tripal_cv.api.inc 27 KB

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  1. <?php
  2. /**
  3. * @file
  4. * Controlled Vocabulary API
  5. *
  6. * @defgroup tripal_cv_api CV Module API
  7. * @ingroup tripal_api
  8. * This module provides a set of functions to simplify working with
  9. * controlled vocabularies. Most of the API functions deal with retrieving
  10. * terms or their parent vocabularies.
  11. *
  12. * However, the API also supports
  13. * generation of trees for browsing a vocabulary as well as generation of
  14. * pie graphs for display of hierarchical counts of terms. Version 0.3b of
  15. * Tripal provides a feature browser and a feature summary chart uses
  16. * the API functions provided here. But in general charts and trees can be
  17. * created for any controlled vocabulary.
  18. *
  19. */
  20. /**
  21. * Purpose: To retrieve a chado controlled vocabulary object
  22. *
  23. * @param $select_values
  24. * An array meant to uniquely select a given controlled vocabulary
  25. *
  26. * @return
  27. * Chado controlled vocabulary object
  28. *
  29. * The controlled vocabulary is selected using tripal_core_chado select and as such the
  30. * $select_values array parameter meant to uniquely identify the controlled vocab to be
  31. * returned follows the same form as when using tripal_core_chado_select directly.
  32. *
  33. * Example Usage:
  34. * @code
  35. $select_values = array(
  36. 'name' => 'feature_property'
  37. );
  38. $cv_object = tripal_cv_get_cv($select_values);
  39. * @endcode
  40. * The above code selects the feature_property cv and returns the following object:
  41. * @code
  42. $cv_object = stdClass Object (
  43. [cv_id] => 13
  44. [name] => feature_property
  45. [definition] =>
  46. );
  47. * @endcode
  48. *
  49. * @ingroup tripal_cv_api
  50. */
  51. function tripal_cv_get_cv($select_values) {
  52. $columns = array(
  53. 'cv_id',
  54. 'name',
  55. 'definition',
  56. );
  57. $results = tripal_core_chado_select('cv', $columns, $select_values);
  58. if (sizeof($results) == 1) {
  59. return $results[0];
  60. }
  61. elseif (empty($results)) {
  62. watchdog('tripal_cv',
  63. 'tripal_cv_get_cv: No cv matches criteria values:%values',
  64. array('%values' => print_r($select_values, TRUE)),
  65. WATCHDOG_WARNING
  66. );
  67. return FALSE;
  68. }
  69. else {
  70. watchdog('tripal_cv',
  71. 'tripal_cv_get_cv: 2+ cvs match criteria values:%values',
  72. array('%values' => print_r($select_values, TRUE)),
  73. WATCHDOG_WARNING
  74. );
  75. }
  76. }
  77. // Purpose: To retrieve a chado cv object
  78. // @param $where_options
  79. // @code
  80. // array(
  81. // <column_name> => array(
  82. // 'type' => <type of column: INT/STRING>,
  83. // 'value' => <the vlaue you want to filter on>,
  84. // 'exact' => <if TRUE use =; if FALSE use ~>,
  85. // )
  86. // )
  87. // @endcode
  88. //
  89. // @return
  90. // Chado cv object with all fields from the chado cv table
  91. //
  92. // @ingroup tripal_cv_api
  93. //
  94. //function tripal_cv_get_cv ($where_options)
  95. /**
  96. * Retrieve a cv given the cv name
  97. *
  98. * @param $name
  99. * The name of the cv to be returned
  100. * @return
  101. * The cv object for the specified CV name
  102. *
  103. * @ingroup tripal_cv_api
  104. */
  105. function tripal_cv_get_cv_by_name($name) {
  106. $r = tripal_core_chado_select('cv', array('*'), array('name' => $name));
  107. return $r[0];
  108. }
  109. /**
  110. * Retrieve the cv object for the specified CV id
  111. *
  112. * NOTE: This function is deprecated.
  113. * @see tripal_core_chado_generate_vars()
  114. *
  115. * @param $cv_id
  116. * The unique identifier for the cv to retrieve
  117. *
  118. * @return
  119. * An object describing the cv
  120. *
  121. * @ingroup tripal_cv_api
  122. */
  123. function tripal_cv_get_cv_by_id($cv_id) {
  124. $r = tripal_core_chado_select('cv', array('*'), array('cv_id' => $cv_id));
  125. return $r;
  126. }
  127. /**
  128. * Retrieve the cv id for the specified CV by name
  129. *
  130. * NOTE: This function is deprecated.
  131. * @see tripal_core_chado_generate_vars()
  132. *
  133. * @param $cv_name
  134. * The unique name for the cv to retrieve
  135. *
  136. * @return
  137. * The numeric cv ID
  138. *
  139. * @ingroup tripal_cv_api
  140. */
  141. function tripal_cv_get_cv_id($cv_name) {
  142. $sql = "
  143. SELECT cv_id FROM {cv} WHERE name = '%s'
  144. ";
  145. $cv = db_fetch_object(chado_query($sql, $cv_name));
  146. return $cv->cv_id;
  147. }
  148. /**
  149. * Create an options array to be used in a form element which provides a
  150. * list of all chado cvs
  151. *
  152. * NOTE: This function is deprecated as of Tripal v1.0
  153. *
  154. * @return
  155. * An array(cv_id => name) for each cv in the chado cv table
  156. *
  157. * @ingroup tripal_cv_api
  158. */
  159. function tripal_cv_get_cv_options() {
  160. $results = tripal_core_chado_select('cv', array('cv_id', 'name'), array());
  161. $options = array();
  162. foreach ($results as $r) {
  163. $options[$r->cv_id] = $r->name;
  164. }
  165. return $options;
  166. }
  167. /**
  168. * Retrieve a chado cvterm object with a given name
  169. *
  170. * @param $name
  171. * the cvterm.name
  172. * @param $cv_id
  173. * the cv_id of the term you are looking for
  174. * @param $cv_name
  175. * the name of the CV
  176. *
  177. * @return
  178. * cvterm object
  179. *
  180. * @ingroup tripal_cv_api
  181. */
  182. function tripal_cv_get_cvterm_by_name($name, $cv_id = 0, $cv_name = 'tripal') {
  183. if ($cv_id) {
  184. $values = array(
  185. 'name' => $name,
  186. 'cv_id' => $cv_id,
  187. );
  188. $options = array(
  189. 'statement_name' => 'sel_cvterm_nacv',
  190. 'case_insensitive_columns' => array('name')
  191. );
  192. $r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
  193. }
  194. elseif ($cv_name) {
  195. $values = array(
  196. 'name' => $name,
  197. 'cv_id' => array(
  198. 'name' => $cv_name,
  199. ),
  200. );
  201. $options = array(
  202. 'statement_name' => 'sel_cvterm_nacv',
  203. 'case_insensitive_columns' => array('name')
  204. );
  205. $r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
  206. }
  207. else {
  208. $values = array(
  209. 'name' => $name,
  210. );
  211. $options = array(
  212. 'statement_name' => 'sel_cvterm_na',
  213. 'case_insensitive_columns' => array('name')
  214. );
  215. $r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
  216. }
  217. if (!$r) {
  218. return FALSE;
  219. }
  220. if (count($r) > 1) {
  221. return FALSE;
  222. }
  223. return $r[0];
  224. }
  225. /**
  226. * Retrieve a chado cvterm object with a given name
  227. *
  228. * @param $synonym
  229. * the synonym of the term
  230. * @param $cv_id
  231. * the cv_id of the term you are looking for
  232. * @param $cv_name
  233. * the name of the CV
  234. *
  235. * @return
  236. * cvterm object
  237. *
  238. * @ingroup tripal_cv_api
  239. */
  240. function tripal_cv_get_cvterm_by_synonym($synonym, $cv_id = NULL, $cv_name = 'tripal') {
  241. // first find the CVTerm synonym
  242. $values = array(
  243. 'synonym' => $synonym,
  244. );
  245. $statement = "sel_cvtermsynonym_sy";
  246. if ($cv_id) {
  247. $values['cvterm_id'] = array('cv_id' => $cv_id);
  248. $statement = "sel_cvtermsynonym_sycv";
  249. }
  250. if ($cv_name) {
  251. $values['cvterm_id'] = array('cv_id' => array('name' => $cv_name));
  252. $statement = "sel_cvtermsynonym_sycv";
  253. }
  254. $options = array(
  255. 'statement_name' => $statement,
  256. 'case_insensitive_columns' => array('name')
  257. );
  258. $synonym = tripal_core_chado_select('cvtermsynonym', array('cvterm_id'), $values, $options);
  259. // if the synonym doens't exist or more than one record is returned then return false
  260. if(count($synonym) == 0) {
  261. return FALSE;
  262. }
  263. if(count($synonym) > 1) {
  264. return FALSE;
  265. }
  266. // get the cvterm
  267. $values = array('cvterm_id' => $synonym[0]->cvterm_id);
  268. $options = array('statement_name' => 'sel_cvterm_id');
  269. $cvterm = tripal_core_chado_select('cvterm', array('*'), $values, $options);
  270. return $cvterm[0];
  271. }
  272. /**
  273. * Create an options array to be used in a form element
  274. * which provides a list of all chado cvterms
  275. *
  276. * @param $cv_id
  277. * The chado cv_id;
  278. * only cvterms with the supplied cv_id will be returned
  279. * @return
  280. * An array(cvterm_id => name)
  281. * for each cvterm in the chado cvterm table where cv_id=that supplied
  282. *
  283. * @ingroup tripal_cv_api
  284. */
  285. function tripal_cv_get_cvterm_options($cv_id = 0) {
  286. if ($cv_id > 0) {
  287. $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array('cv_id' => $cv_id));
  288. }
  289. else {
  290. $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array());
  291. }
  292. $options = array();
  293. foreach ($results as $r) {
  294. $options[$r->cvterm_id] = $r->name;
  295. }
  296. return $options;
  297. }
  298. /**
  299. * Updates the cvtermpath table of Chado for the specified CV.
  300. *
  301. * @param $cv_id
  302. * The chado cv_id;
  303. * @param $job_id
  304. * This function is intended to be used with the Tripal Jobs API.
  305. * When this function is called as a job the $job_id is automatically
  306. * passed to this function.
  307. * @return
  308. * TRUE on success FALSE on failure
  309. *
  310. * @ingroup tripal_cv_api
  311. */
  312. function tripal_cv_update_cvtermpath($cvid, $job_id = NULL) {
  313. // TODO: need better error checking in this function
  314. // first get the controlled vocabulary name:
  315. $cv = db_fetch_object(chado_query("SELECT * FROM {cv} WHERE cv_id = %d", $cvid));
  316. print "\nUpdating cvtermpath for $cv->name...\n";
  317. // now fill the cvtermpath table
  318. // @coder-ignore: using a function rather then tablename therefore table prefixing doesn't apply
  319. $sql = "SELECT * FROM fill_cvtermpath('%s')";
  320. $success = chado_query($sql, $cv->name);
  321. return TRUE;
  322. }
  323. /**
  324. * Adds a controlled vocabular to the CV table of Chado.
  325. *
  326. * @param $name
  327. * The name of the controlled vocabulary. These are typically all lower case
  328. * with no special characters other than an undrescore (for spaces).
  329. * @param $comment
  330. * A description or definition of the vocabulary.
  331. *
  332. * @return
  333. * An object populated with fields from the newly added database.
  334. *
  335. * @ingroup tripal_cv_api
  336. */
  337. function tripal_cv_add_cv($name, $definition) {
  338. // insert/update values
  339. $ins_values = array(
  340. 'name' => $name,
  341. 'definition' => $definition
  342. );
  343. // see if the CV (default-namespace) exists already in the database
  344. $sel_values = array('name' => $name);
  345. $sel_options = array('statement_name' => 'sel_cv_na');
  346. $results = tripal_core_chado_select('cv', array('*'), $sel_values, $sel_options);
  347. // if it does not exists then add it
  348. if (count($results) == 0) {
  349. $ins_options = array('statement_name' => 'ins_cv_nade');
  350. $success = tripal_core_chado_insert('cv', $ins_values, $ins_options);
  351. if (!$success) {
  352. watchdog('tripal_cv', "Failed to create the CV record", NULL, WATCHDOG_WARNING);
  353. return FALSE;
  354. }
  355. $results = tripal_core_chado_select('cv', array('*'), $sel_values, $sel_options);
  356. }
  357. // if it already exists then do an update
  358. else {
  359. $upd_options = array('statement_name' => 'upd_cv_nade');
  360. $success = tripal_core_chado_update('cv', $sel_values, $ins_values, $upd_options);
  361. if (!$success) {
  362. watchdog('tripal_cv', "Failed to update the CV record", NULL, WATCHDOG_WARNING);
  363. return FALSE;
  364. }
  365. $results = tripal_core_chado_select('cv', array('*'), $sel_values, $sel_options);
  366. }
  367. // return the cv object
  368. return $results[0];
  369. }
  370. /**
  371. * Add's a CV term to the cvterm table. If the parent CV does not exist then
  372. * that too is added to the CV table. If the cvterm is a relationship term
  373. * then the $is_relationship argument should be set. The function will try
  374. * to first find the relationship in the relationship ontology for updating and
  375. * if it can't be found will add the relationship to the __global CV. All terms
  376. * must also have a corresponding database. This is specified in the term's
  377. * ID just before the colon (e.g. GO:003824). If the database does not exist
  378. * in the DB table then it will be added automatically. The accession (the
  379. * value just after the colon in the term's ID) will be added to the dbxref
  380. * table. If the CVterm already exists and $update is set (default) then the
  381. * cvterm is updated. If the CVTerm already exists and $update is not set, then
  382. * no changes are made and the CVTerm object is returned.
  383. *
  384. * @param $term
  385. * An associative array with the following keys: 'id', 'name' and 'namespace',
  386. * 'is_obsolete', and 'def'. Where 'id' is the term accession, 'name' is the
  387. * term name, 'namespace' is the CV name for the term, 'def' is the term
  388. * definition and 'is_obsolete' is present and set to 1 if the term is defunct.
  389. * The 'id' must be of the form <DB>:<ACCESSION>, where <DB> is the name of
  390. * the database to which the cvterm belongs and the <ACCESSION> is the
  391. * term's accession number in the database.
  392. * @param $defaultcv
  393. * Optional. The CV name to which the term
  394. * belongs. If this arugment is null or not provided then the function tries
  395. * to find a record in the CV table with the same name provided in the
  396. * $term[namespace]. If this field is provided then it overrides what the
  397. * value in $term[namespace]
  398. * @param $is_relationship
  399. * If this term is a relationship term then this value should be 1.
  400. * @param $update
  401. * By default this is set to 1. If the term exists it is automatically updated.
  402. * @param $dbname
  403. * In some cases the database name will not be part of the $term['id'] and it
  404. * needs to be explicitly set. Use this argument only if the database name
  405. * cannot be specififed in the term ID (e.g. <DB>:<ACCESSION>).
  406. *
  407. * @return
  408. * A CVTerm object
  409. *
  410. * @ingroup tripal_cv_api
  411. */
  412. function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship = 0,
  413. $update = 1, $dbname = 'internal') {
  414. // get the term properties
  415. $id = $term['id'];
  416. $name = '';
  417. $cvname = '';
  418. $definition = '';
  419. $is_obsolete = 0;
  420. $accession = '';
  421. if (array_key_exists('name', $term)) {
  422. $name = $term['name'];
  423. }
  424. else {
  425. $name = $id;
  426. }
  427. if (array_key_exists('namespace', $term)) {
  428. $cvname = $term['namespace'];
  429. }
  430. else {
  431. $cvname = $defaultcv;
  432. }
  433. if (array_key_exists('def', $term)) {
  434. $definition = preg_replace('/^\"(.*)\"/', '\1', $term['def']);
  435. }
  436. else {
  437. $definition = '';
  438. }
  439. if (array_key_exists('is_obsolete', $term)) {
  440. $is_obsolete = $term['is_obsolete'];
  441. if (strcmp($is_obsolete, 'true') == 0) {
  442. $is_obsolete = 1;
  443. }
  444. }
  445. if (!$name and !$id) {
  446. watchdog('tripal_cv', "Cannot find cvterm without 'id' or 'name'", NULL, WATCHDOG_WARNING);
  447. return 0;
  448. }
  449. if (!$id) {
  450. $id = $name;
  451. }
  452. // get the accession and the database from the cvterm id
  453. if ($dbname) {
  454. $accession = $id;
  455. }
  456. if (preg_match('/^.+?:.*$/', $id)) {
  457. $accession = preg_replace('/^.+?:(.*)$/', '\1', $id);
  458. $dbname = preg_replace('/^(.+?):.*$/', '\1', $id);
  459. }
  460. // check that we have a database name, give a different message if it's a relationship
  461. if ($is_relationship and !$dbname) {
  462. watchdog('tripal_cv', "A database name is not provided for this relationship term: $id", NULL, WATCHDOG_WARNING);
  463. return 0;
  464. }
  465. if (!$is_relationship and !$dbname) {
  466. watchdog('tripal_cv', "A database identifier is missing from the term: $id", NULL, WATCHDOG_WARNING);
  467. return 0;
  468. }
  469. // make sure the CV name exists
  470. $cv = tripal_cv_add_cv($cvname, '');
  471. if (!$cv) {
  472. watchdog('tripal_cv', "Cannot find namespace '$cvname' when adding/updating $id", NULL, WATCHDOG_WARNING);
  473. return 0;
  474. }
  475. // this SQL statement will be used a lot to find a cvterm so just set it
  476. // here for easy reference below. Because CV terms can change their names
  477. // but accessions don't change, the following SQL finds cvterms based on
  478. // their accession rather than the name
  479. if (!tripal_core_is_sql_prepared('sel_cvterm_by_accession')) {
  480. $pcvtermsql = "
  481. PREPARE sel_cvterm_by_accession(text, text) AS
  482. SELECT CVT.name, CVT.cvterm_id, CV.cv_id, CV.name as cvname,
  483. DB.name as dbname, DB.db_id, DBX.accession
  484. FROM {cvterm} CVT
  485. INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
  486. INNER JOIN {db} DB on DBX.db_id = DB.db_id
  487. INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
  488. WHERE DBX.accession = $1 and DB.name = $2";
  489. if (!tripal_core_chado_prepare('sel_cvterm_by_accession', $pcvtermsql, array('text', 'text'))) {
  490. watchdog('tripal_cv', "Cannot prepare statement 'sel_cvterm_by_accession'", NULL, WATCHDOG_WARNING);
  491. return 0;
  492. }
  493. }
  494. $cvtermsql = "EXECUTE sel_cvterm_by_accession('%s','%s')";
  495. // add the database. The function will just return the DB object if the
  496. // database already exists.
  497. $db = tripal_db_add_db($dbname);
  498. if (!$db) {
  499. watchdog('tripal_cv', "Cannot find database '$dbname' in Chado.", NULL, WATCHDOG_WARNING);
  500. return 0;
  501. }
  502. // the cvterm table has two unique dependencies. We need to check both.
  503. // first check the (name, cv_id, is_obsolete) constraint
  504. $values = array(
  505. 'name' => $name,
  506. 'is_obsolete' => $is_obsolete,
  507. 'cv_id' => array(
  508. 'name' => $cvname,
  509. ),
  510. );
  511. $options = array('statement_name' => 'sel_cvterm_c1');
  512. $result = tripal_core_chado_select('cvterm', array('*'), $values, $options);
  513. // if the constraint is met then let's check it to see if
  514. // the database name matches the one we have been provided
  515. if (count($result) == 1) {
  516. $cvterm = $result[0];
  517. // get the dbxref record
  518. $values = array('dbxref_id' => $cvterm->dbxref_id);
  519. $options = array('statement_name' => 'sel_dbxref_id');
  520. $result = tripal_core_chado_select('dbxref', array('*'), $values, $options);
  521. $dbxref = $result[0];
  522. // get the db
  523. $values = array('db_id' => $dbxref->db_id);
  524. $options = array('statement_name' => 'sel_db_id');
  525. $result = tripal_core_chado_select('db', array('*'), $values, $options);
  526. $db_check = $result[0];
  527. // the database name for this existing term does not match that of the
  528. // one provided to this function. The CV name matches otherwise we
  529. // wouldn't have made it this far. So, let's swap the database for
  530. // this term
  531. if ($db_check->name != $db->name) {
  532. // look to see if the correct dbxref record already exists for this database
  533. $values = array(
  534. 'db_id' => $db->db_id,
  535. 'accession' => $accession,
  536. );
  537. $options = array('statement_name' => 'sel_dbxref_idac');
  538. $result = tripal_core_chado_select('dbxref', array('*'), $values, $options);
  539. // if we already have a good dbxref then we want to update our cvterm
  540. // to use this dbxref
  541. if (count($result) > 0) {
  542. $dbxref = $result[0];
  543. $match = array('cvterm_id' => $cvterm->cvterm_id);
  544. $values = array('dbxref_id' => $dbxref->dbxref_id);
  545. $options = array('statement_name' => 'upd_cvterm_db');
  546. $success = tripal_core_chado_update('cvterm', $match, $values, $options);
  547. if (!$success) {
  548. watchdog('tripal_cv', "Failed to correct the dbxref id for the cvterm " .
  549. "'$name' (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
  550. return 0;
  551. }
  552. }
  553. // if we don't have the record then we want to delete our cvterm and let the code
  554. // below recreate it with the correct info
  555. else {
  556. $match = array('cvterm_id' => $cvterm->cvterm_id);
  557. $options = array('statement_name' => 'del_cvterm_cv');
  558. tripal_core_chado_delete('cvterm', $match, $options);
  559. }
  560. }
  561. // check that the accession matches. Sometimes an OBO can define the same term
  562. // multiple times but with different accessions. If this is the case we
  563. // can't do an insert or it will violate the constraint in the cvterm table.
  564. // so we'll need to add the record to the cvterm_dbxref table instead
  565. if ($dbxref->accession != $accession) {
  566. // get/add the dbxref fort his term
  567. $dbxref_new = tripal_db_add_dbxref($db->db_id, $accession);
  568. if (!$dbxref_new) {
  569. watchdog('tripal_cv', "Failed to find or insert the dbxref record for cvterm, " .
  570. "$name (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
  571. return 0;
  572. }
  573. // check to see if the cvterm_dbxref record already exists
  574. $values = array(
  575. 'cvterm_id' => $cvterm->cvterm_id,
  576. 'dbxref_id' => $dbxref_new->dbxref_id,
  577. 'is_for_definition' => 1,
  578. );
  579. $options = array('statement_name' => 'sel_cvtermdbxref_cvdbis');
  580. $result = tripal_core_chado_select('cvterm_dbxref', array('*'), $values, $options);
  581. // if the cvterm_dbxref record does not exists then add it
  582. if (count($result)==0) {
  583. $options = array(
  584. 'statement_name' => 'ins_cvtermdbxref_cvdbis',
  585. 'return_record' => FALSE,
  586. );
  587. $success = tripal_core_chado_insert('cvterm_dbxref', $values, $options);
  588. if (!$success) {
  589. watchdog('tripal_cv', "Failed to find or insert the cvterm_dbxref record for a " .
  590. "duplicated cvterm: $name (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
  591. return 0;
  592. }
  593. }
  594. // get the original cvterm with the same name and return that.
  595. $cvterm = db_fetch_object(chado_query($cvtermsql, $dbxref->accession, $dbname));
  596. return $cvterm;
  597. }
  598. // continue on, we've fixed the record if the db_id did not match,
  599. // we can now perform and updated if we need to.
  600. }
  601. // get the CVterm record
  602. $cvterm = db_fetch_object(chado_query($cvtermsql, $accession, $dbname));
  603. //print "$pcvtermsql\n$cvtermsql\n$accession, $dbname\n";
  604. //print "CVTERM:\n";
  605. //print_r($cvterm);
  606. if (!$cvterm) {
  607. // check to see if the dbxref exists if not, add it
  608. $dbxref = tripal_db_add_dbxref($db->db_id, $accession);
  609. if (!$dbxref) {
  610. watchdog('tripal_cv', "Failed to find or insert the dbxref record for cvterm, " .
  611. "$name (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
  612. return 0;
  613. }
  614. // check to see if the dbxref already has an entry in the cvterm table
  615. // this is the second constraint in the cvterm table
  616. $values = array('dbxref_id' => $dbxref->dbxref_id);
  617. $options = array('statement_name' => 'sel_cvterm_db');
  618. $check = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
  619. if (count($check) == 0) {
  620. // now add the cvterm
  621. $ins_values = array(
  622. 'cv_id' => $cv->cv_id,
  623. 'name' => $name,
  624. 'definition' => $definition,
  625. 'dbxref_id' => $dbxref->dbxref_id,
  626. 'is_obsolete' => $is_obsolete,
  627. 'is_relationshiptype' => $is_relationship,
  628. );
  629. $ins_options = array('statement_name' => 'ins_cvterm_all');
  630. $success = tripal_core_chado_insert('cvterm', $ins_values, $ins_options);
  631. if (!$success) {
  632. if (!$is_relationship) {
  633. watchdog('tripal_cv', "Failed to insert the term: $name ($dbname)", NULL, WATCHDOG_WARNING);
  634. return 0;
  635. }
  636. else {
  637. watchdog('tripal_cv', "Failed to insert the relationship term: $name (cv: " . $cvname . " db: $dbname)", NULL, WATCHDOG_WARNING);
  638. return 0;
  639. }
  640. }
  641. }
  642. // this dbxref already exists in the cvterm table
  643. else {
  644. watchdog('tripal_cv', "The dbxref already exists for another cvterm record: $name (cv: " . $cvname . " db: $dbname)", NULL, WATCHDOG_WARNING);
  645. return 0;
  646. }
  647. $cvterm = db_fetch_object(chado_query($cvtermsql, $accession, $dbname));
  648. }
  649. // upate the cvterm
  650. elseif ($update) {
  651. $match = array('cvterm_id' => $cvterm->cvterm_id);
  652. $upd_values = array(
  653. 'name' => $name,
  654. 'definition' => $definition,
  655. 'is_obsolete' => $is_obsolete,
  656. 'is_relationshiptype' => $is_relationship,
  657. );
  658. $upd_options = array('statement_name' => 'upd_cvterm_nadeisis');
  659. $success = tripal_core_chado_update('cvterm', $match, $upd_values, $upd_options);
  660. if (!$success) {
  661. watchdog('tripal_cv', "Failed to update the term: $name", NULL, WATCHDOG_WARNING);
  662. return 0;
  663. }
  664. $cvterm = db_fetch_object(chado_query($cvtermsql, $accession, $dbname));
  665. }
  666. else {
  667. // do nothing, we have the cvterm but we don't want to update
  668. }
  669. // return the cvterm
  670. return $cvterm;
  671. }
  672. /**
  673. * This function defines the custom tables that will be created
  674. * in the chado schema.
  675. *
  676. * @ingroup tripal_cv_api
  677. */
  678. function tripal_cv_get_custom_tables($table = NULL) {
  679. if (!$table or strcmp($table, 'tripal_obo_temp')==0) {
  680. $schema['tripal_obo_temp'] = array(
  681. 'table' => 'tripal_obo_temp',
  682. 'fields' => array(
  683. 'id' => array(
  684. 'type' => 'varchar',
  685. 'length' => '255',
  686. 'not null' => TRUE,
  687. ),
  688. 'stanza' => array(
  689. 'type' => 'text',
  690. 'not null' => TRUE,
  691. ),
  692. 'type' => array(
  693. 'type' => 'varchar',
  694. 'length' => '50',
  695. 'not null' => TRUE,
  696. ),
  697. ),
  698. 'indexes' => array(
  699. 'tripal_obo_temp_idx0' => array('id'),
  700. 'tripal_obo_temp_idx0' => array('type'),
  701. ),
  702. 'unique keys' => array(
  703. 'tripal_obo_temp_uq0' => array('id'),
  704. ),
  705. );
  706. }
  707. return $schema;
  708. }
  709. /**
  710. * This function allows other modules to programatically
  711. * submit an ontology for loading into Chado. This function
  712. * will add a job to the Jobs subsystem for parsing the ontology.
  713. * You can either pass a known OBO ID to the function or the URL
  714. * or full path the the ontology file. If a URL or file name is
  715. * passed then the $obo_name argument must also be provided. If
  716. * this is the first time the ontology has been provided to Tripal
  717. * then it will be added to the database and will be assigned a
  718. * unique OBO ID.
  719. *
  720. * @param $obo_id
  721. * If the ontology is already loaded into the Tripal tables then
  722. * use this argument to specify the unique ID for the ontology
  723. * that will be loaded
  724. * @param $obo_name
  725. * If the OBO has not been added before then use this argument
  726. * to specify the human readable name of the ontology.
  727. * @param $obo_url
  728. * If the OBO to be loaded is located on a remote server then
  729. * use this argument to provide the URL.
  730. * @param $obo_file
  731. * If the OBO is housed on the local file system of the server then
  732. * use this argument to specify the full path.
  733. *
  734. * @return
  735. * returns the job_id of the submitted job or FALSE if the job was not added
  736. *
  737. * @ingroup tripal_cv_api
  738. */
  739. function tripal_cv_submit_obo_job($obo_id = NULL, $obo_name = NULL, $obo_url = NULL, $obo_file = NULL) {
  740. global $user;
  741. if ($obo_id) {
  742. $sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = %d";
  743. $obo = db_fetch_object(db_query($sql, $obo_id));
  744. $args = array($obo_id);
  745. return tripal_add_job("Load OBO $obo->name", 'tripal_cv',
  746. "tripal_cv_load_obo_v1_2_id", $args, $user->uid);
  747. }
  748. else {
  749. if ($obo_url) {
  750. $args = array($obo_name, $obo_url);
  751. return tripal_add_job("Load OBO $obo_name", 'tripal_cv',
  752. "tripal_cv_load_obo_v1_2_url", $args, $user->uid);
  753. }
  754. elseif ($obo_file) {
  755. $args = array($obo_name, $obo_file);
  756. return tripal_add_job("Load OBO $obo_name", 'tripal_cv',
  757. "tripal_cv_load_obo_v1_2_file", $args, $user->uid);
  758. }
  759. }
  760. return FALSE;
  761. }
  762. /**
  763. * Add the obo to the tripal_cv_obo table in the Drupal database
  764. *
  765. * @param $name
  766. * The human readable name of this ontology
  767. * @param $path
  768. * The file path or URL of the ontology
  769. *
  770. * @return
  771. * Returns the ontology ID
  772. *
  773. * @ingroup tripal_cv_api
  774. */
  775. function tripal_cv_add_obo_ref($name, $path) {
  776. $record = new stdClass;
  777. $record->name = $name;
  778. $record->path = $path;
  779. drupal_write_record('tripal_cv_obo', $record);
  780. return $record->obo_id;
  781. }