<?php
function biblio_install() {

  $t = get_t();

  // Define the node type.
  $biblio = array(
    'type' => 'biblio',
    'name' => $t('Biblio'),
    'base' => 'biblio',
    'description' => $t('Use Biblio for scholarly content, such as journal papers and books.'),
    'body_label' => $t('Full text')
  );

  // Complete the node type definition by setting any defaults not explicitly
  // declared above.
  // http://api.drupal.org/api/function/node_type_set_defaults/7
  $content_type = node_type_set_defaults($biblio);
  node_add_body_field($content_type);

  // Save the content type
  node_type_save($content_type);

  set_time_limit(300);

  $result[] = _add_db_field_data();

  $result[] = _add_publication_types();

  $result[] = _add_custom_field_data();

  //_enable_biblio_keyword_vocabulary();

  $result[] = _set_system_weight();


//  if (count($result) == count(array_filter($result))) {
//    drupal_set_message(t('The biblio module has successfully added its tables to the database.'));
//  }
//  else {
//    drupal_set_message(t('Drupal encountered some errors while attempting to install the database tables for the biblio module.'), 'error');
//  }
}

function biblio_enable() {
  if (module_exists('taxonomy')) _enable_biblio_vocabularies();
  _set_system_weight();
  //_enable_biblio_collection_vocabulary();
 // _add_biblio_keywords();
}

function _enable_biblio_vocabularies() {
  $vids = variable_get('biblio_vocabularies', array());
  foreach ($vids as $vid ) {
    if (($voc = taxonomy_vocabulary_load($vid)))  {
      $voc = (array) $voc;
      $voc['nodes']['biblio'] = 1;
      taxonomy_save_vocabulary($voc);
    }
  }
}

function biblio_disable() {
  $vids = array();
  if (module_exists('taxonomy')) {
    $voc = taxonomy_get_vocabularies();
    foreach ($voc as $vid => $vocabulary) {
      if (isset($vocabulary->nodes['biblio']))  {
        $vids[] = $vid;
      }
    }
    variable_set('biblio_vocabularies', $vids);
  }
}

function biblio_uninstall() {
  if (module_exists('taxonomy')) {
    $voc = taxonomy_get_vocabularies();
    foreach ($voc as $vid => $vocabulary) {
      if ($vocabulary->module == 'biblio')  taxonomy_del_vocabulary($vid);
    }
  }

  $result = db_query("SELECT * FROM {node} WHERE type='biblio' ");
  foreach  ($result as $node ) {
    db_query('DELETE FROM {node} WHERE nid = :nid', array(':nid' => $node->nid));
    db_query('DELETE FROM {node_revision} WHERE nid = :nid', array(':nid' => $node->nid));

    // Remove this node from the search index if needed.
    if (function_exists('search_wipe')) {
      search_wipe($node->nid, 'node');
    }
  }


  $vars = db_query("SELECT * FROM {variable} WHERE name LIKE 'biblio_%'");
  foreach ($vars as $var) {
    variable_del($var->name);
  }

  cache_clear_all();

}

function biblio_requirements($phase) {
  $requirements = array();
  $message = '';
 // Ensure translations don't break at install time
  $t = get_t();

  // Report Drupal version
  if ($phase == 'runtime') {
    $dir = drupal_get_path('module', 'biblio');
    $files = file_scan_directory($dir, '/..*.inc$/',  array('recurse' => FALSE));
    if (count($files)) {
      $message = $t('There is a problem with your Biblio installation! There should not be any ".inc" files in the %biblio directory.  You probably forgot to delete the old biblio files when you upgraded the module.  You should remove the following files from that directory...', array('%biblio' => $dir));
      $message .= "<ul>";
      foreach ($files as $file) {
        $message .= "<li>" . $file->filename;
      }
      $message .= "</ul>";
      $requirements['biblio'] = array(
        'title' => $t('Biblio'),
        'value' => BIBLIO_VERSION,
        'severity' => empty($message) ? REQUIREMENT_OK : REQUIREMENT_ERROR,
        'description' => $message,
      );
    }

  }
  return $requirements;
}

function _biblio_helper_modules($mode) {

  $modules = _biblio_get_helper_modules();
  switch ($mode) {
    case 'install':
      module_enable($modules);
      break;
    case 'uninstall':
      foreach ($modules as $module) {
        drupal_uninstall_modules($module);
      }
      break;
  }
}

function _biblio_get_helper_modules() {
  return array(
    'biblio_bibtex',
    'biblio_crossref',
    'biblio_marc',
    'biblio_pm',
    'biblio_ris',
    'biblio_tagged',
    'biblio_xml',
    'biblio_citeproc',
    'biblio_rtf',
  );

}

function _set_system_weight() {
      db_update('system')
              ->fields(array(
                'weight' => 9,
              ))
              ->condition('name', 'biblio')
              ->execute();
   return;
   //return update_sql("UPDATE {system} SET weight = 9 WHERE name = 'biblio'");
}

function _enable_biblio_keyword_vocabulary() {


  if ($vocabulary = taxonomy_vocabulary_load(variable_get('biblio_keyword_vocabulary', 0))) {
      // Existing install. Add back forum node type, if the biblio
    // vocabulary still exists. Keep all other node types intact there.
    $vocabulary = (array) $vocabulary;
    $vocabulary['nodes']['biblio'] = 1;
    taxonomy_save_vocabulary($vocabulary);
  }
//  else {
//    // Create the biblio vocabulary if it does not exist.
//    $vocabulary = array(
//      'name' => 'Biblio Keywords',
//      'description' => t('This is a free tag vocabulary which contains the keywords from all nodes created by the biblio module'),
//      'help' => t('Enter a comma separated list of words. Phrases containing commas should be enclosed in double quotes'),
//      'nodes' => array('biblio' => 1),
//      'hierarchy' => 0,
//      'relations' => 1,
//      'tags' => 1,
//      'multiple' => 0,
//      'required' => 0,
//      'weight' => 0,
//      'module' => 'biblio',
//    );
//    taxonomy_save_vocabulary($vocabulary);
//    variable_set('biblio_keyword_vocabulary', $vocabulary['vid']);
//  }
  return $vocabulary['vid'];
}
function _enable_biblio_collection_vocabulary() {
  if ($vocabulary = taxonomy_vocabulary_load(variable_get('biblio_collection_vocabulary', 0))) {
    // Existing install. Add back forum node type, if the biblio
    // vocabulary still exists. Keep all other node types intact there.
    $vocabulary = (array) $vocabulary;
    $vocabulary['nodes']['biblio'] = 1;
    taxonomy_save_vocabulary($vocabulary);
  }
  else {
    // Create the forum vocabulary if it does not exist. Assign the vocabulary
    // a low weight so it will appear first in forum topic create and edit
    // forms.
    $vocabulary = array(
      'name' => 'Biblio Collections',
      'description' => 'You may organize your publications into collections by adding a collection names to this vocabulary',
      'help' => '',
      'nodes' => array('biblio' => 1),
      'hierarchy' => 0,
      'relations' => 1,
      'tags' => 0,
      'multiple' => 1,
      'required' => 0,
      'weight' => 0,
      'module' => 'biblio',
    );
    taxonomy_save_vocabulary($vocabulary);
    variable_set('biblio_collection_vocabulary', $vocabulary['vid']);
    $default_collection = array(
      'name' => t('Default'),
      'description' => t("This is the collection that all biblio entries will be a part of if no other collection is selected. Deleting this term will render all your biblio entries inaccessable. (You've been warned!)" ),
      'parent' => array(),
      'relations' => array(),
      'synonyms' => '',
      'weight' => 0,
      'vid' => variable_get('biblio_collection_vocabulary', 0),
    );
    taxonomy_save_term($default_collection);
  }
  return $vocabulary['vid'];

}

/**
 * Copies keywords from the biblio_keyword column of the biblio table
 * to a taxonomy vocabulary
 *
 * @return none
 */
function _add_biblio_keywords() {
  set_time_limit(300);
  $kw_sep = variable_get('biblio_keyword_sep', ',');
  $vid = ($vid = variable_get('biblio_keyword_vocabulary', 0))? $vid:_enable_biblio_keyword_vocabulary();
  if ($vid ) {
    $db_result  = db_query("SELECT b.biblio_keywords, b.nid, b.vid FROM {biblio} b");
    $result = array();
    foreach ($db_result as $row) {
      foreach (explode($kw_sep, $row->biblio_keywords) as $keyword) {
        $result[] = array('value' => trim($keyword), 'nid' => $row->nid, 'vid' => $row->vid);
      }
      db_query('DELETE tn.* FROM {term_node} tn INNER JOIN {term_data} td ON tn.tid = td.tid WHERE nid = %d AND td.vid = %d', $row->nid, $vid);
    }
    $inserted = array();
    $count = 0;
    foreach ($result as $keywords) {
      // See if the term exists in the chosen vocabulary
      // and return the tid; otherwise, add a new record.
      $possibilities = taxonomy_get_term_by_name($keywords['value']);
      $term_tid = NULL; // tid match, if any.
      foreach ($possibilities as $possibility) {
        if ($possibility->vid == $vid) {
          $term_tid = $possibility->tid;
        }
      }

      if (!$term_tid) {
        $term = array('vid' => $vid, 'name' => $keywords['value']);
        $status = taxonomy_save_term($term);
        $term_tid = $term['tid'];
      }

      // Defend against duplicate, differently cased tags
      if (!isset($inserted[$keywords['vid']][$term_tid])) {
        db_query('INSERT INTO {term_node} (nid, vid, tid) VALUES (%d, %d, %d)', $keywords['nid'], $keywords['vid'], $term_tid);
        $inserted[$keywords['vid']][$term_tid] = TRUE;
        $count++;
      }
    }
    return array('success' => TRUE, 'query' => 'Added ' . $count . ' keywords to the biblio/taxonomy keyword vocabulary');
  }
  return array('success' => FALSE, 'query' => 'Biblio keyword vocabulary not available');
}


function biblio_schema() {
  $schema['biblio'] = array(
    'fields' => array(
      'nid' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
        'description' => '',
      ),
      'vid' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
        'description' => '',
      ),
      'biblio_type' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
        'description' => '',
      ),
      'biblio_number' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_other_number' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_sort_title' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '64',
        'description' => 'A normalized version of the title, used for sorting on titles. (only first 64 characters saved)',
      ),
      'biblio_secondary_title' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_tertiary_title' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_edition' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_publisher' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_place_published' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_year' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 9999,
        'description' => '',
      ),
      'biblio_volume' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_pages' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_date' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '16',
        'description' => '',
      ),
      'biblio_isbn' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_lang' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '24',
        'default' => 'eng',
        'description' => '',
      ),
      'biblio_abst_e' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_abst_f' => array(
        'not null' => FALSE,
        'type' => 'text',
        'description' => '',
      ),
      'biblio_full_text' => array(
        'type' => 'int',
        'not null' => FALSE,
        'default' => 0,
        'description' => '',
      ),
      'biblio_url' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_issue' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_type_of_work' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_accession_number' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_call_number' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_notes' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_custom1' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_custom2' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_custom3' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_custom4' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_custom5' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_custom6' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_custom7' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_research_notes' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_number_of_volumes' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_short_title' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_alternate_title' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_original_publication' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_reprint_edition' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_translated_title' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_section' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_citekey' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_coins' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_doi' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_issn' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '128',
        'description' => '',
      ),
      'biblio_auth_address' => array(
        'type' => 'text',
        'not null' => FALSE,
        'description' => '',
      ),
      'biblio_remote_db_name' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_remote_db_provider' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_label' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_access_date' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => '',
      ),
      'biblio_refereed' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '20',
        'description' => '',
      ),
      'biblio_md5' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '32',
        'description' => '',
      ),
      'biblio_formats' => array(
        'type' => 'blob',
        'not null' => FALSE,
        'description' => '',
        'serialize' => TRUE,
      ),
    ),
    'foreign keys' => array(
      'node_revision' => array(
        'table' => 'node_revision',
        'columns' => array('vid' => 'vid'),
       ),
      'node' => array(
        'table' => 'node',
        'columns' => array('nid' => 'nid'),
       ),
      'biblio_type' => array(
        'table' => 'biblio_types',
        'columns' => array('biblio_type' => 'tid'),
       ),
     ),
     'primary key' => array(
      'vid'
      ),
    'indexes' => array(
      'nid' => array('nid'),
      'md5' => array('biblio_md5'),
      'year' => array('biblio_year'),
      'title_sort' => array('biblio_sort_title'),
      'date' => array('biblio_date')
      ),
    );

   $schema['biblio_fields'] = array(
    'fields' => array(
      'fid' => array(
        'type' => 'int',
        'not null' => TRUE,
          'unsigned' => TRUE,
        'default' => 0,
        'description' => '{biblio_fields}.fid of the node',
        ),
      'name' => array(
        'type' => 'varchar',
        'length' => '128',
        'not null' => TRUE,
        'default' => ''
        ),
      'type' => array(
        'type' => 'varchar',
        'length' => '128',
        'not null' => TRUE,
        'default' => 'textfield'
        ),
      'size' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 60,
        ),
      'maxsize' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 255,
        ),
        ),
      'primary key' => array('fid'),
        );

   $schema['biblio_field_type'] = array(
    'description' => 'Relational table linking {biblio_fields} with {biblio_field_type_data}',
    'fields' => array(
      'tid' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 0,
        'description' => '{biblio_types}.tid of the node',
        ),
      'fid' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 0,
        'description' => '{biblio_fields}.fid of the node',
        ),
      'ftdid' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 0,
        'description' => '{biblio_field_type_data}.ftdid of the node, points to the current data, default or custom',
        ),
      'cust_tdid' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 0,
        'description' => 'This always points to the custom data for this field. Stored so we can switch back an forth between default and custom',
        ),
      'common' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 0,
        ),
      'vtab' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 0,
        ),
      'autocomplete' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 0,
        ),
        'required' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 0,
        'description' => 'Is input required for this field'
        ),
      'weight' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
        'description' => 'The weight (location) of the field on the input form'
        ),
      'visible' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 0,
        'description' => 'Determines if the field is visible on the input form'
        ),

        ),
    'primary key' => array('tid', 'fid'),
    'indexes' => array(
      'tid' => array('tid')
        ),
        );

   $schema['biblio_field_type_data'] = array(
    'description' => 'Data used to build the form elements on the input form',
    'fields' => array(
      'ftdid' => array(
        'type' => 'int',
        'not null' => TRUE,
          'unsigned' => TRUE,
        'default' => 0,
        'description' => '{biblio_field_type_data}.ftdid of the node',
        ),
      'title' => array(
        'type' => 'varchar',
        'length' => '128',
        'not null' => TRUE,
        'default' => '',
        'description' => 'The title, which will be displayed on the form, for a given field'
        ),
      'hint' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => FALSE,
        'description' => 'The hint text printed below the input widget'
        ),
        ),
    'primary key' => array('ftdid'),
        );

  $schema['biblio_types'] = array(
    'fields' => array(
        'tid' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
        'description' => '{biblio_types}.tid of the publication type',
        ),
      'name' => array(
        'type' => 'varchar',
        'length' => '64',
        'not null' => TRUE,
        'default' => '',
        'description' => 'The name of the publication type'
        ),
      'description' => array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '255',
        'description' => 'Description of the publication type'
        ),
      'weight' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
        'description' => 'Controls the order the types are listed in'
        ),
      'visible' => array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 1,
        'description' => 'Determines if the publication type is visible in the list'
        ),
        ),
      'primary key' => array('tid'),

        );


 $schema['biblio_contributor'] = array(
  'description' => 'Relational table linking authors to biblio entries',
  'fields' => array(
    'nid' => array(
      'type' => 'int',
      'not null' => TRUE,
      'unsigned' => TRUE,
      'default' => 0,
      'description' => '{node}.nid of the node',
    ),
    'vid' => array(
      'type' => 'int',
      'not null' => TRUE,
      'unsigned' => TRUE,
      'default' => 0,
      'description' => '{node}.vid of the node',
    ),
    'cid' => array(
      'type' => 'int',
      'not null' => TRUE,
      'unsigned' => TRUE,
      'default' => 0,
      'description' => '{biblio_contributor_data}.cid of the node',
    ),
    'auth_type' => array(
      'type' => 'int',
      'not null' => TRUE,
      'unsigned' => TRUE,
      'default' => 1,
      'description' => '{biblio_contributor_type}.auth_type of the node',
    ),
    'auth_category' => array(
      'type' => 'int',
      'not null' => TRUE,
      'unsigned' => TRUE,
      'default' => 1,
      'description' => '',
    ),
    'rank' => array(
      'type' => 'int',
      'not null' => TRUE,
      'unsigned' => TRUE,
      'default' => 0,
      'description' => 'Position of the author name on the publication (first,second,third...)',
    )
   ),
   'foreign keys' => array(
     'node_revision' => array(
       'table' => 'node_revision',
       'columns' => array('vid' => 'vid'),
     ),
     'node' => array(
       'table' => 'node',
       'columns' => array('nid' => 'nid'),
     ),
     'biblio_contributor_data' => array(
       'table' => 'biblio_contributor_data',
       'columns' => array('cid' => 'cid'),
     ),
     'biblio_contributor_type' => array(
       'table' => 'biblio_contributor_type',
       'columns' => array('auth_type' => 'auth_type'),
     ),
      'biblio_contributor_category' => array(
       'table' => 'biblio_contributor_type',
       'columns' => array('auth_category' => 'auth_category'),
     ),
   ),
   'primary key' => array(
   		'vid',
   		'cid',
   		'auth_type',
   		'rank'
    ),
   );

  $schema['biblio_contributor_data'] = array(
    'description' => 'Contains Author information for each publication',
    'fields' => array(
      'cid' => array(
        'type' => 'serial',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'description' => 'Primary Key: Author ID',
        ),
      'aka' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default'  => 0,
        'unsigned' => TRUE,
        'description' => 'Also known as, links this author entry with others so you can have variation on the name, but listing by cid will find all other (aka) author entries',
        ),
      'drupal_uid' => array(
        'type' => 'int',
        'not null' => FALSE,
        'unsigned' => TRUE,
        'description' => 'Drupal User ID',
        ),
      'name' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
        'default' => '',
        'description' => 'Full name',
        ),
      'lastname' => array(
        'type' => 'varchar',
        'length' => '128',
        'not null' => TRUE,
        'default' => '',
        'description' => 'Author last name',
        ),
      'firstname' => array(
        'type' => 'varchar',
        'length' => '128',
        'not null' => FALSE,
        'default' => '',
        'description' => 'Author first name',
        ),
      'prefix' => array(
        'type' => 'varchar',
        'length' => '128',
        'not null' => FALSE,
        'default' => '',
        'description' => 'Author name prefix',
        ),
      'suffix' => array(
        'type' => 'varchar',
        'length' => '128',
        'not null' => FALSE,
        'default' => '',
        'description' => 'Author name suffix',
        ),
      'initials' => array(
        'type' => 'varchar',
        'length' => '10',
        'not null' => FALSE,
        'default' => '',
        'description' => 'Author initials (including first name initial)',
        ),
      'affiliation' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => FALSE,
        'default' => '',
        'description' => 'Author affiliation or address',
        ),
      'literal' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default'  => 0,
        'unsigned' => TRUE,
        'description' => 'Determines if the author name is allowed to be reformated by the variaous styles or should be used literally.',
        ),
      'md5' => array(
        'type' => 'varchar',
        'length' => '32',
        'not null' => FALSE,
        'description' => '',
        )
      ),
    'foreign keys' => array(
      'biblio_contributor' => array(
        'table' => 'biblio_contributor',
        'columns' => array('cid' => 'cid'),
       ),
      'node_author' => array(
        'table' => 'users',
        'columns' => array('drupal_uid' => 'uid'),
      ),
     ),
  	'primary key' => array('cid', 'aka'),
    'indexes' => array(
      'lastname' => array('lastname'),
      'firstname' => array('firstname'),
      'initials' => array('initials')
     )
    );
    $schema['biblio_contributor_type'] = array(
      'description' => 'Contains definitions of the contributor types',
      'fields' => array(
        'auth_category' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => 'There are 5 catagoies of author: Primary, Secondary, Tertiery, Subsidary and Corporate  ',
        ),
        'biblio_type' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => '',
        ),
        'auth_type' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => 'This is the pulication type specific verion of a particular catagory',
        ),
    ),
    'foreign keys' => array(
       'biblio' => array(
         'table' => 'biblio',
         'columns' => array('biblio_type' => 'biblio_type'),
       ),
       'biblio_contributor_type' => array(
         'table' => 'biblio_contributor',
         'columns' => array('auth_type' => 'auth_type'),
       ),
      'biblio_contributor_category' => array(
         'table' => 'biblio_contributor',
         'columns' => array('auth_category' => 'auth_category'),
       ),
     ),
     'primary key' => array('auth_category', 'biblio_type', 'auth_type'),
   );

  $schema['biblio_contributor_type_data'] = array(
    'description' => 'Data used to build the form elements on the input form',
    'fields' => array(
      'auth_type' => array(
        'type' => 'serial',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'description' => '{biblio_contributor_type_data} ctdid of the node',
      ),
      'title' => array(
        'type' => 'varchar',
        'length' => '128',
        'not null' => TRUE,
        'default' => '',
        'description' => 'The title, which will be displayed on the form, for a given field'
      ),
      'hint' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => FALSE,
        'description' => 'The hint text printed below the input widget'
      ),
    ),
    'primary key' => array('auth_type'),
   );

    $schema['biblio_keyword'] = array(
      'description' => t('Relational table linking keywords to biblio nodes'),
      'fields' => array(
        'kid' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => t('Primary Key: The {biblio_keyword_data}.kid of the keyword of the node.')
        ),
        'nid' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => t('The {node}.nid of the node.'),
        ),
        'vid' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => t('Primary Key: The {node}.vid of the node.'),
        ),
    ),
    'foreign keys' => array(
     'node_revision' => array(
       'table' => 'node_revision',
       'columns' => array('vid' => 'vid'),
     ),
     'node' => array(
       'table' => 'node',
       'columns' => array('nid' => 'nid'),
     ),
     'keyword' => array(
       'table' => 'biblio_keyword_data',
       'columns' => array('kid' => 'kid'),
     ),
    ),
    'primary key' => array('kid', 'vid'),
      'indexes' => array(
           'vid' => array('vid'),
           'nid' => array('nid'),
        ),
        );

     $schema['biblio_keyword_data'] = array(
      'description' => t('Stores the keywords related to nodes.'),
      'fields' => array(
        'kid' => array(
          'type' => 'serial',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'description' => t('Primary Key: The id of the keyword assigned to the node')
        ),
        'word' => array(
          'type' => 'varchar',
          'length' => 255,
          'not null' => TRUE,
          'default' => '',
          'description' => t('The keyword'),
        ),
        ),
      'primary key' => array('kid'),
      'indexes' => array(
           'kword' => array('word'),
        ),
        );
     $schema['biblio_collection'] = array(
      'description' => t('Relational table grouping biblio nodes into collections'),
      'fields' => array(
        'cid' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => t('Primary Key: The {biblio_collection_data}.cid of the collection')
        ),
        'vid' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => t('Primary Key: The {node}.vid of the node.'),
        ),
        'pid' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => t('The parent id of the collection')
        ),
        'nid' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => t('The {node}.nid of the node.'),
        ),
        ),
      'primary key' => array('cid', 'vid'),
      'indexes' => array(
           'pid' => array('pid'),
           'nid' => array('nid'),
        ),
        );
     $schema['biblio_collection_type'] = array(
      'description' => t('Descriptions of the collections.'),
      'fields' => array(
        'cid' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => t('Primary Key: The id of the collection')
        ),
        'name' => array(
          'type' => 'varchar',
          'length' => 255,
          'not null' => TRUE,
          'default' => '',
          'description' => t('The name of the collection'),
        ),
        'description' => array(
          'type' => 'varchar',
          'length' => 255,
          'not null' => TRUE,
          'default' => '',
          'description' => t('The description of the collection'),
        ),
        ),
      'primary key' => array('cid'),
      'indexes' => array(
           'name' => array('name'),
        ),
        );
    $schema['biblio_duplicates'] = array(
      'description' => t('Relational table linking possible duplicate biblio nodes'),
      'fields' => array(
        'vid' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => t('Primary Key: The {biblio}.nid of the original node')
        ),
        'did' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => t('The {biblio}.nid of the newly imported node which may be a duplicate.'),
        ),
        'type' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => t('The type of duplicate 0=biblio, 1=author.'),
        ),
        ),
      'primary key' => array('vid', 'did'),
        'indexes' => array(
           'did' => array('vid'),
        ),
        );

      $schema['biblio_import_cache'] = array(
        'description' => 'tables used for caching data imported from file and then batch processed',
        'fields' => array(
          'id' => array(
            'type' => 'serial',
            'not null' => TRUE,
            'unsigned' => TRUE),
          'session_id' => array(
            'type' => 'varchar',
            'length' => 45,
            'not null' => TRUE),
          'data' => array(
            'description' => t('A collection of data to cache.'),
            'type' => 'blob',
            'not null' => FALSE,
            'size' => 'big'),
        ),
        'primary key' => array('id'));

  $schema['biblio_type_maps'] = array(
    'description' => 'Table used to store the mapping information between various file formats and the biblio schema',
    'fields' => array(
      'format' => array(
        'description' => 'The import/export file format',
        'type' => 'varchar',
        'length' => 128,
        'not null' => TRUE),
      'type_map' => array(
        'description' => 'The mapping between the publication types in the file format and biblio',
        'type' => 'blob',
        'not null' => FALSE,
        'size' => 'big'),
      'type_names' => array(
        'description' => 'The human readable names of the publication types',
        'type' => 'blob',
        'not null' => FALSE,
        'size' => 'big'),
      'field_map' => array(
        'description' => 'The mapping between the fields in the file format and biblio',
        'type' => 'blob',
        'not null' => FALSE,
        'size' => 'big'),
      'export_map' => array(
        'description' => 'which fields are exported',
        'type' => 'blob',
        'not null' => FALSE,
        'size' => 'big'),
      ),
    'primary key' => array('format'));

   $schema['biblio_vtabs'] = array(
    'description' => 'Table used to store the information to create the vertical tabs on the input form',
    'fields' => array(
        'tab_id' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => ''
        ),
        'weight' => array(
          'type' => 'int',
          'not null' => TRUE,
          'unsigned' => TRUE,
          'default' => 0,
          'description' => ''
        ),
        'title' => array(
          'type' => 'varchar',
          'length' => 128,
          'not null' => TRUE,
          'default' => '',
          'description' => t('The title of the tab'),
        ),
        'description' => array(
          'type' => 'varchar',
          'length' => 255,
          'not null' => TRUE,
          'default' => '',
          'description' => t('The description of the tab'),
        ),
    ),
    'primary key' => array('tab_id'));

   return ($schema);

}

function biblio_reset_types() {
  $result = array();

  db_drop_table('biblio_field_type_data');
  db_drop_table('biblio_field_type');
  db_drop_table('biblio_fields');
  db_drop_table('biblio_contributor_type');
  db_drop_table('biblio_contributor_type_data');

  $schema = biblio_schema();
  db_create_table('biblio_field_type_data', $schema['biblio_field_type_data']);
  db_create_table('biblio_field_type', $schema['biblio_field_type']);
  db_create_table('biblio_fields', $schema['biblio_fields']);
  db_create_table('biblio_contributor_type', $schema['biblio_contributor_type']);
  db_create_table('biblio_contributor_type_data', $schema['biblio_contributor_type_data']);

  variable_set('biblio_last_ftdid', 100); // reset custom field type id too
  //_add_db_field_data_XML();
  _add_db_field_data();
  _add_custom_field_data();
}
function _biblio_add_vtabs() {
  $vtabs = array(
    array('tab_id' => 1, 'weight' => 1, 'title' => 'Authors', 'description' => ''),
    array('tab_id' => 2, 'weight' => 2, 'title' => 'Publication', 'description' => ''),
    array('tab_id' => 3, 'weight' => 3, 'title' => 'Publisher', 'description' => ''),
    array('tab_id' => 4, 'weight' => 4, 'title' => 'Identifiers', 'description' => ''),
    array('tab_id' => 5, 'weight' => 5, 'title' => 'Locators', 'description' => 'URL\'s etc'),
    array('tab_id' => 6, 'weight' => 6, 'title' => 'Keywords', 'description' => ''),
    array('tab_id' => 7, 'weight' => 7, 'title' => 'Notes', 'description' => ''),
    array('tab_id' => 8, 'weight' => 8, 'title' => 'Alternate Titles', 'description' => ''),
    array('tab_id' => 9, 'weight' => 9, 'title' => 'Other', 'description' => ''),
    );

  foreach ($vtabs as $record) {
   db_insert('biblio_vtabs')->fields($record)->execute();
  }


}

function _add_publication_types() {
  $types[] = array(100, 'Book', NULL, 1);
  $types[] = array(101, 'Book Chapter', NULL, 2);
  $types[] = array(102, 'Journal Article', NULL, 3);
  $types[] = array(131,'Journal',NULL,3);
  $types[] = array(103, 'Conference Paper', NULL, 4);
  $types[] = array(104, 'Conference Proceedings', NULL, 5);
  $types[] = array(105, 'Newspaper Article', NULL, 6);
  $types[] = array(106, 'Magazine Article', NULL, 7);
  $types[] = array(107, 'Web Article', NULL, 8);
  $types[] = array(132,'Website',NULL,8);
  $types[] = array(133,'Web service',NULL,8);
  $types[] = array(134,'Web project page',NULL,8);
  $types[] = array(108, 'Thesis', NULL, 9);
  $types[] = array(109, 'Report', NULL, 10);
  $types[] = array(110, 'Film', NULL, 11);
  $types[] = array(111, 'Broadcast', NULL, 12);
  $types[] = array(112, 'Artwork', NULL, 13);
  $types[] = array(113, 'Software', NULL, 14);
  $types[] = array(114, 'Audiovisual', NULL, 15);
  $types[] = array(115, 'Hearing', NULL, 16);
  $types[] = array(116, 'Case', NULL, 17);
  $types[] = array(117, 'Bill', NULL, 18);
  $types[] = array(118, 'Statute', NULL, 19);
  $types[] = array(119, 'Patent', NULL, 20);
  $types[] = array(120, 'Personal', NULL, 21);
  $types[] = array(121, 'Manuscript', NULL, 22);
  $types[] = array(122, 'Map', NULL, 23);
  $types[] = array(123, 'Chart', NULL, 24);
  $types[] = array(124, 'Unpublished', NULL, 25);
  $types[] = array(125, 'Database', NULL, 26);
  $types[] = array(126, 'Government Report', NULL, 27);
  $types[] = array(127, 'Classical'  , NULL, 28);
  $types[] = array(128, 'Legal Ruling', NULL, 29);
  $types[] = array(129, 'Miscellaneous',NULL, 30);
  $types[] = array(130, 'Miscellaneous Section', NULL, 31);
  $types[] = array(135,'Presentation',NULL,8);

  foreach ($types as $record) {
//    $result[] = update_sql("INSERT INTO {biblio_types} (tid, name, description, weight) VALUES ('" . implode("', '", $record) . "')");
        db_insert('biblio_types')->fields(array(
          'tid'           => $record[0],
          'name'          => $record[1],
          'description'   => $record[2],
          'weight'        => $record[3],
        ))->execute();

  }
 return;
}

function _add_db_field_data_XML() {
  $next_ctdid=10; //first contributor_type_data id
  $schema = biblio_schema();
  $fieldnames = array_keys($schema['biblio_fields']['fields']);
  $field_type_fieldnames = array_keys($schema['biblio_field_type']['fields']);
  $field_type_data_fieldnames = array_keys($schema['biblio_field_type_data']['fields']);
  db_query("/*!40000 ALTER TABLE {biblio_field_type_data} DISABLE KEYS */;");
  db_query("/*!40000 ALTER TABLE {biblio_fields} DISABLE KEYS */;");
  for ($type = 1; $type <= 5; $type++) {
    for ($biblio_type = 100; $biblio_type <= 130; $biblio_type++) {
      db_query("INSERT INTO {biblio_contributor_type} (auth_category, biblio_type, auth_type) VALUES (%d, %d, %d)",  $type, $biblio_type, $type);
    }
  }
//  db_query("INSERT INTO {biblio_contributor_type_data} (auth_type, title) VALUES (%d, '%s' )", 1, "Author");
//  db_query("INSERT INTO {biblio_contributor_type_data} (auth_type, title) VALUES (%d, '%s' )", 2, "Secondary Author");
//  db_query("INSERT INTO {biblio_contributor_type_data} (auth_type, title) VALUES (%d, '%s' )", 3, "Tertiary Author ");
//  db_query("INSERT INTO {biblio_contributor_type_data} (auth_type, title) VALUES (%d, '%s' )", 4, "Subsidiary Author ");
//  db_query("INSERT INTO {biblio_contributor_type_data} (auth_type, title) VALUES (%d, '%s' )", 5, "Corporate Author ");
  _id_by_name(NULL, NULL, NULL, array('tablename' => 'biblio_field_type_data', 'name_column' => 'title', 'id_column' => 'ftdid'));
//  _id_by_name(NULL, NULL, NULL, array('tablename' => 'biblio_contributor_type_data', 'name_column' => 'title', 'id_column' => 'auth_type'));

  $xml_file = drupal_get_path('module', 'biblio') . '/field_data.xml';
  $xml = simplexml_load_file($xml_file);
  foreach ($xml->field as $field) {
    $link_data = array(0, $field['fid'], $field['fid'], $field['fid'], $field->common, $field->autocomplete, $field->required, $field->weight, $field->visible);
    db_query("INSERT INTO {biblio_field_type} (" . implode(", ", $field_type_fieldnames) . ")
                  VALUES (%d, %d, %d, %d, %d, %d, %d, %d, %d)", $link_data);
    for ($t = 100; $t <= 130; $t++) {
      $values = array($t, $field['fid'], $field['fid'], $field['fid'], $field->common, $field->autocomplete, $field->required, $field->weight, $field->visible);
      db_query("INSERT INTO {biblio_field_type} (" . implode(", ", $field_type_fieldnames) . ")
                      VALUES('" . implode("', '", $values) . "')");
    }
    $ftd = array($field['fid'], $field->default_name, $field->hint);
    db_query("INSERT INTO {biblio_field_type_data} (" . implode(", ", $field_type_data_fieldnames) . ")
                    VALUES('" . implode("', '", $ftd) . "')");
    $field_data = array($field['fid'], $field->field_name, $field->type, $field->width, $field->maxlength);
    db_query("INSERT INTO {biblio_fields} (" . implode(", ", $fieldnames) . ")
                    VALUES('" . implode("', '", $field_data) . "')");
    foreach ($field->name as $name) {
      if ($name != "~" ) { //&& $field->type != 'contrib_widget') {
        $ftd[0] = ($existing_id = _id_by_name('biblio_field_type_data', $name)) ? $existing_id : variable_get('biblio_last_ftdid', 100); // ftdid
        $ftd[1] = trim($name);                          // title
        $ftd[2] = "";                                     // hint
        db_query("UPDATE {biblio_field_type}
                      SET ftdid = %d, cust_tdid = %d, visible = %d
                      WHERE tid = %d AND fid = %d ", $ftd[0], $ftd[0], 1, $name['tid'], $field['fid'] );
        if (!$existing_id) {
          // if this title doesn't alreay exist, then insert it into the table
          db_query("INSERT INTO {biblio_field_type_data} (" . implode(", ", $field_type_data_fieldnames) . ")
                        VALUES (%d, '%s', '%s')", $ftd);
          _id_by_name('biblio_field_type_data', $name, $ftd[0]);  // cache the new id value for future use
          variable_set('biblio_last_ftdid', $ftd[0] +1); //increment the field type data id by one.
        }

      }
      elseif ($name == "~" ) {
        // turn the visibility off for this (~) type
        db_query("UPDATE {biblio_field_type}
                      SET visible = 0
                      WHERE tid = %d AND fid = %d ", $name['tid'], $field['fid'] );
      }
      if ($field->type == 'contrib_widget' && $name != "~" ) {
//        // also populate biblio_contributor_type tables
//        $title = trim($name);
//        if ($name != "~" ) {
//          // turn the visibility off for this (~) type
//          db_query("UPDATE {biblio_field_type}
//                      SET visible = 0
//                      WHERE tid = %d AND fid = %d ", $name['tid'], $field['fid'] );
//        }else {
//          $ctdid = ($eid = _id_by_name('biblio_field_type_data',$title)) ? $eid :  $next_ctdid;
          db_query("UPDATE {biblio_contributor_type} SET auth_type=%d where auth_category=%d and biblio_type=%d", $ftd[0], $field->contrib_type, $name['tid']);
//          if (!$eid) {
//            db_query("INSERT INTO {biblio_contributor_type_data} (auth_type, title) VALUES (%d, '%s')", $ctdid, $title);
//            _id_by_name('biblio_contributor_type_data',$title, $ctdid);  // cache the new id value for future use
//            $next_ctdid++;
//        }
//        }
      }
    }
  }


  db_query("/*!40000 ALTER TABLE {biblio_field_type_data} ENABLE KEYS */;");
  db_query("/*!40000 ALTER TABLE {biblio_fields} ENABLE KEYS */;");

  return $result;
}

function _add_db_field_data($csv_file = NULL) {
  if (db_driver() == 'mysql' or db_driver() == 'mysqli') {
    db_query("/*!40000 ALTER TABLE {biblio_field_type_data} DISABLE KEYS */;");
    db_query("/*!40000 ALTER TABLE {biblio_fields} DISABLE KEYS */;");
  }
  if (!is_file($csv_file)) {
    $csv_file = drupal_get_path('module', 'biblio') . '/misc/biblio.field.link.data.csv';
  }

  if ($handle = fopen($csv_file, "r")) {
    $header = fgetcsv($handle, 10000, ","); // the first line has the field names
    while (($row = fgetcsv($handle, 10000, ",")) !== FALSE) {
      $column = 0;
      // add link data for default biblio type (0) and all other defined types (100-130)
      foreach (array_merge(array(0), range(100, 136)) as $t) {
        db_insert('biblio_field_type')->fields(array(
          'tid'          => $t,
          'fid'          => $row[0],
          'ftdid'        => $row[0],
          'cust_tdid'    => $row[0],
          'common'       => $row[3],
          'autocomplete' => $row[4],
          'required'     => $row[5],
          'weight'       => $row[6],
          'visible'      => $row[7],
          'vtab'         => $row[12]
        ))->execute();
      }

      db_insert('biblio_field_type_data')->fields(array(
        'ftdid' => $row[0],
        'title' => $row[1],
        'hint'  => $row[2]
      ))->execute();

      db_insert('biblio_fields')->fields(array(
        'fid'     => $row[0],
        'name'    => $row[8],
        'type'    => $row[9],
        'size'    => $row[10],
        'maxsize' => $row[11]
      ))->execute();

      // add contributor type data
      if ($row[9] == 'contrib_widget') {
        // use field name without trailing 's' as initial guess for author type
        $auth_type = (substr($row[1], -1, 1) == 's') ? substr($row[1], 0, -1) : $row[1];

        db_insert('biblio_contributor_type_data')->fields(array(
          'auth_type' => $row[0],
          'title'     => $auth_type
        ))->execute();

        db_insert('biblio_contributor_type')->fields(array(
          'auth_category' => $row[0],
          'biblio_type'   => 0,
          'auth_type'     => $row[0]
        ))->execute();
      }
    }
    fclose($handle);
    $result = array('success' => TRUE, 'query' => 'Added field titles and default values');

  }
  else {
    $result = array('success' => FALSE, 'query' => 'Could not open ' . $csv_file);
  }

  if (db_driver() == 'mysql' or db_driver() == 'mysqli') {
    db_query("/*!40000 ALTER TABLE {biblio_field_type_data} ENABLE KEYS */;");
    db_query("/*!40000 ALTER TABLE {biblio_fields} ENABLE KEYS */;");
  }
  return $result;
}

function _add_custom_field_data() {

  $next_ctdid=10; //first contributor_type_data id
  $schema = biblio_schema();
  $fieldnames = array_keys($schema['biblio_field_type_data']['fields']);

  $query = "SELECT fid, name FROM {biblio_fields} ";
  $res = db_query($query);
  foreach ($res as $row) {
    $fieldmap[$row->name] =  $row->fid;
  }

  $csv_file = drupal_get_path('module', 'biblio') . '/misc/biblio.field.type.data.csv';

  if ($handle = fopen($csv_file, "r")) {
    $header = fgetcsv($handle, 10000, ","); // the first line has the field names
    $generic = fgetcsv($handle, 10000, ","); // the second line has the default titles if none given
    // build cache lookups
    _id_by_name(NULL, NULL, NULL, array('tablename' => 'biblio_field_type_data', 'name_column' => 'title', 'id_column' => 'ftdid'));
    _id_by_name(NULL, NULL, NULL, array('tablename' => 'biblio_contributor_type_data', 'name_column' => 'title', 'id_column' => 'auth_type'));
    // map contributor field titles to field ids
    $res = db_query("SELECT fid,name FROM {biblio_fields} WHERE type='contrib_widget'");
    $contributor_categories = array();
    foreach ($res as $row ) {
      $contributor_categories[$row->name] = $row->fid;
    }
    // process all rows of the file
    while (($row = fgetcsv($handle, 10000, ",")) !== FALSE) {
      $column = 0;
      if (empty($row[1])) continue;

      foreach ($header as $key => $field_name) {
        if (!empty($field_name) && $field_name != 'tid') {
          if (!empty($row[$column]) && $row[$column] != "~" && isset($fieldmap[$field_name])) {
             $ftd[0] = ($existing_id = _id_by_name('biblio_field_type_data', $row[$column])) ? $existing_id : variable_get('biblio_last_ftdid', 100); // ftdid
             $ftd[1] = trim($row[$column]);                    // title
             $ftd[2] = "";                                     // hint

             db_update('biblio_field_type')
               ->fields(array( 'ftdid' => $ftd[0], 'cust_tdid' => $ftd[0], 'visible'   => 1))
               ->condition(db_and()->condition('tid', $row[1])->condition('fid', $fieldmap[$field_name]))
               ->execute();

             if (!$existing_id) {
               // if this title doesn't alreay exist, then insert it into the table
              db_insert('biblio_field_type_data')
              ->fields(array('ftdid' => $ftd[0], 'title' => $ftd[1], 'hint'  => $ftd[2]))
              ->execute();

               _id_by_name('biblio_field_type_data', $row[$column], $ftd[0]);  // cache the new id value for future use
              variable_set('biblio_last_ftdid', $ftd[0] +1); //increment the field type data id by one.
             }

             // also populate biblio_contributor_type tables
             if ((substr($field_name, -7, 7) == 'authors') && $row[$column] != '~' ) {
               $type = $contributor_categories[$field_name];
              $title = trim($row[$column]);
              $biblio_type = $row[1];
              $ctdid = ($eid = _id_by_name('biblio_contributor_type_data', $title)) ? $eid :  $next_ctdid;
              db_update('biblio_contributor_type')
                ->fields(array(
                  'auth_type' => $ctdid))
                ->condition(db_and()->condition('auth_category', $type)->condition('biblio_type', $biblio_type))
                ->execute();

              if (!$eid) {
                db_insert('biblio_contributor_type_data')
                  ->fields(array('auth_type' => $ctdid, 'title' => $title))
                  ->execute();

                _id_by_name('biblio_contributor_type_data', $title, $ctdid);  // cache the new id value for future use
                $next_ctdid++;
              }
             }
          }
          elseif ($row[$column] == "~" && isset($fieldmap[$field_name])) {
            // turn the visibility off for this (~) type

            db_update('biblio_field_type')
              ->fields(array('visible' => 0))
              ->condition(db_and()->condition('tid', $row[1])->condition('fid', $fieldmap[$field_name]))
              ->execute();

          }
          elseif (empty($row[$column]) && isset($fieldmap[$field_name])) {
            // use the default field title when the title is blank
            db_update('biblio_field_type')
              ->fields(array('visible' => 1))
              ->condition(db_and()->condition('tid', $row[1])->condition('fid', $fieldmap[$field_name]))
              ->execute();
          }
        }
        $column++;
      }
    }
    fclose($handle);
    $result = array('success' => TRUE, 'query' => 'Added type specific field titles');
  }
  else {
    $result = array('success' => FALSE, 'query' => 'Could not open ' . $csv_file);
  }

  return $result;
}
function _id_by_name($table, $name, $id = NULL, $build = NULL) {
  static $result = NULL;
  if (!empty($build)) { //refresh cache from table
    unset($result[$build['tablename']]);
    $res = db_query("SELECT " . $build['name_column'] . ", " . $build['id_column'] . " FROM {" . $build['tablename'] . "}", array(), array('fetch' => PDO::FETCH_ASSOC));
    foreach ($res as $row ) {
      $result[$build['tablename']][$row[$build['name_column']]] = $row[$build['id_column']];
    }
    return;
  }
  $name = trim($name);
  if (isset($result[$table][$name])) return $result[$table][$name];
  if ($id) $result[$table][$name] = $id;
  return FALSE;
}
/*
 * Removed updates 1 - 27 since they were from 5.x biblio
 */

/*
 * Removed updates 6000 - 6023 only upgrades from  biblio 6.x-1.9 are supported
 */
/* add the new field -refereed- on the biblio table
*/
function biblio_update_6024() {
  $result = array();

  db_add_field($result, 'biblio', 'biblio_refereed', array('type' => 'varchar', 'length' => '20') );

  /* add the field data for -refereed- on the biblo_fields table
   you need to get the last inserted record from biblio_fields and increment it by one
   so you don't step on customized fields added via the user online interface */

  $sql = 'SELECT fid FROM {biblio_fields} ORDER BY fid DESC LIMIT 1';
  $lastfid = db_result(db_query($sql));
  $newfid  = $lastfid + 1;

  $result[] = update_sql("INSERT INTO {biblio_fields} (fid, name, type, size, maxsize) VALUES
                        ($newfid, 'biblio_refereed', 'select', 0, 125)");

  /*use the same fid and insert an entry in the biblio_field_type_data */
  $result[] = update_sql("INSERT INTO {biblio_field_type_data}
       (ftdid, title, hint) VALUES ($newfid, 'Refereed Designation', NULL)");

  /* get a list of unique tids from the biblio_field_type table.  You want to
   insert a tid,fid using the new fid for every available tid */

  $newsql = "SELECT DISTINCT tid FROM {biblio_field_type} ORDER BY tid DESC";

  $tidlist = db_query($newsql);
  while ($db_result = db_fetch_array($tidlist)) {
    $newtid = $db_result['tid'] ;
    db_query('INSERT INTO {biblio_field_type}
       (tid, fid, ftdid, cust_tdid, common, autocomplete, required, weight, visible)
        VALUES (%d, %d, %d, %d, %d, %d, %d, %d, %d)',
    $newtid, $newfid, $newfid, $newfid, 1, 1, 0, 1, 1);
  }

  return $result;
}
function biblio_update_6025() {
  $result = array();
  $schema = biblio_schema();
  db_create_table($result, 'biblio_type_maps', $schema['biblio_type_maps']);
  return $result;
}

function biblio_update_6026() {
  $result = array();
  // move custom block titles stored in variable "biblio_block_title" to the block table if the title has not already been overriden
  $custom_title = variable_get('biblio_block_title', '');
  if (!empty($custom_title)) {
    $db_result = db_query("SELECT bid,title FROM {blocks} b where module='biblio' ");
    while ($block = db_fetch_object($db_result)) {
      if (empty ($block->title)) {
        $block->title = $custom_title;
        $result[] = update_sql("UPDATE {blocks} SET title='" . $block->title . "' WHERE bid=" . $block->bid);
      }
    }
    variable_del('biblio_block_title');
  }
  return $result;
}
function biblio_update_6027() {
  // renunmber the author rank such that it is zero based accross all categories
  // this only needs to be done for entries that actually have auth_categories other than 1
  require_once(drupal_get_path('module', 'biblio') . '/biblio.contributors.inc');
  $result =  array();
  $count = 0;
  $db_result = db_query("SELECT DISTINCT(vid),nid FROM {biblio_contributor} WHERE auth_category IN (2,3,4,5) ");
  $db_count_result = db_query("SELECT COUNT(DISTINCT(vid)) FROM {biblio_contributor} WHERE auth_category IN (2,3,4,5) ");
  $count_success = db_result($db_count_result);
  while ($node = db_fetch_object($db_result)) {
    $contributors = biblio_load_contributors($node->vid);
    _save_contributors($contributors, $node->nid, $node->vid, $update = FALSE) ;
    $count++;
  }
  $mesg = "Reordered the authors on $count/$count_success nodes";
  $result[] = array('success' => ($count_success == $count),
                    'query' => $mesg);
  return $result;
}

function biblio_update_6028() {
  $ret = array();

  $table = drupal_get_schema_unprocessed('system', 'cache');
  $table['description'] = 'Cache table for biblio to store pre-built csl objects';
  $table['fields']['serialized']['default'] = 1;

  return $ret;
}

function biblio_update_6029() {
  $spec = array(
        'type' => 'blob',
        'not null' => FALSE,
        'default'  => NULL,
        'size' => 'big',
        'description' => 'Stores the mapping between biblio fields and external file formats',
        );
  db_add_field('biblio_type_maps', 'export_map', $spec);
}

function biblio_update_6030() {

  $spec = array(
        'type' => 'int',
        'not null' => TRUE,
        'default'  => 0,
        'unsigned' => TRUE,
        'description' => 'Determines if the author name is allowed to be reformated by the variaous styles or should be used literally.',
        );
  db_add_field('biblio_contributor_data', 'literal', $spec);

}

function biblio_update_6031() {
  $result = array();
  $types[] = array(131,'Journal',NULL,3);
  $types[] = array(132,'Web site',NULL,8);
  $types[] = array(133,'Web service','e.g. Google, Yahoo',8);
  $types[] = array(134,'Web project page',NULL,8);
  $types[] = array(135,'Presentation',NULL,8);
  $types[] = array(136,'Newspaper',NULL,8);

  foreach($types as $record)
  {
    db_query("INSERT INTO {biblio_types} (tid, name, description, weight) VALUES ('" . implode("', '", $record) . "')");
  }
    db_query("DELETE FROM {biblio_types} WHERE tid=-1");

 return $result;
}
function biblio_update_6032() {
  $spec = array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
        'default' => '',
        'description' => 'Full name',
        );
  db_change_field('biblio_contributor_data', 'name', 'name', $spec);
}
function biblio_update_6033() {
  $spec = array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '64',
        'description' => 'A normalized version of the title, used for sorting on titles. (only first 64 characters saved)',
  );
  db_add_field('biblio', 'biblio_sort_title', $spec);
}

function biblio_update_7000() {

  _biblio_helper_modules('install');

}
/**
 * Add new column to biblio_contributor_data table
 */
function biblio_update_7001() {
  if (!db_field_exists('biblio_contributor_data', 'literal')) {
    $spec = array(
        'type' => 'int',
        'not null' => TRUE,
        'default'  => 0,
        'unsigned' => TRUE,
        'description' =>'Determines if the author name is allowed to be reformated by the variaous styles or should be used literally.',
        );
    db_add_field('biblio_contributor_data', 'literal', $spec);
  }
}
/**
 *
 * Adds export_map column to biblio_type_maps table
 */
function biblio_update_7002() {
  if (!db_field_exists('biblio_type_maps', 'export_map')) {
    biblio_update_6029();
  }
}
/**
 *
 * Adds some new publication types
 */
function biblio_update_7003() {
  $result = db_query('SELECT tid FROM {biblio_types} WHERE tid = :tid', array(':tid' => 136))->fetchField();
  if (!$result) {
    biblio_update_6031();
  }
}
function _biblio_update_field_link_data($range, $vtabs = FALSE){
  $csv_file = drupal_get_path('module', 'biblio') . '/misc/biblio.field.link.data.csv';

  if ($handle = fopen($csv_file, "r")) {
    $header = fgetcsv($handle, 10000, ","); // the first line has the field names
    while (($row = fgetcsv($handle, 10000, ",")) !== FALSE) {
      if ($vtabs) {
        // add link data for default biblio type (0) and all other defined types (100-130)
        foreach (array_merge(array(0), range($range[0], $range[1])) as $t) {
          db_update('biblio_field_type')
          ->fields(array(
                'vtab' => $row[12]
          ))
          ->condition(db_and()->condition('tid', $t)->condition('fid', $row[0]))
          ->execute();
        }
      }
      else {
        foreach (range($range[0], $range[1]) as $t) {
          db_insert('biblio_field_type')->fields(array(
          'tid'          => $t,
          'fid'          => $row[0],
          'ftdid'        => $row[0],
          'cust_tdid'    => $row[0],
          'common'       => $row[3],
          'autocomplete' => $row[4],
          'required'     => $row[5],
          'weight'       => $row[6],
          'visible'      => $row[7],
          'vtab'         => $row[12]
          ))->execute();
        }
      }
    }
  }

}

/**
 * Add information to manage vtabs on input form.
*/
function biblio_update_7005() {
  $spec = array(
        'type' => 'int',
        'not null' => TRUE,
        'unsigned' => TRUE,
        'default' => 0,
  );
  db_add_field('biblio_field_type', 'vtab', $spec);
  _biblio_update_field_link_data(array(100, 130), TRUE);
  cache_clear_all();
}

function biblio_update_7006() {
  $result = db_query('SELECT fid FROM {biblio_field_type} WHERE tid = :tid', array(':tid' => 136))->fetchField();
  if (!$result) {
    _biblio_update_field_link_data(array(131, 136));
    cache_clear_all();
  }
}
/**
 * Increases the size of the {biblio_contributor_data}.name column to 255 characters
*/
function biblio_update_7007() {
  $spec = array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
        'default' => '',
        'description' => 'Full name',
        );
  db_change_field('biblio_contributor_data', 'name', 'name', $spec);
}
/**
 * Adds new "biblio_sort_title" column to the biblio table, which is used for title sorting.
*/
function biblio_update_7008() {
  if (!db_field_exists('biblio', 'biblio_sort_title')) {
    biblio_update_6033();
  }
}

/**
 * Populates the  new "biblio_sort_title" column, which is used for title sorting.
*/
function biblio_update_7009(&$sandbox) {
  $sandbox['#finished'] = 0;
  module_load_include('inc', 'biblio', '/includes/biblio.util');

  if (!isset($sandbox['max'])) {
    $sandbox['max'] = db_query('SELECT COUNT(DISTINCT vid) FROM {node} n WHERE n.type = :type', array(':type' => 'biblio'))->fetchField();
    $sandbox['current_vid'] = 0;
  }

  $nodes = db_select('node', 'n')
    ->fields('n', array('vid', 'title'))
    ->condition('vid', $sandbox['current_vid'], '>')
    ->condition('type', 'biblio')
    ->range(0, 20)
    ->orderBy('vid', 'ASC')
    ->execute();

  foreach ($nodes as $node) {
    $node->biblio_sort_title = biblio_normalize_title($node->title);
    db_update('biblio')
      ->fields(array('biblio_sort_title' => $node->biblio_sort_title))
      ->condition('vid', $node->vid)
      ->execute();

    $sandbox['progress']++;
    $sandbox['current_vid'] = $node->vid;
  }

  $sandbox['#finished'] = empty($sandbox['max']) ? 1 : ($sandbox['progress'] / $sandbox['max']);
}
/**
 * Removes "biblio_inlinemode_in_links" variable
 */
function biblio_update_7010() {
  variable_del('biblio_inlinemode_in_links');
}
/**
 * Add a body field instance
 */
function biblio_update_7011() {
  $content_type = node_type_load('biblio');
  node_add_body_field($content_type, 'Full text');
}
/**
 * Update biblio_field_type table
 */
function biblio_update_7012() {

  // there was a problem with update 7006 and it might no have done anything so lets try again.
  biblio_update_7006();
}

function biblio_update_7013() {
  db_add_index('biblio', 'title_sort', array('biblio_sort_title'));
  db_add_index('biblio', 'date', array('biblio_date'));

}

/**
 *
 * Widen the biblio_date column to 64 characters
 */
function biblio_update_7014() {
  $spec =  array(
        'type' => 'varchar',
        'not null' => FALSE,
        'length' => '64',
        'description' => '',
  );
  db_change_field('biblio', 'biblio_date', 'biblio_date', $spec);

}
/**
 *
 * Add biblio_formats column to biblio table to hold the format information for each text area
 */
function biblio_update_7015() {
  if (!db_field_exists('biblio', 'biblio_formats')) {
    $spec =  array(
              'type' => 'blob',
              'not null' => FALSE,
              'description' => '',
              'serialize' => TRUE,
      );
    db_add_field('biblio', 'biblio_formats', $spec);
  }
}
/**
 * Convert textarea fields to text_format
 */
function biblio_update_7016() {
    db_update('biblio_fields')
      ->fields(array('type' => 'text_format'))
      ->condition('type', 'textarea')
      ->execute();
}

/**
 * Remove views export handlers in sub-modules (if they still exist)
 */
function biblio_update_7017() {
  $dirs = array('bibtexParse', 'endnote', 'RIS', 'rtf');
  foreach ($dirs as $dir) {
    $path = drupal_get_path('module', 'biblio') . '/modules/'.$dir.'/views';
    if (is_dir($path)) {
      $message = t('You have an inconsistancy in your installation, the directory: @path, should not exist!', array('@path' => $path));
      drupal_set_message($message, 'error');
    }
  }
  if (module_exists('views')) { // rebuild the data tables
    views_invalidate_cache();
  }
}