Functions
	tripal_db_views_data ()
	tripal_db_views_default_views ()

Function Documentation

tripal_db_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_db.views.inc.

                                 {
  $data = array();

  if (module_exists('tripal_views')) {
    // Base Tables
    $tables = array(
      'db',
      'dbxref'
    );
    foreach ($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
        if ($tablename == 'db') {
          $table_integration_array['fields']['name']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_string';
        }

        tripal_views_integration_add_entry($table_integration_array);
      }
    }

    // Additional Tables
    $tables = array(
      'dbxrefprop'
    );
    foreach ($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_db_views_default_views ( )

Definition at line 76 of file tripal_db.views.inc.

                                         {
  $views = array();

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

  // Main DB default view
  $view = new view;
  $view->name = 'db_listing';
  $view->description = 'A listing of all databases.';
  $view->tag = 'chado default';
  $view->base_table = 'db';
  $view->core = 6;
  $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(
    'name' => array(
      'label' => 'Name',
      '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,
      'type' => 'separator',
      'separator' => ', ',
      'exclude' => 0,
      'id' => 'name',
      'table' => 'db',
      'field' => 'name',
      'relationship' => 'none',
    ),
    'description' => array(
      'label' => 'Description',
      '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,
      'type' => 'separator',
      'separator' => ', ',
      'exclude' => 0,
      'id' => 'description',
      'table' => 'db',
      'field' => 'description',
      'relationship' => 'none',
    ),
    'url' => array(
      'label' => 'Url',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 1,
        'path' => '[url]',
        'absolute' => 1,
        'link_class' => '',
        'alt' => '',
        'rel' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '_blank',
        '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,
      'type' => 'separator',
      'separator' => ', ',
      'exclude' => 0,
      'id' => 'url',
      'table' => 'db',
      'field' => 'url',
      'relationship' => 'none',
    ),
    'urlprefix' => array(
      'label' => 'Urlprefix',
      '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,
      'type' => 'separator',
      'separator' => ', ',
      'exclude' => 0,
      'id' => 'urlprefix',
      'table' => 'db',
      'field' => 'urlprefix',
      'relationship' => 'none',
    ),
  ));
  $handler->override_option('filters', array(
    'name' => array(
      'operator' => '~',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'name_op',
        'identifier' => 'name',
        'label' => 'Name Contains',
        'remember' => 0,
      ),
      'case' => 0,
      'id' => 'name',
      'table' => 'db',
      'field' => 'name',
      'relationship' => 'none',
      'values_form_type' => 'textfield',
      'multiple' => 0,
      'optional' => 0,
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 0,
      ),
    ),
    'description' => array(
      'operator' => '~',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'description_op',
        'identifier' => 'description',
        'label' => 'Description Contains',
        'remember' => 0,
      ),
      'case' => 0,
      'id' => 'description',
      'table' => 'db',
      'field' => 'description',
      'relationship' => 'none',
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 0,
      ),
    ),
    'search_results' => array(
      'operator' => '=',
      'value' => '',
      'group' => '0',
      'exposed' => FALSE,
      'expose' => array(
        'operator' => FALSE,
        'label' => '',
      ),
      'id' => 'search_results',
      'table' => 'views',
      'field' => 'search_results',
      'relationship' => 'none',
      'apply_button' => 'Show',
      'no_results_text' => 'Click "Show" to see a list of all databases matching the entered criteria. If you leave a any of the criteria blank then the databases will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all databases will be listed.',
    ),
  ));
  $handler->override_option('access', array(
    'type' => 'perm',
    'perm' => 'access chado_db content',
  ));
  $handler->override_option('cache', array(
    'type' => 'none',
  ));
  $handler->override_option('title', 'Databases');
  $handler->override_option('header', 'Click "Show" to see a list of all databases matching the entered criteria. If you leave a any of the criteria blank then the databases will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all databases will be listed.');
  $handler->override_option('header_format', '2');
  $handler->override_option('header_empty', 0);
  $handler->override_option('empty', 'No databases match the supplied criteria.');
  $handler->override_option('empty_format', '2');
  $handler->override_option('items_per_page', 50);
  $handler->override_option('use_pager', '1');
  $handler->override_option('style_plugin', 'table');
  $handler->override_option('style_options', array(
    'grouping' => '',
    'override' => 1,
    'sticky' => 0,
    'order' => 'asc',
    'summary' => '',
    'columns' => array(
      'name' => 'name',
      'url' => 'url',
      'urlprefix' => 'urlprefix',
      'description' => 'description',
    ),
    'info' => array(
      'name' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'url' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'urlprefix' => array(
        'sortable' => 0,
        'separator' => '',
      ),
      'description' => array(
        'sortable' => 0,
        'separator' => '',
      ),
    ),
    'default' => 'name',
  ));
  $handler = $view->new_display('page', 'Page', 'page_1');
  $handler->override_option('path', 'admin/tripal/tripal_db/list_dbs');
  $handler->override_option('menu', array(
    'type' => 'normal',
    'title' => 'DB Listing',
    'description' => 'Lists all databases available to create database references for.',
    'weight' => '10',
    'name' => 'navigation',
  ));
  $handler->override_option('tab_options', array(
    'type' => 'none',
    'title' => '',
    'description' => '',
    'weight' => 0,
    'name' => 'navigation',
  ));
  $views[$view->name] = $view;

  // Main dbxref default view
  $view = new view;
  $view->name = 'dbxref_listing';
  $view->description = 'A listing of all database references filtered by database';
  $view->tag = 'chado default';
  $view->base_table = 'dbxref';
  $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(
    'name' => array(
      'label' => 'Database',
      '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' => 'name',
      'table' => 'db',
      'field' => 'name',
      'relationship' => 'none',
    ),
    'accession' => array(
      'label' => 'Accession',
      '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' => 'accession',
      'table' => 'dbxref',
      'field' => 'accession',
      'relationship' => 'none',
    ),
    'description' => array(
      'label' => 'Description',
      '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' => 'description',
      'table' => 'dbxref',
      'field' => 'description',
      'relationship' => 'none',
    ),
    'version' => array(
      'label' => 'Version',
      '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' => 'version',
      'table' => 'dbxref',
      'field' => 'version',
      'relationship' => 'none',
    ),
    'urlprefix' => array(
      'label' => 'External Link',
      'alter' => array(
        'alter_text' => 1,
        'text' => '[name]:[accession]',
        'make_link' => 1,
        'path' => '[urlprefix][accession]',
        'absolute' => 1,
        'link_class' => '',
        'alt' => '',
        'rel' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '_blank',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 1,
      'empty_zero' => 0,
      'hide_alter_empty' => 1,
      'type' => 'separator',
      'separator' => ', ',
      'exclude' => 0,
      'id' => 'urlprefix',
      'table' => 'db',
      'field' => 'urlprefix',
      'relationship' => 'none',
    ),
  ));
  $handler->override_option('sorts', array(
    'name' => array(
      'order' => 'ASC',
      'id' => 'name',
      'table' => 'db',
      'field' => 'name',
      'relationship' => 'none',
    ),
    'accession' => array(
      'order' => 'ASC',
      'id' => 'accession',
      'table' => 'dbxref',
      'field' => 'accession',
      'relationship' => 'none',
    ),
  ));
  $handler->override_option('filters', array(
    'name' => array(
      'operator' => '=',
      'value' => array(),
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'name_op',
        'identifier' => 'db',
        'label' => 'Database',
        'remember' => 0,
      ),
      'case' => 1,
      'id' => 'name',
      'table' => 'db',
      'field' => 'name',
      'relationship' => 'none',
      'values_form_type' => 'select',
      'multiple' => 1,
      'optional' => 0,
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
    ),
    'accession' => array(
      'operator' => '~',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'accession_op',
        'identifier' => 'accession',
        'label' => 'Accession Contains',
        'remember' => 0,
      ),
      'case' => 0,
      'id' => 'accession',
      'table' => 'dbxref',
      'field' => 'accession',
      'relationship' => 'none',
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
    ),
    'search_results' => array(
      'operator' => '=',
      'value' => '',
      'group' => '0',
      'exposed' => FALSE,
      'expose' => array(
        'operator' => FALSE,
        'label' => '',
      ),
      'id' => 'search_results',
      'table' => 'views',
      'field' => 'search_results',
      'relationship' => 'none',
      'apply_button' => 'Show',
      'no_results_text' => 'Click "Show" to see a list of all database references matching the entered criteria. If you leave a any of the criteria blank then the database references will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all database references will be listed.',
    ),
  ));
  $handler->override_option('access', array(
    'type' => 'perm',
    'perm' => 'access chado_db content',
  ));
  $handler->override_option('cache', array(
    'type' => 'none',
  ));
  $handler->override_option('title', 'Database References');
  $handler->override_option('header', 'Click "Show" to see a list of all database references matching the entered criteria. If you leave a any of the criteria blank then the database references will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all database references will be listed.');
  $handler->override_option('header_format', '2');
  $handler->override_option('header_empty', 0);
  $handler->override_option('empty', 'There are no database references matching the above criteria. Please select a database in order to display all references to that database.');
  $handler->override_option('empty_format', '1');
  $handler->override_option('items_per_page', 50);
  $handler->override_option('use_pager', '1');
  $handler->override_option('style_plugin', 'table');
  $handler->override_option('style_options', array(
    'grouping' => '',
    'override' => 1,
    'sticky' => 0,
    'order' => 'asc',
    'columns' => array(
      'name' => 'name',
      'accession' => 'accession',
      'description' => 'description',
      'version' => 'version',
    ),
    'info' => array(
      'name' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'accession' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'description' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'version' => array(
        'sortable' => 1,
        'separator' => '',
      ),
    ),
    'default' => '-1',
  ));
  $handler = $view->new_display('page', 'Page', 'page_1');
  $handler->override_option('path', 'admin/tripal/tripal_db/list_dbxrefs');
  $handler->override_option('menu', array(
    'type' => 'normal',
    'title' => 'DB Reference Listing',
    'description' => 'A listing of all database references associated with a given database',
    'weight' => '10',
    'name' => 'navigation',
  ));
  $handler->override_option('tab_options', array(
    'type' => 'none',
    'title' => '',
    'description' => '',
    'weight' => 0,
    'name' => 'navigation',
  ));
  $views[$view->name] = $view;

  return $views;
}

Functions

Function Documentation