tripal_core.module 13 KB

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  1. <?php
  2. /**
  3. * @file
  4. * The Tripal Core module
  5. */
  6. /**
  7. * @defgroup tripal_modules Tripal Modules
  8. * @{
  9. * All documented functions for the various Tripal Modules excluding API functions and Views Integration functions.
  10. * @}
  11. */
  12. /**
  13. * @defgroup tripal_api Tripal API
  14. * @{
  15. * Provides an application programming interface (API) for Tripal
  16. *
  17. * The Tripal API currently provides generic insert/update/select functions for all chado content as
  18. * well as some module specific functions that insert/update/delete/select specific chado content.
  19. *
  20. * This API is currently in its infancy and some necessary functions might be missing. If you find
  21. * a missing function that you think should be included go to the sourceforge feature request
  22. * page and request it's inclusion in the API. Such feature requests with a working function
  23. * definition will be given priority.
  24. * @}
  25. */
  26. /**
  27. * @defgroup tripal_core_api Core Module API
  28. * @ingroup tripal_api
  29. */
  30. /**
  31. * @defgroup tripal_core Tripal Core Module
  32. * @ingroup tripal_modules
  33. */
  34. require_once "api/tripal_core_chado.api.inc";
  35. require_once "api/tripal_core_files.api.inc";
  36. require_once "api/tripal_core_ahah.api.inc";
  37. require_once "api/tripal_core_custom_tables.api.inc";
  38. require_once "api/tripal_core_jobs.api.inc";
  39. require_once "api/tripal_core_mviews.api.inc";
  40. require_once "api/tripal_core_misc.api.inc";
  41. require_once "includes/jobs.inc";
  42. require_once "includes/mviews.inc";
  43. require_once "includes/custom_tables.inc";
  44. require_once "includes/chado_install.inc";
  45. require_once "includes/form_elements.inc";
  46. /**
  47. * Implements hook_init().
  48. * Used to set the search_path, create default content and set default variables.
  49. *
  50. * @ingroup tripal_core
  51. */
  52. function tripal_core_init() {
  53. global $base_url;
  54. // we need to declare here the persistent_chado global variable
  55. global $persistent_chado;
  56. global $prepared_statements;
  57. $persistent_chado = NULL;
  58. $prepared_statements = array();
  59. // add javascript files
  60. drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/tripal.ahah.js');
  61. // create the 'tripal' controlled volcabulary in chado but only if it doesn't already exist, and
  62. // only if the chado database is present.
  63. if (tripal_core_is_chado_installed()) {
  64. // make sure the current version of chado is set
  65. tripal_core_set_chado_version();
  66. if (!db_fetch_object(chado_query("SELECT * FROM {cv} WHERE name = 'tripal'"))) {
  67. $results = chado_query(
  68. "INSERT INTO {cv} (name,definition) ".
  69. "VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc')");
  70. }
  71. if (!db_fetch_object(chado_query("SELECT * FROM {db} WHERE name = 'tripal'"))) {
  72. $results = chado_query(
  73. "INSERT INTO {db} (name,description) ".
  74. "VALUES ('tripal', 'Used as a database placeholder for tripal defined objects such as tripal cvterms')");
  75. }
  76. }
  77. // add some variables for all javasript to use for building URLs
  78. global $base_url;
  79. $theme_dir = drupal_get_path('theme', 'tripal');
  80. $clean_urls = variable_get('clean_url', 0);
  81. drupal_add_js(
  82. " var baseurl = '$base_url';
  83. var themedir = '$theme_dir';
  84. var isClean = $clean_urls;",
  85. 'inline', 'header');
  86. // make sure the date time settings are the way Tripal will insert them
  87. // otherwise PostgreSQL version that may have a different datestyle setting
  88. // will fail when inserting or updating a date column in a table.
  89. db_query("SET DATESTYLE TO '%s'", 'MDY');
  90. // in the event that an errant Tripal or extension function fails to
  91. // set the postgres search_path back to noraml we do it here on
  92. // init of the core
  93. tripal_db_set_default_search_path();
  94. // create a persistent connection
  95. $connection = tripal_db_persistent_chado();
  96. // If we want AHAH elements on the node forms (e.g. chado_pub form) then we need to include
  97. // the node.pages file. Otherwise this error message is given:
  98. //
  99. // warning: call_user_func_array() expects parameter 1 to be a valid callback,
  100. // function 'node_form' not found or invalid function name
  101. // in /var/www/includes/form.inc on line 382.
  102. module_load_include('inc', 'node', 'node.pages');
  103. }
  104. /**
  105. * Implements hook_menu().
  106. * Defines all menu items needed by Tripal Core
  107. *
  108. * @ingroup tripal_core
  109. */
  110. function tripal_core_menu() {
  111. $items = array();
  112. // Triapl setting groups
  113. $items['admin/tripal'] = array(
  114. 'title' => 'Tripal Management',
  115. 'description' => "Manage the behavior or Tripal and its various modules.",
  116. 'position' => 'right',
  117. 'weight' => -5,
  118. 'page callback' => 'system_admin_menu_block_page',
  119. 'access arguments' => array('administer site configuration'),
  120. 'file' => 'system.admin.inc',
  121. 'file path' => drupal_get_path('module', 'system'),
  122. );
  123. $items['admin/tripal/customize'] = array(
  124. 'title' => 'Customize Tripal',
  125. 'position' => 'right',
  126. 'page callback' => 'theme',
  127. 'page arguments' => array('tripal_core_customize'),
  128. 'access arguments' => array('administer site configuration'),
  129. );
  130. $items['tripal_toggle_box_menu/%/%/%'] = array(
  131. 'title' => 'Toggle Box',
  132. 'page callback' => 'tripal_toggle_box_menu',
  133. 'page arguments' => array(1, 2, 3),
  134. 'access arguments' => array('access administration pages'),
  135. 'type' => MENU_CALLBACK | MENU_LINKS_TO_PARENT
  136. );
  137. $items['admin/tripal/chado_install'] = array(
  138. 'title' => 'Install Chado Schema',
  139. 'description' => 'Installs the Chado database tables, views, etc., inside the current Drupal database',
  140. 'page callback' => 'drupal_get_form',
  141. 'page arguments' => array('tripal_core_chado_load_form'),
  142. 'access arguments' => array('install chado'),
  143. 'type' => MENU_NORMAL_ITEM,
  144. );
  145. // Jobs Management
  146. $items['admin/tripal/tripal_jobs'] = array(
  147. 'title' => 'Jobs',
  148. 'description' => 'Jobs managed by Tripal',
  149. 'page callback' => 'tripal_jobs_report',
  150. 'access arguments' => array('access administration pages'),
  151. 'type' => MENU_NORMAL_ITEM,
  152. );
  153. $items['admin/tripal/tripal_jobs/cancel/%'] = array(
  154. 'title' => 'Jobs',
  155. 'description' => 'Cancel a pending job',
  156. 'page callback' => 'tripal_jobs_cancel',
  157. 'page arguments' => array(4),
  158. 'access arguments' => array('access administration pages'),
  159. 'type' => MENU_CALLBACK,
  160. );
  161. $items['admin/tripal/tripal_jobs/rerun/%'] = array(
  162. 'title' => 'Jobs',
  163. 'description' => 'Re-run an existing job.',
  164. 'page callback' => 'tripal_jobs_rerun',
  165. 'page arguments' => array(4),
  166. 'access arguments' => array('access administration pages'),
  167. 'type' => MENU_CALLBACK,
  168. );
  169. $items['admin/tripal/tripal_jobs/view/%'] = array(
  170. 'title' => 'Jobs Details',
  171. 'description' => 'View job details.',
  172. 'page callback' => 'tripal_jobs_view',
  173. 'page arguments' => array(4),
  174. 'access arguments' => array('access administration pages'),
  175. 'type' => MENU_CALLBACK,
  176. );
  177. // Materialized Views
  178. $items['admin/tripal/mviews'] = array(
  179. 'title' => 'MViews',
  180. 'description' => 'Materialized views are used to improve speed of large or complex queries.',
  181. 'page callback' => 'tripal_mviews_report',
  182. 'access arguments' => array('access administration pages'),
  183. 'type' => MENU_NORMAL_ITEM,
  184. );
  185. $items['admin/tripal/mviews/report/%'] = array(
  186. 'title' => 'Materialized View',
  187. 'description' => 'Materialized views are used to improve speed of large or complex queries.',
  188. 'page callback' => 'tripal_mview_report',
  189. 'page arguments' => array(4),
  190. 'access arguments' => array('access administration pages'),
  191. 'type' => MENU_NORMAL_ITEM,
  192. );
  193. $items['admin/tripal/mviews/new'] = array(
  194. 'title' => 'Create MView',
  195. 'description' => 'Materialized views are used to improve speed of large or complex queries.',
  196. 'page callback' => 'drupal_get_form',
  197. 'page arguments' => array('tripal_mviews_form'),
  198. 'access arguments' => array('access administration pages'),
  199. 'type' => MENU_CALLBACK,
  200. );
  201. $items['admin/tripal/mviews/edit/%'] = array(
  202. 'title' => 'Edit MView',
  203. 'page callback' => 'drupal_get_form',
  204. 'page arguments' => array('tripal_mviews_form', 4),
  205. 'access arguments' => array('access administration pages'),
  206. 'type' => MENU_NORMAL_ITEM,
  207. );
  208. $items['admin/tripal/mviews/action/%/%'] = array(
  209. 'title' => 'Create MView',
  210. 'description' => 'Materialized views are used to improve speed of large or complex queries.',
  211. 'page callback' => 'tripal_mviews_action',
  212. 'page arguments' => array(4, 5, "1"),
  213. 'access arguments' => array('access administration pages'),
  214. 'type' => MENU_CALLBACK,
  215. );
  216. // Custom Tables
  217. $items['admin/tripal/custom_tables'] = array(
  218. 'title' => 'Custom Tables',
  219. 'description' => 'Custom tables are added to Chado.',
  220. 'page callback' => 'tripal_custom_tables_list',
  221. 'access arguments' => array('access administration pages'),
  222. 'type' => MENU_NORMAL_ITEM,
  223. );
  224. $items['admin/tripal/custom_tables/view/%'] = array(
  225. 'title' => 'Custom Tables',
  226. 'description' => 'Custom tables are added to Chado.',
  227. 'page callback' => 'tripal_custom_table_view',
  228. 'page arguments' => array(4),
  229. 'access arguments' => array('access administration pages'),
  230. 'type' => MENU_NORMAL_ITEM,
  231. );
  232. $items['admin/tripal/custom_tables/new'] = array(
  233. 'title' => 'Create Custom Table',
  234. 'description' => 'Custom tables are added to Chado.',
  235. 'page callback' => 'drupal_get_form',
  236. 'page arguments' => array('tripal_custom_tables_form'),
  237. 'access arguments' => array('access administration pages'),
  238. 'type' => MENU_CALLBACK,
  239. );
  240. $items['admin/tripal/custom_tables/edit/%'] = array(
  241. 'title' => 'Edit Custom Table',
  242. 'page callback' => 'drupal_get_form',
  243. 'page arguments' => array('tripal_custom_tables_form', 4),
  244. 'access arguments' => array('access administration pages'),
  245. 'type' => MENU_NORMAL_ITEM,
  246. );
  247. $items['admin/tripal/custom_tables/action/%/%'] = array(
  248. 'title' => 'Create Custom TAble',
  249. 'description' => 'Custom tables are added to Chado.',
  250. 'page callback' => 'tripal_custom_tables_action',
  251. 'page arguments' => array(4, 5, "1"),
  252. 'access arguments' => array('access administration pages'),
  253. 'type' => MENU_CALLBACK,
  254. );
  255. return $items;
  256. }
  257. /**
  258. * Set the permission types that the chado module uses. Essentially we
  259. * want permissionis that protect creation, editing and deleting of chado
  260. * data objects
  261. *
  262. * @ingroup tripal_core
  263. */
  264. function tripal_core_perm() {
  265. return array('install chado');
  266. }
  267. /**
  268. * Implements hook_theme().
  269. * Registers template files/functions used by this module.
  270. *
  271. * @ingroup tripal_core
  272. */
  273. function tripal_core_theme() {
  274. return array(
  275. 'tripal_core_job_view' => array(
  276. 'arguments' => array('job_id' => NULL),
  277. 'template' => 'tripal_core_job_view',
  278. ),
  279. 'tripal_core_customize' => array(
  280. 'arguments' => array('job_id' => NULL),
  281. 'template' => 'tripal_core_customize',
  282. 'path' => drupal_get_path('module', 'tripal_core') . '/theme'
  283. ),
  284. );
  285. }
  286. /**
  287. * Implements hook_job_describe_args().
  288. * Describes the arguements for the tripal_update_mview job to allow for greater
  289. * readability in the jobs details pages.
  290. *
  291. * @param $callback
  292. * The callback of the current tripal job (this is the function that will be executed
  293. * when tripal_launch_jobs.php is run.
  294. * @param $args
  295. * An array of arguments passed in when the job was registered.
  296. *
  297. * @return
  298. * A more readable $args array
  299. *
  300. * @ingroup tripal_core
  301. */
  302. function tripal_core_job_describe_args($callback, $args) {
  303. $new_args = array();
  304. if ($callback == 'tripal_update_mview') {
  305. // get this mview details
  306. $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d ";
  307. $mview = db_fetch_object(db_query($sql, $args[0]));
  308. $new_args['View Name'] = $mview->name;
  309. }
  310. elseif ($callback == 'tripal_core_install_chado') {
  311. $new_args['Action'] = $args[0];
  312. }
  313. return $new_args;
  314. }
  315. /**
  316. * this is just a wrapper for backwards compatibility with a naming mistake.
  317. * it can go away in the future as it only is useful for jobs created by v0.3b
  318. *
  319. * @todo remove this function
  320. */
  321. function tripal_core_load_gff3($gff_file, $organism_id, $analysis_id, $add_only = 0,
  322. $update = 0, $refresh = 0, $remove = 0, $job = NULL) {
  323. tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id, $add_only,
  324. $update, $refresh, $remove, $job);
  325. }
  326. /**
  327. * Implements hook_coder_ignore().
  328. * Defines the path to the file (tripal_core.coder_ignores.txt) where ignore rules for coder are stored
  329. */
  330. function tripal_core_coder_ignore() {
  331. return array(
  332. 'path' => drupal_get_path('module', 'tripal_core'),
  333. 'line prefix' => drupal_get_path('module', 'tripal_core'),
  334. );
  335. }