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- <?php
- /* Typically in a Tripal template, the data needed is retrieved using a call to
- * chado_expand_var function. For example, to retrieve all
- * of the feature relationships for this node, the following function call would be made:
- *
- * $feature = chado_expand_var($feature,'table','feature_relationship');
- *
- * However, this function call can be extremely slow when there are numerous relationships.
- * This is because the chado_expand_var function is recursive and expands
- * all data following the foreign key relationships tree. Therefore, to speed retrieval
- * of data, a special variable is provided to this template:
- *
- * $feature->all_relationships;
- *
- * This variable is an array with two sub arrays with the keys 'object' and 'subject'. The array with
- * key 'object' contains relationships where the feature is the object, and the array with
- * the key 'subject' contains relationships where the feature is the subject
- */
- $feature = $variables['node']->feature;
- $all_relationships = $feature->all_relationships;
- $object_rels = $all_relationships['object'];
- $subject_rels = $all_relationships['subject'];
- if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
- <div class="tripal_feature-data-block-desc tripal-data-block-desc"></div> <?php
- // first add in the subject relationships.
- foreach ($subject_rels as $rel_type => $rels) {
- foreach ($rels as $obj_type => $objects) {
- // Make the verb in the sentence make sense in English.
- switch ($rel_type) {
- case 'integral part of':
- case 'instance of':
- $verb = 'is an';
- break;
- case 'proper part of':
- case 'transformation of':
- case 'genome of':
- case 'part of':
- case 'position of':
- case 'sequence of':
- case 'variant of':
- $verb = 'is a';
- break;
- case 'derives from':
- case 'connects on':
- case 'contains':
- case 'finishes':
- case 'guides':
- case 'has origin':
- case 'has part':
- case 'has quality':
- case 'is consecutive sequence of':
- case 'maximally overlaps':
- case 'overlaps':
- case 'starts':
- $verb = '';
- break;
- default:
- $verb = 'is';
- } ?>
- <p>
- This <?php print $feature->type_id->name; ?> <?php print $verb ?> <?php print $rel_type ?>
- the following <b><?php print $obj_type ?></b> feature(s): <?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 = ['Feature Name', 'Unique Name', 'Species', 'Type'];
- // 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
- $rows = [];
- foreach ($objects as $object) {
- // link the feature to it's node
- $feature_name = $object->record->object_id->name;
- if (property_exists($object->record, 'nid')) {
- $feature_name = l($feature_name, "node/" . $object->record->nid, ['attributes' => ['target' => "_blank"]]);
- }
- // link the organism to it's node
- $organism = $object->record->object_id->organism_id;
- $organism_name = $organism->genus . " " . $organism->species;
- if (property_exists($organism, 'nid')) {
- $organism_name = l("<i>" . $organism->genus . " " . $organism->species . "</i>", "node/" . $organism->nid, ['html' => TRUE]);
- }
- $rows[] = [
- ['data' => $feature_name, 'width' => '30%'],
- [
- 'data' => $object->record->object_id->uniquename,
- 'width' => '30%',
- ],
- ['data' => $organism_name, 'width' => '30%'],
- [
- 'data' => $object->record->object_id->type_id->name,
- 'width' => '10%',
- ],
- ];
- }
- // 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' => $rows,
- 'attributes' => [
- 'id' => 'tripal_feature-table-relationship-object',
- 'class' => 'tripal-data-table',
- ],
- 'sticky' => FALSE,
- 'caption' => '',
- 'colgroups' => [],
- 'empty' => '',
- ];
- // once we have our table array structure defined, we call Drupal's theme_table()
- // function to generate the table.
- print theme_table($table); ?>
- </p>
- <br><?php
- }
- }
- // second add in the object relationships.
- foreach ($object_rels as $rel_type => $rels) {
- foreach ($rels as $subject_type => $subjects) {
- // Make the verb in the sentence make sense in English.
- switch ($rel_type) {
- case 'integral part of':
- case 'instance of':
- $verb = 'are an';
- break;
- case 'proper part of':
- case 'transformation of':
- case 'genome of':
- case 'part of':
- case 'position of':
- case 'sequence of':
- case 'variant of':
- $verb = 'are a';
- break;
- case 'derives from':
- case 'connects on':
- case 'contains':
- case 'finishes':
- case 'guides':
- case 'has origin':
- case 'has part':
- case 'has quality':
- case 'is consecutive sequence of':
- case 'maximally overlaps':
- case 'overlaps':
- case 'starts':
- $verb = '';
- break;
- default:
- $verb = 'are';
- } ?>
- <p>The following
- <b><?php print $subjects[0]->record->subject_id->type_id->name ?></b>
- feature(s) <?php print $verb ?> <?php print $rel_type ?>
- this <?php print $feature->type_id->name; ?>: <?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 = ['Feature Name', 'Unique Name', 'Species', 'Type'];
- // 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
- $rows = [];
- foreach ($subjects as $subject) {
- // link the feature to it's node
- $feature_name = $subject->record->subject_id->name;
- if (property_exists($subject->record, 'nid')) {
- $feature_name = l($feature_name, "node/" . $subject->record->nid, ['attributes' => ['target' => "_blank"]]);
- }
- // link the organism to it's node
- $organism = $subject->record->subject_id->organism_id;
- $organism_name = $organism->genus . " " . $organism->species;
- if (property_exists($organism, 'nid')) {
- $organism_name = l("<i>" . $organism->genus . " " . $organism->species . "</i>", "node/" . $organism->nid, ['html' => TRUE]);
- }
- $rows[] = [
- ['data' => $feature_name, 'width' => '30%'],
- [
- 'data' => $subject->record->subject_id->uniquename,
- 'width' => '30%',
- ],
- ['data' => $organism_name, 'width' => '30%'],
- [
- 'data' => $subject->record->subject_id->type_id->name,
- 'width' => '10%',
- ],
- ];
- }
- // 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' => $rows,
- 'attributes' => [
- 'id' => 'tripal_feature-table-relationship-subject',
- 'class' => 'tripal-data-table',
- ],
- 'sticky' => FALSE,
- 'caption' => '',
- 'colgroups' => [],
- 'empty' => '',
- ];
- // once we have our table array structure defined, we call Drupal's theme_table()
- // function to generate the table.
- print theme_table($table); ?>
- </p>
- <br><?php
- }
- }
- }
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