chado_linker__contact.inc 12 KB

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  1. <?php
  2. class chado_linker__contact extends ChadoField {
  3. // --------------------------------------------------------------------------
  4. // EDITABLE STATIC CONSTANTS
  5. //
  6. // The following constants SHOULD be set for each descendent class. They are
  7. // used by the static functions to provide information to Drupal about
  8. // the field and it's default widget and formatter.
  9. // --------------------------------------------------------------------------
  10. // The default label for this field.
  11. public static $default_label = 'Contacts';
  12. // The default description for this field.
  13. public static $description = 'Associates an indviddual or organization with
  14. this record';
  15. // Provide a list of instance specific settings. These can be accessed within
  16. // the instanceSettingsForm. When the instanceSettingsForm is submitted
  17. // then Drupal will automatically change these settings for the instance.
  18. // It is recommended to put settings at the instance level whenever possible.
  19. // If you override this variable in a child class be sure to replicate the
  20. // term_name, term_vocab, term_accession and term_fixed keys as these are
  21. // required for all TripalFields.
  22. public static $default_instance_settings = [
  23. // The short name for the vocabulary (e.g. schema, SO, GO, PATO, etc.).
  24. 'term_vocabulary' => 'local',
  25. // The name of the term.
  26. 'term_name' => 'contact',
  27. // The unique ID (i.e. accession) of the term.
  28. 'term_accession' => 'contact',
  29. // Set to TRUE if the site admin is allowed to change the term
  30. // type. This will create form elements when editing the field instance
  31. // to allow the site admin to change the term settings above.
  32. 'term_fixed' => FALSE,
  33. ];
  34. // The default widget for this field.
  35. public static $default_widget = 'chado_linker__contact_widget';
  36. // The default formatter for this field.
  37. public static $default_formatter = 'chado_linker__contact_formatter';
  38. // --------------------------------------------------------------------------
  39. // PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE
  40. // --------------------------------------------------------------------------
  41. // An array containing details about the field. The format of this array
  42. // is the same as that returned by field_info_fields()
  43. protected $field;
  44. // An array containing details about an instance of the field. A field does
  45. // not have to have an instance. But if dealing with an instance (such as
  46. // when using the widgetForm, formatterSettingsForm, etc.) it should be set.
  47. protected $instance;
  48. /**
  49. * @see TripalField::elements()
  50. */
  51. public function elementInfo() {
  52. $field_term = $this->getFieldTermID();
  53. $type_term = chado_get_semweb_term('contact', 'type_id');
  54. $name_term = chado_get_semweb_term('contact', 'name');
  55. $description_term = chado_get_semweb_term('contact', 'description');
  56. return [
  57. $field_term => [
  58. 'operations' => ['eq', 'contains', 'starts'],
  59. 'sortable' => TRUE,
  60. 'searchable' => TRUE,
  61. 'type' => 'xs:complexType',
  62. 'readonly' => FALSE,
  63. 'elements' => [
  64. $type_term => [
  65. 'searchable' => TRUE,
  66. 'label' => 'Contact Type',
  67. 'help' => 'The type of contact',
  68. 'operations' => ['eq', 'ne', 'contains', 'starts'],
  69. 'sortable' => TRUE,
  70. 'type' => 'xs:string',
  71. 'readonly' => FALSE,
  72. 'required' => TRUE,
  73. ],
  74. $name_term => [
  75. 'searchable' => TRUE,
  76. 'label' => 'Contact Name',
  77. 'help' => 'The name of the contact.',
  78. 'operations' => ['eq', 'ne', 'contains', 'starts'],
  79. 'sortable' => TRUE,
  80. 'type' => 'xs:string',
  81. 'readonly' => FALSE,
  82. 'required' => TRUE,
  83. ],
  84. $description_term => [
  85. 'searchable' => TRUE,
  86. 'label' => 'Contact Description',
  87. 'help' => 'A descriptoin of the contact.',
  88. 'operations' => ['contains'],
  89. 'sortable' => TRUE,
  90. 'type' => 'xs:string',
  91. 'readonly' => TRUE,
  92. 'required' => FALSE,
  93. ],
  94. 'entity' => [
  95. 'searchable' => FALSE,
  96. ],
  97. ],
  98. ],
  99. ];
  100. }
  101. /**
  102. *
  103. * @see TripalField::load()
  104. */
  105. public function load($entity) {
  106. $record = $entity->chado_record;
  107. $field_name = $this->field['field_name'];
  108. $field_type = $this->field['type'];
  109. $field_table = $this->instance['settings']['chado_table'];
  110. $field_column = $this->instance['settings']['chado_column'];
  111. $base_table = $this->instance['settings']['base_table'];
  112. $type_term = chado_get_semweb_term('contact', 'type_id');
  113. $name_term = chado_get_semweb_term('contact', 'name');
  114. $description_term = chado_get_semweb_term('contact', 'description');
  115. // Get the FK that links to the base record.
  116. $schema = chado_get_schema($field_table);
  117. $pkey = $schema['primary key'][0];
  118. if (!isset($schema['foreign keys'][$base_table]['columns'])) {
  119. return;
  120. }
  121. $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
  122. $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
  123. // If we don't have a chado record return before creating a stub for this field!
  124. if (!$record) {
  125. return;
  126. }
  127. // Set some defaults for the empty record.
  128. $entity->{$field_name}['und'][0] = [
  129. 'value' => [],
  130. 'chado-' . $field_table . '__' . $pkey => '',
  131. 'chado-' . $field_table . '__' . $fkey_lcolumn => $record->$fkey_lcolumn,
  132. 'chado-' . $field_table . '__' . 'contact_id' => '',
  133. // Ignore the synonym_sgml column for now.
  134. ];
  135. $linker_table = $base_table . '_contact';
  136. $options = [
  137. 'return_array' => 1,
  138. 'include_fk' => [
  139. 'contact_id' => [
  140. 'type_id' => [
  141. 'dbxref_id' => [
  142. 'db_id' => TRUE,
  143. ],
  144. ],
  145. ],
  146. $fkey_lcolumn => TRUE,
  147. ],
  148. ];
  149. $record = chado_expand_var($record, 'table', $linker_table, $options);
  150. $contact_linkers = $record->$linker_table;
  151. if ($contact_linkers) {
  152. foreach ($contact_linkers as $i => $contact_linker) {
  153. $contact = $contact_linker->contact_id;
  154. $entity->{$field_name}['und'][$i] = [
  155. 'value' => [
  156. $type_term => $contact->type_id ? $contact->type_id->name : '',
  157. $name_term => $contact->name,
  158. $description_term => $contact->description,
  159. ],
  160. // Add elements that are not part of the values but used by
  161. // the chado storage back-end for saving values.
  162. 'chado-' . $field_table . '__' . $pkey => $contact_linker->$pkey,
  163. 'chado-' . $field_table . '__' . $fkey_lcolumn => $record->$fkey_lcolumn,
  164. 'chado-' . $field_table . '__' . 'contact_id' => $contact->contact_id,
  165. ];
  166. if (property_exists($contact, 'entity_id')) {
  167. $entity->{$field_name}['und'][$i]['value']['entity'] = 'TripalEntity:' . $contact->entity_id;
  168. }
  169. }
  170. }
  171. }
  172. /**
  173. * @see ChadoField::query()
  174. */
  175. public function query($query, $condition) {
  176. $alias = $this->field['field_name'];
  177. $operator = $condition['operator'];
  178. $field_term_id = $this->getFieldTermID();
  179. $type_term = chado_get_semweb_term('contact', 'type_id');
  180. $name_term = chado_get_semweb_term('contact', 'name');
  181. $description_term = chado_get_semweb_term('contact', 'description');
  182. $contact_linker = $this->instance['settings']['chado_table'];
  183. $base_table = $this->instance['settings']['base_table'];
  184. // Get the FK that links to the base record.
  185. $schema = chado_get_schema($contact_linker);
  186. $pkey = $schema['primary key'][0];
  187. $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
  188. $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
  189. // Join the contact linker table and then join the contact table.
  190. $calias = $contact_linker . '_contact';
  191. $this->queryJoinOnce($query, $contact_linker, $alias, "base.$fkey_rcolumn = $alias.$fkey_lcolumn");
  192. $this->queryJoinOnce($query, 'contact', $calias, "$calias.contact_id = $alias.contact_id");
  193. // Search by the contact name
  194. if ($condition['column'] == $field_term_id or
  195. $condition['column'] == $field_term_id . ',' . $name_term) {
  196. $query->condition("$calias.name", $condition['value'], $operator);
  197. }
  198. // Search on the contact description.
  199. if ($condition['column'] == $field_term_id . ',' . $description_term) {
  200. $query->condition("$calias.description", $condition['value'], $operator);
  201. }
  202. // Search on the contact type.
  203. if ($condition['column'] == $field_term_id . ',' . $type_term) {
  204. $talias = $contact_linker . '_contact_type';
  205. $this->queryJoinOnce($query, 'cvterm', $talias, "$calias.type_id = $talias.cvterm_id");
  206. $query->condition("$talias.name", $condition['value'], $operator);
  207. }
  208. }
  209. /**
  210. * @see ChadoField::queryOrder()
  211. */
  212. public function queryOrder($query, $order) {
  213. $alias = $this->field['field_name'];
  214. $field_term_id = $this->getFieldTermID();
  215. $type_term = chado_get_semweb_term('contact', 'type_id');
  216. $name_term = chado_get_semweb_term('contact', 'name');
  217. $description_term = chado_get_semweb_term('contact', 'description');
  218. $contact_linker = $this->instance['settings']['chado_table'];
  219. $base_table = $this->instance['settings']['base_table'];
  220. // Get the FK that links to the base record.
  221. $schema = chado_get_schema($contact_linker);
  222. $pkey = $schema['primary key'][0];
  223. $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
  224. $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
  225. // Join the contact linker table and then join the contact table.
  226. $calias = $contact_linker . '_contact';
  227. $this->queryJoinOnce($query, $contact_linker, $alias, "base.$fkey_rcolumn = $alias.$fkey_lcolumn", "LEFT OUTER");
  228. $this->queryJoinOnce($query, 'contact', $calias, "$calias.contact_id = $alias.contact_id", "LEFT OUTER");
  229. // Search by the contact name
  230. if ($order['column'] == $field_term_id or
  231. $order['column'] == $field_term_id . ',' . $name_term) {
  232. $query->orderBy("$calias.name", $order['direction']);
  233. }
  234. // Search on the contact description.
  235. if ($order['column'] == $field_term_id . ',' . $description_term) {
  236. $query->orderBy("$calias.description", $order['direction']);
  237. }
  238. // Search on the contact type.
  239. if ($order['column'] == $field_term_id . ',' . $type_term) {
  240. $talias = $contact_linker . '_contact_type';
  241. $this->queryJoinOnce($query, 'cvterm', $talias, "$calias.type_id = $talias.cvterm_id", "LEFT OUTER");
  242. $query->orderBy("$talias.name", $order['direction']);
  243. }
  244. }
  245. }
  246. /**
  247. * An Ajax callback for the pub widget.
  248. */
  249. function chado_linker__contact_widget_form_ajax_callback($form, $form_state) {
  250. $field_name = $form_state['triggering_element']['#parents'][0];
  251. $delta = $form_state['triggering_element']['#parents'][2];
  252. return $form[$field_name]['und'][$delta];
  253. }
  254. /**
  255. * Theme function for the pub widget.
  256. *
  257. * @param $variables
  258. */
  259. function theme_chado_linker__contact_widget($variables) {
  260. $element = $variables['element'];
  261. // These two fields were added to the widget to help identify the fields
  262. // for layout.
  263. $table_name = $element['#table_name'];
  264. $fkey = $element['#fkey_field'];
  265. $layout = "
  266. <div class=\"pub-widget\">
  267. <div class=\"pub-widget-item\">" .
  268. drupal_render($element['name']) . "
  269. </div>
  270. </div>
  271. ";
  272. return $layout;
  273. }