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- <?php
- $feature = $variables['node']->feature;
- $references = [];
- // First, get the dbxref record from feature record itself if one exists
- if ($feature->dbxref_id) {
- $feature->dbxref_id->is_primary = 1; // add this new property so we know it's the primary reference
- $references[] = $feature->dbxref_id;
- }
- // Second, expand the feature object to include the records from the feature_dbxref table
- $options = ['return_array' => 1];
- $feature = chado_expand_var($feature, 'table', 'feature_dbxref', $options);
- $feature_dbxrefs = $feature->feature_dbxref;
- if (count($feature_dbxrefs) > 0) {
- foreach ($feature_dbxrefs as $feature_dbxref) {
- if ($feature_dbxref->dbxref_id->db_id->name == 'GFF_source') {
- // check to see if the reference 'GFF_source' is there. This reference is
- // used to if the Chado Perl GFF loader was used to load the features
- }
- else {
- $references[] = $feature_dbxref->dbxref_id;
- }
- }
- }
- if (count($references) > 0) { ?>
- <div class="tripal_feature-data-block-desc tripal-data-block-desc">External
- references for this <?php print $feature->type_id->name ?></div><?php
- // the $headers array is an array of fields to use as the colum headers.
- // additional documentation can be found here
- // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
- $headers = ['Database', 'Accession'];
- // the $rows array contains an array of rows where each row is an array
- // of values for each column of the table in that row. Additional documentation
- // can be found here:
- // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
- $rows = [];
- foreach ($references as $dbxref) {
- // skip the GFF_source entry as this is just needed for the GBrowse chado adapter
- if ($dbxref->db_id->name == 'GFF_source') {
- continue;
- }
- $dbname = $dbxref->db_id->name;
- if ($dbxref->db_id->url) {
- $dbname = l($dbname, $dbxref->db_id->url, ['attributes' => ['target' => '_blank']]);
- }
- $accession = $dbxref->accession;
- if ($dbxref->db_id->urlprefix) {
- $accession = l($accession, $dbxref->db_id->urlprefix . $dbxref->accession, ['attributes' => ['target' => '_blank']]);
- }
- if (property_exists($dbxref, 'is_primary')) {
- $accession .= " <i>(primary cross-reference)</i>";
- }
- $rows[] = [
- $dbname,
- $accession,
- ];
- }
- // 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 = [
- 'header' => $headers,
- 'rows' => $rows,
- 'attributes' => [
- 'id' => 'tripal_feature-table-references',
- 'class' => 'tripal-data-table',
- ],
- 'sticky' => FALSE,
- 'caption' => '',
- 'colgroups' => [],
- 'empty' => '',
- ];
- // once we have our table array structure defined, we call Drupal's theme_table()
- // function to generate the table.
- print theme_table($table);
- } ?>
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