<?php

/**
 * Implements hook_install().
 */
function darwincore_install(){
  // Clear the errors.
  drupal_get_messages('warning');
}

/**
 * Implements hook_enable().
 * 
 * Re-enable any content types or views that might have been disabled previously
 */
function darwincore_enable(){
  // Enable/re-enable all the features of this module.
  $feature = features_get_features('darwincore');
  $components = array_keys($feature->info['features']);
  features_revert(array(
    'darwincore' => $components
  ));
}

/**
 * Implements hook_disable().
 * 
 * Remove content types defined by this module
 * 
 */
function darwincore_disable(){
  // If there is no data, remove the fields and content type. Normal users
  // should not reach this point if there is content as the Tools module will
  // prevent the module being turned off.
  if(!db_select('node', 'n')->condition('n.type', array(
    'location',
    'specimen_observation'
  ))->countQuery()->execute()->fetchField()){
    node_type_delete('location');
    variable_del('node_preview_location');
    node_type_delete('specimen_observation');
    variable_del('node_preview_specimen_observation');
  }
}

/**
 * Change the input format for the date collected field.
 */
function darwincore_update_7001(){
  $field_instance = field_info_instance('node', 'field_date_collected', 'specimen_observation');
  $field_instance['widget']['settings']['input_format'] = 'Y/m/d - H:i:s';
  field_update_instance($field_instance);
}

/**
 * Change the node_type table to reflect the bug in features.
 */
function darwincore_update_7002(){
  db_update('node_type')->fields(array(
    'base' => ''
  ))->condition('module', 'darwincore')->execute();
}

/**
 * Update the specimen/observation instance of the field_media field to alter
 * its display.
 */
function darwincore_update_7003(){
  $field_instance = field_info_instance('node', 'field_media', 'specimen_observation');
  $field_instance['display'] = array(
    'default' => array(
      'label' => 'above',
      'module' => 'file_entity',
      'settings' => array(
        'file_view_mode' => 'file_styles_square_thumbnail'
      ),
      'type' => 'file_rendered',
      'weight' => '12'
    ),
    'linked_node' => array(
      'label' => 'above',
      'settings' => array(),
      'type' => 'hidden',
      'weight' => 1
    ),
    'teaser' => array(
      'label' => 'above',
      'settings' => array(),
      'type' => 'hidden',
      'weight' => 0
    )
  );
  field_update_instance($field_instance);
}

/**
 * Update the specimen/observation instance of the field_media field to alter
 * the widget it uses.
 */
function darwincore_update_7004(){
  $field_instance = field_info_instance('node', 'field_media', 'specimen_observation');
  $field_instance['widget'] = array(
    'active' => 1,
    'module' => 'media_multiselect',
    'settings' => array(
      'allowed_schemes' => array(),
      'allowed_types' => array(
        'audio' => 'audio',
        'default' => 0,
        'image' => 'image',
        'video' => 'video'
      ),
      'browser_plugins' => array(
        'media_default--media_browser_1' => 0,
        'media_default--media_browser_my_files' => 0,
        'upload' => 0
      ),
      'progress_indicator' => 'throbber'
    ),
    'type' => 'media_multiselect',
    'weight' => '-3'
  );
  field_update_instance($field_instance);
}

/**
 * Update the user_reference fields so that they can actually be used!
 */
function darwincore_update_7005(){
  foreach(array(
    'field_collector',
    'field_identified_by'
  ) as $field_name){
    $field = field_info_field($field_name);
    if($field){
      $field['settings'] = array(
        'referenceable_roles' => array(),
        'referenceable_status' => array(),
        'view' => array(
          'view_name' => 'users_references',
          'display_name' => 'references_1',
          'args' => array()
        )
      );
      field_update_field($field);
    }
  }
}

/**
 * Set the collector field to be 1:n
 */
function darwincore_update_7006(){
  $field = field_info_field('field_collector');
  if($field){
    $field['cardinality'] = -1;
    field_update_field($field);
  }
}

/**
 * Update the user_reference fields for newly created sites since update 7005
 */
function darwincore_update_7007(){
  foreach(array(
    'field_collector',
    'field_identified_by'
  ) as $field_name){
    $field = field_info_field($field_name);
    if($field){
      $field['settings'] = array(
        'referenceable_roles' => array(),
        'referenceable_status' => array(),
        'view' => array(
          'view_name' => 'users_references',
          'display_name' => 'references_1',
          'args' => array()
        )
      );
      field_update_field($field);
    }
  }
}

/**
 * Update the display of the field_country field.
 */
function darwincore_update_7010(){
  // Update the display of the field_country field.
  module_load_include('features.field.inc', 'darwincore');
  $fields = darwincore_field_default_fields();
  foreach($fields as $key => $field){
    if(substr($key, 0, 13) == 'node-location'){
      if(field_info_field($field['field_instance']['field_name'])){
        field_update_instance($field['field_instance']);
      }
    }
  }
}

/**
 * Update the Widget used by the user reference fields
 * (field_identified_by and field_collector)
 */
function darwincore_update_7011(){
  $user_fields = array(
    'field_collector',
    'field_identified_by'
  );
  foreach($user_fields as $user_field){
    $info = field_info_field($user_field);
    // If the field doesn't exist, or isn't a user_reference (if the maintainers have changed it), skip it
    if(!$info || $info['type'] != 'user_reference'){
      continue;
    }
    $field_instance = field_info_instance('node', $user_field, 'specimen_observation');
    // If the field instance doesn't exist, or isn't using the widget we'd expect it to use
    // (if the maintainers have changed it), skip it
    if(!$field_instance || $field_instance['widget']['module'] != 'options' || $field_instance['widget']['type'] != 'options_select'){
      continue;
    }
    $field_instance['widget']['module'] = 'user_reference';
    $field_instance['widget']['type'] = 'user_reference_autocomplete';
    $field_instance['widget']['settings'] = array(
      'autocomplete_match' => 'contains',
      'autocomplete_path' => 'user_reference/autocomplete',
      'size' => '60'
    );
    field_update_instance($field_instance);
  }
}

/**
 * Update the specimen/observation instance of the field_genbank_number field.
 */
function darwincore_update_7012(){
  $field_instance = field_info_instance('node', 'field_genbank_number', 'specimen_observation');
  if($field_instance){
    $field_instance['label'] = 'GenBank number(s)';
    $field_instance['description'] = t('Enter a comma separated list of numbers. For example: FN554775, FR694013');
    $field_instance['display']['default']['type'] = 'darwincore_link_to_ncbi';
    field_update_instance($field_instance);
  }
}

/**
 * Ensure all fields exist, and lock them!
 */
function darwincore_update_7013(){
  $fields_to_lock = array();
  module_load_include('features.field.inc', 'darwincore');
  foreach(darwincore_field_default_fields() as $field){
    $fields_to_lock[] = $field['field_config']['field_name'];
    if(!field_info_field($field['field_config']['field_name'])){
      field_create_field($field['field_config']);
    }
    try{
      field_create_instance($field['field_instance']);
    }
    catch(Exception $e){
    }
  }
  db_update('field_config')->fields(array(
    'locked' => 1
  ))->condition('field_name', $fields_to_lock)->execute();
}

/**
 * Update the display of the Collector and Identified-By fields.
 */
function darwincore_update_7014(){
  module_load_include('features.field.inc', 'darwincore');
  $fields = darwincore_field_default_fields();
  field_update_instance($fields['node-specimen_observation-field_collector']['field_instance']);
  field_update_instance($fields['node-specimen_observation-field_identified_by']['field_instance']);
}

/**
 * Alter the Remarks field so that the text is processed and it uses the WYSIWYG
 * editor
 */
function darwincore_update_7015(){
  module_load_include('features.field.inc', 'darwincore');
  $fields = darwincore_field_default_fields();
  field_update_instance($fields['node-specimen_observation-field_remarks']['field_instance']);
}

/**
 * Update to the token module requires a change to our ANT pattern.
 */
function darwincore_update_7016(){
  variable_set('ant_pattern_specimen_observation', '[node:field_institution_code] - [node:field_collection_code] - [node:field_catalogue_number]');
}

/**
 * Tweak the entityconnectpreview display of the location node.
 */
function darwincore_update_7017(){
  module_load_include('features.field.inc', 'darwincore');
  $fields = darwincore_field_default_fields();
  field_update_instance($fields['node-location-field_map']['field_instance']);
}

/**
 * Update field field_media description
 */
function darwincore_update_7018(){
  if(field_info_instance('node', 'field_media', 'specimen_observation')){
    module_load_include('features.field.inc', 'darwincore');
    $fields = darwincore_field_default_fields();
    field_update_instance($fields['node-specimen_observation-field_media']['field_instance']);
  }
}

/**
 * Fix an issue with migration that resulted in Collector and Identifier fields
 * being created as text fields, and not user reference fields.
 */
function darwincore_update_7019(){
  // First check if we need to do this update by counting the number of rows
  // from the field_config table (0, 1 or 2) that have module = 'text' and 
  // field_name of field_collector or field_identified_by
  $condition = db_or()->condition('field_name', 'field_collector')->condition('field_name', 'field_identified_by');
  $rows = db_select('field_config', 'f')->condition($condition)->condition('module', 'text')->fields('f', array(
    'field_name'
  ))->execute()->fetchCol();
  if(count($rows)){
    foreach($rows as $field_name){
      // We need to do the update.  We create a new field for copying the data
      // across, then delete the old field, and create the correct fields.  Note,
      // this update does not copy the data across to the new field, that is for
      // the user to do.  We will not allow nodes to be saved with data in these
      // new fields, so they will eventually be deleted.
      $current_field = field_info_field($field_name);
      $current_field['field_name'] .= '_copy';
      if(!field_info_field($current_field['field_name'])){
        field_create_field($current_field);
      }
      $current_field_instance = field_info_instance('node', $field_name, 'specimen_observation');
      $current_field_instance['field_name'] .= '_copy';
      $current_field_instance['label'] .= ' (COPY)';
      $current_field_instance['description'] .= ' This field must be EMPTY before this node can be saved.';
      $current_field_instance['widget']['module'] = 'text';
      $current_field_instance['widget']['type'] = 'text_textfield';
      $current_field_instance['display'] = array(
        'default' => array(
          'label' => 'above',
          'type' => 'text_default',
          'weight' => 5,
          'settings' => array(),
          'module' => 'text'
        )
      );
      unset($current_field_instance['widget']['settings']['autocomplete_match']);
      unset($current_field_instance['widget']['settings']['autocomplete_path']);
      if(!field_info_instance('node', $current_field_instance['field_name'], 'specimen_observation')){
        field_create_instance($current_field_instance);
      }
      // Now we copy the data, using a simple SQL query.
      foreach(array(
        'field_revision_',
        'field_data_'
      ) as $table){
        // If this query fails, then the update must fail.  We do not want to
        // get to a point where we've created a new field, not copied the data
        // across, and then deleted the old field.
        $select_query = db_select($table . $field_name, 's')->fields('s');
        $schema = drupal_get_schema($table . $field_name . '_copy');
        $query = db_insert($table . $field_name . '_copy')->fields(array_keys($schema['fields']))->from($select_query);
        $query->execute();
      }
      // Next we delete the old version of the field and all of its instances, and
      // then we create the new user_reference version of the field.
      field_delete_field($field_name);
      // Purge the deleted field
      module_load_include('crud.inc', 'field');
      field_purge_batch(10000);
      // Finally, create the new version of the field.
      module_load_include('features.field.inc', 'darwincore');
      $fields = darwincore_field_default_fields();
      field_create_field($fields['node-specimen_observation-' . $field_name]['field_config']);
      field_create_instance($fields['node-specimen_observation-' . $field_name]['field_instance']);
    }
    // Finally, we flush all caches
    drupal_flush_all_caches();
  }
}

/**
 * Prepare for switch to GBIF names
 *
 * We are going to update fields on (potentially) all entities, so we won't be using
 * the entity API but changing the database directly to avoid timeouts.
 */
function darwincore_update_7020(){
  module_enable(array(
    'scratchpads_vocabularies'
  ));
  module_load_include('features.field.inc', 'darwincore');
  $definitions = darwincore_field_default_fields();
  // See #3185 for the map
  $map = array(
    'field_basis_of_record' => array(
      'Fossil Specimen' => 'FossilSpecimen',
      'Human Observation' => 'HumanObservation',
      'Living Specimen' => 'LivingSpecimen',
      'Preserved Specimen' => 'PreservedSpecimen',
      'Machine Observation' => 'MachineObservation',
      'Moving Image' => 'MachineObservation',
      'Other Specimen' => 'PreservedSpecimen',
      'Sound Recording' => 'MachineObservation',
      'Still Image' => 'MachineObservation',
      'Frozen specimen' => 'PreservedSpecimen',
      'Pinned Specimen' => 'PreservedSpecimen',
      'Specimen in vial' => 'PreservedSpecimen',
      'Specimen in vial (70% ethanol)' => 'PreservedSpecimen',
      'Specimen in vial + genital' => 'PreservedSpecimen'
    ),
    'field_type_status' => array(
      'Holotype' => 'holotype',
      'Isotype' => 'isotype',
      'Lectotype' => 'lectotype',
      'Neotype' => 'neotype',
      'Nontype' => NULL,
      'nontype' => NULL,
      'Not Provided' => NULL,
      'Paralectotype' => 'paralectotype',
      'paraLectotype' => 'paralectotype',
      'Paratype' => 'paratype',
      'Syntype' => 'syntype',
      'Syntypes of T. pacificum wilsoni' => 'syntype',
      'Type status' => NULL,
      'Neotype' => 'neotype',
      'Not a Type' => 'notatype',
      'female' => NULL,
      '1 ex. holotype on slide 80/49 at Berlese Acaroteca, Cascine del Riccio, Firenze, Italy' => 'holotype',
      '1 ex., holotype on slide 23/9 inside finger-like air bubbles but recognizable, 1 ex. on 23/10, 1 ex. on 23/8 and 1 ex. on 23/11 in poor condition, 1 ex. on 23/7, useful, at Berlese Acaroteca, Cascine del Riccio, Firenze, Italy' => 'holotype',
      '3 females' => NULL,
      '3 specimens' => NULL,
      'des adultes des deux sexes (les mâles étant aussi nombreux que les femelles), les 3 sortes de nymphes et un exemplaire de la larve.' => NULL,
      'des adultes, les 3 sortes de nymphes et la larve. Les adultes étaient peu nombreux, et je n\'ai pu en examiner que 9 (8 femelles et 1 mâle)' => NULL,
      'female — Holotype and 2 females — paratypes' => NULL,
      'holotype as Alicus oblongus on a slide' => 'holotype',
      'holotype on slide N1952109' => 'holotype',
      'holotype on slide no. 20.02/7560' => 'holotype',
      'Holotype specimen # 2 of Protacarus crani Hirst, 1923' => 'holotype',
      'lost' => NULL,
      'male — Holotype, male — paratype, female — paratype and I paratype tritonymph' => 'type',
      'Material estudiado: Holotipo fem. (28 -X-81); 9 paratipos: 4 fem. (7-VIII-81; 28-X-81); 2 deutoninfas (7-VIII-81; 14-III-82) y 3 tritoninfas (20-XI-81; 14-III-82).' => 'type',
      'not stated' => NULL
    )
  );
  $stats = array(
    '@rev_deleted' => 0,
    '@data_deleted' => 0,
    '@rev_updated' => 0,
    '@data_updated' => 0
  );
  foreach($map as $field_name => $map){
    // Change the field definition
    $field = field_info_field($field_name);
    $field['settings']['allowed_values'] = $definitions['node-specimen_observation-' . $field_name]['field_config']['settings']['allowed_values'];
    $data = $field;
    unset($data['columns'], $data['field_name'], $data['type'], $data['locked'], $data['module'], $data['cardinality'], $data['active'], $data['deleted']);
    unset($data['bundles']);
    $field['data'] = $data;
    $primary_key = array(
      'id'
    );
    drupal_write_record('field_config', $field, $primary_key);
    //field_cache_clear(TRUE);
    //module_invoke_all('field_update_field', $new_field, $field_info['field'], field_has_data($new_field));
    // Update values
    foreach($map as $old => $new){
      $data_table = "{field_data_" . $field_name . "}";
      $revision_table = "{field_revision_" . $field_name . "}";
      $field_value = $field_name . "_value";
      if($new === NULL){
        $result = db_query("
          DELETE r.* FROM $revision_table r
          INNER JOIN $data_table d ON d.entity_id = r.entity_id AND d.revision_id = r.revision_id
          WHERE BINARY r.$field_value = :old
        ", array(
          ':old' => $old
        ));
        $stats['@rev_deleted'] += $result->rowCount();
        $result = db_query("
          DELETE FROM $data_table
          WHERE BINARY $field_value = :old
        ", array(
          ':old' => $old
        ));
        $stats['@data_deleted'] += $result->rowCount();
      }else{
        $result = db_query("
        UPDATE $revision_table r
        INNER JOIN $data_table d ON d.entity_id = r.entity_id AND d.revision_id = r.revision_id
        SET r.$field_value = :new
        WHERE BINARY r.$field_value = :old
     ", array(
          ':new' => $new,
          ':old' => $old
        ));
        $stats['@rev_updated'] += $result->rowCount();
        db_query("
        UPDATE $data_table
        SET $field_value = :new
        WHERE BINARY $field_value = :old
     ", array(
          ':new' => $new,
          ':old' => $old
        ));
        $stats['@data_updated'] += $result->rowCount();
      }
    }
  }
  watchdog('darwincore', "Vocbularies update statistics. Number of field revisions that were deleted: @rev_deleted ; Number of field entries that were deleted: @data_deleted ; Number of of field revisions that were updated: @rev_updated ; Number of field entries that were updated: @data_updated", $stats);
  // We've worked on the database directly, so ensure everything is cleaned up.
  drupal_flush_all_caches();
}

/**
 * Enable the auto_entitylabel module
 */
function darwincore_update_7021(){
  darwincore_update_7015();
  module_enable(array(
    'auto_entitylabel'
  ));
  module_disable(array(
    'auto_nodetitle'
  ), FALSE);
  drupal_uninstall_modules(array(
    'auto_nodetitle'
  ), FALSE);
}

/**
 * Remove the allowed_scheme options from the field_example_of_handwriting field
 */
function darwincore_update_7022(){
  $field_instance = field_info_instance('node', 'field_media', 'specimen_observation');
  if($field_instance){
    $field_instance['widget']['settings']['allowed_schemes'] = array();
    field_update_instance($field_instance);
  }
}

/**
 * The field_media field should not be required (it appears it doesn't fail when
 * not populated, but does alter the UI)
 */
function darwincore_update_7023(){
  $instance = field_info_instance('node', 'field_media', 'specimen_observation');
  if($instance){
    $instance['required'] = 0;
    field_update_instance($instance);
  }
}

/**
 * Update gm3 settings
 */
function darwincore_update_7024(){
  if(field_info_instance('node', 'field_map', 'location')){
    module_load_include('features.field.inc', 'darwincore');
    $fields = darwincore_field_default_fields();
    field_update_instance($fields['node-location-field_map']['field_instance']);
  }
}