tripal_chado.field_storage.inc 27 KB

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  1. <?php
  2. /**
  3. * Implements hook_field_storage_info().
  4. */
  5. function tripal_chado_field_storage_info() {
  6. return array(
  7. 'field_chado_storage' => array(
  8. 'label' => t('Chado'),
  9. 'description' => t('Stores fields in the local Chado database.'),
  10. 'settings' => array(),
  11. // The logo_url key is supported by Tripal. It's not a Drupal key. It's
  12. // used for adding a logo or picture for the data store to help make it
  13. // more easily recognized on the field_ui_field_overview_form. Ideally
  14. // the URL should point to a relative path on the local Drupal site.
  15. 'logo_url' => url(drupal_get_path('module', 'tripal') . '/theme/images/250px-ChadoLogo.png'),
  16. ),
  17. );
  18. }
  19. /**
  20. * Implements hook_field_storage_write().
  21. */
  22. function tripal_chado_field_storage_write($entity_type, $entity, $op, $fields) {
  23. // Get the bundle and the term for this entity.
  24. $bundle = tripal_load_bundle_entity(array('name' => $entity->bundle));
  25. $term = entity_load('TripalTerm', array('id' => $entity->term_id));
  26. $term = reset($term);
  27. // Convert the Tripal term entity into the appropriate record in Chado.
  28. $dbxref = tripal_get_dbxref(array('accession' => $term->accession, 'db_id' => array('name' => $term->vocab->vocabulary)));
  29. $cvterm = tripal_get_cvterm(array('dbxref_id' => $dbxref->dbxref_id));
  30. // Get the base table, type field and record_id from the entity.
  31. $base_table = $entity->chado_table;
  32. $type_field = $entity->chado_column;
  33. $record = $entity->chado_record;
  34. $record_id = $entity->chado_record_id;
  35. $base_schema = chado_get_schema($base_table);
  36. $base_pkey = $base_schema['primary key'][0];
  37. // Convert the fields into a key/value list of fields and their values.
  38. $field_vals = tripal_chado_field_storage_write_merge_fields($fields, $entity_type, $entity);
  39. // First, write the record for the base table. If we have a record id then
  40. // this is an update and we need to set the primary key. If not, then this
  41. // is an insert and we need to set the type_id if the table supports it.
  42. $values = $field_vals[$base_table];
  43. if ($record_id) {
  44. $values[$base_pkey] = $record_id;
  45. }
  46. elseif ($type_field) {
  47. $values[$type_field] = $cvterm->cvterm_id;
  48. }
  49. $base_record_id = tripal_chado_field_storage_write_table($base_table, $values);
  50. // If this is an insert then add the chado_entity record.
  51. if ($op == FIELD_STORAGE_INSERT) {
  52. // Add a record to the chado_entity table so that the data for the
  53. // fields can be pulled from Chado when loaded the next time.
  54. $record = array(
  55. 'entity_id' => $entity->id,
  56. 'record_id' => $base_record_id,
  57. 'data_table' => $base_table,
  58. );
  59. $success = drupal_write_record('chado_entity', $record);
  60. if (!$success) {
  61. drupal_set_message('Unable to insert new Chado entity.', 'error');
  62. }
  63. }
  64. // Now that we have handled the base table, we need to handle linking tables.
  65. foreach ($field_vals as $table_name => $details) {
  66. // Skip the base table as we've already dealt with it.
  67. if ($table_name == $base_table) {
  68. continue;
  69. }
  70. foreach ($details as $delta => $values) {
  71. $record_id = tripal_chado_field_storage_write_table($table_name, $values);
  72. }
  73. }
  74. }
  75. /**
  76. * Write (inserts/updates/deletes) values for a Chado table.
  77. *
  78. * The $values array is of the same format used by chado_insert_record() and
  79. * chado_update_record(). However, both of those methods will use any nested
  80. * arrays (i.e. representing foreign keys) to select an appropriate record ID
  81. * that can be substituted as the value. Here, the nested arrays are
  82. * either inserted or updated as well, but the choice is determined if the
  83. * primary key value is present. If present an update occurs, if not present
  84. * then an insert occurs.
  85. *
  86. * This function is recursive and nested arrays from the lowest point of the
  87. * "tree" are dealt with first.
  88. *
  89. * @param $table_name
  90. * The name of the table on which the insertion/update is performed.
  91. * @param $values
  92. * The values array for the insertion.
  93. *
  94. * @throws Exception
  95. *
  96. * @return
  97. * The unique record ID.
  98. */
  99. function tripal_chado_field_storage_write_table($table_name, $values) {
  100. $schema = chado_get_schema($table_name);
  101. $fkeys = $schema['foreign keys'];
  102. $pkey = $schema['primary key'][0];
  103. // Fields with a cardinality greater than 1 will often submit an
  104. // empty form. We want to remove these empty submissions. We can detect
  105. // them if all of the fields are empty.
  106. $num_empty = 0;
  107. foreach ($values as $column => $value) {
  108. if (!$value) {
  109. $num_empty++;
  110. }
  111. }
  112. if ($num_empty == count(array_keys($values))) {
  113. return '';
  114. }
  115. // If the primary key column has a value but all other values are empty then
  116. // this is a delete.
  117. if (array_key_exists($pkey, $values) and $values[$pkey]) {
  118. $num_vals = 0;
  119. foreach ($values as $value) {
  120. if ($value) {
  121. $num_vals++;
  122. }
  123. }
  124. if ($num_vals == 1) {
  125. $new_vals[$pkey] = $values[$pkey];
  126. if (!chado_delete_record($table_name, $new_vals)) {
  127. throw new Exception('Could not delete record from table: "' . $table_name . '".');
  128. }
  129. return '';
  130. }
  131. }
  132. // If the primary key column does not have a value then this is an insert.
  133. if (!array_key_exists($pkey, $values) or !$values[$pkey] or !isset($values[$pkey])) {
  134. // Before inserting, we want to make sure the record does not
  135. // already exist. Using the unique constraint check for a matching record.
  136. $options = array('is_duplicate' => TRUE);
  137. $is_duplicate = chado_select_record($table_name, array('*'), $values, $options);
  138. if($is_duplicate) {
  139. $record = chado_select_record($table_name, array('*'), $values);
  140. return $record[0]->$pkey;
  141. }
  142. // Insert the values array as a new record in the table but remove the
  143. // pkey as it should be set.
  144. $new_vals = $values;
  145. unset($new_vals[$pkey]);
  146. $record = chado_insert_record($table_name, $new_vals);
  147. if ($record === FALSE) {
  148. throw new Exception('Could not insert Chado record into table: "' . $table_name . '".');
  149. }
  150. return $record[$pkey];
  151. }
  152. // If we've made it to this point then this is an update.
  153. // TODO: what if the unique constraint matches another record? That is
  154. // not being tested for here.
  155. $match[$pkey] = $values[$pkey];
  156. if (!chado_update_record($table_name, $match, $values)) {
  157. drupal_set_message("Could not update Chado record in table: $table_name.", 'error');
  158. }
  159. return $values[$pkey];
  160. }
  161. /**
  162. * Implements hook_field_storage_load().
  163. *
  164. * Responsible for loading the fields from the Chado database and adding
  165. * their values to the entity.
  166. */
  167. function tripal_chado_field_storage_load($entity_type, $entities, $age,
  168. $fields, $options) {
  169. $load_current = $age == FIELD_LOAD_CURRENT;
  170. global $language;
  171. $langcode = $language->language;
  172. foreach ($entities as $id => $entity) {
  173. if (property_exists($entity, 'chado_table')) {
  174. // Get the base table and record id for the fields of this entity.
  175. $base_table = $entity->chado_table;
  176. $type_field = $entity->chado_column;
  177. $record_id = $entity->chado_record_id;
  178. }
  179. else {
  180. $bundle = tripal_load_bundle_entity(array('name' => $entity->bundle));
  181. $base_table = $bundle->data_table;
  182. $type_field = $bundle->type_column;
  183. // Get the base table and record id for the fields of this entity.
  184. $details = db_select('chado_entity', 'ce')
  185. ->fields('ce')
  186. ->condition('entity_id', $entity->id)
  187. ->execute()
  188. ->fetchObject();
  189. if (!$details) {
  190. // TODO: what to do if record is missing!
  191. }
  192. $record_id = isset($details->record_id) ? $details->record_id : '';
  193. }
  194. // Get this table's schema.
  195. $schema = chado_get_schema($base_table);
  196. $pkey_field = $schema['primary key'][0];
  197. // Get the base record if one exists
  198. $columns = array('*');
  199. $match = array($pkey_field => $record_id);
  200. $record = chado_generate_var($base_table, $match);
  201. $entity->chado_record = $record;
  202. // Iterate through the entity's fields so we can get the column names
  203. // that need to be selected from each of the tables represented.
  204. $tables = array();
  205. foreach ($fields as $field_id => $ids) {
  206. // By the time this hook runs, the relevant field definitions have been
  207. // populated and cached in FieldInfo, so calling field_info_field_by_id()
  208. // on each field individually is more efficient than loading all fields in
  209. // memory upfront with field_info_field_by_ids().
  210. $field = field_info_field_by_id($field_id);
  211. $field_name = $field['field_name'];
  212. $field_type = $field['type'];
  213. $field_module = $field['module'];
  214. // Get the instance for this field. If no instance exists then skip
  215. // loading of this field. This can happen when a field is deleted from
  216. // a bundle using the user UI form.
  217. // TODO: how to deal with deleted fields?
  218. $instance = field_info_instance($entity_type, $field_name, $entity->bundle);
  219. if (!$instance) {
  220. continue;
  221. }
  222. // Skip fields that don't map to a Chado table.
  223. if (!array_key_exists('settings', $instance) or
  224. !array_key_exists('chado_table', $instance['settings'])) {
  225. continue;
  226. }
  227. // Get the Chado table and column for this field.
  228. $field_table = $instance['settings']['chado_table'];
  229. $field_column = $instance['settings']['chado_column'];
  230. // There are only two types of fields: 1) fields that represent a single
  231. // column of the base table, or 2) fields that represent a linked record
  232. // in a many-to-one relationship with the base table.
  233. // Type 1: fields from base tables.
  234. if ($field_table == $base_table) {
  235. // Set an empty value by default, and if there is a record, then update.
  236. $entity->{$field_name}['und'][0]['value'] = '';
  237. if ($record and property_exists($record, $field_column)) {
  238. // If the field column is an object then it's a FK to another table.
  239. // and because $record object is created by the chado_generate_var()
  240. // function we must go one more level deeper to get the value
  241. if (is_object($record->$field_column)) {
  242. $fkey_column = $field_column;
  243. foreach($schema['foreign keys'] as $table => $fk_details) {
  244. foreach($fk_details['columns'] as $lfkey => $rfkey) {
  245. if ($lfkey == $field_column) {
  246. $fkey_column = $rfkey;
  247. }
  248. }
  249. }
  250. $entity->{$field_name}['und'][0]['chado-' . $field_table . '__' . $field_column] = $record->$field_column->$fkey_column;
  251. }
  252. else {
  253. // For non FK fields we'll make the field value be the same
  254. // as the column value.
  255. $entity->{$field_name}['und'][0]['value'] = $record->$field_column;
  256. $entity->{$field_name}['und'][0]['chado-' . $field_table . '__' . $field_column] = $record->$field_column;
  257. }
  258. }
  259. // Allow the creating module to alter the value if desired. The
  260. // module should do this if the field has any other form elements
  261. // that need populationg besides the value which was set above.
  262. tripal_load_include_field_class($field_type);
  263. if (class_exists($field_type) and is_subclass_of($field_type, 'TripalField')) {
  264. $tfield = new $field_type($field, $instance);
  265. $tfield->load($entity, array('record' => $record));
  266. }
  267. // For text fields that were not handled by a TripalField class we
  268. // want to automatically expand those fields.
  269. else {
  270. if ($schema['fields'][$field_column]['type'] == 'text') {
  271. $record = chado_expand_var($record, 'field', "$field_table.$field_column");
  272. $entity->{$field_name}['und'][0]['value'] = $record->$field_column;
  273. // Text fields that have a text_processing == 1 setting need a
  274. // special 'format' element too:
  275. if (array(key_exists('text_processing', $instance['settings']) and
  276. $instance['settings']['text_processing'] == 1)) {
  277. // TODO: we need a way to write the format back to the
  278. // instance settings if the user changes it when using the form.
  279. $entity->{$field_name}['und'][0]['format'] = array_key_exists('format', $instance['settings']) ? $instance['settings']['format'] : 'full_html';
  280. }
  281. }
  282. }
  283. }
  284. // Type 2: fields for linked records. These fields will have any number
  285. // of form elements that might need populating so we'll offload the
  286. // loading of these fields to the field itself.
  287. if ($field_table != $base_table) {
  288. // Set an empty value by default, and let the hook function update it.
  289. $entity->{$field_name}['und'][0]['value'] = '';
  290. tripal_load_include_field_class($field_type);
  291. if (class_exists($field_type) && method_exists($field_type, 'load')) {
  292. $tfield = new $field_type($field, $instance);
  293. $tfield->load($entity, array('record' => $record));
  294. }
  295. }
  296. } // end: foreach ($fields as $field_id => $ids) {
  297. } // end: foreach ($entities as $id => $entity) {
  298. }
  299. /**
  300. * Merges the values of all fields into a single array keyed by table name.
  301. */
  302. function tripal_chado_field_storage_write_merge_fields($fields, $entity_type, $entity) {
  303. $all_fields = array();
  304. $base_fields = array();
  305. // Iterate through all of the fields and organize them into a
  306. // new fields array keyed by the table name
  307. foreach ($fields as $field_id => $ids) {
  308. // Get the field name and information about it.
  309. $field = field_info_field_by_id($field_id);
  310. $field_name = $field['field_name'];
  311. $instance = field_info_instance('TripalEntity', $field['field_name'], $entity->bundle);
  312. // Some fields (e.g. chado_linker_cvterm_adder) don't add data to
  313. // Chado so they don't have a table, but they are still attached to the
  314. // entity. Just skip these.
  315. if (!array_key_exists('chado_table', $instance['settings'])) {
  316. continue;
  317. }
  318. $chado_table = $instance['settings']['chado_table'];
  319. $chado_column = $instance['settings']['chado_column'];
  320. $base_table = $instance['settings']['base_table'];
  321. // Iterate through the field's items. Fields with cardinality ($delta) > 1
  322. // are multi-valued.
  323. $items = field_get_items($entity_type, $entity, $field_name);
  324. $temp = array();
  325. foreach ($items as $delta => $item) {
  326. // A field may have multiple items. The field can use items
  327. // indexed with "chado-" to represent values that should map directly
  328. // to chado tables and fields.
  329. foreach ($item as $item_name => $value) {
  330. $matches = array();
  331. if (preg_match('/^chado-(.*?)__(.*?)$/', $item_name, $matches)) {
  332. $table_name = $matches[1];
  333. $column_name = $matches[2];
  334. // If this field belongs to the base table then we just add
  335. // those values in... there's no delta.
  336. if ($table_name == $base_table) {
  337. $base_fields[$table_name][$column_name] = $value;
  338. }
  339. else {
  340. $temp[$table_name][$delta][$column_name] = $value;
  341. }
  342. }
  343. }
  344. // If there is no value set for the field using the
  345. // chado-[table_name]__[field name] naming schema then check if a 'value'
  346. // item is present and if so use that for the table column value.
  347. if ((!array_key_exists($chado_table, $temp) or
  348. !array_key_exists($delta, $temp[$chado_table]) or
  349. !array_key_exists($chado_column, $temp[$chado_table][$delta])) and
  350. array_key_exists('value', $items[$delta]) and
  351. !is_array($items[$delta]['value'])) {
  352. // If this field belongs to the base table then we just add
  353. // those values in... there's no delta.
  354. if ($base_table == $chado_table) {
  355. $base_fields[$chado_table][$chado_column] = $item['value'];
  356. }
  357. else {
  358. $temp[$chado_table][$delta][$chado_column] = $item['value'];
  359. }
  360. }
  361. }
  362. // Now merge the records for this field with the $new_fields array
  363. foreach ($temp as $table_name => $details) {
  364. foreach ($details as $delta => $list) {
  365. $all_fields[$table_name][] = $list;
  366. }
  367. }
  368. }
  369. $all_fields = array_merge($base_fields, $all_fields);
  370. return $all_fields;
  371. }
  372. /**
  373. * Implements hook_field_storage_query().
  374. */
  375. function tripal_chado_field_storage_query($query) {
  376. // Initialize the result array.
  377. $result = array(
  378. 'TripalEntity' => array()
  379. );
  380. // There must always be an entity filter that includes the bundle. Otherwise
  381. // it would be too overwhelming to search every table of every content type
  382. // for a matching field.
  383. if (!array_key_exists('bundle', $query->entityConditions)) {
  384. return $result;
  385. }
  386. $bundle = tripal_load_bundle_entity(array('name' => $query->entityConditions['bundle']));
  387. $data_table = $bundle->data_table;
  388. $type_column = $bundle->type_column;
  389. $type_id = $bundle->type_id;
  390. $schema = chado_get_schema($data_table);
  391. $pkey = $schema['primary key'][0];
  392. // Initialize the Query object.
  393. $cquery = chado_db_select($data_table, 'base');
  394. $cquery->fields('base', array($pkey));
  395. // Iterate through all the conditions and add to the filters array
  396. // a chado_select_record compatible set of filters.
  397. foreach ($query->fieldConditions as $index => $condition) {
  398. $field = $condition['field'];
  399. $field_name = $field['field_name'];
  400. $field_type = $field['type'];
  401. // Skip conditions that don't belong to this storage type.
  402. if ($field['storage']['type'] != 'field_chado_storage') {
  403. continue;
  404. }
  405. // The Chado settings for a field are part of the instance and each bundle
  406. // can have the same field but with different Chado mappings. Therefore,
  407. // we need to iterate through the bundles to get the field instances.
  408. foreach ($field['bundles']['TripalEntity'] as $bundle_name) {
  409. // If there is a bundle filter for the entity and if the field is not
  410. // associated with the bundle then skip it.
  411. if (array_key_exists('bundle', $query->entityConditions)) {
  412. if (strtolower($query->entityConditions['bundle']['operator']) == 'in' and
  413. !array_key_exists($bundle_name, $query->entityConditions['bundle']['value'])) {
  414. continue;
  415. }
  416. else if ($query->entityConditions['bundle']['value'] != $bundle_name) {
  417. continue;
  418. }
  419. }
  420. // Allow the field to update the query object.
  421. $instance = field_info_instance('TripalEntity', $field['field_name'], $bundle_name);
  422. if (tripal_load_include_field_class($field_type)) {
  423. $field_obj = new $field_type($field, $instance);
  424. $field_obj->query($cquery, $condition);
  425. }
  426. }
  427. } // end foreach ($query->fieldConditions as $index => $condition) {
  428. // Now get the list for sorting.
  429. foreach ($query->order as $index => $sort) {
  430. // We only handle ordering by field type here.
  431. if ($sort['type'] != 'field') {
  432. continue;
  433. }
  434. $field = $sort['specifier']['field'];
  435. $field_type = $field['type'];
  436. $field_name = $field['field_name'];
  437. // Skip sorts that don't belong to this storage type.
  438. if ($field['storage']['type'] != 'field_chado_storage') {
  439. continue;
  440. }
  441. $column = $sort['specifier']['column'];
  442. $direction = $sort['direction'];
  443. // The Chado settings for a field are part of the instance and each bundle
  444. // can have the same field but with different Chado mappings. Therefore,
  445. // we need to iterate through the bundles to get the field instances.
  446. foreach ($field['bundles']['TripalEntity'] as $bundle_name) {
  447. // If there is a bundle filter for the entity and if the field is not
  448. // associated with the bundle then skip it.
  449. if (array_key_exists('bundle', $query->entityConditions)) {
  450. if (strtolower($query->entityConditions['bundle']['operator']) == 'in' and
  451. !array_key_exists($bundle_name, $query->entityConditions['bundle']['value'])) {
  452. continue;
  453. }
  454. else if ($query->entityConditions['bundle']['value'] != $bundle_name) {
  455. continue;
  456. }
  457. }
  458. // See if there is a ChadoField class for this instance. If not then do
  459. // our best to order the field.
  460. $instance = field_info_instance('TripalEntity', $field_name, $bundle_name);
  461. if (tripal_load_include_field_class($field_type)) {
  462. $field_obj = new $field_type($field, $instance);
  463. $field_obj->queryOrder($cquery, array('column' => $column, 'direction' => $direction));
  464. }
  465. // There is no class so do our best to order the data by this field
  466. else {
  467. $base_table = $instance['settings']['base_table'];
  468. $chado_table = $instance['settings']['chado_table'];
  469. $table_column = tripal_get_chado_semweb_column($chado_table, $column);
  470. if ($table_column) {
  471. if ($chado_table == $base_table) {
  472. $cquery->orderBy('base.' . $table_column, $direction);
  473. }
  474. else {
  475. // TODO: how do we handle a field that doesn't map to the base table.
  476. // We would expect that all of these would be custom field and
  477. // the ChadoField::queryOrder() function would be implemented.
  478. }
  479. }
  480. else {
  481. // TODO: handle when the name can't be matched to a table column.
  482. }
  483. }
  484. }
  485. }
  486. // Now join with the chado_entity table to get published records only.
  487. $cquery->join('chado_entity', 'CE', "CE.record_id = base.$pkey");
  488. $cquery->join('tripal_entity', 'TE', "CE.entity_id = TE.id");
  489. $cquery->fields('CE', array('entity_id'));
  490. $cquery->fields('TE', array('bundle'));
  491. $cquery->condition('CE.data_table', $data_table);
  492. if (array_key_exists('start', $query->range)) {
  493. $cquery->range($query->range['start'], $query->range['length']);
  494. }
  495. $records = $cquery->execute();
  496. $result = array();
  497. while ($record = $records->fetchObject()) {
  498. $ids = array($record->entity_id, 0, $record->bundle);
  499. $result['TripalEntity'][$record->entity_id] = entity_create_stub_entity('TripalEntity', $ids);
  500. }
  501. return $result;
  502. }
  503. /**
  504. * @return
  505. * An array containing the chado_select_record() compatible array.
  506. */
  507. function tripal_chado_field_storage_query_build_sql(&$sql, $prev_table, $prev_column, $prev_term, $chado_table, $query_terms, $condition, $value, $depth = 0) {
  508. // Get schema information for the previous (linker) Chado table.
  509. $pschema = chado_get_schema($prev_table);
  510. $ppkey = $pschema['primary key'][0];
  511. $pfkeys = $pschema['foreign keys'];
  512. // Get schema information for the current Chado table.
  513. $schema = chado_get_schema($chado_table);
  514. $pkey = $schema['primary key'][0];
  515. $fkeys = $schema['foreign keys'];
  516. // Get the first query term from the list and find out what column this
  517. // term maps to in the Chado table.
  518. $term = array_shift($query_terms);
  519. $chado_column = tripal_get_chado_semweb_column($chado_table, $term);
  520. if (!$chado_column) {
  521. // TODO: we could get to this point because a field has a value that
  522. // doesn't map to a database column but is a manually created
  523. // element. How do we deal with those?
  524. return FALSE;
  525. }
  526. // reformat that term so it's compatible with SQL
  527. $term = preg_replace('/[^\w]/', '_', $term);
  528. // A query can be an array of column names separated by a period. We
  529. // want to split them apart and just deal with the column at the head
  530. // of the array. But before dealing with that head, we will recurse so that
  531. // we build our filters array from the bottom up.
  532. if (count($query_terms) > 0) {
  533. // Since the $query_terms is not a single element that implies this
  534. // query term represents a foreign key.
  535. // We don't know which direction the foreign key is going, so we'll have
  536. // to check both the previous and current tables to build the join
  537. // statement correctly.
  538. if (array_key_exists($prev_table, $fkeys) and
  539. array_key_exists($chado_column, $fkeys[$prev_table]['columns'])) {
  540. $fkey = $fkeys[$prev_table]['columns'][$chado_column];
  541. $sql['join'][] = 'INNER JOIN {' . $chado_table . '} ' . $term . ' ON ' . $prev_term . '.' . $fkey . ' = ' . $term . '.' . $chado_column;
  542. }
  543. else {
  544. $sql['join'][] = 'INNER JOIN {' . $chado_table . '} ' . $term . ' ON ' . $prev_term . '.' . $prev_column . ' = ' . $term . '.' . $chado_column;
  545. }
  546. // Get the table that this foreign key links to.
  547. $next_table = '';
  548. foreach ($fkeys as $fktable_name => $fk_details) {
  549. foreach ($fk_details['columns'] as $lfkey => $rfkey) {
  550. if ($lfkey == $chado_column) {
  551. $next_table = $fktable_name;
  552. }
  553. }
  554. }
  555. if ($next_table) {
  556. tripal_chado_field_storage_query_build_sql($sql, $chado_table, $chado_column, $term, $next_table, $query_terms, $condition, $value, $depth++);
  557. }
  558. else {
  559. // TODO: we could get to this point because a field has a value that
  560. // doesn't map to a database column but is a manually created
  561. // element. How do we deal with those?
  562. return FALSE;
  563. }
  564. return FALSE;
  565. }
  566. // We don't know which direction the foreign key is going, so we'll have
  567. // to check both the previous and current tables to build the join
  568. // statement correctly.
  569. if (array_key_exists($prev_table, $fkeys) and
  570. array_key_exists($chado_column, $fkeys[$prev_table]['columns'])) {
  571. $fkey = $fkeys[$prev_table]['columns'][$chado_column];
  572. $sql['join'][] = 'INNER JOIN {' . $chado_table . '} ' . $term . ' ON ' . $prev_term . '.' . $fkey . ' = ' . $term . '.' . $chado_column;
  573. }
  574. else {
  575. $sql['join'][] = 'INNER JOIN {' . $chado_table . '} ' . $term . ' ON ' . $prev_term . '.' . $prev_column . ' = ' . $term . '.' . $chado_column;
  576. }
  577. // Use the appropriate operator.
  578. $operator = $condition['operator'] ? $condition['operator'] : '=';
  579. switch ($operator) {
  580. case '=':
  581. $sql['where'][] = "$term.$chado_column = :value";
  582. $sql['args'][':value'] = $value;
  583. break;
  584. case '>':
  585. case '>=':
  586. case '<':
  587. case '<=':
  588. $sql['where'][] = "$term.$chado_column $op :value";
  589. $sql['args'][':value'] = $value;
  590. break;
  591. case '<>':
  592. $sql['where'][] = "$term.$chado_column $op :value";
  593. $sql['args'][':value'] = $value;
  594. break;
  595. case 'CONTAINS':
  596. $sql['where'][] = "$term.$chado_column LIKE :value";
  597. $sql['args'][':value'] = '%' . $value . '%';
  598. break;
  599. case 'NOT':
  600. $subfilters[$chado_column] = array(
  601. 'op' => 'NOT LIKE',
  602. 'data' => '%' . $value . '%',
  603. );
  604. $sql['where'][] = "$term.$chado_column NOT LIKE :value";
  605. $sql['args'][':value'] = '%' . $value . '%';
  606. break;
  607. case 'STARTS WITH':
  608. $sql['where'][] = "$term.$chado_column LIKE :value";
  609. $sql['args'][':value'] = $value . '%';
  610. break;
  611. case 'NOT STARTS':
  612. $sql['where'][] = "$term.$chado_column NOT LIKE :value";
  613. $sql['args'][':value'] = $value . '%';
  614. break;
  615. case 'ENDS WITH':
  616. $sql['where'][] = "$term.$chado_column LIKE :value";
  617. $sql['args'][':value'] = '%' . $value;
  618. break;
  619. case 'NOT ENDS':
  620. $sql['where'][] = "$term.$chado_column NOT LIKE :value";
  621. $sql['args'][':value'] = '%' . $value;
  622. break;
  623. default:
  624. // unrecognized operation.
  625. break;
  626. }
  627. }