<?php
/**
 * Copyright 2012(c) OBiBa, All rights reserved.
 *
 * This program and the accompanying materials are made available under the terms of the GNU Public License v3.0.
 * You should have received a copy of the GNU General Public License along with
 * this program. If not, see <http://www.gnu.org/licenses/>.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
 * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
 * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
 * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
 * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
 * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
 * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */
/**
 * @file
 * Code for the mica_studies feature.
 */

require_once('mica_studies.features.inc');

/**
 * Implements hook_menu().
 */
function mica_studies_menu() {
  $items = array();
  $items['export'] = array(
    'title' => 'Export',
    'page callback' => 'mica_studies_export_page',
    'access callback' => 'mica_studies_export_page_access',
    'file' => 'mica_studies.pages.inc',
  );
  return $items;
}

/**
 * Implements hook_menu_local_tasks_alter().
 */
function mica_studies_menu_local_tasks_alter(&$data, $router_item, $root_path) {
  $links = array();

  switch ($root_path) {
    case 'studies':
      if (node_access('create', 'study')) {
        $node_type = node_type_load('study');
        $links['add-study'] = array(
          '#theme' => 'menu_local_action',
          '#link' => array(
            'title' => t('Add a !name', array('!name' => $node_type->name)),
            'href' => 'node/add/study',
          ),
        );
      }
      $links['search-studies'] = array(
        '#weight' => 30,
        '#theme' => 'menu_local_action',
        '#link' => array(
          'title' => t('<a class="highlight" href="@url">!name</a>',
            array('!name' => t('Search cohorts'), '@url' => url('studies-search'))
          ),
          'localized_options' => array('html' => TRUE),
        ),
      );
      break;

    case 'documents':
      if (node_access('create', 'documents')) {
        $links['add-documents'] = array(
          '#theme' => 'menu_local_action',
          '#link' => array(
            'title' => t('Add some Documents'),
            'href' => 'node/add/documents',
          ),
        );
      }
      break;
  }

  $data['actions']['output'] = array_merge($data['actions']['output'], $links);
}

/**
 * Implements feeds_permission().
 */
function mica_studies_permission() {
  $perms = array(
    'export data' => array(
      'title' => t('Export Data'),
      'description' => t('Allow exportation of data.')
    ),
  );
  return $perms;
}

/**
 * Menu access callback.
 */
function mica_studies_export_page_access() {
  return user_access('export data');
}

/**
 * Implements hook_node_insert()
 */
function mica_studies_node_insert($node) {
  if ($node->type === 'study') {
    mica_core_create_node_default_menu($node, TRUE, FALSE, 0, 'studies');
  }
}

/**
 * Implements hook_node_view()
 */
function mica_studies_node_view($node, $view_mode, $langcode) {
  switch ($node->type) {
    case 'study':
      _mica_studies_study_view($node, $view_mode, $langcode);
      break;
    case 'contact':
      _mica_studies_contact_view($node, $view_mode, $langcode);
      break;
  }
}

function _mica_studies_study_view($node, $view_mode, $langcode) {
  if ($view_mode === 'full') return;

  // Show moderation state messages if we're on a node page.
  if (node_is_page($node) && $view_mode === 'banner_area' && empty($node->in_preview)) {
    workbench_moderation_messages('view', $node);
  }

  $wrapper = entity_metadata_wrapper('node', $node);

  $bindings = array(
    'field_design_other_sp' => array(
      'field' => 'field_design',
      'key' => 'other',
      'label_as_prefix' => FALSE,
      'enclosed' => FALSE,
    ),
    'field_recruitment_other_sp' => array(
      'field' => 'field_recruitment',
      'key' => 'other',
      'label_as_prefix' => FALSE,
      'enclosed' => FALSE,
    ),
    'field_current_part_nb_date' => array(
      'field' => 'field_current_participants_nb',
      'key' => 0, // To specify to add the specified field to the first item
      'label_as_prefix' => TRUE,
    ),
    'field_current_samples_date' => array(
      'field' => 'field_current_samples_nb',
      'key' => 0,
      'label_as_prefix' => TRUE,
    ),
    'field_recruitment_other' => array(
      'field' => 'field_recruitment_sources',
      'key' => 'other',
      'label_as_prefix' => FALSE,
      'enclosed' => FALSE,
    ),
    'field_data_sources_sp' => array(
      'field' => 'field_data_sources',
      'key' => 'others',
      'label_as_prefix' => FALSE,
      'enclosed' => FALSE,
    ),
    'field_tissues_sp' => array(
      'field' => 'field_bio_samples_management',
      'key' => 'tissues',
      'label_as_prefix' => FALSE,
      'enclosed' => FALSE,
    ),
    'field_samples_man_other_sp' => array(
      'field' => 'field_bio_samples_management',
      'key' => 'others',
      'label_as_prefix' => FALSE,
      'enclosed' => FALSE,
    ),
    'field_access_other_sp' => array(
      'field' => 'field_access_other',
      'key' => '1',
      'label_as_prefix' => FALSE,
      'enclosed' => FALSE,
    ),
  );

  _mica_bind_other_specify($node, $bindings);

  $status_dates = array(
    'field_preparation_start_year' => 'field_preparation_end_year',
    'field_baseline_start_year' => 'field_baseline_end_year',
    'field_followup_start_year' => 'field_followup_end_year',
  );
  _mica_studies_display_status_dates($node, $status_dates);

  $fields = array(
    'field_target_number_participants',
    'field_target_number_biosamples',
    'field_current_participants_nb',
    'field_current_samples_nb',
  );
  _mica_remove_suffix($node, $fields);

  $bindings = array(
    'field_no_limits_participants' => 'field_target_number_participants',
    'field_no_limits_samples' => 'field_target_number_biosamples',
  );
  _mica_remove_exclusive_fields($node, $bindings);

  // Hide the fields "No limits in the number of..." when they are false
  if (isset($node->content['field_no_limits_participants']) && isset($node->content['field_no_limits_participants']['#items'])) {
    if ($node->content['field_no_limits_participants']['#items'][0]['value']) {
      $node->content['field_no_limits_participants'][0]['#markup'] = $node->content['field_no_limits_participants']['#title'];
    }
    else {
      $node->content['field_no_limits_participants']['#access'] = FALSE;
    }
  }
  if (isset($node->content['field_no_limits_samples']) && isset($node->content['field_no_limits_samples']['#items'])) {
    if ($node->content['field_no_limits_samples']['#items'][0]['value']) {
      $node->content['field_no_limits_samples'][0]['#markup'] = $node->content['field_no_limits_samples']['#title'];
    }
    else {
      $node->content['field_no_limits_samples']['#access'] = FALSE;
    }
  }

  // selection criteria
  _mica_studies_study_view_selection_criteria($node, $view_mode, $langcode, $wrapper);

  // authorization fields
  _mica_studies_study_view_authorization($node, $view_mode, $langcode, $wrapper);

}

function _mica_studies_contact_view($node, $view_mode, $langcode) {
  $wrapper = entity_metadata_wrapper('node', $node);
  $node->content['field_daco']['#access'] = $wrapper->field_daco->value();
}

function _mica_studies_study_view_selection_criteria(&$node, $view_mode, $langcode, $wrapper) {
  if (isset($node->content['#groups']['group_participants_selection'])
    && $node->content['#groups']['group_participants_selection']->format_type !== 'hidden') {

    if (!isset($node->content['field_select_criteria'])) {
      // create empty field_select_criteria if it has no values
      // Load instance of the field for the node.
      $instances = _field_invoke_get_instances('node', $node->type, array(
        'field_name' => 'field_select_criteria',
        'default' => TRUE,
        'deleted' => FALSE));
      $select_criteria_instance = $instances[0];
      $display_mode = $node->content['#groups']['group_participants_selection']->mode;
      $display = field_get_display($select_criteria_instance, $display_mode, $node);
      $select_criteria_info = field_info_field('field_select_criteria');
      $node->content['field_select_criteria'] = array(
        '#theme' => 'field',
        '#title' => $select_criteria_instance['label'],
        '#label_display' => 'above',
        '#field_type' => $select_criteria_info['type'],
        '#field_name' => $select_criteria_instance['field_name'],
        '#bundle' => $node->type,
        '#object' => $node,
        '#items' => array(),
        '#entity_type' => 'node',
        '#weight' => $display['weight'],
        0 => array('#markup' => ''),
      );
    }

    _mica_studies_study_view_selection_criteria_item($node, $wrapper, 'field_gender', 'Gender:');

    if (isset($node->content['field_age_min']) || isset($node->content['field_age_max'])) {
      $index = count($node->content['field_select_criteria']['#items']);
      $age_min = $wrapper->field_age_min->value();
      $age_max = $wrapper->field_age_max->value();
      if (!empty($age_min) || !empty($age_max)) {
        $age_items = array();
        $age_markup = '';
        if (!empty($age_min)) {
          $age_items['age_min'] = $node->content['field_age_min']['#items'][0];
          $age_markup .= t('minimum') . ' ' . $node->content['field_age_min'][0]['#markup'];
        }
        if (!empty($age_max)) {
          if (!empty($age_min)) $age_markup .= ', ';
          $age_items['age_max'] = $node->content['field_age_max']['#items'][0];
          $age_markup .= t('maximum') . ' ' . $node->content['field_age_max'][0]['#markup'];
        }
        $node->content['field_age_max']['#access'] = FALSE;
        $node->content['field_age_min']['#access'] = FALSE;
        $node->content['field_select_criteria']['#items'][$index] = $age_items;
        $node->content['field_select_criteria'][$index++]['#markup'] = t('Age:') . '<br />&nbsp;&nbsp;&nbsp;&nbsp;'
          . ucfirst($age_markup);
      }
    }

    _mica_studies_study_view_selection_criteria_item($node, $wrapper, 'field_country', 'Country:', 'Countries:');
    _mica_studies_study_view_selection_criteria_item($node, $wrapper, 'field_territory', 'Territory:', 'Territories:');
    _mica_studies_study_view_selection_criteria_item($node, $wrapper, 'field_ethnic_origin', 'Ethnic origin:', 'Ethnic origins:');
    _mica_studies_study_view_selection_criteria_item($node, $wrapper, 'field_health_status', 'Health status:');
    _mica_studies_study_view_selection_criteria_item($node, $wrapper, 'field_selection_others_sp', 'Other:');

    if (strlen($node->content['field_select_criteria'][0]['#markup']) === 0) {
      $node->content['field_select_criteria']['#access'] = FALSE;
    }

  }

}

function _mica_studies_study_view_selection_criteria_item(&$node, $wrapper, $field, $label, $label_plural = '') {
  if (!isset($node->content[$field])) return;
  $value = $wrapper->$field->value();
  if (!empty($value)) {
    $nb_items = count($value);
    $index = count($node->content['field_select_criteria']['#items']);
    $node->content['field_select_criteria']['#items'][$index] = $node->content[$field]['#items'];
    $markup = '';
    for ($i = 0; $i < $nb_items; $i++) {
      $markup .= $node->content[$field][$i]['#markup'];
      if ($i < $nb_items - 1) $markup .= ', ';
    }
    $markup_label = $label;
    if ($nb_items > 1 && strlen($label_plural) > 0) {
      $markup_label = $label_plural;
    }
    $node->content['field_select_criteria'][$index++]['#markup'] = t($markup_label)
      . '<br />&nbsp;&nbsp;&nbsp;&nbsp;' . $markup;
    $node->content[$field]['#access'] = FALSE;
  }
}


function _mica_studies_study_view_authorization(&$node, $view_mode, $langcode, $wrapper) {
  if (isset($node->content['field_authorization_specific'])) {
    $authorization_specific = $wrapper->field_authorization_specific->value();
    $node->content['field_authorization_specific']['#access'] = $authorization_specific;
    $node->content['field_authorising_person_name']['#access'] = FALSE;
    $node->content['field_authorising_date']['#access'] = FALSE;
    if ($authorization_specific) {
      $person_name = $wrapper->field_authorising_person_name->value();
      $site_name = variable_get('site_name', "[SPECIFIC NETWORK]");
      if (empty($person_name)) {
        $txt = t("Contribution to @site authorised", array('@site' => $site_name));
      }
      else {
        $txt = t("@name authorised the contribution to @site", array('@name' => $person_name, '@site' => $site_name));
      }
      $node->content['field_authorization_specific'][0]['#markup'] = $txt;
      if (!empty($node->content['field_authorising_date'][0]['#markup'])) {
        $node->content['field_authorization_specific'][0]['#markup'] .= ' ' . t('on') . ' '
          . $node->content['field_authorising_date'][0]['#markup'];
      }
    }
  }
  if (isset($node->content['field_authorization_maelstrom'])) {
    $authorization_maelstrom = $wrapper->field_authorization_maelstrom->value();
    $node->content['field_authorization_maelstrom']['#access'] = $authorization_maelstrom;
    $node->content['field_authorising_person_name_m']['#access'] = FALSE;
    $node->content['field_authorising_date_m']['#access'] = FALSE;
    if ($authorization_maelstrom) {
      $person_name = $wrapper->field_authorising_person_name_m->value();
      if (empty($person_name)) {
        $txt = t("Contribution to Maelstrom Research authorised");
      }
      else {
        $txt = t("@name authorised the contribution to Maelstrom Research", array('@name' => $person_name));
      }
      $node->content['field_authorization_maelstrom'][0]['#markup'] = $txt;
      if (!empty($node->content['field_authorising_date_m'][0]['#markup'])) {
        $node->content['field_authorization_maelstrom'][0]['#markup'] .= ' ' . t('on') . ' '
          . $node->content['field_authorising_date_m'][0]['#markup'];
      }
    }
  }
}

/**
 * Implements hook_form_alter
 * To add dependent fields when filling out the form
 */
function mica_studies_form_alter(&$form, &$form_state, $form_id) {
  switch ($form_id) {
    case 'study_node_form':
      _mica_studies_study_form_alter($form, $form_state, $form_id);
      break;
    case 'contact_node_form':
      _mica_studies_contact_form_alter($form, $form_state, $form_id);
      break;
  }
}

function _mica_studies_study_form_alter(&$form, &$form_state, $form_id) {
  $form['#validate'][] = '_mica_studies_form_validate';
  _mica_add_dependent_field_checked($form, 'field_design', 'field_design_other_sp', 'other');
  _mica_add_dependent_field_checked($form, 'field_recruitment', 'field_recruitment_other_sp', 'other');
  _mica_add_dependent_field_checked($form, 'field_access_other', 'field_access_other_sp', '1');
  _mica_add_dependent_field_checked($form, 'field_bio_samples_management', 'field_samples_man_other_sp', 'others');
  _mica_add_dependent_field_checked($form, 'field_bio_samples_management', 'field_tissues_sp', 'tissues');
  _mica_add_dependent_field_checked($form, 'field_data_sources', 'field_data_sources_sp', 'others');

  // Add dependent field "Please specify other source of recruitment" to taxonomy checkbox identified by its tid
  $terms = taxonomy_get_term_by_name('Other source', 'sources_of_recruitment');
  if (!empty($terms)) {
    $k = array_keys($terms);
    _mica_add_dependent_field_checked($form, 'field_recruitment_sources', 'field_recruitment_other', $k[0]);
  }
}

function _mica_studies_contact_form_alter(&$form, &$form_state, $form_id) {
  $form['title']['#type'] = 'value';
  $form['title']['#required'] = FALSE;
}

/**
 * Implements hook_node_submit
 */
function mica_studies_node_submit($node, $form, &$form_state) {
  if ($node->type === 'contact' && _mica_studies_contact_title_is_needed($node)) {
    _mica_studies_set_contact_title($node);
  }
}

/**
 * Implements hook_node_presave().
 */
function mica_studies_node_presave($node) {
  if ($node->type === 'contact' && _mica_studies_contact_title_is_needed($node)) {
    _mica_studies_set_contact_title($node);
  }
}

function _mica_studies_set_contact_title(&$node) {

  if (isset($node->field_contact_name)) {

    $wrapper = entity_metadata_wrapper('node', $node);
    $institution = $wrapper->field_institution_name->value();

    // cannot use entity_metadata_wrapper for Name fields because of http://drupal.org/node/1423160
    $language = $node->language;
    $field_contact_name = $node->field_contact_name;

    if (array_key_exists($language, $field_contact_name)) {

      $name = $field_contact_name[$language][0];
      $full_name = isset($name['title']) ? trim($name['title']) : '';
      if (isset($name['given'])) {
        if (!empty($full_name)) $full_name .= ' ';
        $full_name .= trim($name['given']);
      }
      if (isset($name['family'])) {
        if (!empty($full_name)) $full_name .= ' ';
        $full_name .= trim($name['family']);
      }

      if (strlen(trim($full_name)) > 0) {

        $node->title = $full_name;
        if (!empty($institution)) $node->title .= ' (' . trim($institution) . ')';

        // set title for current node revision
        $node->title = substr($node->title, 0, 255);

        // With that flag we ensure we don't apply the title two times to the same
        // node. See _mica_studies_contact_title_is_needed().
        $node->contact_title_applied = TRUE;
      }
    }
  }
}

/**
 * Returns whether the contact title has to be set.
 */
function _mica_studies_contact_title_is_needed($node) {
  return empty($node->contact_title_applied);
}


/**
 * Implement hook_field_group_pre_render
 * Used to show/hide a fieldset based on another field selection
 */
function mica_field_group_pre_render(&$element, $group, &$form) {

  if (isset($form['#form_id']) && $form['#form_id'] === 'study_node_form') {

    $group_name = $group->group_name;
    $lang = key_exists('#default_value', $form['language']) ? $form['language']['#default_value'] : LANGUAGE_NONE;
    $to_hide = array(
      'group_authorising_person' => array(
        'dependee' => 'field_authorization_specific[' . $lang . ']',
        'condition' => 'checked',
        'value' => TRUE,
      ),
      'group_authorising_person_m' => array(
        'dependee' => 'field_authorization_maelstrom[' . $lang . ']',
        'condition' => 'checked',
        'value' => TRUE,
      ),
    );

    if (array_key_exists($group_name, $to_hide)) {
      $element['#states'] = array(
        'visible' => array(
          'input[name="' . $to_hide[$group_name]['dependee'] . '"]' => array(
            $to_hide[$group_name]['condition'] => $to_hide[$group_name]['value']
          ),
        ),
      );
    }
  }
}

function _mica_add_dependent_field_checked(&$form, $dependee, $dependent, $key_selected) {
  if (array_key_exists($dependee, $form) && array_key_exists($dependent, $form)) {
    $lang = $form[$dependee]['#language'];
    $type = $form[$dependee][$lang]['#type'];
    $input = ':input[name="' . $dependee . '[' . $lang . ']';
    $rule = array();
    if ($type != 'radios') {
      $input = $input . '[' . $key_selected . ']';
      $rule['checked'] = TRUE;
    }
    else {
      $rule['value'] = $key_selected;
    }
    $input = $input . '"]';
    $form[$dependent]['#states'] = array(
      'visible' => array(
        $input => $rule,
      ),
    );
  }
  else {
    debug('dependee "' . $dependee . '" or dependent "' . $dependent . '"not found');
  }
}

/**
 * Displays dates as: 'start date' to 'end date' as the start date value.
 * And hide end date.
 */
function _mica_studies_display_status_dates(&$node, $status_dates) {
  $wrapper = entity_metadata_wrapper('node', $node);
  foreach ($status_dates as $start_date => $end_date) {
    $start = $wrapper->$start_date->value();
    if (!empty($start)) {
      if (isset($node->content[$start_date])) {
        $node->content[$start_date][0]['#markup'] = t('From') . ' ' . $node->content[$start_date][0]['#markup'];
      }
      $end = $wrapper->$end_date->value();
      if (!empty($end) && isset($node->content[$end_date])) {
        $node->content[$start_date][0]['#markup'] .= ' ' . t('to') . ' ' . $node->content[$end_date][0]['#markup'];
      }
      $node->content[$end_date]['#access'] = FALSE;
    }
  }
}


function _mica_bind_other_specify(&$node, $bindings) {

  foreach ($bindings as $other_sp => $options) {
    $field = $options['field'];
    if (isset($node->content[$field]) && (isset($node->content[$other_sp]) || isset($options['field_sp']))) {
      $key = $options['key'];
      $delimiter = ', ';

      if (!isset($options['enclosed']) || $options['enclosed']) {
        $start = ' (';
        $end = ')';
      }

      if (isset($key)) {
        // get the array index of the key
        foreach ($node->content[$field]['#items'] as $i => $items) {
          if ($i === $key || $items['value'] === $key) {
            $index = $i;
            break;
          }
        }
      }
      else {
        $node->content[$field]['#items'][] = array('value' => 'extraone');
        $index = count($node->content[$field]['#items']) - 1;
      }

      if (isset($index)) {
        // bind the other specify with the other option
        $content = '';
        $specifies = array();
        if (isset($options['field_sp'])) {
          // add each field
          foreach ($options['field_sp'] as $f) {
            if (isset($node->content[$f])) {
              $prefix = '';
              if ($options['label_as_prefix']) {
                // If a display field as been defined, take this title instead
                $field_info = field_info_instance('node', $f, 'study');
                if (isset($field_info['display_label']) && strlen(trim($field_info['display_label'])) > 0) {
                  $prefix = $field_info['display_label'] . ' ';
                }
                else {
                  $prefix = $node->content[$f]['#title'] . ' ';
                }
              }
              if (isset($options['indent']) && $options['indent']) {
                $prefix .= '<br />&nbsp;&nbsp;&nbsp;&nbsp;';
              }
              foreach ($node->content[$f] as $k => $value) {
                if (is_int($k)) $specifies[] = $prefix . $value['#markup'];
              }
            }
          }
          $content = implode($delimiter, $specifies);

        }
        else {

          for ($i = 0; $i < count($node->content[$other_sp]); $i++) {
            if (isset($node->content[$other_sp][$i])) {
              $prefix = '';
              if ($options['label_as_prefix']) {
                $prefix = $node->content[$other_sp]['#title'] . ' ';
                // If a display field as been defined, take this title instead
                $field_info = field_info_instance('node', $other_sp, 'study');
                if (isset($field_info['display_label']) && strlen(trim($field_info['display_label'])) > 0) {
                  $prefix = $field_info['display_label'] . ' ';
                }
              }
              $specifies[] = $prefix . $node->content[$other_sp][$i]['#markup'];
            }
          }

          $node->content[$other_sp]['#access'] = FALSE;
          $content = implode($delimiter, $specifies);
        }
        if (strlen(trim($content)) > 0) {
          if (key_exists($index, $node->content[$field])) {
            if (isset($options['enclosed']) && !$options['enclosed']) {
              $node->content[$field][$index]['#markup'] = $content;
            }
            else {
              $node->content[$field][$index]['#markup'] .= $start . $content . $end;
            }
          }
          else {
            if (isset($key)) {
              if (isset($options['enclosed']) && !$options['enclosed']) {
                $node->content[$field][0]['#markup'] = $content;
              }
              else {
                $node->content[$field][0]['#markup'] .= $start . $content . $end;
              }
            }
            else {
              if (key_exists('custom_prefix', $options)) {
                $node->content[$field][] = array('#markup' => $options['custom_prefix'] . ': ' . $content);
              }
              else {
                $node->content[$field][] = array('#markup' => $content);
              }
            }
          }
        }
      }
    }

    // hide the field_sp always
    if (isset($node->content[$field]) && isset($options['field_sp'])) {
      foreach ($options['field_sp'] as $f) {
        $node->content[$f]['#access'] = FALSE;
      }
    }

    if (isset($node->content[$field]) && isset($node->content[$other_sp])) {
      $node->content[$other_sp]['#access'] = FALSE;
    }
  }
}

function _mica_remove_suffix(&$node, $fields) {
  foreach ($fields as $field) {
    if (isset($node->content[$field])) {
      // find the last integer index...
      $index = 0;
      for (; $index < count($node->content[$field]); $index++) {
        if (!isset($node->content[$field][$index])) {
          break;
        }
      }
      $index--;

      $suffix = '';
      $field_info = field_info_instance('node', $field, 'study');
      if (isset($field_info['settings']['suffix']) && strlen(trim($field_info['settings']['suffix'])) > 0) {
        $suffix = $field_info['settings']['suffix'];
      }

      $node->content[$field][$index]['#markup'] = str_replace($suffix, '', $node->content[$field][$index]['#markup']);
    }
  }
}

/**
 * Hide a field if another field has a value
 */
function _mica_remove_exclusive_fields(&$node, $bindings) {
  // Hide the field if the other field as a value
  foreach ($bindings as $field => $other_field) {
    if (isset($node->content[$other_field])) {
      $node->content[$field]['#access'] = FALSE;
    }
  }
}

/**
 * Clear dependent field if dependee field selection is not checked.
 */
function _mica_studies_form_validate($form, &$form_state) {
  _mica_studies_form_validate_field($form, $form_state, 'field_design', 'field_design_other_sp', 'other');
  _mica_studies_form_validate_field($form, $form_state, 'field_recruitment', 'field_recruitment_other_sp', 'other');
  _mica_studies_form_validate_field($form, $form_state, 'field_access_other', 'field_access_other_sp', '1');
  _mica_studies_form_validate_field($form, $form_state, 'field_bio_samples_management', 'field_samples_man_other_sp', 'others');
  _mica_studies_form_validate_field($form, $form_state, 'field_bio_samples_management', 'field_tissues_sp', 'tissues');
  _mica_studies_form_validate_field($form, $form_state, 'field_data_sources', 'field_data_sources_sp', 'others');

  // Add dependent field "Please specify other source of recruitment" to taxonomy checkbox identified by its tid
  $terms = taxonomy_get_term_by_name('Other source', 'sources_of_recruitment');
  if (!empty($terms)) {
    $k = array_keys($terms);
    _mica_add_dependent_field_checked($form, 'field_recruitment_sources', 'field_recruitment_other', $k[0]);
  }
}

/**
 * Clear dependent field if dependee field selection is not checked in any language.
 */
function _mica_studies_form_validate_field($form, &$form_state, $dependee, $dependent, $selection) {
  if (array_key_exists($dependee, $form_state['values']) && array_key_exists($dependent, $form_state['values'])) {
    $flangs = array_keys($form_state['values'][$dependee]);
    $flang = $flangs[0];
    $values = array();
    foreach ($form_state['values'][$dependee][$flang] as $value) {
      if (array_key_exists('value', $value)) {
        $values[] = $value['value'];
      }
      else if (array_key_exists('tid', $value)) {
        $values[] = $value['tid'];
      }

    }

    if (in_array($selection, $values) == FALSE) {
      $empty_value = array();
      $lgs = array_keys($form_state['values'][$dependent]);
      foreach ($lgs as $lg) {
        $empty_value[$lg] = array(array('value' => ''));
      }
      form_set_value($form[$dependent], $empty_value, $form_state);
    }
  }
  else {
    debug('dependee "' . $dependee . '" or dependent "' . $dependent . '"not found');
  }
}

/**
 * Implements hook_block_view_alter()
 */
function mica_studies_block_view_alter(&$data, $block) {
  if (!empty($block) && $block->delta === 'study_current_search' && $block->module === 'current_search') {
    _mica_studies_study_current_search($data, $block);
  }
}

function _mica_studies_study_current_search(&$data, $block) {
  if (isset($data['content']['field_group'])) {
    $data['content']['results']['#markup'] .= ' - ' . l(
      t('Clear all criteria') . ' [X]',
      'studies-search',
      array(
        'attributes' => array(
          'rel' => 'nofollow',
          'class' => array('current-search-clear-all'),
        )
      )
    );
    foreach ($data['content']['field_group'] as $field => $field_group) {
      $field_info = field_info_instance('node', $field, 'study');
      if (isset($field_info['display_label']) && strlen(trim($field_info['display_label'])) > 0) {
        $data['content']['field_group'][$field]['title']['#markup'] = '<h4 class="current-search-group-title">'
          . $field_info['display_label'] . ':</h4>';
      }
    }
  }
}

/**
 * Implements hook_node_validate()
 */
function mica_studies_node_validate($node, $form, &$form_state) {
  // check study node title is unique
  if (!isset($node->nid) && $node->type === 'study') {
    if (mica_core_node_title_exists($node->type, $node->title)) {
      form_set_error('title', t('Study name \'!title\' is already given.', array('!title' => $node->title)));
    }
  }
}

/**
 * Creates default content after Features successfully installed
 * Implements hook_features_rebuild_completed()
 */
function mica_studies_features_rebuild_completed() {
  if (!variable_get('mica_studies_features_rebuild_completed', FALSE)) {
    _mica_studies_create_default_content();
    variable_set('mica_studies_features_rebuild_completed', TRUE);
  }
}

function _mica_studies_create_default_content() {
  $study_menu = mica_core_create_menu(st('Studies'), 'studies', 'studies', FALSE, FALSE, 5);

  $base_path = drupal_get_path('module', 'mica_studies') . '/taxonomies/';
  mica_core_taxonomy_import('sources_of_recruitment.csv', $base_path, 'Source of Recruitment');

  mica_core_set_menu_option('study', $study_menu['mlid']);
}

/**
 * When creating studies via noderefcreate, set the complete name form the title because of auto_node_title
 * Implements hook_noderefcreate_alter()
 */
function mica_studies_noderefcreate_alter(&$newnode, $element, $form_state) {
  $wrapper = entity_metadata_wrapper('node', $newnode);
  $wrapper->field_complete_name->set($wrapper->title->value());
}