tripal_feature.chado_node.inc 33 KB

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  1. <?php
  2. /**
  3. * @file
  4. * Implementation of hooks to create a feature content type
  5. */
  6. /**
  7. * Implements hook_node_info().
  8. *
  9. * Provide information to drupal about the node types that we're creating
  10. * in this module
  11. *
  12. * @ingroup tripal_feature
  13. */
  14. function tripal_feature_node_info() {
  15. $nodes = array();
  16. $nodes['chado_feature'] = array(
  17. 'name' => t('Feature'),
  18. 'base' => 'chado_feature',
  19. 'description' => t('A feature from the chado database'),
  20. 'has_title' => TRUE,
  21. 'locked' => TRUE,
  22. 'chado_node_api' => array(
  23. 'base_table' => 'feature',
  24. 'hook_prefix' => 'chado_feature',
  25. 'record_type_title' => array(
  26. 'singular' => t('Feature'),
  27. 'plural' => t('Features')
  28. ),
  29. 'sync_filters' => array(
  30. 'type_id' => TRUE,
  31. 'organism_id' => TRUE
  32. ),
  33. )
  34. );
  35. return $nodes;
  36. }
  37. /**
  38. * Implementation of hook_form().
  39. *
  40. * @ingroup tripal_feature
  41. */
  42. function chado_feature_form($node, &$form_state) {
  43. $form = array();
  44. // Default values can come in the following ways:
  45. //
  46. // 1) as elements of the $node object. This occurs when editing an existing feature
  47. // 2) in the $form_state['values'] array which occurs on a failed validation or
  48. // ajax callbacks from non submit form elements
  49. // 3) in the $form_state['input'[ array which occurs on ajax callbacks from submit
  50. // form elements and the form is being rebuilt
  51. //
  52. // set form field defaults
  53. $feature = null;
  54. $feature_id = null;
  55. $uniquename = '';
  56. $fname = '';
  57. $feature_type = '';
  58. $organism_id = '';
  59. $residues = '';
  60. $is_obsolete = '';
  61. $analyses = '';
  62. $references = '';
  63. $synonyms = '';
  64. // if we are editing an existing node then the feature is already part of the node
  65. if (property_exists($node, 'feature')) {
  66. $feature = $node->feature;
  67. $feature = chado_expand_var($feature, 'field', 'feature.residues');
  68. $feature_id = $feature->feature_id;
  69. $uniquename = $feature->uniquename;
  70. $fname = $feature->name;
  71. $feature_type = $feature->type_id->name;
  72. $organism_id = $feature->organism_id->organism_id;
  73. $residues = $feature->residues;
  74. $is_obsolete = $feature->is_obsolete;
  75. // get the synonyms from a previous post
  76. $synonyms = '';
  77. if(property_exists($node, 'synonyms')) {
  78. $synonyms = $node->synonyms;
  79. }
  80. // get synonyms from the database if we don't already have them
  81. if (!$synonyms) {
  82. $options = array('return_array' => 1);
  83. $feature = chado_expand_var($feature, 'table', 'feature_synonym', $options);
  84. $feature_synonyms = (isset($feature->feature_synonym)) ? $feature->feature_synonym : array();
  85. foreach ($feature_synonyms as $index => $synonym) {
  86. $synonyms .= $synonym->synonym_id->name . "\n";
  87. }
  88. }
  89. // keep track of the feature id
  90. $form['feature_id'] = array(
  91. '#type' => 'value',
  92. '#value' => $feature_id,
  93. );
  94. }
  95. // if we are re constructing the form from a failed validation or ajax callback
  96. // then use the $form_state['values'] values
  97. if (array_key_exists('values', $form_state) and isset($form_state['values']['uniquename'])) {
  98. $uniquename = $form_state['values']['uniquename'];
  99. $fname = $form_state['values']['fname'];
  100. $feature_type = $form_state['values']['feature_type'];
  101. $organism_id = $form_state['values']['organism_id'];
  102. $residues = $form_state['values']['residues'];
  103. $is_obsolete = $form_state['values']['is_obsolete'];
  104. $synonyms = $form_state['values']['synonyms'];
  105. }
  106. // if we are re building the form from after submission (from ajax call) then
  107. // the values are in the $form_state['input'] array
  108. if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
  109. $uniquename = $form_state['input']['uniquename'];
  110. $fname = $form_state['input']['fname'];
  111. $feature_type = $form_state['input']['feature_type'];
  112. $organism_id = $form_state['input']['organism_id'];
  113. $residues = $form_state['input']['residues'];
  114. $is_obsolete = array_key_exists('is_obsolete', $form_state['input']) ? $form_state['input']['is_obsolete'] : FALSE;
  115. $synonyms = $form_state['input']['synonyms'];
  116. }
  117. $form['fname']= array(
  118. '#type' => 'textfield',
  119. '#title' => t('Feature Name'),
  120. '#required' => TRUE,
  121. '#default_value' => $fname,
  122. '#description' => t('Enter the name used by humans to refer to this feature.'),
  123. '#maxlength' => 255
  124. );
  125. $form['uniquename']= array(
  126. '#type' => 'textfield',
  127. '#title' => t('Unique Feature Name'),
  128. '#required' => TRUE,
  129. '#default_value' => $uniquename,
  130. '#description' => t('Enter a unique name for this feature. This name must be unique for the organism and feature type.'),
  131. '#maxlength' => 255
  132. );
  133. // get the sequence ontology CV ID
  134. $values = array('name' => 'sequence');
  135. $cv = chado_select_record('cv', array('cv_id'), $values);
  136. $cv_id = $cv[0]->cv_id;
  137. $form['feature_type'] = array(
  138. '#title' => t('Feature Type'),
  139. '#type' => 'textfield',
  140. '#description' => t("Choose the feature type."),
  141. '#required' => TRUE,
  142. '#default_value' => $feature_type,
  143. '#autocomplete_path' => "admin/tripal/chado/tripal_cv/cvterm/auto_name/$cv_id",
  144. );
  145. // get the list of organisms
  146. $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
  147. $org_rset = chado_query($sql);
  148. $organisms = array();
  149. $organisms[''] = '';
  150. while ($organism = $org_rset->fetchObject()) {
  151. $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
  152. }
  153. $form['organism_id'] = array(
  154. '#title' => t('Organism'),
  155. '#type' => t('select'),
  156. '#description' => t("Choose the organism with which this feature is associated"),
  157. '#required' => TRUE,
  158. '#default_value' => $organism_id,
  159. '#options' => $organisms,
  160. );
  161. // Get synonyms
  162. $syn_text = '';
  163. if ($synonyms) {
  164. if (is_array($synonyms)) {
  165. foreach ($synonyms as $synonym) {
  166. $syn_text .= "$synonym->name\n";
  167. }
  168. }
  169. else {
  170. $syn_text = $synonyms;
  171. }
  172. }
  173. $form['synonyms']= array(
  174. '#type' => 'textarea',
  175. '#title' => t('Synonyms'),
  176. '#required' => FALSE,
  177. '#default_value' => $syn_text,
  178. '#description' => t('Enter alternate names (synonmys) for this feature to help in searching and identification. You may enter as many alternate names as needed each on different lines.'),
  179. );
  180. $form['residues']= array(
  181. '#type' => 'textarea',
  182. '#title' => t('Residues'),
  183. '#required' => FALSE,
  184. '#default_value' => $residues,
  185. '#description' => t('Enter the nucelotide sequences for this feature'),
  186. );
  187. $checked = '';
  188. if ($is_obsolete == 't') {
  189. $checked = '1';
  190. }
  191. $form['is_obsolete']= array(
  192. '#type' => 'checkbox',
  193. '#title' => t('Is Obsolete'),
  194. '#required' => FALSE,
  195. '#default_value' => $checked,
  196. '#description' => t('Check this box if this sequence should be retired'),
  197. );
  198. // PROPERTIES FORM
  199. //---------------------------------------------
  200. $details = array(
  201. 'property_table' => 'featureprop', // the name of the prop table
  202. 'chado_id' => $feature_id, // the value of feature_id for this record
  203. 'cv_name' => 'feature_property' // the cv.name of the cv governing featureprop.type_id
  204. );
  205. // Adds the form elements to your current form
  206. chado_add_node_form_properties($form, $form_state, $details);
  207. // ADDITIONAL DBXREFS FORM
  208. //---------------------------------------------
  209. $details = array(
  210. 'linking_table' => 'feature_dbxref', // the name of the _dbxref table
  211. 'base_foreign_key' => 'feature_id', // the name of the key in your base chado table
  212. 'base_key_value' => $feature_id // the value of feature_id for this record
  213. );
  214. // Adds the form elements to your current form
  215. chado_add_node_form_dbxrefs($form, $form_state, $details);
  216. return $form;
  217. }
  218. /**
  219. * Implementation of hook_validate().
  220. *
  221. * This validation is being used for three activities:
  222. * CASE A: Update a node that exists in both drupal and chado
  223. * CASE B: Synchronizing a node from chado to drupal
  224. * CASE C: Inserting a new node that exists in niether drupal nor chado
  225. *
  226. * @ingroup tripal_feature
  227. */
  228. function chado_feature_validate($node, $form, &$form_state) {
  229. // remove surrounding white-space on submitted values
  230. $node->uniquename = trim($node->uniquename);
  231. $node->fname = trim($node->fname);
  232. $node->feature_type = trim($node->feature_type);
  233. $node->residues = trim($node->residues);
  234. // if this is a delete then don't validate
  235. if($node->op == 'Delete') {
  236. return;
  237. }
  238. // we are syncing if we do not have a node ID but we do have a feature_id. We don't
  239. // need to validate during syncing so just skip it.
  240. if (is_null($node->nid) and property_exists($node, 'feature_id') and $node->feature_id != 0) {
  241. return;
  242. }
  243. // Validating for an update
  244. if (property_exists($node, 'nid')) {
  245. // make sure the feature type is a real sequence ontology term
  246. $type = tripal_cv_get_cvterm_by_name($node->feature_type, NULL, 'sequence');
  247. if (!$type) {
  248. form_set_error('feature_type', t("The feature type is not a valid name from the Sequence Ontology."));
  249. }
  250. // if this is an update, we want to make sure that a different feature for
  251. // the organism doesn't already have this uniquename. We don't want to give
  252. // two sequences the same uniquename
  253. if (property_exists($node, 'feature_id') and $node->feature_id != 0) {
  254. $sql = "
  255. SELECT *
  256. FROM {feature} F
  257. INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
  258. WHERE
  259. F.uniquename = :uname AND
  260. F.organism_id = :organism_id AND
  261. CVT.name = :cvtname AND
  262. NOT f.feature_id = :feature_id
  263. ";
  264. $args = array(':uname' => $node->uniquename, ':organism_id' => $node->organism_id,
  265. ':cvtname' => $node->feature_type, ':feature_id' => $node->feature_id);
  266. $result = chado_query($sql, $args)->fetchObject();
  267. if ($result) {
  268. form_set_error('uniquename', t("Feature update cannot proceed. The feature name '$node->uniquename' is not unique for this organism. Please provide a unique name for this feature."));
  269. }
  270. }
  271. }
  272. // Validating for an insert
  273. else {
  274. // make sure the feature type is a real sequence ontology term
  275. $type = tripal_cv_get_cvterm_by_name($node->feature_type, NULL, 'sequence');
  276. if (!$type) {
  277. form_set_error('feature_type', t("The feature type is not a valid name from the Sequence Ontology."));
  278. }
  279. // if this is an insert then we just need to make sure this name doesn't
  280. // already exist for this organism if it does then we need to throw an error
  281. $sql = "
  282. SELECT *
  283. FROM {feature} F
  284. INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
  285. WHERE
  286. F.uniquename = :name AND
  287. F.organism_id = :organism_id AND
  288. CVT.name = :cvtname
  289. ";
  290. $args = array(':name' => $node->uniquename, ':organism_id' => $node->organism_id, ':cvtname' => $node->feature_type);
  291. $result = chado_query($sql, $args)->fetchObject();
  292. if ($result) {
  293. form_set_error('uniquename', t("Feature insert cannot proceed. The feature name '$node->uniquename' already exists for this organism. Please provide a unique name for this feature."));
  294. }
  295. }
  296. }
  297. /**
  298. * Implement hook_node_access().
  299. *
  300. * This hook allows node modules to limit access to the node types they define.
  301. *
  302. * @param $node
  303. * The node on which the operation is to be performed, or, if it does not yet exist, the
  304. * type of node to be created
  305. *
  306. * @param $op
  307. * The operation to be performed
  308. *
  309. * @param $account
  310. * A user object representing the user for whom the operation is to be performed
  311. *
  312. * @return
  313. * If the permission for the specified operation is not set then return FALSE. If the
  314. * permission is set then return NULL as this allows other modules to disable
  315. * access. The only exception is when the $op == 'create'. We will always
  316. * return TRUE if the permission is set.
  317. *
  318. * @ingroup tripal_feature
  319. */
  320. function chado_feature_node_access($node, $op, $account) {
  321. if ($op == 'create') {
  322. if (!user_access('create chado_feature content', $account)) {
  323. return FALSE;
  324. }
  325. return TRUE;
  326. }
  327. if ($op == 'update') {
  328. if (!user_access('edit chado_feature content', $account)) {
  329. return FALSE;
  330. }
  331. }
  332. if ($op == 'delete') {
  333. if (!user_access('delete chado_feature content', $account)) {
  334. return FALSE;
  335. }
  336. }
  337. if ($op == 'view') {
  338. if (!user_access('access chado_feature content', $account)) {
  339. return FALSE;
  340. }
  341. }
  342. return NULL;
  343. }
  344. /**
  345. * Implements hook_insert().
  346. *
  347. * When a new chado_feature node is created we also need to add information
  348. * to our chado_feature table. This function is called on insert of a new node
  349. * of type 'chado_feature' and inserts the necessary information.
  350. *
  351. * @ingroup tripal_feature
  352. */
  353. function chado_feature_insert($node) {
  354. $node->uniquename = trim($node->uniquename);
  355. $node->fname = trim($node->fname);
  356. $node->feature_type = trim($node->feature_type);
  357. $node->residues = trim($node->residues);
  358. // remove spaces, newlines from residues
  359. $residues = preg_replace("/[\n\r\s]/", "", $node->residues);
  360. $obsolete = 'FALSE';
  361. if ($node->is_obsolete) {
  362. $obsolete = 'TRUE';
  363. }
  364. // get the feature type id
  365. $values = array(
  366. 'cv_id' => array(
  367. 'name' => 'sequence'
  368. ),
  369. 'name' => $node->feature_type
  370. );
  371. $type = chado_select_record('cvterm', array('cvterm_id'), $values);
  372. $feature_id = '';
  373. // if there is an feature_id in the $node object then this must be a sync so
  374. // we can skip adding the feature as it is already there, although
  375. // we do need to proceed with the rest of the insert
  376. if (!property_exists($node, 'feature_id')) {
  377. $values = array(
  378. 'organism_id' => $node->organism_id,
  379. 'name' => $node->fname,
  380. 'uniquename' => $node->uniquename,
  381. 'residues' => $residues,
  382. 'seqlen' => drupal_strlen($residues),
  383. 'is_obsolete' => $obsolete,
  384. 'type_id' => $type[0]->cvterm_id,
  385. 'md5checksum' => md5($residues)
  386. );
  387. $feature = chado_insert_record('feature', $values);
  388. if (!$feature) {
  389. drupal_set_message(t('Unable to add feature.'), 'warning');
  390. tripal_report_error('tripal_feature', TRIPAL_WARNING, 'Insert feature: Unable to create feature where values: %values',
  391. array('%values' => print_r($values, TRUE)));
  392. return;
  393. }
  394. $feature_id = $feature['feature_id'];
  395. // add the genbank accession and synonyms
  396. chado_feature_add_synonyms($node->synonyms, $feature_id);
  397. // * Properties Form *
  398. $details = array(
  399. 'property_table' => 'featureprop', // the name of the prop table
  400. 'base_table' => 'feature', // the name of your chado base table
  401. 'foreignkey_name' => 'feature_id', // the name of the key in your base table
  402. 'foreignkey_value' => $feature_id // the value of the feature_id key
  403. );
  404. chado_update_node_form_properties($node, $details);
  405. // * Additional DBxrefs Form *
  406. $details = array(
  407. 'linking_table' => 'feature_dbxref', // the name of your _dbxref table
  408. 'foreignkey_name' => 'feature_id', // the name of the key in your base table
  409. 'foreignkey_value' => $feature_id // the value of the feature_id key
  410. );
  411. chado_update_node_form_dbxrefs($node, $details);
  412. }
  413. else {
  414. $feature_id = $node->feature_id;
  415. }
  416. // Make sure the entry for this feature doesn't already exist in the
  417. // chado_feature table if it doesn't exist then we want to add it.
  418. $check_org_id = chado_get_id_from_nid('feature', $node->nid);
  419. if (!$check_org_id) {
  420. $record = new stdClass();
  421. $record->nid = $node->nid;
  422. $record->vid = $node->vid;
  423. $record->feature_id = $feature_id;
  424. drupal_write_record('chado_feature', $record);
  425. }
  426. }
  427. /**
  428. * Implements hook_update().
  429. *
  430. * @ingroup tripal_feature
  431. */
  432. function chado_feature_update($node) {
  433. $node->uniquename = trim($node->uniquename);
  434. $node->fname = trim($node->fname);
  435. $node->feature_type = trim($node->feature_type);
  436. $node->residues = trim($node->residues);
  437. $residues = preg_replace("/[\n\r\s]/", "", $node->residues);
  438. $obsolete = 'FALSE';
  439. if ($node->is_obsolete) {
  440. $obsolete = 'TRUE';
  441. }
  442. // get the feature type id
  443. $values = array(
  444. 'cv_id' => array(
  445. 'name' => 'sequence'
  446. ),
  447. 'name' => $node->feature_type
  448. );
  449. $type = chado_select_record('cvterm', array('cvterm_id'), $values);
  450. $feature_id = chado_get_id_from_nid('feature', $node->nid) ;
  451. if (sizeof($type) > 0) {
  452. $match = array(
  453. 'feature_id' => $feature_id,
  454. );
  455. $values = array(
  456. 'organism_id' => $node->organism_id,
  457. 'name' => $node->fname,
  458. 'uniquename' => $node->uniquename,
  459. 'residues' => $residues,
  460. 'seqlen' => drupal_strlen($residues),
  461. 'is_obsolete' => $obsolete,
  462. 'type_id' => $type[0]->cvterm_id,
  463. 'md5checksum' => md5($residues)
  464. );
  465. $options = array('return_record' => TRUE);
  466. $status = chado_update_record('feature', $match, $values, $options);
  467. // add the genbank synonyms
  468. chado_feature_add_synonyms($node->synonyms, $feature_id);
  469. // * Properties Form *
  470. $details = array(
  471. 'property_table' => 'featureprop', // the name of the prop table
  472. 'base_table' => 'feature', // the name of your chado base table
  473. 'foreignkey_name' => 'feature_id', // the name of the key in your base table
  474. 'foreignkey_value' => $feature_id // the value of the feature_id key
  475. );
  476. chado_update_node_form_properties($node, $details);
  477. // * Additional DBxrefs Form *
  478. $details = array(
  479. 'linking_table' => 'feature_dbxref', // the name of your _dbxref table
  480. 'foreignkey_name' => 'feature_id', // the name of the key in your base table
  481. 'foreignkey_value' => $feature_id // the value of the feature_id key
  482. );
  483. chado_update_node_form_dbxrefs($node, $details);
  484. }
  485. else {
  486. drupal_set_message(t('Unable to update feature.'), 'warning');
  487. tripal_report_error('tripal_feature', TRIPAL_WARNING,
  488. 'Update feature: Unable to update feature where values: %values',
  489. array('%values' => print_r($values, TRUE))
  490. );
  491. }
  492. }
  493. /**
  494. * Implements hook_delete().
  495. *
  496. * @ingroup tripal_feature
  497. */
  498. function chado_feature_delete($node) {
  499. $feature_id = chado_get_id_from_nid('feature', $node->nid);
  500. // if we don't have a library id for this node then this isn't a node of
  501. // type chado_library or the entry in the chado_library table was lost.
  502. if (!$feature_id) {
  503. return;
  504. }
  505. // remove the drupal content
  506. $sql_del = "DELETE FROM {chado_feature} WHERE nid = :nid AND vid = :vid";
  507. db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
  508. $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
  509. db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
  510. $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid";
  511. db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
  512. // Remove data from feature tables of chado database. This will
  513. // cause a cascade delete and remove all data in referencing tables
  514. // for this feature
  515. chado_query("DELETE FROM {feature} WHERE feature_id = :feature_id", array(':feature_id' => $feature_id));
  516. drupal_set_message(t("The feature and all associated data were removed from") .
  517. "chado");
  518. }
  519. /**
  520. * Add synonyms to a feature
  521. *
  522. * @param $synonyms
  523. * A string containing synonyms separated by a return character
  524. * @param $feature_id
  525. * The feature to attach the synonyms to
  526. *
  527. * @ingroup tripal_feature
  528. */
  529. function chado_feature_add_synonyms($synonyms, $feature_id) {
  530. // separate synomys by carriage returns
  531. $synonyms = preg_replace("/[\n\r]+/", " ", $synonyms);
  532. // split the synonyms into an array based on a space as the delimieter
  533. $syn_array = array();
  534. $syn_array = explode(" ", $synonyms);
  535. // remove any old synonyms
  536. $feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = :feature_id";
  537. if (!chado_query($feature_syn_dsql, array(':feature_id' => $feature_id))) {
  538. tripal_report_error('tripal_feature', TRIPAL_ERROR, "Could not remove synonyms from feature. ", array());
  539. return;
  540. }
  541. // return if we don't have any synonmys to add
  542. if (!$synonyms) {
  543. return;
  544. }
  545. // iterate through each synonym and add it to the database
  546. foreach ($syn_array as $syn) {
  547. // skip this item if it's empty
  548. if (!$syn) {
  549. break;
  550. }
  551. // check to see if we have this accession number already in the database
  552. // if so then don't add it again. it messes up drupal if the insert fails.
  553. // It is possible for the accession number to be present and not the feature
  554. $synonym_sql = "SELECT synonym_id FROM {synonym} WHERE name = :name";
  555. $synonym = chado_query($synonym_sql, array(':name' => $syn))->fetchObject();
  556. if (!$synonym) {
  557. $synonym_isql = "
  558. INSERT INTO {synonym} (name, synonym_sgml, type_id)
  559. VALUES (:name, :synonym_sgml,
  560. (SELECT cvterm_id
  561. FROM {cvterm} CVT
  562. INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
  563. WHERE CV.name = 'feature_property' and CVT.name = 'synonym')
  564. )
  565. ";
  566. if (!chado_query($synonym_isql, array(':name' => $syn, ':synonym_sgml' => $syn))) {
  567. tripal_report_error('tripal_feature', "Could not add synonym. ", array(), TRIPAL_WARNING);
  568. return;
  569. }
  570. // now get the synonym we just added
  571. $synonym_sql = "SELECT synonym_id FROM {synonym} WHERE name = :name";
  572. $synonym = chado_query($synonym_sql, array(':name' => $syn))->fetchObject();
  573. }
  574. // now add in our new sysnonym
  575. $feature_syn_isql = "
  576. INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id)
  577. VALUES (:synonym_id, :feature_id, :pub_id)";
  578. $args = array(':synonym_id' => $synonym->synonym_id, ':feature_id' => $feature_id, ':pub_id'=> 1);
  579. if (!chado_query($feature_syn_isql, $args)) {
  580. tripal_report_error('tripal_feature', "Could not associate synonym with feature. ", array(), TRIPAL_WARNING);
  581. return;
  582. }
  583. }
  584. }
  585. /**
  586. * Implements hook_load().
  587. *
  588. * When a node is requested by the user this function is called to allow us
  589. * to add auxiliary data to the node object.
  590. *
  591. * @ingroup tripal_feature
  592. */
  593. function chado_feature_load($nodes) {
  594. foreach ($nodes as $nid => $node) {
  595. // find the feature and add in the details
  596. $feature_id = chado_get_id_from_nid('feature', $nid);
  597. // build the feature variable
  598. $values = array('feature_id' => $feature_id);
  599. $feature = chado_generate_var('feature', $values);
  600. $nodes[$nid]->feature = $feature;
  601. // by default, the titles are saved using the unique constraint. We will
  602. // keep it the same, but remove the duplicate name if the unique name and name
  603. // are identical. This doesn't change the title saved in the database, just what is shown
  604. // to the user on the page
  605. $title_type = variable_get('chado_feature_title', 'unique_constraint');
  606. if ($title_type == 'unique_constraint') {
  607. if (strcmp($feature->name, $feature->uniquename)==0) {
  608. $node->title = $feature->name . " (" . $feature->type_id->name . ") " . $feature->organism_id->genus . " " . $feature->organism_id->species ;
  609. }
  610. // in previous version of Tripal, the feature title was simply the unique name.
  611. // so, we recreate the title just to be sure all of our feature pages are consistent
  612. else {
  613. $node->title = $feature->name . ", " . $feature->uniquename . " (" . $feature->type_id->name . ") " . $feature->organism_id->genus . " " . $feature->organism_id->species ;
  614. }
  615. }
  616. // set the title to be the feature name or uniquename as configured
  617. if ($title_type == 'feature_name') {
  618. $node->title = $feature->name;
  619. }
  620. if ($title_type == 'feature_unique_name') {
  621. $node->title = $feature->uniquename;
  622. }
  623. }
  624. }
  625. /**
  626. * Implements hook_node_presave().
  627. * Acts on all content types.
  628. *
  629. * @ingroup tripal_feature
  630. */
  631. function tripal_feature_node_presave($node) {
  632. // set the title to ensure it is always unique
  633. switch ($node->type) {
  634. case 'chado_feature':
  635. // for a form submission the fields are part of the node object
  636. // but for a sync the fields are in an object of the node
  637. $name = '';
  638. $uname = '';
  639. $type = '';
  640. $organism_id = null;
  641. if(property_exists($node, 'uniquename')) {
  642. $organism_id = $node->organism_id;
  643. $name = $node->name;
  644. $uname = $node->uniquename;
  645. $type = $node->feature_type;
  646. }
  647. else {
  648. $organism_id = $node->feature->organism_id;
  649. $name = $node->feature->name;
  650. $uname = $node->feature->uniquename;
  651. $type_id = $node->feature->type_id;
  652. $values = array('cvterm_id' => $type_id);
  653. $ftype = chado_select_record('cv', array('name'), $values);
  654. $type = $ftype[0]->name;
  655. }
  656. $values = array('organism_id' => $organism_id);
  657. $organism = chado_select_record('organism', array('genus', 'species'), $values);
  658. $node->title = "$name, $uname ($type) " . $organism[0]->genus . ' ' . $organism[0]->species;
  659. if ($name == $uname) {
  660. $node->title = "$name ($type) " . $organism[0]->genus . ' ' . $organism[0]->species;
  661. }
  662. break;
  663. }
  664. }
  665. /**
  666. * Implements hook_node_insert().
  667. * Acts on all content types.
  668. *
  669. * @ingroup tripal_feature
  670. */
  671. function tripal_feature_node_insert($node) {
  672. // set the URL path after inserting. We do it here because we do not
  673. // know the feature_id in the presave
  674. switch ($node->type) {
  675. case 'chado_feature':
  676. if (!property_exists($node,'feature_id')) {
  677. $sql = "SELECT * FROM {chado_feature} WHERE nid = :nid";
  678. $chado_feature = db_query($sql, array(':nid' => $node->nid))->fetchObject();
  679. $node->feature_id = $chado_feature->feature_id;
  680. }
  681. // remove any previous alias
  682. db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
  683. // set the URL for this feature page
  684. $url_alias = tripal_feature_get_feature_url($node);
  685. $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
  686. path_save($path_alias);
  687. break;
  688. }
  689. }
  690. /**
  691. * Return the url alias for a feature
  692. *
  693. * @param $node
  694. * A node object containing at least the feature_id and nid
  695. * @param $url_alias
  696. * Optional. This should be the URL alias syntax string that contains
  697. * placeholders such as [id], [genus], [species], [name], [uniquename],
  698. * and [type]. These placeholders will be substituted for actual values.
  699. * If this parameter is not provided then the value of the
  700. * chado_feature_url_string Drupal variable will be used.
  701. *
  702. * @ingroup tripal_feature
  703. */
  704. function tripal_feature_get_feature_url($node, $url_alias = NULL) {
  705. // get the starting URL alias
  706. if(!$url_alias) {
  707. $url_alias = variable_get('chado_feature_url_string', '/feature/[genus]/[species]/[type]/[uniquename]');
  708. if (!$url_alias) {
  709. $url_alias = '/feature/[genus]/[species]/[type]/[uniquename]';
  710. }
  711. $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash
  712. }
  713. // get the feature
  714. $values = array('feature_id' => $node->feature_id);
  715. $feature = chado_select_record('feature', array('*'), $values);
  716. if (!$feature) {
  717. tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find feature when setting URL alias for feature: %id", array('%id' => $node->feature_id));
  718. return FALSE;
  719. }
  720. $feature = (object) $feature[0];
  721. // get the organism
  722. $values = array('organism_id' => $feature->organism_id);
  723. $organism = chado_select_record('organism', array('*'), $values);
  724. if (!$organism) {
  725. tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find organism when setting URL alias for feature: %id", array('%id' => $node->feature_id));
  726. return FALSE;
  727. }
  728. $genus = preg_replace('/\s/', '_', strtolower($organism[0]->genus));
  729. $species = preg_replace('/\s/', '_', strtolower($organism[0]->species));
  730. // get the type
  731. $values = array('cvterm_id' => $feature->type_id);
  732. $cvterm = chado_select_record('cvterm', array('name'), $values);
  733. if (!$cvterm) {
  734. tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find type when setting URL alias for feature: %id", array('%id' => $node->feature_id));
  735. return FALSE;
  736. }
  737. $type = preg_replace('/\s/', '_', $cvterm[0]->name);
  738. // now substitute in the values
  739. $url_alias = preg_replace('/\[id\]/', $feature->feature_id, $url_alias);
  740. $url_alias = preg_replace('/\[genus\]/', $genus, $url_alias);
  741. $url_alias = preg_replace('/\[species\]/', $species, $url_alias);
  742. $url_alias = preg_replace('/\[type\]/', $type, $url_alias);
  743. $url_alias = preg_replace('/\[name\]/', $feature->name, $url_alias);
  744. $url_alias = preg_replace('/\[uniquename\]/', $feature->uniquename, $url_alias);
  745. // the dst field of the url_alias table is only 128 characters long.
  746. // if this is the case then simply return the node URL, we can't set this one
  747. if (strlen($url_alias) > 128) {
  748. tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot set alias longer than 128 characters: %alias.", array('%alias' => $url_alias));
  749. return "node/" . $node->nid;
  750. }
  751. return $url_alias;
  752. }
  753. /**
  754. * Implements hook_node_view().
  755. * Acts on all content types.
  756. *
  757. * @ingroup tripal_feature
  758. */
  759. function tripal_feature_node_view($node, $view_mode, $langcode) {
  760. switch ($node->type) {
  761. case 'chado_feature':
  762. // Show feature browser and counts
  763. if ($view_mode == 'full') {
  764. $node->content['tripal_feature_alignments'] = array(
  765. '#markup' => theme('tripal_feature_alignments', array('node' => $node)),
  766. '#tripal_toc_id' => 'alignments',
  767. '#tripal_toc_title' => 'Alignments',
  768. );
  769. $node->content['tripal_feature_analyses'] = array(
  770. '#markup' => theme('tripal_feature_analyses', array('node' => $node)),
  771. '#tripal_toc_id' => 'analyses',
  772. '#tripal_toc_title' => 'Analyses',
  773. );
  774. $node->content['tripal_feature_base'] = array(
  775. '#markup' => theme('tripal_feature_base', array('node' => $node)),
  776. '#tripal_toc_id' => 'base',
  777. '#tripal_toc_title' => 'Overview',
  778. '#weight' => -100,
  779. );
  780. $node->content['tripal_feature_properties'] = array(
  781. '#markup' => theme('tripal_feature_properties', array('node' => $node)),
  782. '#tripal_toc_id' => 'properties',
  783. '#tripal_toc_title' => 'Properties',
  784. );
  785. $node->content['tripal_feature_publications'] = array(
  786. '#markup' => theme('tripal_feature_publications', array('node' => $node)),
  787. '#tripal_toc_id' => 'publications',
  788. '#tripal_toc_title' => 'Publications',
  789. );
  790. $node->content['tripal_feature_references'] = array(
  791. '#markup' => theme('tripal_feature_references', array('node' => $node)),
  792. '#tripal_toc_id' => 'references',
  793. '#tripal_toc_title' => 'Cross References',
  794. );
  795. $node->content['tripal_feature_relationships'] = array(
  796. '#markup' => theme('tripal_feature_relationships', array('node' => $node)),
  797. '#tripal_toc_id' => 'relationships',
  798. '#tripal_toc_title' => 'Relationships',
  799. );
  800. $node->content['tripal_feature_seqence'] = array(
  801. '#markup' => theme('tripal_feature_sequence', array('node' => $node)),
  802. '#tripal_toc_id' => 'sequence',
  803. '#tripal_toc_title' => 'Sequence',
  804. );
  805. $node->content['tripal_feature_synonyms'] = array(
  806. '#markup' => theme('tripal_feature_synonyms', array('node' => $node)),
  807. '#tripal_toc_id' => 'synonyms',
  808. '#tripal_toc_title' => 'Synonyms',
  809. );
  810. $node->content['tripal_feature_terms'] = array(
  811. '#markup' => theme('tripal_feature_terms', array('node' => $node)),
  812. '#tripal_toc_id' => 'terms',
  813. '#tripal_toc_title' => 'Annotated Terms',
  814. );
  815. }
  816. if ($view_mode == 'teaser') {
  817. $node->content['tripal_feature_teaser'] = array(
  818. '#markup' => theme('tripal_feature_teaser', array('node' => $node)),
  819. );
  820. }
  821. break;
  822. case 'chado_organism':
  823. // Show feature browser and counts
  824. if ($view_mode == 'full') {
  825. $node->content['tripal_organism_feature_counts'] = array(
  826. '#markup' => theme('tripal_organism_feature_counts', array('node' => $node)),
  827. '#tripal_toc_id' => 'feature_counts',
  828. '#tripal_toc_title' => 'Data Type Summary',
  829. );
  830. $node->content['tripal_organism_feature_browser'] = array(
  831. '#markup' => theme('tripal_organism_feature_browser', array('node' => $node)),
  832. '#tripal_toc_id' => 'feature_browser',
  833. '#tripal_toc_title' => 'Feature Browser',
  834. );
  835. }
  836. break;
  837. // TODO: handle these node types. Should we also have a feature browser?
  838. case 'chado_library':
  839. break;
  840. case 'chado_stock':
  841. break;
  842. case 'chado_analysis':
  843. break;
  844. }
  845. }
  846. /**
  847. * Implements hook_node_update().
  848. * Acts on all content types.
  849. *
  850. * @ingroup tripal_feature
  851. */
  852. function tripal_feature_node_update($node) {
  853. // add items to other nodes, build index and search results
  854. switch ($node->type) {
  855. case 'chado_feature':
  856. // remove any previous alias
  857. db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
  858. // set the URL for this feature page
  859. $url_alias = tripal_feature_get_feature_url($node);
  860. $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
  861. path_save($path_alias);
  862. break;
  863. }
  864. }