scholar.module

<?php

/**
 * @file
 */
/**
 * Constants
 */
define('ISLANDORA_SCHOLAR_JOURNAL_FORM_NAME', 'Islandora Scholar Journal Form');
define('ISLANDORA_SCHOLAR_THESIS_FORM_NAME', 'Islandora Scholar Thesis Form');
define('MENU_SCHOLAR_HOME', 'scholar');
define('MENU_SCHOLAR_ADVANCED_SEARCH_ADD_FIELD', 'scholar/search/advanced/field/add');
define('MENU_SCHOLAR_ADVANCED_SEARCH_REMOVE_FIELD', 'scholar/search/advanced/field/remove');
define('THEME_SCHOLAR_HOME', 'scholar_home');
define('THEME_SCHOLAR_SEARCH_ITEM', 'scholar_search_item');
define('THEME_SCHOLAR_SEARCH_TABLE', 'scholar_search_results_table');
define('THEME_SCHOLAR_OVERVIEW_PANEL_CITATION', 'scholar_overview_panel_citation');

module_load_include('php', 'scholar', 'IrClass');

function scholar_edit_refworks($pid) {
  return drupal_get_form('scholar_edit_refworks_form', $pid);
}

function scholar_edit_refworks_form($form_state, $pid) {

  $edit_refworks_form = new IrClass();
  return $edit_refworks_form->buildRefworksEditForm($pid);
}

function scholar_edit_refworks_form_submit($form, &$form_state) {
  $irClass = new IrClass();
  $form_state['redirect'] = $irClass->updateRefworksMetaData($form_state['values']);
}

function scholar_by_name($type, $query) {
  $irClass = new IrClass();
  $user = $irClass->get_user_by_username($query);
  $output = "<h4 align='center'>$user</h4>";
  $output .= '<center><table class="table-form"><tr>' . drupal_get_form('scholar_browse_by_user_form') . '</tr></table></center>';
  $output .= scholar_custom_search($type, $query, 0);
  return $output;
}

function scholar_role($type, $query) {
  $role = $query; //
  $irClass = new IrClass();
//real bad hack to change home economics and ohters to something different (ldap groups are incorrect in ldap server so they say)
  $department = $query;

  if ('Home Economics' == $department) {
    $department = 'Family and Nutritional Sciences';
  }
  elseif ('Anatomy Physiology' == $department) {
    $department = 'Biomedical Sciences';
  }
  elseif ('Womens Studies' == $department) {
    $department = "Women's Studies";
  }
  elseif ('Path Micro' == $department) {
    $department = "Pathology and Microbiology";
  }
  elseif ('Soc Anth' == $department) {
    $department = "Sociology and Anthropology";
  }
  $output = "<h4 align='center'>$department</h4>";
  $usersArray = array();

  $results = scholar_custom_search($type, $query, 0, 0, $usersArray);
  $output .= '<center><table class="table-form"><tr>' . drupal_get_form('scholar_browse_by_user_form', $role, $usersArray) . '</tr></table></center>';

  return $output . $results;
}

function scholar_add_ir_datastream_form($form_state, $pid) {
  $datastream_form = new IrClass();
  return $datastream_form->build_add_datastream_form($pid);
}

function scholar_add_ir_datastream_form_submit($form, &$form_state) {
  $ir = new IrClass();
  $ir->addStreamFormSubmit($form_state['values']['form_id'], $form_state['values']);
}

/*
 * defines the list of paths and hooks/callbacks for the scholar module
 */

function scholar_menu() {

  $items = array();

  $items[MENU_SCHOLAR_ADVANCED_SEARCH_ADD_FIELD] = array(
    'file' => 'SearchForm.inc',
    'page callback' => 'scholar_search_advanced_add_field',
    'access callback' => 'user_access',
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK,
  );

  $items[MENU_SCHOLAR_ADVANCED_SEARCH_REMOVE_FIELD] = array(
    'file' => 'SearchForm.inc',
    'page callback' => 'scholar_search_advanced_remove_field',
    'access callback' => 'user_access',
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK,
  );

  $items['admin/settings/scholar'] = array(
    'title' => t('Islandora Scholar Settings'),
    'description' => t('Configure Islandora Scholar settings.'),
    'file' => 'includes/scholar.admin.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('scholar_admin_settings'),
    'access callback' => 'user_access',
    'access arguments' => array('administer scholar settings'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['add_users/%'] = array(
    'title' => t('Add Users'),
    'file' => 'Users.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('scholar_get_ldap_users_form', 1),
    'access callback' => 'user_access',
    'access arguments' => array('add users'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['search_users'] = array(
    'title' => t('Import Users'),
    'file' => 'Users.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('scholar_ldap_users_search_form'),
    'access callback' => 'user_access',
    'access arguments' => array('add users'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['browse_authors/%'] = array(
    'title' => t('Browse Authors'),
    'file' => 'BrowseByUserForm.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('scholar_browse_by_user_form', 1),
    'access callback' => 'user_access',
    'access arguments' => array('access content'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['browse_scholars'] = array(
    'title' => t('Scholars'),
    'file' => 'BrowseByUserForm.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_scholar_browse_by_author_form'),
    'access callback' => 'user_access',
    'access arguments' => array('access content'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['browse_scholars/%'] = array(
    'title' => t('Scholars'),
    'file' => 'BrowseByUserForm.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_scholar_browse_by_author_form', 1),
    'access callback' => 'user_access',
    'access arguments' => array('access content'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['browse_users_dept/%'] = array(
    'title' => t('Browse Users by Dept'),
    'file' => 'BrowseByUserForm.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('scholar_browse_by_user_dept_form', 1),
    'access callback' => 'user_access',
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK,
  );

  $items['browse_dept'] = array(
    'title' => t('Browse Organizations'),
    'file' => 'BrowseByDeptForm.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('scholar_browse_by_dept_form'),
    'access callback' => 'user_access',
    'access arguments' => array('access content'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['islandora_autocomplete/%/%/%'] = array(
    'title' => 'Auto Complete',
    'description' => 'Islandora autocomplete',
    'file' => 'includes/scholar.autocomplete.inc',
    'page callback' => 'islandora_autocomplete',
    'page arguments' => array(1, 2, 3),
    'access arguments' => array('view fedora collection'), // Use something fedora specific.
    'type' => MENU_CALLBACK,
  );

  $items['islandora_autocomplete/%/%'] = array(
    'title' => 'Auto Complete',
    'description' => 'Islandora autocomplete',
    'file' => 'includes/scholar.autocomplete.inc',
    'page callback' => 'islandora_autocomplete',
    'page arguments' => array(1, 2),
    'access arguments' => array('view fedora collection'), // Use something fedora specific.
    'type' => MENU_CALLBACK,
  );

  $items['rss/%'] = array(
    'title' => 'RSS feed',
    'description' => 'RSS feed',
    'file' => 'SearchForm.inc',
    'page callback' => 'scholar_rss_feed',
    'page arguments' => array(1),
    'access arguments' => array('view fedora collection'), // Use something fedora specific.
    'type' => MENU_CALLBACK,
  );

  $items['refworks_migrate'] = array(
    'title' => 'Refworks migrate',
    'description' => 'Migrate content from refworks',
    'file' => 'includes/scholar.migrate.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('scholar_migrate_refworks_form'),
    'access callback' => 'user_access',
    'access arguments' => array('migrate content'), // Use something fedora specific.
    'type' => MENU_NORMAL_ITEM,
  );

  $items['refworks_entry/%'] = array(
    'title' => 'Refworks entry',
    'description' => 'Page to display refworks entry for a given pid',
    'file' => 'refworks.inc',
    'page callback' => 'scholar_refworks_add_form',
    'page arguments' => array(1),
    'access callback' => 'user_access',
    'access arguments' => array('refworks entry'), // Use something fedora specific.
    'type' => MENU_CALLBACK,
  );

  $items['users_suggest'] = array(
    'title' => 'Users suggest',
    'description' => 'Migrate content from refworks',
    'file' => 'Users.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_scholar_researcher_compare_form'),
    'access callback' => 'user_access',
    'access arguments' => array('migrate content'), // Use something fedora specific.
    'type' => MENU_NORMAL_ITEM,
  );

  $items['scholar_associate/%'] = array(
    'title' => 'Associate citation',
    'description' => 'Associate citation with researcher and department',
    'file' => 'Users.inc',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('islandora_scholar_associate_citation_form', 1),
    'access callback' => 'user_access',
    'access arguments' => array('migrate content'), // Use something fedora specific.
    'type' => MENU_CALLBACK,
  );

  return $items;
}

/**
 * Valid permissions for this module
 * @return array An array of valid permissions for the IR module
 */
function scholar_perm() {
  return array(
    'view signature tab',
    'add scholarly research',
    'view scholarly research',
    'administer scholarly research',
    'add users',
    'migrate content',
    'refworks entry',
    'manage tracking',
    'administer scholar settings',
  );
}

/**
 * implement our own query block so we can style it
 * @return type 
 */
function scholar_islandora_solr_query_blocks() {
  return array(
    'scholar_current_query' => array(
      'name' => t('Scholar Current Query'),
      'module' => 'scholar',
      'file' => 'includes/scholar.blocks.inc',
      'class' => 'ScholarSearchResults',
      'function' => 'currentQuery',
      'form' => NULL,
    ),
  );
}

/**
 * Alter the login block to say UPEI
 * 
 * @param type $form
 * @param type $form_state
 * @param type $form_id 
 */
function scholar_form_alter(&$form, &$form_state, $form_id) {
  if ($form_id == 'user_login') {
    $form['name']['#attributes']['placeholder'] = t('Username');
    $form['pass']['#attributes']['placeholder'] = t('Password');
    $form['name']['#description'] = t('Enter your UPEI username.');
  }
}

/**
 * alter the user creation form.
 *
 * 
 */
function scholar_form_user_register_alter(&$form, &$form_state) {
  $form['scholar'] = array(
    '#type' => 'fieldset',
    '#title' => t('Scholar'),
    '#weight' => 5,
    '#collapsible' => TRUE,
    '#collapsed' => FALSE,
  );
  $form['scholar']['given_name'] = array(
    '#type' => 'textfield',
    '#title' => t('Given Name'),
    '#maxlength' => '128',
      //'#required' => TRUE,
  );
  $form['scholar']['family_name'] = array(
    '#type' => 'textfield',
    '#title' => t('Family Name'),
    '#maxlength' => '128',
      //'#required' => TRUE,
  );
  $form['scholar']['display_name'] = array(
    '#type' => 'textfield',
    '#title' => t('Display Name'),
    '#maxlength' => '128',
    // '#required' => TRUE,
    '#description' => 'Enter the name as you would like to see it displayed.  ie. John Doe.  If this field is blank then no Authority object will be created in the repository.
      A drupal user will still be created.'
  );
  $form['scholar']['date'] = array(
    '#type' => 'textfield',
    '#title' => t('Date'),
    '#maxlength' => '128',
    //'#required' => TRUE,
    '#description' => t('Birth date - death date'),
  );
  $form['scholar']['department'] = array(
    '#type' => 'textfield',
    '#title' => t('Department'),
    '#maxlength' => '128',
      //'#required' => TRUE,
  );
  $form['scholar']['position'] = array(
    '#type' => 'select',
    '#title' => t('Position'),
    '#maxlength' => '128',
    //'#required' => TRUE,
    '#options' => array(
      'EmeritusFaculty' => t('Emeritus Faculty'),
      'Emeritis Librarian' => t('Emeritus Librarian'),
      'Faculty Member' => t('Faculty Member'),
      'Librarian' => t('Librarian'),
      'NonAcademic' => t('Non Academic'),
      'Postdoc' => t('Postdoc'),
      'GraduateStudent' => t('Graduate Student'),
      'UndergraduateStudent' => t('Under Graduate Student'),
    ),
  );
  $form['scholar']['phone'] = array(
    '#type' => 'textfield',
    '#title' => t('Phone'),
    '#maxlength' => '128',
      //'#required' => TRUE,
  );
  $form['scholar']['start_date'] = array(
    '#type' => 'date',
    '#title' => t('Start Date at UPEI'),
    '#required' => TRUE,
  );
  $form['scholar']['end_date'] = array(
    '#type' => 'date',
    '#title' => t('End Date at UPEI'),
      //'#required' => TRUE,
  );
  $form['scholar']['scholar_status'] = array(
    '#type' => 'select',
    '#title' => t('Status'),
    '#options' => array(
      'Current' => t('Current'),
      'Retired' => t('Retired'),
      'Other' => t('Other'),
    ),
  );
  $form['scholar']['notes'] = array(
    '#type' => 'textarea',
    '#title' => t('Notes'),
    '#maxlength' => '128',
      //'#required' => TRUE,
  );
  $form['scholar']['url'] = array(
    '#type' => 'textfield',
    '#title' => t('URL'),
    '#maxlength' => '255',
      //'#required' => TRUE,
  );
//$form['#validate'][] = 'scholar_add_user_to_fedora_validate';
  $form['#submit'][] = 'scholar_add_user_to_fedora';
}

//function scholar_add_user_to_fedora_validate(&$form, &$form_state) {
//}

function scholar_add_user_to_fedora(&$form, &$form_state) {
  module_load_include('inc', 'scholar', 'includes/scholar.user');
  scholar_create_user_object($form, $form_state);
}

function scholar_uninstall() {
  return drupal_uninstall_schema('scholar');
}

// end function scholar_uninstall

function fedora_repository_scholar_settings_page() {
  
}

/**
 * Function specifying all of the required objects and database
 * entries for Fedora/Islandora
 * @return type 
 */
function scholar_required_fedora_objects() {

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

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

  $result2 = db_result(db_query('Select content_model from {islandora_content_model_forms} where  content_model = "%s" and form_name = "%s"', 'islandora:researcherCModel', 'Islandora Scholar MADS Form'));
  if (!$result2) {
    $object2 = new stdClass();
    $object2->content_model = 'islandora:researcherCModel';
    $object2->form_name = 'Islandora Scholar 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(
    'scholar' => array(
      'module' => 'scholar',
      'title' => 'Islandora Scholar Module',
      'objects' => array(
        array(
          'pid' => 'ir:scholar',
          'label' => 'Institutional Repository',
          'cmodel' => 'islandora:collectionCModel',
//          'parent' => variable_get('fedora_repository_pid', 'islandora:root'),
          'datastreams' => array(
            array(
              'dsid' => 'TN',
              'datastream_file' => "$module_path/images/Crystal_Clear_filesystem_folder_grey.png",
              'mimetype' => 'image/png',
            ),
            array(
              'dsid' => 'COLLECTION_POLICY',
              'datastream_file' => "$module_path/xml/COLLECTION-COLLECTION POLICY.xml",
            ),
          ),
        ),
        array(
          'pid' => 'islandora:citationCModel',
          'label' => 'Islandora Scholar Citation Content Model',
          'dsid' => 'ISLANDORACM',
          'datastream_file' => "$module_path/models/citationCModel.xml",
          'cmodel' => 'fedora-system:ContentModel-3.0',
        ),
        array(
          'pid' => 'islandora:thesisCModel',
          'label' => 'Islandora Scholar Thesis Content Model',
          'dsid' => 'ISLANDORACM',
          'datastream_file' => "$module_path/models/thesisCModel.xml",
          'cmodel' => 'fedora-system:ContentModel-3.0',
        ),
        array(
          'pid' => 'islandora:researcherCModel',
          'label' => 'Islandora Scholar Authority Content Model',
          'dsid' => 'ISLANDORACM',
          'datastream_file' => "$module_path/models/researcherCModel.xml",
          'cmodel' => 'fedora-system:ContentModel-3.0',
        ),
        array(
          'pid' => 'islandora:departmentCModel',
          'label' => 'Islandora Scholar Department Content Model',
          'dsid' => 'ISLANDORACM',
          'datastream_file' => "$module_path/models/departmentCModel.xml",
          'cmodel' => 'fedora-system:ContentModel-3.0',
        ),
        array(
          'pid' => 'ir:citationCollection',
          'label' => 'Citation Collection',
          'cmodel' => 'islandora:collectionCModel',
          'parent' => 'ir:scholar',
          'datastreams' => array(
            array(
              'dsid' => 'TN',
              'datastream_file' => "$module_path/images/Crystal_Clear_filesystem_folder_grey.png",
              'mimetype' => 'image/png',
            ),
            array(
              'dsid' => 'COLLECTION_POLICY',
              'datastream_file' => "$module_path/xml/CITATION-COLLECTION POLICY.xml",
            ),
            array(
              'dsid' => 'COLLECTION_VIEW',
              'datastream_file' => "$module_path/xsl/citation_collection_view.xsl",
            ),
          ),
        ),
        array(
          'pid' => 'ir:thesisCollection',
          'label' => 'Thesis Collection',
          'cmodel' => 'islandora:collectionCModel',
          'parent' => 'ir:scholar',
          'datastreams' => array(
            array(
              'dsid' => 'TN',
              'datastream_file' => "$module_path/images/Crystal_Clear_filesystem_folder_grey.png",
              'mimetype' => 'image/png',
            ),
            array(
              'dsid' => 'COLLECTION_POLICY',
              'datastream_file' => "$module_path/xml/THESIS-COLLECTION POLICY.xml",
            ),
            array(
              'dsid' => 'CHILD_SECURITY',
              'datastream_file' => "$module_path/xacml/both-embargo.xml",
            ),
          ),
        ),
        array(
          'pid' => 'ir:authorityCollection',
          'label' => 'IR Authority Collection',
          'cmodel' => 'islandora:collectionCModel',
          'parent' => 'ir:scholar',
          'datastreams' => array(
            array(
              'dsid' => 'TN',
              'datastream_file' => "$module_path/images/Crystal_Clear_filesystem_folder_grey.png",
              'mimetype' => 'image/png',
            ),
            array(
              'dsid' => 'COLLECTION_POLICY',
              'datastream_file' => "$module_path/xml/AUTHORITY-COLLECTION POLICY.xml",
            ),
          ),
        ),
      ),
    ),
  );
}

function scholar_form_fedora_repository_ingest_form_alter(array &$form, array &$form_state) {
  if ($form_state['storage']['step'] == 1 && isset($form['indicator'])) {
    $models = array('islandora:citationCModel/ISLANDORACM');
    $show_bulk_ingest = FALSE;
    foreach ($form['indicator']['models']['#options'] as $model => $label) {
      if (array_search($model, $models) !== FALSE) {
        $show_bulk_ingest = TRUE;
      }
    }
    if ($show_bulk_ingest) {
      $bulk_ingest = scholar_bulk_ingest_form($form_state, $form['collection_pid']['#value']);
// Move the next button within the field set to make it clearer.
      $form['indicator']['submit'] = $form['submit'];
      unset($form['submit']);
      array_unshift($form, $bulk_ingest);
      $form['#attributes'] = array('enctype' => 'multipart/form-data'); // Allow the uploading of files.
      $form['#validate'] = array('scholar_bulk_ingest_form_validate');
    }
  }
//add a handler so we can update the rels-ext
  $form['#submit'][] = 'scholar_auto_associate';
}

function scholar_auto_associate(&$form, &$form_state) {
  module_load_include('inc', 'fedora_repository', 'api/fedora_item');
  $item = new Fedora_Item($form_state['values']['pid']);
  if (!empty($form_state['values']['identifier_u1_tags'])) {
    foreach ($form_state['values']['identifier_u1_tags'] as $user) {
// add a rels relationship
//add_relationship($relationship, $object, $namespaceURI = RELS_EXT_URI, $literal_value = RELS_TYPE_URI) {
      $item->add_relationship('hasResearcher', $user['identifier_u1'], 'info:fedora/fedora-system:def/relations-external#');
    }
  }
  if (!empty($form_state['values']['identifier_u2_tags'])) {
    foreach ($form_state['values']['identifier_u2_tags'] as $department) {
// add a rels relationship
      $value = str_replace(' ', '_', $department['identifier_u2']);
      $item->add_relationship('hasDepartment', $value, 'info:fedora/fedora-system:def/relations-external#');
    }
  }
}

/**
 * Performs a bulk ingestion.
 * 
 * This is not meant to be called from drupal_get_form, 
 * this is a sub-form that part of the content_model_viewer_ingest_metadata
 * 
 * @param array $form_state
 *   The Drupal form state.
 * @param string $collection_pid 
 *   The pid of the collection we will ingest into.
 * 
 * @return array
 *   The Drupal form.
 */
function scholar_bulk_ingest_form(array &$form_state, $collection_pid) {
  $path = drupal_get_path('module', 'scholar');
  drupal_add_js("$path/js/islandora_scholar.js");
  drupal_add_css("$path/css/scholar.css");
  $potential_models = scholar_bulk_ingest_get_potential_models($collection_pid);
  reset($potential_models);
  $identifier = key($potential_models);
  $selected_model = isset($form_state['values']['models']) ? $form_state['values']['models'] : $identifier;
  $markup = '<div id = "scholar_choice_buttons">';
  $markup .= '<button id = "single" class = "scholar_button">Create Single Citation</button><br />';
  $markup .= '<button id = "RIS" class = "scholar_button">RIS, Endnote or RefWorks</button><br />';
  $markup .= '<button id = "PUBMD" class = "scholar_button">Import using PMIDs</button><br />';
  $markup .= '<button id = "DOI" class = "scholar_button">Import using DOIs</button>';

  $form['buttons'] = array(
    '#type' => 'markup',
    '#value' => $markup,
    '#attributes' => array('class' => 'myclass')
  );
  $form['bulk_ingest'] = array(
    '#type' => 'fieldset',
    '#title' => t('Ingest digital objects generated by RIS, EndNote or RefWorks into collection_pid Step #1', array('collection_pid' => $collection_pid)),
    '#attributes' => array('id' => 'bulk_ingest', 'class' => 'scholar_choice'),
    'file' => array(
      '#type' => 'file',
      '#title' => t('Upload "RIS", "EndNote XML" or "RefWorks XML" Document'),
      '#description' => t('A RIS, EndNote XML, or RefWorks XML document that will generate multiple digital objects on ingest. One for each record within the RIS, EndNote XML, or RefWorks document.'),
      '#element_validate' => array('scholar_bulk_ingest_file_upload_validate'),
    ),
    'content_model_pid' => array(
      '#type' => 'select',
      '#title' => t('Content models available'),
      '#options' => $potential_models,
      '#default_value' => $selected_model,
      '#description' => t('Content models define datastream composition, relationships between this and other content models, and the mandatory behaviors associated with each digital object.<br /> Additional information may be found <a href="https://wiki.duraspace.org/display/FEDORACREATE/Content+Models+Overview">here.</a> '),
    ),
    'submit' => array(
      '#type' => 'submit',
      '#executes_submit_callback' => TRUE,
      '#submit' => array('scholar_bulk_ingest_form_submit'),
      '#value' => t('Create objects from document.'),
      '#attributes' => array('class' => 'file_submit', 'source' => 'ris'),
    ),
  );

  // Harvest records from pubmed.
  $form['pubmed'] = array(
    '#type' => 'fieldset',
    '#title' => t('Pubmed IDs'),
    '#description' => t('A list Pubmed IDs.'),
    '#attributes' => array('id' => 'pubmed', 'class' => 'scholar_choice'),
  );

  $form['pubmed']['pubmed_file'] = array(
    '#type' => 'file',
    '#title' => t('Pubmed Batch Importer'),
    '#description' => t("Give either a list of Pubmed IDs in a file, or enter the list in the textarea. In either case, the items in the list should be separated by either whitespace or commas (or some combination thereof)."),
    '#element_validate' => array('scholar_bulk_ingest_file_upload_validate'),
  );

  $form['pubmed']['pubmed_list'] = array(
    '#type' => 'textarea',
    '#title' => t('Pubmed IDs'),
    '#description' => t('A list Pubmed IDs.'),
    '#element_validate' => array('scholar_bulk_ingest_file_upload_validate'),
  );
  $form['pubmed']['submit'] = array(
    '#type' => 'submit',
    '#executes_submit_callback' => TRUE,
    '#submit' => array('scholar_bulk_ingest_form_submit'),
    '#value' => t('Create Pubmed Objects'),
    '#attributes' => array('class' => 'file_submit', 'source' => 'pubmed'),
  );

  // Harvest records from DOI
  $form['doi'] = array(
    '#type' => 'fieldset',
    '#title' => t('DOI IDs'),
    '#description' => t('A list DOI IDs.'),
    '#attributes' => array('id' => 'doi', 'class' => 'scholar_choice'),
  );

  $form['doi']['doi_file'] = array(
    '#type' => 'file',
    '#title' => t('DOI Batch Importer'),
    '#description' => t('Provide either a list of Digital Object Identifiers in a file, or enter DOIs in the textarea below. In either case, the DOIs in the list should be separated by either whitespace or commas (or some combination thereof). NOTE: Presently, only journal (articles) are supported.'),
    '#element_validate' => array('scholar_bulk_ingest_file_upload_validate'),
  );

  $form['doi']['doi_list'] = array(
    '#type' => 'textarea',
    '#title' => t('DOI IDs'),
    '#description' => t('Provide a list Digital Object Identifiers (DOI) - eg. 10.1016/j.jorganchem.2011.11.018, 10.1016/j.tiv.2011.10.017, 10.1111/j.1540-4560.2012.01733.x '),
    '#element_validate' => array('scholar_bulk_ingest_file_upload_validate'),
  );
  $form['doi']['submit'] = array(
    '#type' => 'submit',
    '#executes_submit_callback' => TRUE,
    '#submit' => array('scholar_bulk_ingest_form_submit'),
    '#value' => t('Create DOI Objects'),
    '#attributes' => array('class' => 'file_submit', 'source' => 'doi'),
  );


  return $form;
}

/**
 * Get Potential Models that can be part of the given collection.
 * 
 * @param string $collection_pid
 *   The pid of the collection.
 * @return array
 *   Where the key is the Content Model PID and the value is the human readable name for the Content Model.
 */
function scholar_bulk_ingest_get_potential_models($collection_pid) {
  if (($collection_policy = CollectionPolicy::loadFromCollection($collection_pid)) === FALSE) {
    drupal_set_message(t("Unable to load collection policy '@collection_pid'", array('@collection_pid' => $collection_pid)));
    return FALSE;
  }
  if (!($content_models = $collection_policy->getContentModels())) {
    drupal_set_message(t('No content models associated with this collection: @collection_pid. Please contact your administrator.', array('@collection_pid' => $collection_pid)), 'error');
    return FALSE;
  }
  $potential_models = array();
  foreach ($content_models as $content_model) {
    $identifier = $content_model->getIdentifier();
    $pid = $content_model->getPidFromIdentifier($identifier);
    $name = $content_model->name;
    $potential_models["$pid"] = "$name";
  }
  unset($potential_models['islandora:contentCModel']);
  return $potential_models;
}

/**
 * Over writes the default 'content_model_viewer_ingest_metadata_form_validate' function.
 * 
 * @param array $form
 *   The Drupal form.
 * @param array $form_state 
 *   The Drupal form state.
 */
function scholar_bulk_ingest_form_validate(array &$form, array &$form_state) {

  $bulk_ingest_clicked = $form_state['clicked_button']['#attributes']['class'] == 'file_submit';
  if (!$bulk_ingest_clicked) {
    if ($form_state['storage']['step'] == 1) {
      $form_state['storage']['step']++;
      $form_state['rebuild'] = TRUE;
    }
    else {
      module_load_include('inc', 'xml_form_api', 'XMLForm');
      $xml_form = new XMLForm($form_state);
      $xml_form->validate($form, $form_state);
    }
  }
}

/**
 * Makes sure the file was uploaded and is of the right type.
 * 
 * @param array $element
 *   The file upload field
 * @param array $form_state 
 *   The Drupal form state.
 */
function scholar_bulk_ingest_file_upload_validate(array $element, array &$form_state) {
  if ($form_state['clicked_button']['#attributes']['source'] == 'pubmed') {
    if (!isset($_FILES['files']['name']['pubmed_file']) && $form_state['values']['pubmed_list'] == '' && $element['#title'] == "DOI Batch Importer") {
      form_error($element, t("You must either add a file or input one or more pubmed id's."));
      $path = drupal_get_path('module', 'scholar');
      drupal_add_js("$path/js/islandora_scholar.js");
    }
    return;
  }
  if ($form_state['clicked_button']['#attributes']['source'] == 'doi') {
    if (!isset($_FILES['files']['name']['doi_file']) && $form_state['values']['doi_list'] == '' && $element['#title'] == "Pubmed Batch Importer") {
      form_error($element, t("You must either add a file or input one or more pubmed id's."));
      $path = drupal_get_path('module', 'scholar');
      drupal_add_js("$path/js/islandora_scholar.js");
    }
    return;
  }

  module_load_include('inc', 'fedora_repository', 'MimeClass');
  $bulk_ingest_clicked = $form_state['clicked_button']['#attributes']['class'] == 'file_submit';
  $file_uploaded = isset($_FILES['files']['error']['file']) && $_FILES['files']['error']['file'] == 0;
  if ($bulk_ingest_clicked) {
    if (!$file_uploaded) {
      form_error($element, t('You must upload a "RIS" or "EndNote XML" document.'));
    }
    else { // Only support for one file.
//      $mime_type = $_FILES['files']['type']['file'];
      $file = file_save_upload('file');
      $filename = $file->filepath;
      $mime = new MimeClass();
      $mime_type = $mime->get_mimetype($filename);
      $valid_types = array('text/xml', 'text/plain', 'application/x-research-info-systems');
      if (array_search($mime_type, $valid_types) === FALSE) {
        form_error($element, t('The upload file is not the correct type. You must upload a "RIS" or "EndNote XML" document.'));
      }
    }
  }
}

/**
 * Bulk Ingest object.
 * 
 * @param array $form
 *   The Drupal form.
 * @param array $form_state 
 *   The Drupal form state.
 */
function scholar_bulk_ingest_form_submit(array &$form, array &$form_state) {
  module_load_include('inc', 'fedora_repository', 'MimeClass');
  $collection_pid = $form_state['values']['collection_pid'];
  $content_model_pid = $form_state['values']['content_model_pid'];
  // Build full pubmed list from textfield and/or file.
  $contents_as_string = '';
  if ($form_state['clicked_button']['#attributes']['source'] == 'pubmed') {
// From the textarea
    if ($form_state['values']['pubmed_list'] != '') {
      $contents_as_string .= $form_state['values']['pubmed_list'] . ' ';
    }
    if (!empty($_FILES['files']['name']['pubmed_file'])) {
      $file = file_save_upload('pubmed_file');
      $contents_as_string .= file_get_contents($file->filepath);
    }
    $pubmed_list_ids = preg_split('/[\s,]+/', $contents_as_string, NULL, PREG_SPLIT_NO_EMPTY);
    $context = array();
    foreach ($pubmed_list_ids as $id) {
      $operations[] = array(islandora_scholar_build_pubmed_object, array(trim($id)), $context);
    }
    $batch = array(
      'title' => t('Ingesting PUBMED Files'),
      'operations' => $operations,
      'file' => drupal_get_path('module', 'scholar') . '/Batch.inc',
      'finished' => 'islandora_scholar_build_pubmed_object_finished',
    );

    batch_set($batch);
    unset($form_state['storage']);
    return;
  }

  // Build full DOI list from textfield and/or file.
  if ($form_state['clicked_button']['#attributes']['source'] == 'doi') {
// From the textarea
    if ($form_state['values']['doi_list'] != '') {
      $contents_as_string .= $form_state['values']['doi_list'] . ' ';
    }
    if (!empty($_FILES['files']['name']['doi_file'])) {
      $file = file_save_upload('doi_file');
      $contents_as_string .= file_get_contents($file->filepath);
    }
    $doi_list_ids = preg_split('/[\s,]+/',  $contents_as_string, NULL, PREG_SPLIT_NO_EMPTY);
    $context = array();
    foreach ($doi_list_ids as $id) {
      $operations[] = array(islandora_scholar_build_doi_object, array(trim($id)), $context);
    }
    $batch = array(
      'title' => t('Ingesting DOI Files'),
      'operations' => $operations,
      'file' => drupal_get_path('module', 'scholar') . '/Batch.inc',
      'finished' => 'islandora_scholar_build_doi_object_finished',
    );

    batch_set($batch);
    unset($form_state['storage']);
    return;
  }

  $file = file_save_upload('file');
  $filename = $file->filepath;
  $mime = new MimeClass();
  $mime_type = $mime->get_mimetype($filename);
//need to inspect this to see if it is refworks or end note
  $doc = new DOMDocument();
  $raw_xml = file_get_contents($filename);
  $xml = trim($raw_xml); //refworks has a nasty habit of outputing an xml file with 
// the xml declartion being the second line, the first line being blank
  $success = $doc->loadXML($xml);
  $root = $doc->documentElement;
  $nodeName = $root->nodeName;
  if ($success && $root->nodeName == 'refworks') {
    $function = 'scholar_batch_ingest_refworks_document';
  }
  else {
    $function = ($mime_type == 'text/xml') ? 'scholar_batch_ingest_endnote_document' : 'scholar_batch_ingest_ris_document';
  }
  $operations = array(
    array($function, array($filename, $collection_pid, $content_model_pid))
  );
  $batch = array(
    'title' => t('Ingesting Files'),
    'operations' => $operations,
    'file' => drupal_get_path('module', 'scholar') . '/Batch.inc',
  );
  batch_set($batch);
  unset($form_state['storage']); // Return to the viewer.  
}

/**
 * Implementation of solr_primary_display hook to customise the results
 * display.
 * @return type 
 */
function scholar_islandora_solr_primary_display() {
  return array(
    'scholar' => array(
      'name' => t('Scholar'),
      'module' => 'scholar',
      'file' => 'SolrResultsScholar.inc',
      'class' => "ScholarSolrResults",
      'function' => "displayResultsScholar",
      'description' => t("Results displayed for Islandscholar."),
    )
  );
}

function scholar_block($op = 'list', $delta = 0, $edit = array()) {
  module_load_include('inc', 'scholar', 'includes/scholar.blocks');
  switch ($op) {

    case 'list':
      $blocks[0]['info'] = t('Recently added items');
      $blocks[0]['cache'] = BLOCK_NO_CACHE;

      $blocks[1]['info'] = t('Total records added');
      $blocks[1]['cache'] = BLOCK_NO_CACHE;

      $blocks[2]['info'] = t('Total citation views');
      $blocks[2]['cache'] = BLOCK_NO_CACHE;

      $blocks[3]['info'] = t('Total full-text downloads');
      $blocks[3]['cache'] = BLOCK_NO_CACHE;

      $blocks[4]['info'] = t('Top viewed citations');
      $blocks[4]['cache'] = BLOCK_NO_CACHE;

      $blocks[5]['info'] = t('Random citation');
      $blocks[5]['cache'] = BLOCK_NO_CACHE;

//$blocks[6]['info'] = t('Scholar Scrape');
//$blocks[6]['cache'] = BLOCK_NO_CACHE;

      return $blocks;

    case 'view':

      if ($delta == 0) {

        $block['subject'] = t('Recently added items');

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

        $block['subject'] = t('Total records added');

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

        $block['subject'] = t('Total citation views');

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

        $block['subject'] = t('Total full-text downloads');

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

        $block['subject'] = t('Top viewed citations');

        $block['content'] = drupal_get_form('scholar_top_viewed');
      }
      elseif ($delta == 5) {

        $block['subject'] = t('Random citation');

        $block['content'] = drupal_get_form('scholar_random_citation');
      }
      /* elseif ($delta == 6) {

        $block['subject'] = t('Scholar Scrape');

        $block['content'] = scholar_scrape_get_content();
        } */

      return $block;
  }
}

function scholar_cron() {
  module_load_include('inc', 'scholar', 'includes/scholar.cron');
  scholar_cron_embargo_check();
  scholar_cron_citations_update();
}

/**
 * 
 */
function scholar_form_islandora_extended_search_form_alter(&$form, &$form_state) {
  module_load_include('inc', 'scholar', 'includes/scholar.query');
  $form['terms']['#prefix'] = '<div id="islandora-extended-search-terms">';
//unset($form['terms']['#suffix']);
  $query = 'select $object $title
    from <#ri>
    where $object <info:fedora/fedora-system:def/model#label> $title
    and $object <fedora-rels-ext:isMemberOfCollection> <info:fedora/ir:scholarCollection>';
  $options = islandora_scholar_query($query, TRUE);
  $options['AAAA'] = 'Any'; //we want any to show up first
  ksort($options);
//override the score fields to match our solr index.
  $score_fields = array(
    'score' => 'Relevance',
    'mods_title_sv' => 'Title',
    'mods_date_issued_dt' => 'Date',
  );
  $form['controls']['sort']['#options'] = $score_fields;

  $form['collections'] = array(
    '#type' => 'select',
    '#title' => t('Collection'),
    '#options' => $options,
    '#weight' => 0,
  );
//we are overriding the orginal handler so we can append to the query
  $form['#submit'][0] = 'islandora_scholar_handle_search';
}

/**
 * get a list of collections to display in a dropdown. 
 */
function islandora_scholar_handle_search(&$form, &$form_state) {
  module_load_include('inc', 'scholar', 'includes/scholar.blocks');
  $_SESSION['islandora_extended_search']['values'] = $form_state['values'];
//$_SESSION['islandora_extended_search']['sort'] = $form_state['values']['sort'];
//$_SESSION['islandora_extended_search']['order'] = $form_state['values']['order'];
  $query = scholar_extended_search_form_build_query($form_state);
  $collection = $form_state['values']['collections'];

  if ($collection != 'AAAA') {
//TODO fix temporary hack here
    if ($collection == "Faculty/Staff Works") {
      $collection = "Institutional Repository Collection";
    }
    $query .= " AND collection_title:" . "(\"$collection\")";
  }
  $collection = scholar_escape_phrase($collection);
  $sort_field = check_plain($form_state['values']['sort']);
  $sort_dir = check_plain($form_state['values']['order']);
  $query = urlencode($query);
  $sort = array("sort" => "$sort_field $sort_dir"); //"?sort=$sort_field%20$sort_dir";
  drupal_goto("islandora/solr/search/$query", $sort);
//$form_state['redirect'] = 'islandora/solr/search/' . $query; // Redirect to the search.
}

function scholar_theme() {
  return array(
    'scholar' => array(
      'template' => 'templates/scholar',
      'file' => 'scholar.inc',
      'arguments' => array(
        'pid' => NULL,
        'type' => 'citation',
      ),
    ),
    'supplemental' => array(
      'template' => 'templates/supplemental',
      'file' => 'scholar.inc',
      'arguments' => array(
        'pid' => NULL,
      ),
    ),
    'tracking' => array(
      'template' => 'templates/tracking',
      'file' => 'scholar.inc',
      'arguments' => array(
        'pid' => NULL,
        'dsid' => NULL,
      ),
    ),
    'scholar_profile' => array(
      'template' => 'templates/profile',
      'file' => 'scholar.inc',
      'arguments' => array(
        'vars' => NULL,
      ),
    ),
  );
}