Functions
	tripal_organism_views_data ()
	tripal_organism_views_handlers ()
	tripal_organism_views_default_views ()

Function Documentation

tripal_organism_views_data ( )

Implements hook_views_data() Purpose: Describe chado/tripal tables & fields to views

Returns:: : a data array which follows the structure outlined in the views2 documentation for this hook. Essentially, it's an array of table definitions keyed by chado/tripal table name. Each table definition includes basic details about the table, fields in that table and relationships between that table and others (joins)

Definition at line 29 of file tripal_organism.views.inc.

                                       {
  $data = array();

  if (module_exists('tripal_views')) {
    // Base Table
    $tables = array(
      'organism'
    );
    foreach ($tables as $tablename) {
      $priority = 9;

      // check to see if the table is integrated. If it is then integrate it's
      // corresponding 'chado_[table]' table.
      if (!tripal_views_is_integrated($tablename, $priority)) {
        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE, $priority);

        // Add specialty handlers
        $table_integration_array['fields']['common_name']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_string';
        $table_integration_array['fields']['genus']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_string';
        $table_integration_array['fields']['species']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_string';
        $table_integration_array['fields']['abbreviation']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_string';

        // Add in node relationships if chado is in the same db as drupal
        if (tripal_core_chado_schema_exists()) {
          $integrations = tripal_views_add_node_relationship_to_chado_table_integration($table_integration_array);
          foreach ($integrations as $integration) {
            tripal_views_integration_add_entry($integration);
          }
        }
        else {
          tripal_views_integration_add_entry($table_integration_array);
        }
      }
    }

    // Additional Tables
    $tables = array(
      'organismprop',
      'organism_dbxref'
    );
    foreach ($tables as $tablename) {
      $priority = 9;
      if (!tripal_views_is_integrated($tablename, $priority)) {
        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, FALSE, $priority);
        tripal_views_integration_add_entry($table_integration_array);
      }
    }
  }

  return $data;
}

tripal_organism_views_default_views ( )

$filters = $view->get_items('filter', 'default'); $filters['status'] = array( 'operator' => '=', 'value' => '1', 'group' => '0', 'exposed' => FALSE, 'expose' => array( 'operator' => FALSE, 'label' => '', ), 'id' => 'status', 'table' => 'node', 'field' => 'status', 'relationship' => 'none', ); $default_handler->override_option('filters', $filters);

Definition at line 136 of file tripal_organism.views.inc.

                                               {
  $views = array();

  if (!module_exists('tripal_views')) {
    return $views;
  }

  // Main default view
  $view = new view;
  $view->name = 'organism_listing';
  $view->description = 'A listing of all organism in chado';
  $view->tag = 'chado default';
  $view->base_table = 'organism';
  $view->core = 0;
  $view->api_version = '2';
  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
  $handler = $view->new_display('default', 'Defaults', 'default');
  $handler->override_option('fields', array(
    'common_name' => array(
      'label' => 'Common Name',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'link_class' => '',
        'alt' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'link_to_node' => 1,
      'exclude' => 0,
      'id' => 'common_name',
      'table' => 'organism',
      'field' => 'common_name',
      'relationship' => 'none',
    ),
    'genus' => array(
      'label' => 'Genus',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'link_class' => '',
        'alt' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'exclude' => 0,
      'id' => 'genus',
      'table' => 'organism',
      'field' => 'genus',
      'relationship' => 'none',
    ),
    'species' => array(
      'label' => 'Species',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'link_class' => '',
        'alt' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'exclude' => 0,
      'id' => 'species',
      'table' => 'organism',
      'field' => 'species',
      'relationship' => 'none',
    ),
    'abbreviation' => array(
      'label' => 'Abbreviation',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'link_class' => '',
        'alt' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'link_to_node' => 0,
      'exclude' => 0,
      'id' => 'abbreviation',
      'table' => 'organism',
      'field' => 'abbreviation',
      'relationship' => 'none',
    ),
  ));
  $handler->override_option('sorts', array(
    'genus' => array(
      'order' => 'ASC',
      'id' => 'genus',
      'table' => 'organism',
      'field' => 'genus',
      'relationship' => 'none',
    ),
    'species' => array(
      'order' => 'ASC',
      'id' => 'species',
      'table' => 'organism',
      'field' => 'species',
      'relationship' => 'none',
    ),
  ));
  $handler->override_option('access', array(
    'type' => 'perm',
    'perm' => 'access chado_organism content',
  ));
  $handler->override_option('cache', array(
    'type' => 'none',
  ));
  $handler->override_option('title', 'Organisms');
  $handler->override_option('empty', 'No organisms matched the supplied criteria.');
  $handler->override_option('empty_format', '1');
  $handler->override_option('items_per_page', 0);
  $handler->override_option('style_plugin', 'table');
  $handler->override_option('style_options', array(
    'grouping' => '',
    'override' => 1,
    'sticky' => 0,
    'order' => 'asc',
    'summary' => '',
    'columns' => array(
      'common_name' => 'common_name',
      'genus' => 'genus',
      'species' => 'species',
      'abbreviation' => 'abbreviation',
    ),
    'info' => array(
      'common_name' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'genus' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'species' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'abbreviation' => array(
        'sortable' => 1,
        'separator' => '',
      ),
    ),
    'default' => '-1',
  ));
  $default_handler = $handler;
  $handler = $view->new_display('page', 'Page', 'page_1');
  $handler->override_option('path', 'chado/organisms');
  $handler->override_option('menu', array(
    'type' => 'normal',
    'title' => 'Organisms',
    'description' => 'A biological organism.',
    'weight' => '10',
    'name' => 'navigation',
  ));
  $handler->override_option('tab_options', array(
    'type' => 'none',
    'title' => '',
    'description' => '',
    'weight' => 0,
    'name' => 'navigation',
  ));
  // Add code specific to a local chado installation
  // NOTE: Edit $handler above to $default_handler for the default display
  if (tripal_core_chado_schema_exists()) {
    // Add nid field
    $fields = $view->get_items('field', 'default');
    $new_fields = array(
      'nid' => array(
        'label' => 'Nid',
        'alter' => array(
          'alter_text' => 0,
          'text' => '',
          'make_link' => 0,
          'path' => '',
          'absolute' => 0,
          'link_class' => '',
          'alt' => '',
          'rel' => '',
          'prefix' => '',
          'suffix' => '',
          'target' => '',
          'help' => '',
          'trim' => 0,
          'max_length' => '',
          'word_boundary' => 1,
          'ellipsis' => 1,
          'html' => 0,
          'strip_tags' => 0,
        ),
        'empty' => '',
        'hide_empty' => 0,
        'empty_zero' => 0,
        'hide_alter_empty' => 1,
        'link_to_node' => 0,
        'exclude' => 1,
        'id' => 'nid',
        'table' => 'node',
        'field' => 'nid',
        'relationship' => 'none',
      )
    );
    $fields = $new_fields + $fields;
    // Adds organism => Node relationship
    $default_handler->override_option('relationships', array(
      'nid' => array(
        'label' => 'Organism to Node',
        'required' => 0,
        'id' => 'nid',
        'table' => 'chado_organism',
        'field' => 'nid',
        'relationship' => 'none',
      ),
    ));
    // Change analysis.name to have a link to the node
    $fields['common_name']['alter']['link_to_node'] = 1;
    $default_handler->override_option('fields', $fields);
    // Only show records with published nodes
  }
  $views[$view->name] = $view;

  return $views;
}

tripal_organism_views_handlers ( )

Implements hook_views_handlers() Purpose: Register all custom handlers with views where a handler describes either "the type of field", "how a field should be filtered", "how a field should be sorted"

Returns:: : An array of handler definitions

Definition at line 90 of file tripal_organism.views.inc.

                                          {
  return array(
    'info' => array(
      'path' => drupal_get_path('module', 'tripal_organism') . '/views/handlers',
    ),
    'handlers' => array(
      'views_handler_field_computed_organism_nid' => array(
        'parent' => 'views_handler_field_numeric',
      ),
      'views_handler_filter_organism_common_name' => array(
      'parent' => 'views_handler_filter_string',
    ),
    ),
  );
}

Functions

Function Documentation