sbo__relationship_formatter.inc 5.1 KB

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  1. <?php
  2. class sbo__relationship_formatter extends ChadoFieldFormatter {
  3. // The default lable for this field.
  4. public static $default_label = 'Relationship Statements';
  5. // The list of field types for which this formatter is appropriate.
  6. public static $field_types = ['sbo__relationship'];
  7. public static $default_settings = [
  8. 'title' => 'Relationship',
  9. 'empty' => 'There are no relationships',
  10. ];
  11. /**
  12. *
  13. * @see TripalFieldFormatter::settingsForm()
  14. */
  15. public function settingsForm($view_mode, $form, &$form_state) {
  16. $display = $this->instance['display'][$view_mode];
  17. $settings = $display['settings'];
  18. $element = [];
  19. $element['title'] = [
  20. '#type' => 'textfield',
  21. '#title' => 'Table Header',
  22. '#default_value' => array_key_exists('title', $settings) ? $settings['title'] : 'Relationship',
  23. ];
  24. $element['empty'] = [
  25. '#type' => 'textfield',
  26. '#title' => 'Empty text',
  27. '#default_value' => array_key_exists('empty', $settings) ? $settings['empty'] : 'There are no relationships',
  28. ];
  29. return $element;
  30. }
  31. /**
  32. * @see TripalFieldFormatter::settingsSummary()
  33. */
  34. public function settingsSummary($view_mode) {
  35. $display = $this->instance['display'][$view_mode];
  36. $settings = $display['settings'];
  37. $summary = t('Title: @title<br>Empty: @empty',
  38. [
  39. '@title' => $settings['title'],
  40. '@empty' => $settings['empty'],
  41. ]
  42. );
  43. return $summary;
  44. }
  45. /**
  46. *
  47. * @see TripalFieldFormatter::view()
  48. */
  49. public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
  50. // Get the settings
  51. $settings = $display['settings'];
  52. $rows = [];
  53. $headers = [$settings['title']];
  54. foreach ($items as $delta => $item) {
  55. if (empty($item['value'])) {
  56. continue;
  57. }
  58. $subject_name = $item['value']['local:relationship_subject']['schema:name'];
  59. $subject_type = $item['value']['local:relationship_subject']['rdfs:type'];
  60. $object_name = $item['value']['local:relationship_object']['schema:name'];
  61. $object_type = $item['value']['local:relationship_object']['rdfs:type'];
  62. $phrase = $item['value']['SIO:000493'];
  63. // Handle some special cases.
  64. // For mRNA objects we don't want to show the CDS, exons, 5' UTR, etc.
  65. // we want to show the parent gene and the protein.
  66. if ($object_type == 'mRNA' and
  67. (in_array($subject_type, [
  68. 'CDS',
  69. 'exon',
  70. 'five_prime_UTR',
  71. 'three_prime_UTR',
  72. ]))) {
  73. continue;
  74. }
  75. // Add bold font to the object and subject names.
  76. // @todo add back in bolding...
  77. // @todo Fix Current Bug: if type name is in the object name, wierd bolding happens.
  78. // $phrase = preg_replace("/$subject_type/", "<b>$subject_type</b>", $phrase);
  79. // $phrase = preg_replace("/$object_type/", "<b>$object_type</b>", $phrase);
  80. // Convert the object/subject to a link if an entity exists for it.
  81. if (array_key_exists('entity', $item['value']['local:relationship_object'])) {
  82. list($entity_type, $object_entity_id) = explode(':', $item['value']['local:relationship_object']['entity']);
  83. if ($object_entity_id != $entity->id) {
  84. $link = l($object_name, 'bio_data/' . $object_entity_id);
  85. $phrase = str_replace($object_name, $link, $phrase);
  86. }
  87. }
  88. if (array_key_exists('entity', $item['value']['local:relationship_subject'])) {
  89. list($entity_type, $subject_entity_id) = explode(':', $item['value']['local:relationship_subject']['entity']);
  90. if ($subject_entity_id != $entity->id) {
  91. $link = l($subject_name, 'bio_data/' . $subject_entity_id);
  92. $phrase = str_replace($subject_name, $link, $phrase);
  93. }
  94. }
  95. $rows[][] = [
  96. 'data' => $phrase,
  97. //'class' => array('tripal-entity-unattached field-items')
  98. ];
  99. }
  100. // Build the pager
  101. $items_per_page = array_key_exists('items_per_page', $this->instance['settings']) ? $this->instance['settings']['items_per_page'] : 10;
  102. $total_records = count($rows);
  103. $total_pages = (int) ($total_records / $items_per_page) + 1;
  104. $pelement = 0;
  105. $current_page = pager_default_initialize($total_records, $items_per_page, $pelement);
  106. $pager = theme('pager', [
  107. 'tags' => [],
  108. 'element' => $pelement,
  109. 'parameters' => [],
  110. 'quantity' => $total_pages,
  111. ]);
  112. $pager = $this->ajaxifyPager($pager, $entity);
  113. $page_items = array_chunk($rows, $items_per_page);
  114. $caption = '';
  115. if ($total_records == 1) {
  116. $caption = 'There is ' . count($rows) . ' relationship.';
  117. }
  118. else {
  119. $caption = 'There are ' . count($rows) . ' relationships.';
  120. }
  121. $content = theme_table([
  122. 'header' => $headers,
  123. 'rows' => count($rows) > 0 ? $page_items[$current_page] : [],
  124. 'attributes' => [
  125. 'class' => 'tripal-data-table',
  126. ],
  127. 'sticky' => FALSE,
  128. 'caption' => $caption,
  129. 'colgroups' => [],
  130. 'empty' => $settings['empty'],
  131. ]);
  132. $element[0] = [
  133. '#type' => 'markup',
  134. '#markup' => $content . $pager,
  135. ];
  136. }
  137. }