tripal_chado.views.inc

<?php
/**
 * @file
 * Integrates many of the core database tables with drupal views
 */

/**
 * Describe various Tripal Core systems to Views for the creation of
 * administrative views.
 *
 * @ingroup tripal
 */
function tripal_chado_views_data() {
  $data = array();

  // Custom Tables Management
  $data = tripal_chado_views_data_custom_tables($data);

  // Materialized Views Management
  $data = tripal_chado_views_data_mviews($data);

  return $data;
}

// /**
//  * Implements hook_views_data_alter().
//  */
// function tripal_chado_views_data_alter(&$data) {

//   // Adds integration for chado-based fields.
//   tripal_chado_add_field_views_data($data);

//   return $data;
// }

// /**
//  * Adds integration for chado-based fields.
//  *
//  * We can't use hook_field_view_data since this only works when the
//  * storage engine is of type 'field_sql_storage' and of course,
//  * ours is not. Thus we create our own implementation of field_views_data()
//  * for our storage engine.
//  */
// function tripal_chado_add_field_views_data(&$data) {
//   foreach (field_info_fields() as $field) {
//     if ($field['storage']['type'] != 'field_chado_storage') {
//       continue;
//     }

//     $field_name = $field['field_name'];
//     $field_type = $field['type'];


//     // Currently, we only handle integration of chado fields with TripalEntity.
//     // @todo: extend this to work with other entities in the future.
//     if (isset($field['bundles']['TripalEntity']) AND isset($field['settings']['chado_column'])) {

//       // We currently don't support prop tables for views integration due
//       // in part to the multiple values but also b/c we can't indicate which
//       // type of property to show. Thus, instead of warning the user,
//       // we just won't integrate it at this time.
//       // @todo: Handle property fields.
//       if (preg_match('/prop$/', $field['settings']['chado_table'])) {
//         continue;
//       }

//       // Get some information about the chado table in order to make good
//       // default choices for handlers.
//       $table_desc = chado_get_schema($field['settings']['chado_table']);
//       $field_defn = $table_desc['fields'][ $field['settings']['chado_column'] ];

//       // We also need to know if this field is a foreign key.
//       $fk_defn = FALSE;
//       foreach ($table_desc['foreign keys'] as $details) {
//         foreach ($details['columns'] as $left_field => $right_field) {
//           if ($left_field == $field['settings']['chado_column']) {
//             $fk_defn = array(
//               'left_table' => $field['settings']['chado_table'],
//               'left_field' => $left_field,
//               'right_table' => $details['table'],
//               'right_field' => $right_field,
//             );
//           }
//         }
//       }

//       // Unfortunatly we can't use the field label since that is set at the
//       // instance level and fields are integrated at the field level (independant of bundle).
//       // Thus we will simply make the most readable and informative field name we can.
//       $data['tripal_entity'][$field_name]['title'] = ucfirst(str_replace('_',' ',$field['settings']['chado_table']))
//         . ': ' .ucfirst(str_replace('_',' ',$field['settings']['chado_column']));

//       // The help should be 'Appears in: TripalEntity: gene, organism'
//       // so that users know where they can use it. This requires a little extra work since all
//       // we have access to at this point is bio_data_2, bio_data_4 but since that's not very
//       // informative, extra work is worth it ;-).
//       $entity_info = entity_get_info('TripalEntity');
//       $bundle_labels = array();
//       foreach ($field['bundles']['TripalEntity'] as $bundle_id) {
//         $bundle_labels[] = $entity_info['bundles'][$bundle_id]['label'];
//       }
//       $data['tripal_entity'][$field_name]['help'] = 'Appears in: TripalEntity:' . implode(', ', $bundle_labels);

//       // Define the field.
//       $data['tripal_entity'][$field_name]['field']['chado_field'] = $field['settings']['chado_column'];
//       $data['tripal_entity'][$field_name]['field']['chado_table'] = $field['settings']['chado_table'];
//       $data['tripal_entity'][$field_name]['field']['field_name'] = $field['field_name'];
//       $data['tripal_entity'][$field_name]['field']['entity_table'] = 'tripal_entity';
//       $data['tripal_entity'][$field_name]['field']['entity_type'] = 'TripalEntity';
//       $data['tripal_entity'][$field_name]['field']['bundles'] = $field['bundles']['TripalEntity'];
//       $data['tripal_entity'][$field_name]['field']['handler'] = 'chado_views_handler_field';
//       $data['tripal_entity'][$field_name]['field']['click sortable'] = FALSE;

//       // Define the Filter.
//       $data['tripal_entity'][$field_name]['filter']['chado_field'] = $field['settings']['chado_column'];
//       $data['tripal_entity'][$field_name]['filter']['chado_table'] = $field['settings']['chado_table'];
//       $data['tripal_entity'][$field_name]['filter']['field_name'] = $field['field_name'];
//       $data['tripal_entity'][$field_name]['filter']['entity_table'] = 'tripal_entity';
//       $data['tripal_entity'][$field_name]['filter']['entity_type'] = 'TripalEntity';
//       $data['tripal_entity'][$field_name]['filter']['bundles'] = $field['bundles']['TripalEntity'];
//       $data['tripal_entity'][$field_name]['filter']['handler'] = 'chado_views_handler_filter_string';

//       // Define sorting.
//       $data['tripal_entity'][$field_name]['sort']['chado_field'] = $field['settings']['chado_column'];
//       $data['tripal_entity'][$field_name]['sort']['chado_table'] = $field['settings']['chado_table'];
//       $data['tripal_entity'][$field_name]['sort']['field_name'] = $field['field_name'];
//       $data['tripal_entity'][$field_name]['sort']['entity_table'] = 'tripal_entity';
//       $data['tripal_entity'][$field_name]['sort']['entity_type'] = 'TripalEntity';
//       $data['tripal_entity'][$field_name]['sort']['bundles'] = $field['bundles']['TripalEntity'];
//       $data['tripal_entity'][$field_name]['sort']['handler'] = 'chado_views_handler_sort';

//       // Specify special handlers.
//       if ($fk_defn) {
//         $data['tripal_entity'][$field_name]['filter']['handler'] = 'chado_views_handler_filter_fk';
//         $data['tripal_entity'][$field_name]['filter']['foreign_key'] = $fk_defn;
//       }
//       if ($field_defn['type'] == 'boolean') {
//         $data['tripal_entity'][$field_name]['filter']['handler'] = 'chado_views_handler_filter_boolean';
//         $data['tripal_entity'][$field_name]['filter']['label'] = $field['settings']['chado_column'];
//         $data['tripal_entity'][$field_name]['filter']['type'] = 'yes-no';
//       }
//       elseif ($field_defn['type'] == 'datetime') {
//         $data['tripal_entity'][$field_name]['filter']['handler'] = 'chado_views_handler_filter_date';
//       }

//       // Allow the fields to alter the default selections from above.
//       tripal_load_include_field_type($field_type);
//       if (preg_match('/^chado/', $field_type) and class_exists($field_type)) {
//         $field_obj = new $field_type($field);
//         $field_obj->views_data_alter($data['tripal_entity'][$field_name], $field, $entity_info);
//       }
//     }
//   }
// }

/**
 * Provides the data array for the tripal custom tables management
 *
 * @param $data
 *   Previously generated tripal views data array
 * return
 *   $data array with custom tables management described
 *
 * @ingroup tripal
 */
function tripal_chado_views_data_custom_tables($data) {

  $data['tripal_custom_tables']['table']['group'] = t('Tripal Custom Tables');
  $data['tripal_custom_tables']['table']['base'] = array(
    'field' => 'table_id', // This is the identifier field for the view.
    'title' => t('Tripal Custom Tables'),
    'help' => t('Custom Tables in Chado created by this Tripal Installation.'),
    'weight' => 10,
  );

  // Table ID
  $data['tripal_custom_tables']['table_id'] = array(
    'title' => t('Custom Table ID'),
    'help' => t('Custom table primary key.'),
    'field' => array(
      'handler' => 'views_handler_field_numeric',
      'click sortable' => TRUE,
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_numeric',
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
  );

  // Table Name
  $data['tripal_custom_tables']['table_name'] = array(
    'title' => t('Table Name'),
    'help' => t('The name of the table in the database.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  // Schema
  $data['tripal_custom_tables']['schema'] = array(
    'title' => t('Table Schema'),
    'help' => t('The schema definition of the table.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  // Table ID
  $data['tripal_custom_tables']['mview_id'] = array(
    'title' => t('Materialized View ID'),
    'help' => t('Foreign key to tripal_mviews table for the materialized view.'),
    'field' => array(
      'handler' => 'views_handler_field_numeric',
      'click sortable' => TRUE,
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_numeric',
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
  );


  return $data;
}

/**
 * Provides the data array for the tripal custom tables management
 *
 * @param $data
 *   Previously generated tripal views data array
 * return
 *   $data array with custom tables management described
 *
 * @ingroup tripal
 */
function tripal_chado_views_data_mviews($data) {

  $data['tripal_mviews']['table']['group'] = t('Tripal Materialized Views');
  $data['tripal_mviews']['table']['base'] = array(
    'field' => 'mview_id', // This is the identifier field for the view.
    'title' => t('Tripal Materialized Views'),
    'help' => t('Materialized Views in Chado created by this Tripal Installation.'),
    'weight' => 10,
  );

    // Implicit Join to Tripal Views
  $data['tripal_mviews']['table']['join'] = array(
    'tripal_views' => array(
      'left_field' => 'mview_id',
      'field' => 'mview_id',
    ),
  );

  // Mview ID
  $data['tripal_mviews']['mview_id'] = array(
    'title' => t('Materialized View ID'),
    'help' => t('The primary key.'),
    'field' => array(
      'handler' => 'views_handler_field_numeric',
      'click sortable' => TRUE,
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_numeric',
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
  );

  // name
  $data['tripal_mviews']['name'] = array(
    'title' => t('Name'),
    'help' => t('Human-readable name of the materialized view.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  // modulename
  $data['tripal_mviews']['modulename'] = array(
    'title' => t('Module Name'),
    'help' => t('The module that created the materialized view.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  // mv_table
  $data['tripal_mviews']['mv_table'] = array(
    'title' => t('Table'),
    'help' => t('The database table the materialized view is stored in.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  // mv_specs
  $data['tripal_mviews']['mv_specs'] = array(
    'title' => t('Specification'),
    'help' => t('Materialized View Specification.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  // mv_schema
  $data['tripal_mviews']['mv_schema'] = array(
    'title' => t('Schema'),
    'help' => t('Schema definition for the materialized view table.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  // indexed
  $data['tripal_mviews']['indexed'] = array(
    'title' => t('Indices'),
    'help' => t('Any indices for this materialized view.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  // query
  $data['tripal_mviews']['query'] = array(
    'title' => t('Query'),
    'help' => t('The query used to populate the materialized view.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  // special_index
  $data['tripal_mviews']['special_index'] = array(
    'title' => t('Special Index'),
    'help' => t('Any special indices for the materialized view.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  // last_update
  $data['tripal_mviews']['last_update'] = array(
    'title' => t('Updated'),
    'help' => t('Date Last Updated.'),
    'field' => array(
      'handler' => 'views_handler_field_date',
      'click sortable' => TRUE,
    ),
    'sort' => array(
      'handler' => 'views_handler_sort_date',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_date',
    ),
  );

  // status
  $data['tripal_mviews']['status'] = array(
    'title' => t('Status'),
    'help' => t('The status of the materialized view.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  // comment
  $data['tripal_mviews']['comment'] = array(
    'title' => t('Description'),
    'help' => t('Human-Readable Admin Description.'),
    'field' => array(
      'handler' => 'views_handler_field',
      'click sortable' => TRUE, // This is use by the table display plugin.
    ),
    'sort' => array(
      'handler' => 'views_handler_sort',
    ),
    'filter' => array(
      'handler' => 'views_handler_filter_string',
    ),
    'argument' => array(
      'handler' => 'views_handler_argument_string',
    ),
  );

  return $data;
}