organism; // get the list of available sequence ontology terms for which // we will build drupal pages from features in chado. If a feature // is not one of the specified typse we won't build a node for it. $allowed_types = variable_get('chado_browser_feature_types'); $allowed_types = preg_replace("/[\s\n\r]+/", " ", $allowed_types); $so_terms = explode(' ', $allowed_types); // Don't show the browser if there are no terms if (count($so_terms) > 0) { // get the feature_id's of the feature that belong to this organism. But we only // want 25 and we want a pager to let the user cycle between pages of features. // so we, use the chado_select_record API function to get the results and // generate the pager. The function is smart enough to know which page the user is // on and retrieves the proper set of features $element = 0; // an index to specify the pager if more than one is on the page $num_per_page = 25; // the number of features to show per page $values = array( 'organism_id' => $organism->organism_id, 'type_id' => array( 'name' => $so_terms ), ); $columns = array('feature_id'); $options = array( 'pager' => array( 'limit' => $num_per_page, 'element' => $element ), 'order_by' => array('name' => 'ASC'), ); $results = chado_select_record('feature', $columns, $values, $options); // now that we have all of the feature IDs, we want to expand each one so that we // have all of the neccessary values, including the node ID, if one exists, and the // cvterm type name. $features = array(); foreach ($results as $result) { $values = array('feature_id' => $result->feature_id); $options = array( 'include_fk' => array( 'type_id' => 1 ) ); $features[] = chado_generate_var('feature', $values, $options); } if (count($features) > 0) { ?>
The following browser provides a quick view for new visitors. Use the searching mechanism to find specific features.
array('target' => '_blank'))), TRIPAL_INFO, array('return_html' => 1) ); foreach ($features as $feature){ $fname = $feature->name; if (property_exists($feature, 'nid')) { $fname = l($fname, "node/$feature->nid", array('attributes' => array('target' => '_blank'))); } $rows[] = array( $fname, $feature->uniquename, $feature->type_id->name ); } // the $table array contains the headers and rows array as well as other // options for controlling the display of the table. Additional // documentation can be found here: // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7 $table = array( 'header' => $headers, 'rows' => $rows, 'attributes' => array( 'id' => 'tripal_organism-table-features', 'class' => 'tripal-data-table' ), 'sticky' => FALSE, 'caption' => '', 'colgroups' => array(), 'empty' => '', ); // once we have our table array structure defined, we call Drupal's theme_table() // function to generate the table. print theme_table($table); // the $pager array values that control the behavior of the pager. For // documentation on the values allows in this array see: // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7 // here we add the paramter 'block' => 'feature_browser'. This is because // the pager is not on the default block that appears. When the user clicks a // page number we want the browser to re-appear with the page is loaded. $pager = array( 'tags' => array(), 'element' => $element, 'parameters' => array( 'block' => 'feature_browser' ), 'quantity' => $num_per_page, ); print theme_pager($pager); print tripal_set_message(" Administrators, please note that the feature browser will be retired in a future version of Tripal.", TRIPAL_INFO, array('return_html' => 1)); } }