tripal_pub.module 15 KB

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  1. <?php
  2. require_once "api/tripal_pub.api.inc";
  3. require_once "includes/tripal_pub.admin.inc";
  4. require_once "includes/pubmed.inc";
  5. require_once "includes/pub_sync.inc";
  6. require_once "includes/pub_form.inc";
  7. /**
  8. * @file
  9. *
  10. * The Tripal Publication module allows you to search the PubMed databse for academic articles,
  11. * that relate to user specified tpoic\s. As well, it allows management of publications so that
  12. * a user can enter specified details regarding a desired publication. This allows all of the important
  13. * information that is unique to a Academic Publication to be stored for access.
  14. */
  15. /**
  16. *
  17. * @ingroup tripal_pub
  18. */
  19. function tripal_pub_init() {
  20. drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/tripal_pub.js');
  21. drupal_add_css(drupal_get_path('theme', 'tripal') . '/css/tripal_pub.css');
  22. }
  23. /**
  24. * Implementation of hook_tripal_pub_node_info().
  25. *
  26. * This node_info, is a simple node that describes the functionallity of the module.
  27. *
  28. */
  29. function tripal_pub_node_info() {
  30. return array(
  31. 'chado_pub' => array(
  32. 'name' => t('Publication'),
  33. 'module' => 'chado_pub',
  34. 'description' => t('A publication from the Chado database'),
  35. 'title_label' => t('Article Title'),
  36. 'body_label' => t('Abstract'),
  37. 'has_title' => TRUE,
  38. 'has_body' => FALSE,
  39. ),
  40. );
  41. }
  42. /**
  43. * Tripal-Publication-Menu
  44. *
  45. * Implemets hook_menu(): Adds menu items for the tripal_pub module menu. This section
  46. * gives the outline for the main menu of the Tripal-Publication module
  47. *
  48. * @return
  49. * An array of menu items that is visible within the Drupal Menu, returned as soon
  50. * as the program is ran
  51. */
  52. function tripal_pub_menu() {
  53. $items = array();
  54. $items[ 'admin/tripal/tripal_pub' ]= array(
  55. 'title' => 'Publications',
  56. 'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
  57. 'page callback' => 'theme',
  58. 'page arguments' => array('tripal_pub_admin'),
  59. 'access arguments' => array('administer tripal pubs'),
  60. 'type' => MENU_NORMAL_ITEM
  61. );
  62. $items['admin/tripal/tripal_pub/sync'] = array(
  63. 'title' => ' Sync Publications',
  64. 'description' => 'Sync publications in Chado with Drupal',
  65. 'page callback' => 'drupal_get_form',
  66. 'page arguments' => array('tripal_pub_sync_form'),
  67. 'access arguments' => array('administer tripal pubs'),
  68. 'type' => MENU_NORMAL_ITEM,
  69. );
  70. $items['admin/tripal/tripal_pub/import_list'] = array(
  71. 'title' => t('Importers List'),
  72. 'description' => t('List all publication importers'),
  73. 'page callback' => 'tripal_pub_importers_list',
  74. 'access arguments' => array('administer tripal pubs'),
  75. 'type ' => MENU_CALLBACK,
  76. );
  77. $items['admin/tripal/tripal_pub/import/new'] = array(
  78. 'title' => t('Add an Importer'),
  79. 'description' => t('Add a new publication importer.'),
  80. 'page callback' => 'tripal_pub_importer_setup',
  81. 'page arguments' => array(4, NULL),
  82. 'access arguments' => array('administer tripal pubs'),
  83. 'type ' => MENU_CALLBACK,
  84. );
  85. $items['admin/tripal/tripal_pub/import/edit/%'] = array(
  86. 'page callback' => 'tripal_pub_importer_setup',
  87. 'page arguments' => array(4, 5),
  88. 'access arguments' => array('administer tripal pubs'),
  89. 'type ' => MENU_CALLBACK,
  90. );
  91. $items['admin/tripal/tripal_pub/import/delete/%'] = array(
  92. 'page callback' => 'tripal_pub_importer_delete',
  93. 'page arguments' => array(5),
  94. 'access arguments' => array('administer tripal pubs'),
  95. 'type ' => MENU_CALLBACK,
  96. );
  97. $items['admin/tripal/tripal_pub/import/criteria/%/%'] = array(
  98. 'page callback' => 'tripal_pub_importer_setup_page_update_criteria',
  99. 'page arguments' => array(5, 6),
  100. 'access arguments' => array('administer tripal pubs'),
  101. 'type ' => MENU_CALLBACK,
  102. );
  103. $items['tripal_pub/properties/add/%'] = array(
  104. 'page callback' => 'tripal_pub_property_add',
  105. 'page arguments' => array(3),
  106. 'access arguments' => array('edit chado_pub content'),
  107. 'type ' => MENU_CALLBACK,
  108. );
  109. $items['tripal_pub/properties/minus/%'] = array(
  110. 'page callback' => 'tripal_pub_property_delete',
  111. 'page arguments' => array(3),
  112. 'access arguments' => array('edit chado_pub content'),
  113. 'type ' => MENU_CALLBACK,
  114. );
  115. return $items;
  116. }
  117. /**
  118. * Implements hook_theme(): Register themeing functions for this module
  119. *
  120. *
  121. * @return
  122. * An array of themeing functions to register
  123. *
  124. */
  125. function tripal_pub_theme() {
  126. return array(
  127. 'tripal_pub_base' => array(
  128. 'arguments' => array('node' => NULL),
  129. ),
  130. 'tripal_pub_properties' => array(
  131. 'arguments' => array('node' => NULL)
  132. ),
  133. 'tripal_pub_authors' => array(
  134. 'arguments' => array('node' => NULL)
  135. ),
  136. 'tripal_pub_references' => array(
  137. 'arguments' => array('node' => NULL)
  138. ),
  139. 'tripal_pub_relationships' => array(
  140. 'arguments' => array('node' => NULL)
  141. ),
  142. 'tripal_pub_importer_setup_form' => array(
  143. 'arguments' => array('form'),
  144. ),
  145. 'chado_pub_node_form' => array(
  146. 'arguments' => array('form'),
  147. ),
  148. 'tripal_pub_admin' => array(
  149. 'template' => 'tripal_pub_admin',
  150. 'arguments' => array(NULL),
  151. 'path' => drupal_get_path('module', 'tripal_pub') . '/theme'
  152. ),
  153. );
  154. }
  155. /**
  156. * Implement hook_perm().
  157. */
  158. function tripal_pub_perm() {
  159. return array(
  160. 'access chado_pub content',
  161. 'create chado_pub content',
  162. 'delete chado_pub content',
  163. 'edit chado_pub content',
  164. 'administer tripal pubs',
  165. );
  166. }
  167. /**
  168. * Implement hook_access().
  169. *
  170. * This hook allows node modules to limit access to the node types they define.
  171. *
  172. * @param $op
  173. * The operation to be performed
  174. *
  175. * @param $node
  176. * The node on which the operation is to be performed, or, if it does not yet exist, the
  177. * type of node to be created
  178. *
  179. * @param $account
  180. * A user object representing the user for whom the operation is to be performed
  181. *
  182. * @return
  183. * TRUE
  184. *
  185. */
  186. function chado_pub_access($op, $node, $account ) {
  187. if ($op == 'create') {
  188. if (!user_access('create chado_pub content', $account)) {
  189. return FALSE;
  190. }
  191. }
  192. if ($op == 'update') {
  193. if (!user_access('edit chado_pub content', $account)) {
  194. return FALSE;
  195. }
  196. }
  197. if ($op == 'delete') {
  198. if (!user_access('delete chado_pub content', $account)) {
  199. return FALSE;
  200. }
  201. }
  202. if ($op == 'view') {
  203. if (!user_access('access chado_pub content', $account)) {
  204. return FALSE;
  205. }
  206. }
  207. return NULL;
  208. }
  209. /**
  210. * Implementation of tripal_pub_insert().
  211. *
  212. * This function inserts user entered information pertaining to the Publication instance into the
  213. * 'pubauthor', 'pubprop', 'chado_pub', 'pub' talble of the database.
  214. *
  215. * @parm $node
  216. * Then node which contains the information stored within the node-ID
  217. *
  218. *
  219. */
  220. function chado_pub_insert($node) {
  221. // if a pub_id already exists for this node then it already exists in Chado and
  222. // we get here because we are syncing the node. Therefore, we can skip the insert
  223. if ($node->pub_id) {
  224. $pub['pub_id'] = $node->pub_id;
  225. }
  226. else {
  227. $values = array(
  228. 'title' => $node->title,
  229. 'volumetitle' => $node->volumetitle,
  230. 'volume' => $node->volume,
  231. 'series_name' => $node->series_name,
  232. 'issue' => $node->issue,
  233. 'pyear' => $node->pyear,
  234. 'pages' => $node->pages,
  235. 'miniref' => $node->miniref,
  236. 'type_id' => $node->type_id,
  237. 'is_obsolete' => $node->is_obsolete,
  238. 'publisher' => $node->publisher,
  239. 'pubplace' => $node->pubplace,
  240. 'uniquename' => $node->uniquename,
  241. 'type_id' => $node->type_id
  242. );
  243. $pub = tripal_core_chado_insert('pub', $values);
  244. }
  245. if ($pub) {
  246. // make sure the entry for this feature doesn't already exist in the chado_pub table
  247. // if it doesn't exist then we want to add it.
  248. $pub_id = chado_get_id_for_node('pub', $node) ;
  249. if (!$pub_id) {
  250. // next add the item to the drupal table
  251. $sql = "INSERT INTO {chado_pub} (nid, vid, pub_id) ".
  252. "VALUES (%d, %d, %d)";
  253. db_query($sql, $node->nid, $node->vid, $pub['pub_id']);
  254. }
  255. }
  256. else {
  257. drupal_set_message(t('Unable to add publication.', 'warning'));
  258. watchdog('tripal_pub', 'Insert publication: Unable to create pub where values: %values',
  259. array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING);
  260. }
  261. }
  262. /*
  263. *
  264. * Implements hook_update
  265. *
  266. * The purpose of the function is to allow the module to take action when an edited node is being
  267. * updated. It updates any name changes to the database tables that werec reated upon registering a Publication.
  268. * As well, the database will be changed, so the user changed information will be saved to the database.
  269. *
  270. * @param $node
  271. * The node being updated
  272. *
  273. * @ingroup tripal_pub
  274. */
  275. function chado_pub_update($node) {
  276. if ($node->revision) {
  277. // there is no way to handle revisions in Chado but leave
  278. // this here just to make not we've addressed it.
  279. }
  280. $pub_id = chado_get_id_for_node('pub', $node) ;
  281. // update the pub record
  282. $match = array(
  283. 'pub_id' => $pub_id,
  284. );
  285. $values = array(
  286. 'title' => $node->title,
  287. 'volumetitle' => $node->volumetitle,
  288. 'volume' => $node->volume,
  289. 'series_name' => $node->series_name,
  290. 'issue' => $node->issue,
  291. 'pyear' => $node->pyear,
  292. 'pages' => $node->pages,
  293. 'miniref' => $node->miniref,
  294. 'uniquename' => $node->uniquename,
  295. 'type_id' => $node->type_id,
  296. 'is_obsolete' => $node->is_obsolete,
  297. 'publisher' => $node->publisher,
  298. 'pubplace' => $node->pubplace,
  299. 'type_id' => $node->type_id
  300. );
  301. $status = tripal_core_chado_update('pub', $match, $values);
  302. }
  303. /**
  304. * Implementation of tripal_pub_load().
  305. *
  306. *
  307. * @param $node
  308. * The node that is to be accessed from the database
  309. *
  310. * @return $node
  311. * The node with the information to be loaded into the database
  312. *
  313. */
  314. function chado_pub_load($node) {
  315. // get the feature details from chado
  316. $pub_id = chado_get_id_for_node('pub', $node);
  317. $values = array('pub_id' => $pub_id);
  318. $pub = tripal_core_generate_chado_var('pub', $values);
  319. $additions = new stdClass();
  320. $additions->pub = $pub;
  321. return $additions;
  322. }
  323. /**
  324. * Implementation of tripal_pub_delete().
  325. *
  326. * This function takes a node and if the delete button has been chosen by the user, the publication
  327. * and it's details will be removed.Following,given the node-ID, the instance will be deleted from
  328. * the 'chado_pub' table.
  329. *
  330. * @parm $node
  331. * Then node which contains the information stored within the node-ID
  332. *
  333. */
  334. function chado_pub_delete(&$node) {
  335. $pub_id = chado_get_id_for_node('pub', $node);
  336. // if we don't have a pub id for this node then this isn't a node of
  337. // type chado_pub or the entry in the chado_pub table was lost.
  338. if (!$pub_id) {
  339. return;
  340. }
  341. // Remove data from {chado_pub}, {node} and {node_revisions} tables of
  342. // drupal database
  343. $sql_del = "DELETE FROM {chado_pub} ".
  344. "WHERE nid = %d ".
  345. "AND vid = %d";
  346. db_query($sql_del, $node->nid, $node->vid);
  347. $sql_del = "DELETE FROM {node_revisions} ".
  348. "WHERE nid = %d ".
  349. "AND vid = %d";
  350. db_query($sql_del, $node->nid, $node->vid);
  351. $sql_del = "DELETE FROM {node} ".
  352. "WHERE nid = %d ".
  353. "AND vid = %d";
  354. db_query($sql_del, $node->nid, $node->vid);
  355. // Remove data from pub and pubprop tables of chado database as well
  356. chado_query("DELETE FROM {pubprop} WHERE pub_id = %d", $pub_id);
  357. chado_query("DELETE FROM {pub} WHERE pub_id = %d", $pub_id);
  358. }
  359. /*
  360. *
  361. */
  362. function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
  363. if ($form_id == "tripal_pub_importer_setup_form") {
  364. // updating the form through the ahah callback sets the action of
  365. // the form to the ahah callback URL. We need to set it back
  366. // to the normal form URL
  367. if ($form_state['values']['action'] == 'edit') {
  368. $form['#action'] = url("admin/tripal/tripal_pub/import/edit/" . $form['pub_import_id']);
  369. }
  370. if ($form_state['values']['action'] == 'new') {
  371. $form['#action'] = url("admin/tripal/tripal_pub/import/new");
  372. }
  373. }
  374. }
  375. /**
  376. *
  377. *
  378. * @ingroup tripal_pub
  379. */
  380. function tripal_pub_preprocess_tripal_pub_relationships(&$variables) {
  381. // we want to provide a new variable that contains the matched pubs.
  382. $pub = $variables['node']->pub;
  383. // normally we would use tripal_core_expand_chado_vars to expand our
  384. // organism object and add in the relationships, however whan a large
  385. // number of relationships are present this significantly slows the
  386. // query, therefore we will manually perform the query
  387. $sql = "
  388. SELECT P.title, P.pub_id, CP.nid, CVT.name as rel_type
  389. FROM pub_relationship PR
  390. INNER JOIN {pub} P ON PR.object_id = P.pub_id
  391. INNER JOIN {cvterm} CVT ON PR.type_id = CVT.cvterm_id
  392. LEFT JOIN public.chado_pub CP ON P.pub_id = CP.pub_id
  393. WHERE PR.subject_id = %d
  394. ";
  395. $as_subject = chado_query($sql, $pub->pub_id);
  396. $sql = "
  397. SELECT P.title, P.pub_id, CP.nid, CVT.name as rel_type
  398. FROM pub_relationship PR
  399. INNER JOIN {pub} P ON PR.subject_id = P.pub_id
  400. INNER JOIN {cvterm} CVT ON PR.type_id = CVT.cvterm_id
  401. LEFT JOIN public.chado_pub CP ON P.pub_id = CP.pub_id
  402. WHERE PR.object_id = %d
  403. ";
  404. $as_object = chado_query($sql, $pub->pub_id);
  405. // combine both object and subject relationshisp into a single array
  406. $relationships = array();
  407. $relationships['object'] = array();
  408. $relationships['subject'] = array();
  409. // iterate through the object relationships
  410. while ($relationship = db_fetch_object($as_object)) {
  411. // get the relationship and child types
  412. $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
  413. $sub_type = t(preg_replace('/_/', " ", $relationship->sub_type));
  414. if (!array_key_exists($rel_type, $relationships['object'])) {
  415. $relationships['object'][$rel_type] = array();
  416. }
  417. if (!array_key_exists($sub_type, $relationships['object'][$rel_type])) {
  418. $relationships['object'][$rel_type][$sub_type] = array();
  419. }
  420. $relationships['object'][$rel_type][$sub_type][] = $relationship;
  421. }
  422. // now add in the subject relationships
  423. while ($relationship = db_fetch_object($as_subject)) {
  424. // get the relationship and child types
  425. $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
  426. $obj_type = t(preg_replace('/_/', " ", $relationship->obj_type));
  427. if (!array_key_exists($rel_type, $relationships['subject'])) {
  428. $relationships['subject'][$rel_type] = array();
  429. }
  430. if (!array_key_exists($obj_type, $relationships['subject'][$rel_type])) {
  431. $relationships['subject'][$rel_type][$obj_type] = array();
  432. }
  433. $relationships['subject'][$rel_type][$obj_type][] = $relationship;
  434. }
  435. $pub->all_relationships = $relationships;
  436. }