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@@ -5,141 +5,126 @@ $organism = $variables['node']->organism;
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// get the list of available sequence ontology terms for which
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// we will build drupal pages from features in chado. If a feature
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// is not one of the specified typse we won't build a node for it.
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-$allowed_types = variable_get('chado_browser_feature_types', 'gene mRNA');
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+$allowed_types = variable_get('chado_browser_feature_types');
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$allowed_types = preg_replace("/[\s\n\r]+/", " ", $allowed_types);
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$so_terms = explode(' ', $allowed_types);
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-// get the feature_id's of the feature that belong to this organism. But we only
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-// want 25 and we want a pager to let the user cycle between pages of features.
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-// so we, use the chado_select_record API function to get the results and
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-// generate the pager. The function is smart enough to know which page the user is
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-// on and retrieves the proper set of features
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-$element = 0; // an index to specify the pager if more than one is on the page
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-$num_per_page = 25; // the number of features to show per page
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-$values = array(
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- 'organism_id' => $organism->organism_id,
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- 'type_id' => array(
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- 'name' => $so_terms
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- ),
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-);
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-$columns = array('feature_id');
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-$options = array(
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- 'pager' => array(
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- 'limit' => $num_per_page,
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- 'element' => $element
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- ),
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- 'order_by' => array('name' => 'ASC'),
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-);
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-$results = chado_select_record('feature', $columns, $values, $options);
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+// Don't show the browser if there are no terms
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+if (count($so_terms) > 0) {
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-// now that we have all of the feature IDs, we want to expand each one so that we
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-// have all of the neccessary values, including the node ID, if one exists, and the
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-// cvterm type name.
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-$features = array();
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-foreach ($results as $result) {
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- $values = array('feature_id' => $result->feature_id);
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+ // get the feature_id's of the feature that belong to this organism. But we only
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+ // want 25 and we want a pager to let the user cycle between pages of features.
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+ // so we, use the chado_select_record API function to get the results and
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+ // generate the pager. The function is smart enough to know which page the user is
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+ // on and retrieves the proper set of features
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+ $element = 0; // an index to specify the pager if more than one is on the page
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+ $num_per_page = 25; // the number of features to show per page
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+ $values = array(
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+ 'organism_id' => $organism->organism_id,
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+ 'type_id' => array(
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+ 'name' => $so_terms
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+ ),
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+ );
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+ $columns = array('feature_id');
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$options = array(
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- 'include_fk' => array(
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- 'type_id' => 1
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- )
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+ 'pager' => array(
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+ 'limit' => $num_per_page,
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+ 'element' => $element
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+ ),
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+ 'order_by' => array('name' => 'ASC'),
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);
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- $features[] = chado_generate_var('feature', $values, $options);
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-}
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+ $results = chado_select_record('feature', $columns, $values, $options);
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-if (count($features) > 0) { ?>
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- <div class="tripal_organism-data-block-desc tripal-data-block-desc">The following browser provides a quick view for new visitors. Use the searching mechanism to find specific features.</div> <?php
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+ // now that we have all of the feature IDs, we want to expand each one so that we
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+ // have all of the neccessary values, including the node ID, if one exists, and the
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+ // cvterm type name.
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+ $features = array();
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+ foreach ($results as $result) {
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+ $values = array('feature_id' => $result->feature_id);
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+ $options = array(
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+ 'include_fk' => array(
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+ 'type_id' => 1
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+ )
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+ );
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+ $features[] = chado_generate_var('feature', $values, $options);
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+ }
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- // the $headers array is an array of fields to use as the colum headers.
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- // additional documentation can be found here
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- // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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- $headers = array('Feature Name' ,'Unique Name', 'Type');
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+ if (count($features) > 0) { ?>
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+ <div class="tripal_organism-data-block-desc tripal-data-block-desc">The following browser provides a quick view for new visitors. Use the searching mechanism to find specific features.</div> <?php
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- // the $rows array contains an array of rows where each row is an array
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- // of values for each column of the table in that row. Additional documentation
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- // can be found here:
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- // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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- $rows = array();
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+ // the $headers array is an array of fields to use as the colum headers.
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+ // additional documentation can be found here
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+ // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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+ $headers = array('Feature Name' ,'Unique Name', 'Type');
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- // let admins know they can customize the terms that appear in the list
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- print tripal_set_message("Administrators, you can specify the feature types ".
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- "that should appear in this browser or remove it from the list of resources ".
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- "by navigating to the ".
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- l("Tripal feature settings page", "admin/tripal/chado/tripal_feature/configuration", array('attributes' => array('target' => '_blank'))),
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- TRIPAL_INFO,
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- array('return_html' => 1)
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- );
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+ // the $rows array contains an array of rows where each row is an array
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+ // of values for each column of the table in that row. Additional documentation
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+ // can be found here:
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+ // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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+ $rows = array();
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+
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+ // let admins know they can customize the terms that appear in the list
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+ print tripal_set_message("Administrators, you can specify the feature types ".
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+ "that should appear in this browser or remove it from the list of resources ".
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+ "by navigating to the ".
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+ l("Tripal feature settings page", "admin/tripal/chado/tripal_feature/configuration", array('attributes' => array('target' => '_blank'))),
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+ TRIPAL_INFO,
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+ array('return_html' => 1)
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+ );
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- foreach ($features as $feature){
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- $fname = $feature->name;
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- if (property_exists($feature, 'nid')) {
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- $fname = l($fname, "node/$feature->nid", array('attributes' => array('target' => '_blank')));
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+ foreach ($features as $feature){
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+ $fname = $feature->name;
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+ if (property_exists($feature, 'nid')) {
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+ $fname = l($fname, "node/$feature->nid", array('attributes' => array('target' => '_blank')));
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+ }
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+ $rows[] = array(
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+ $fname,
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+ $feature->uniquename,
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+ $feature->type_id->name
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+ );
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}
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- $rows[] = array(
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- $fname,
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- $feature->uniquename,
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- $feature->type_id->name
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+ // the $table array contains the headers and rows array as well as other
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+ // options for controlling the display of the table. Additional
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+ // documentation can be found here:
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+ // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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+ $table = array(
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+ 'header' => $headers,
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+ 'rows' => $rows,
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+ 'attributes' => array(
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+ 'id' => 'tripal_organism-table-features',
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+ 'class' => 'tripal-data-table'
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+ ),
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+ 'sticky' => FALSE,
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+ 'caption' => '',
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+ 'colgroups' => array(),
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+ 'empty' => '',
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);
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- }
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- // the $table array contains the headers and rows array as well as other
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- // options for controlling the display of the table. Additional
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- // documentation can be found here:
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- // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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- $table = array(
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- 'header' => $headers,
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- 'rows' => $rows,
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- 'attributes' => array(
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- 'id' => 'tripal_organism-table-features',
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- 'class' => 'tripal-data-table'
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- ),
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- 'sticky' => FALSE,
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- 'caption' => '',
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- 'colgroups' => array(),
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- 'empty' => '',
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- );
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- // once we have our table array structure defined, we call Drupal's theme_table()
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- // function to generate the table.
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- print theme_table($table);
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+ // once we have our table array structure defined, we call Drupal's theme_table()
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+ // function to generate the table.
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+ print theme_table($table);
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- // the $pager array values that control the behavior of the pager. For
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- // documentation on the values allows in this array see:
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- // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
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- // here we add the paramter 'block' => 'feature_browser'. This is because
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- // the pager is not on the default block that appears. When the user clicks a
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- // page number we want the browser to re-appear with the page is loaded.
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- $pager = array(
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- 'tags' => array(),
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- 'element' => $element,
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- 'parameters' => array(
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- 'block' => 'feature_browser'
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- ),
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- 'quantity' => $num_per_page,
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- );
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- print theme_pager($pager);
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-}
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-else { ?>
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- <p>There are no results.</p><?php
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- print tripal_set_message("
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- Administrators, perform the following to show features in this browser:
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- <ul>
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- <li>Load features for this organism using the " .
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- l("FASTA loader", 'admin/tripal/loaders/fasta_loader') . ", ".
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- l("GFF Loader", 'admin/tripal/loaders/gff3_load') . " or ".
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- l("Bulk Loader", 'admin/tripal/loaders/bulk'). "</li>
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- <li>Sync the features that should have pages using the ".
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- l("Sync features page", 'admin/tripal/chado/tripal_feature/sync'). "</li>
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- <li>Return to this page to browse features.</li>
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- <li>Ensure the user " .
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- l("has permission", 'admin/people/permissions') . " to view the feature content</li>
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- </ul>
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- <br>
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- <br>
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- You can specify the feature types
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- that should appear in this browser or remove it from the list of resources by navigating to the " .
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- l("Tripal feature settings page", "admin/tripal/chado/tripal_feature/configuration", array('attributes' => array('target' => '_blank'))) . "
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- The feature browser will not appear to site visitors unless features are present. ",
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- TRIPAL_INFO,
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- array('return_html' => 1));
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-}
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+ // the $pager array values that control the behavior of the pager. For
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+ // documentation on the values allows in this array see:
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+ // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
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+ // here we add the paramter 'block' => 'feature_browser'. This is because
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+ // the pager is not on the default block that appears. When the user clicks a
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+ // page number we want the browser to re-appear with the page is loaded.
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+ $pager = array(
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+ 'tags' => array(),
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+ 'element' => $element,
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+ 'parameters' => array(
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+ 'block' => 'feature_browser'
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+ ),
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+ 'quantity' => $num_per_page,
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+ );
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+ print theme_pager($pager);
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+ print tripal_set_message("
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+ Administrators, please note that the feature browser will be retired in
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+ a future version of Tripal.",
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+ TRIPAL_INFO,
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+ array('return_html' => 1));
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+ }
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+}
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Stephen Ficklin