAME)) {
    $definition = new DOMDocument();
    $definition->load($module_path . '/xml/mods_chem.xml');
    XMLFormDatabase::Create(ISLANDORA_CHEM_SP_MODS_FORM_NAME, $definition);
  }
  if (!XMLFormDatabase::Exists(ISLANDORA_CHEM_SP_MADS_FORM_NAME)) {
    $definition = new DOMDocument();
    $definition->load($module_path . '/xml/mads_chem.xml');
    XMLFormDatabase::Create(ISLANDORA_CHEM_SP_MADS_FORM_NAME, $definition);
  }
  // Associates the form with the content model
  $result = db_result(db_query('Select content_model from {islandora_content_model_forms} where  content_model = "%s" and form_name = "%s"', 'islandora:sp_chem_CM', 'Islandora Chem MODS Form'));
  if (!$result) {
    $object = new stdClass();
    $object->content_model = 'islandora:sp_chem_CM';
    $object->form_name = 'Islandora Chem MODS Form';
    $object->dsid = 'MODS';
    $object->title_field = "['titleInfo']['title']";
    $object->transform = 'mods_to_dc.xsl';
    $result = drupal_write_record('islandora_content_model_forms', $object);
  }

  $result2 = db_result(db_query('Select content_model from {islandora_content_model_forms} where  content_model = "%s" and form_name = "%s"', 'islandora:sp_chem_researcher_CM', 'Islandora Chem MADS Form'));
  if (!$result2) {
    $object2 = new stdClass();
    $object2->content_model = 'islandora:sp_chem_researcher_CM';
    $object2->form_name = 'Islandora Chem MADS Form';
    $object2->dsid = 'MADS';
    $object2->title_field = "['titleInfo']['title']";
    $object2->transform = 'mads_to_dc.xsl';
    $result2 = drupal_write_record('islandora_content_model_forms', $object2);
  }

  return array(
    'islandora_chem_sp' => array(
      'module' => 'islandora_chem_sp',
      'title' => 'Islandora Chem Solution Pack',
      'objects' => array(
        array(
          'pid' => 'islandora:sp_chem_CM',
          'label' => 'Islandora chemistry content model',
          'dsid' => 'ISLANDORACM',
          'datastream_file' => "$module_path/xml/CHEMCM.xml",
          'cmodel' => 'fedora-system:ContentModel-3.0',
        ),
        array(
          'pid' => 'islandora:sp_chem_researcher_CM',
          'label' => 'Islandora chemistry researcher content model',
          'dsid' => 'ISLANDORACM',
          'datastream_file' => "$module_path/xml/CHEMRSCM.xml",
          'cmodel' => 'fedora-system:ContentModel-3.0',
        ),
        array(
          'pid' => 'quantumchem:sp_collection',
          'label' => 'Quantumchem',
          'cmodel' => 'islandora:collectionCModel',
          'datastreams' => array(
            array(
              'dsid' => 'TN',
              'datastream_file' => "$module_path/images/Crystal_Clear_filesystem_folder_chem.png",
              'mimetype' => 'image/png',
            ),
            array(
              'dsid' => 'COLLECTION_POLICY',
              'datastream_file' => "$module_path/xml/COLLECTION-COLLECTION POLICY.xml",
            ),
          ),
        ),
        array(
          'pid' => 'quantumchem:sp_chem_calculations',
          'label' => 'Calculations',
          'cmodel' => 'islandora:collectionCModel',
          'parent' => 'quantumchem:sp_collection',
          'datastreams' => array(
            array(
              'dsid' => 'TN',
              'datastream_file' => "$module_path/images/Crystal_Clear_filesystem_folder_chem.png",
              'mimetype' => 'image/png',
            ),
            array(
              'dsid' => 'COLLECTION_POLICY',
              'datastream_file' => "$module_path/xml/CHEM-COLLECTION POLICY.xml",
            ),
          ),
        ),
        array(
          'pid' => 'quantumchem:sp_chem_researchers',
          'label' => 'Researchers',
          'cmodel' => 'islandora:collectionCModel',
          'parent' => 'quantumchem:sp_collection',
          'datastreams' => array(
            array(
              'dsid' => 'TN',
              'datastream_file' => "$module_path/images/Crystal_Clear_filesystem_folder_chem.png",
              'mimetype' => 'image/png',
            ),
            array(
              'dsid' => 'COLLECTION_POLICY',
              'datastream_file' => "$module_path/xml/CHEM_RESEARCHER_POLICY.xml",
            ),
          ),
        ),
      ),
    ),
  );
}

/**
 * Create the callbacks for each of the pages
 * @return array 
 */
function islandora_chem_sp_menu() {
  $items = array();
  $items['structure_search'] = array(
    'title' => t('Structure search'),
    'file' => 'islandora_chem_sp_search.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_chem_sp_structure_search_form'),
    'type' => MENU_NORMAL_ITEM, //MENU_CALLBACK,
    'access arguments' => array('structure search'),
  );

  $items['inchi_search'] = array(
    'title' => t('Structure search'),
    'file' => 'islandora_chem_sp_search.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_chem_sp_inchi_search_form'),
    'type' => MENU_CALLBACK,
    'access arguments' => array('structure search'),
  );

  $items['fragment_search'] = array(
    'title' => t('Fragment search'),
    'file' => 'islandora_chem_sp_search.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_chem_sp_fragment_search_form'),
    'type' => MENU_CALLBACK,
    'access arguments' => array('structure search'),
  );

  $items['substructure'] = array(
    'title' => t('Substructure search intermeditate page'),
    'file' => 'islandora_chem_sp_search.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_chem_sp_substructure_search_intermediate_form'),
    'type' => MENU_CALLBACK,
    'access arguments' => array('structure search'),
  );

  $items['substructure_search'] = array(
//    'title' => t('Substructure search'),
    'file' => 'islandora_chem_sp_search.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_chem_sp_substructure_search_form'),
    'type' => MENU_CALLBACK,
    'access arguments' => array('structure search'),
  );

  $items['mw_search'] = array(
    'title' => t('Molecular weight search'),
    'file' => 'islandora_chem_sp_search.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_chem_sp_mw_search_form'),
    'type' => MENU_CALLBACK,
    'access arguments' => array('view fedora collection'),
  );

  $items['download'] = array(
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_chem_sp_download_form'),
    'type' => MENU_CALLBACK,
    'access arguments' => array('view fedora collection'),
  );

  $items['r_autocomplete'] = array(
    'title' => 'Auto Complete List of Researchers.',
    'description' => 'Lists Researchers.',
    'file' => 'autocomplete.inc',
    'page callback' => 'islandora_content_model_forms_autocomplete_researchers',
    'access arguments' => array('view fedora collection'), // Use something fedora specific.
    'type' => MENU_CALLBACK,
  );

  $items['i_autocomplete'] = array(
    'title' => 'Auto Complete List of Institutions.',
    'description' => 'Lists Institutions.',
    'file' => 'autocomplete.inc',
    'page callback' => 'islandora_content_model_forms_autocomplete_institutions',
    'access arguments' => array('view fedora collection'), // Use something fedora specific.
    'type' => MENU_CALLBACK,
  );

  $items['ingest'] = array(
    'title' => t('Ingest'),
    'file' => 'islandora_chem_sp_blocks.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_chem_sp_ingest_form'),
    'type' => MENU_NORMAL_ITEM, //MENU_CALLBACK,
    'access arguments' => array('ingest new fedora objects'),
  );

  $items['advanced_search'] = array(
    'title' => t('Advanced search'),
    'file' => 'islandora_chem_sp_search.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_chem_sp_advanced_search_form'),
    'type' => MENU_NORMAL_ITEM, //MENU_CALLBACK,
    'access arguments' => array('view fedora collection'),
  );

  $items['advanced_search/field/add'] = array(
    'file' => 'islandora_chem_sp_search.inc',
    'page callback' => 'islandora_chem_sp_search_advanced_add_field',
    'access callback' => 'user_access',
    'access arguments' => array('view fedora collection'),
    'type' => MENU_CALLBACK,
  );

  $items['advanced_search/field/remove'] = array(
    'file' => 'islandora_chem_sp_search.inc',
    'page callback' => 'islandora_chem_sp_search_advanced_remove_field',
    'access callback' => 'user_access',
    'access arguments' => array('view fedora collection'),
    'type' => MENU_CALLBACK,
  );

  return $items;
}

function islandora_chem_sp_perm() {
  return array(
    'structure search',
  );
}

function islandora_chem_sp_cron() {
  module_load_include('inc', 'islandora_chem_sp', 'islandora_chem_sp_cron');

  islandora_chem_cron();
}

function islandora_chem_sp_download_form($form_state, $pid) {
  module_load_include('inc', 'fedora_repository', 'api/fedora_item');
  module_load_include('inc', 'islandora_chem_sp', 'FileConversion');
  $object = new Fedora_Item($pid);
  $list = $object->get_datastreams_list_as_array();
//  $ext = ltrim(strstr($list['OBJ']['MIMEType'], '-'), '-');
  $ext = system_mime_type_extension($list['OBJ']['MIMEType']);
  $fedora_url = variable_get('fedora_base_url', 'http://localhost:8080/fedora');
  $file = $fedora_url . '/objects/' . $pid . '/datastreams/OBJ/content';
  $name = str_replace(':', '-', $pid);
  header("Content-type: " . $mime);
  header("Content-disposition: attachment; filename=" . $name . '.' . $ext . ";");
  readfile($file);
  exit;
}

function islandora_chem_sp_block($op = 'list', $delta = 0, $edit = array()) {
  module_load_include('inc', 'islandora_chem_sp', 'islandora_chem_sp_search');
  module_load_include('inc', 'islandora_chem_sp', 'islandora_chem_sp_blocks');
  module_load_include('inc', 'islandora_chem_sp', 'islandora_chem_sp_home');

  switch ($op) {

    case 'list':
      $blocks[0]['info'] = t('Molecular weight search');
      $blocks[0]['cache'] = BLOCK_NO_CACHE;

      $blocks[1]['info'] = t('Ingest block');
      $blocks[1]['cache'] = BLOCK_NO_CACHE;
      
      $blocks[2]['info'] = t('My files');
      $blocks[2]['cache'] = BLOCK_NO_CACHE;
      
      $blocks[3]['info'] = t('People');
      $blocks[3]['cache'] = BLOCK_NO_CACHE;
      
      $blocks[4]['info'] = t('Groups');
      $blocks[4]['cache'] = BLOCK_NO_CACHE;

      return $blocks;

    case 'view':

      if ($delta == 0) {

        $block['subject'] = t('Molecular weight search');

        $block['content'] = drupal_get_form('islandora_chem_sp_mw_search_form');
      }
      elseif ($delta == 1) {

        $block['subject'] = t('Upload structures');

        $block['content'] = drupal_get_form('islandora_chem_sp_ingest_form');
      }
      elseif ($delta == 2) {

        $block['subject'] = t('My files');

        $block['content'] = drupal_get_form('islandora_chem_sp_object_form');
      }
      elseif ($delta == 3) {

        $block['subject'] = t('People');

        $block['content'] = drupal_get_form('islandora_chem_sp_people_form');
      }
      elseif ($delta == 4) {

        $block['subject'] = t('Groups');

        $block['content'] = drupal_get_form('islandora_chem_sp_group_form');
      }
      
      return $block;
  }
}

function islandora_chem_sp_islandora_solr_primary_display() {
  return array(
    'islandora_chem_sp' => array(
      'name' => t('Chemistry'),
      'module' => 'islandora_chem_sp',
      'file' => 'IslandoraSolrResultsChem.inc',
      'class' => "IslandoraSolrResultsChem",
      'function' => "displayResultsChem",
      'description' => t("Results displayed in a format suited for chemistry."),
    )
  );
}

/**
* Implementation of hook_form_alter().
*/
function islandora_chem_sp_form_alter(&$form, &$form_state, $form_id) {
  switch($form_id) {
    case 'user_admin_settings':
      if (is_array($form['email']) && $form['email']['#type'] == 'fieldset') {
        foreach ($form['email'] AS $key => $value) {
          if (is_array($value) && $value['#type'] == 'fieldset') {
            $form['email'][$key]['#description'] .= '<br />' . t('Also available variables are: ') . '!profile_first_name, !profile_last_name, !profile_full_name, !profile_title';
          }
        }
      }
      break;
  }
}

/**
* Implementation of hook_mail_alter().
*/
function islandora_chem_sp_mail_alter(&$message) {
  switch ($message['id']) {
    case "user_register_admin_created":
    case "user_register_no_approval_required": 
    case "user_register_pending_approval":
    case "user_password_reset": 
    case "user_status_activated":
    case "user_status_blocked":
    case "user_status_deleted":
    case "logintoboggan_register_no_approval_required":
      $token_replacements = array(
        '!profile_first_name' => $message['params']['account']->profile_firstname,
        '!profile_last_name' => $message['params']['account']->profile_lastname,
        '!profile_full_name' => $message['params']['account']->profile_firstname . ' ' . $message['params']['account']->profile_lastname,
        '!profile_title' => $message['params']['account']->profile_title,
      );
      // You can also use $message['params']['account']->uid to get more values related to the user like number of new messages (privatemsg) he/she got on the site
      $message['subject'] = strtr($message['subject'], $token_replacements);
      $message['body'][0] = strtr($message['body'][0], $token_replacements);
      break;
  }
}