Functions
	tripal_cv_views_data ()
	tripal_cv_views_handlers ()
	tripal_cv_views_default_views ()

Function Documentation

tripal_cv_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 32 of file tripal_cv.views.inc.

                                {
  $data = array();

  if (module_exists('tripal_views')) {
    // Base Tables
    $tables = array(
      'cv',
      'cvterm'
    );
    foreach ($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)) {
        // get default integration array
        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE, $priority);

        // add specialty handlers
        if ($tablename == 'cvterm') {
          $table_integration_array['fields']['name']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_string';
        }
        elseif ($tablename == 'cv') {
          $table_integration_array['fields']['name']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_string';
        }

        // add integration
        tripal_views_integration_add_entry($table_integration_array);
      }
    }

    // Additional Tables
    $tables = array(
      'cvterm_dbxref',
      'cvterm_relationship',
      'cvtermpath',
      'cvtermprop',
      'cvtermsynonym'
    );
    foreach ($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_cv_views_default_views ( )

Definition at line 112 of file tripal_cv.views.inc.

                                         {
  $views = array();

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

  // Main default view
  // List all cvterms based on cv
  $view = new view;
  $view->name = 'cvterm_listing';
  $view->description = 'A listing of all controlled vocabulary terms filtered by controlled vocabulary';
  $view->tag = 'chado default';
  $view->base_table = 'cvterm';
  $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_1' => array(
      'label' => 'Vocabulary',
      '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_1',
      'table' => 'cv',
      'field' => 'name',
      'relationship' => 'none',
    ),
    'name' => array(
      'label' => '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,
      'exclude' => 0,
      'id' => 'name',
      'table' => 'cvterm',
      'field' => 'name',
      'relationship' => 'none',
    ),
    'definition' => array(
      'label' => 'Definition',
      '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' => 'definition',
      'table' => 'cvterm',
      'field' => 'definition',
      'relationship' => 'none',
    ),
    'is_obsolete' => array(
      'label' => 'Is Obsolete',
      '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,
      'type' => 'yes-no',
      'not' => 0,
      'exclude' => 0,
      'id' => 'is_obsolete',
      'table' => 'cvterm',
      'field' => 'is_obsolete',
      'relationship' => 'none',
    ),
    'is_relationshiptype' => array(
      'label' => 'Is Relationship',
      '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,
      'type' => 'yes-no',
      'not' => 0,
      'exclude' => 0,
      'id' => 'is_relationshiptype',
      'table' => 'cvterm',
      'field' => 'is_relationshiptype',
      'relationship' => 'none',
    ),
  ));
  $handler->override_option('sorts', array(
    'name' => array(
      'order' => 'ASC',
      'id' => 'name',
      'table' => 'cv',
      'field' => 'name',
      'relationship' => 'none',
    ),
    'name_1' => array(
      'order' => 'ASC',
      'id' => 'name_1',
      'table' => 'cvterm',
      'field' => 'name',
      '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' => 'cv',
        'label' => 'Vocabulary',
        'remember' => 0,
      ),
      'case' => 1,
      'id' => 'name',
      'table' => 'cv',
      'field' => 'name',
      'relationship' => 'none',
      'values_form_type' => 'select',
      'multiple' => 1,
      'optional' => 0,
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
    ),
    'name_1' => array(
      'operator' => '~',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => '',
        'identifier' => 'name',
        'label' => 'Name Contains',
        'remember' => 0,
      ),
      'case' => 0,
      'id' => 'name_1',
      'table' => 'cvterm',
      'field' => 'name',
      'relationship' => 'none',
      'values_form_type' => 'textfield',
      'multiple' => 0,
      'optional' => 0,
      'show_all' => 0,
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
    ),
    'definition' => array(
      'operator' => '~',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'definition_op',
        'identifier' => 'definition',
        'label' => 'Definition Contains',
        'remember' => 0,
      ),
      'case' => 0,
      'id' => 'definition',
      'table' => 'cvterm',
      'field' => 'definition',
      '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 controlled vocabulary terms matching the entered criteria. If you leave a any of the criteria blank then the controlled vocabulary terms will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all controlled vocabulary terms will be listed.',
    ),
  ));
  $handler->override_option('access', array(
    'type' => 'perm',
    'perm' => 'access chado_cv content',
  ));
  $handler->override_option('cache', array(
    'type' => 'none',
  ));
  $handler->override_option('title', 'Controlled Vocabulary Terms');
  $handler->override_option('header', 'Click "Show" to see a list of all controlled vocabulary terms matching the entered criteria. If you leave a any of the criteria blank then the controlled vocabulary terms will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all controlled vocabulary terms will be listed.');
  $handler->override_option('header_format', '2');
  $handler->override_option('header_empty', 0);
  $handler->override_option('empty', 'There are no terms associated with the selected controlled vocabulary. Please select a different vocabulary from the list above.');
  $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',
    'summary' => '',
    'columns' => array(
      'name_1' => 'name_1',
      'name' => 'name',
      'definition' => 'definition',
      'is_obsolete' => 'is_obsolete',
      'is_relationshiptype' => 'is_relationshiptype',
    ),
    'info' => array(
      'name_1' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'name' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'definition' => array(
        'sortable' => 0,
        'separator' => '',
      ),
      'is_obsolete' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'is_relationshiptype' => array(
        'sortable' => 1,
        'separator' => '',
      ),
    ),
    'default' => '-1',
  ));
  $handler = $view->new_display('page', 'Page', 'page_1');
  $handler->override_option('path', 'admin/tripal/tripal_cv/list_cvterms');
  $handler->override_option('menu', array(
    'type' => 'normal',
    'title' => 'Term Listing',
    'description' => 'A listing of a controlled vocabulary terms for a given vocabulary',
    'weight' => '10',
    'name' => 'navigation',
  ));
  $handler->override_option('tab_options', array(
    'type' => 'none',
    'title' => '',
    'description' => '',
    'weight' => 0,
    'name' => 'navigation',
  ));
  $views[$view->name] = $view;

  // Main cv default listing
  $view = new view;
  $view->name = 'cv_listing';
  $view->description = 'A listing of all controlled vocabularies';
  $view->tag = 'chado default';
  $view->base_table = 'cv';
  $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' => 'cv',
      'field' => 'name',
      'relationship' => 'none',
    ),
    'definition' => array(
      'label' => 'Definition',
      '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' => 'definition',
      'table' => 'cv',
      'field' => 'definition',
      'relationship' => 'none',
    ),
    'nothing' => array(
      'label' => 'Terms',
      'alter' => array(
        'text' => 'view',
        'make_link' => 1,
        'path' => 'admin/tripal/tripal_cv/list_cvterms?cv%5B%5D=[name]',
        '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,
      'exclude' => 0,
      'id' => 'nothing',
      'table' => 'views',
      'field' => 'nothing',
      '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' => 'cv',
      'field' => 'name',
      'relationship' => 'none',
      'values_form_type' => 'textfield',
      'multiple' => 0,
      'optional' => 0,
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 0,
      ),
    ),
    'definition' => array(
      'operator' => '~',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'definition_op',
        'identifier' => 'definition',
        'label' => 'Definition Contains',
        'remember' => 0,
      ),
      'case' => 0,
      'id' => 'definition',
      'table' => 'cv',
      'field' => 'definition',
      '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 controlled vocabularies matching the entered criteria. If you leave a any of the criteria blank then the controlled vocabularies will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all controlled vocabularies will be listed.',
    ),
  ));
  $handler->override_option('access', array(
    'type' => 'perm',
    'perm' => 'access chado_cv content',
  ));
  $handler->override_option('cache', array(
    'type' => 'none',
  ));
  $handler->override_option('title', 'Controlled Vocabularies');
  $handler->override_option('header', 'Click "Show" to see a list of all controlled vocabularies matching the entered criteria. If you leave a any of the criteria blank then the controlled vocabularies will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all controlled vocabularies will be listed.');
  $handler->override_option('header_format', '2');
  $handler->override_option('header_empty', 0);
  $handler->override_option('empty', 'No controlled vocabularies match the supplied criteria.');
  $handler->override_option('empty_format', '2');
  $handler->override_option('items_per_page', 50);
  $handler->override_option('style_plugin', 'table');
  $handler->override_option('style_options', array(
    'grouping' => '',
    'override' => 1,
    'sticky' => 0,
    'order' => 'asc',
    'summary' => '',
    'columns' => array(
      'name' => 'name',
      'definition' => 'definition',
      'nothing' => 'nothing',
    ),
    'info' => array(
      'name' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'definition' => array(
        'sortable' => 0,
        'separator' => '',
      ),
      'nothing' => array(
        'separator' => '',
      ),
    ),
    'default' => 'name',
  ));
  $handler = $view->new_display('page', 'Page', 'page_1');
  $handler->override_option('path', 'admin/tripal/tripal_cv/list_cvs');
  $handler->override_option('menu', array(
    'type' => 'normal',
    'title' => 'CV Listing',
    'description' => 'A listing of all controlled vocabularies',
    'weight' => '10',
    'name' => 'navigation',
  ));
  $handler->override_option('tab_options', array(
    'type' => 'none',
    'title' => '',
    'description' => '',
    'weight' => 0,
    'name' => 'navigation',
  ));
  $views[$view->name] = $view;

  return $views;
}

tripal_cv_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 95 of file tripal_cv.views.inc.

                                    {
  return array(
    'info' => array(
      'path' => drupal_get_path('module', 'tripal_cv') . '/views/handlers',
    ),
    'handlers' => array(
      'views_handler_field_tf_boolean' => array(
       'parent' => 'views_handler_field',
      ),
    ),
  );
}

Functions

Function Documentation