Tripal v1.0 (6.x-1.0)
|
00001 <?php 00041 require_once "api/tripal_core_chado.api.inc"; 00042 require_once "api/tripal_core_files.api.inc"; 00043 require_once "api/tripal_core_ahah.api.inc"; 00044 require_once "api/tripal_core_custom_tables.api.inc"; 00045 require_once "api/tripal_core_jobs.api.inc"; 00046 require_once "api/tripal_core_mviews.api.inc"; 00047 require_once "includes/jobs.php"; 00048 require_once "includes/mviews.php"; 00049 require_once "includes/custom_tables.php"; 00050 require_once "includes/chado_install.php"; 00051 00058 function tripal_core_init() { 00059 global $base_url; 00060 00061 // we need to declare here the persistent_chado global variable 00062 global $persistent_chado; 00063 global $prepared_statements; 00064 $persistent_chado = NULL; 00065 $prepared_statements = array(); 00066 00067 // add javascript files 00068 drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/tripal.ahah.js'); 00069 00070 // create the 'tripal' controlled volcabulary in chado but only if it doesn't already exist, and 00071 // only if the chado database is present. 00072 if (tripal_core_is_chado_installed()) { 00073 00074 // make sure the current version of chado is set 00075 tripal_core_set_chado_version(); 00076 00077 if (!db_fetch_object(chado_query("SELECT * FROM {cv} WHERE name = 'tripal'"))) { 00078 $results = chado_query( 00079 "INSERT INTO {cv} (name,definition) ". 00080 "VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc')"); 00081 } 00082 if (!db_fetch_object(chado_query("SELECT * FROM {db} WHERE name = 'tripal'"))) { 00083 $results = chado_query( 00084 "INSERT INTO {db} (name,description) ". 00085 "VALUES ('tripal', 'Used as a database placeholder for tripal defined objects such as tripal cvterms')"); 00086 } 00087 } 00088 00089 // add some variables for all javasript to use for building URLs 00090 global $base_url; 00091 $theme_dir = drupal_get_path('theme', 'tripal'); 00092 $clean_urls = variable_get('clean_url', 0); 00093 drupal_add_js( 00094 " var baseurl = '$base_url'; 00095 var themedir = '$theme_dir'; 00096 var isClean = $clean_urls;", 00097 'inline', 'header'); 00098 00099 // make sure the date time settings are the way Tripal will insert them 00100 // otherwise PostgreSQL version that may have a different datestyle setting 00101 // will fail when inserting or updating a date column in a table. 00102 db_query("SET DATESTYLE TO '%s'", 'MDY'); 00103 00104 // in the event that an errant Tripal or extension function fails to 00105 // set the postgres search_path back to noraml we do it here on 00106 // init of the core 00107 tripal_db_set_default_search_path(); 00108 00109 // create a persistent connection 00110 $connection = tripal_db_persistent_chado(); 00111 } 00112 00119 function tripal_core_menu() { 00120 $items = array(); 00121 00122 // Triapl setting groups 00123 $items['admin/tripal'] = array( 00124 'title' => 'Tripal Management', 00125 'description' => "Manage the behavior or Tripal and its various modules.", 00126 'position' => 'right', 00127 'weight' => -5, 00128 'page callback' => 'system_admin_menu_block_page', 00129 'access arguments' => array('administer site configuration'), 00130 'file' => 'system.admin.inc', 00131 'file path' => drupal_get_path('module', 'system'), 00132 ); 00133 $items['admin/tripal/customize'] = array( 00134 'title' => 'Customize Tripal', 00135 'position' => 'right', 00136 'page callback' => 'theme', 00137 'page arguments' => array('tripal_core_customize'), 00138 'access arguments' => array('administer site configuration'), 00139 ); 00140 $items['tripal_toggle_box_menu/%/%/%'] = array( 00141 'title' => 'Toggle Box', 00142 'page callback' => 'tripal_toggle_box_menu', 00143 'page arguments' => array(1, 2, 3), 00144 'access arguments' => array('access administration pages'), 00145 'type' => MENU_CALLBACK | MENU_LINKS_TO_PARENT 00146 ); 00147 $items['admin/tripal/chado_install'] = array( 00148 'title' => 'Install Chado Schema', 00149 'description' => 'Installs the Chado database tables, views, etc., inside the current Drupal database', 00150 'page callback' => 'drupal_get_form', 00151 'page arguments' => array('tripal_core_chado_load_form'), 00152 'access arguments' => array('install chado'), 00153 'type' => MENU_NORMAL_ITEM, 00154 ); 00155 00156 // Jobs Management 00157 $items['admin/tripal/tripal_jobs'] = array( 00158 'title' => 'Jobs', 00159 'description' => 'Jobs managed by Tripal', 00160 'page callback' => 'tripal_jobs_report', 00161 'access arguments' => array('access administration pages'), 00162 'type' => MENU_NORMAL_ITEM, 00163 ); 00164 $items['admin/tripal/tripal_jobs/cancel/%'] = array( 00165 'title' => 'Jobs', 00166 'description' => 'Cancel a pending job', 00167 'page callback' => 'tripal_jobs_cancel', 00168 'page arguments' => array(4), 00169 'access arguments' => array('access administration pages'), 00170 'type' => MENU_CALLBACK, 00171 ); 00172 $items['admin/tripal/tripal_jobs/rerun/%'] = array( 00173 'title' => 'Jobs', 00174 'description' => 'Re-run an existing job.', 00175 'page callback' => 'tripal_jobs_rerun', 00176 'page arguments' => array(4), 00177 'access arguments' => array('access administration pages'), 00178 'type' => MENU_CALLBACK, 00179 ); 00180 $items['admin/tripal/tripal_jobs/view/%'] = array( 00181 'title' => 'Jobs Details', 00182 'description' => 'View job details.', 00183 'page callback' => 'tripal_jobs_view', 00184 'page arguments' => array(4), 00185 'access arguments' => array('access administration pages'), 00186 'type' => MENU_CALLBACK, 00187 ); 00188 00189 // Materialized Views 00190 $items['admin/tripal/mviews'] = array( 00191 'title' => 'MViews', 00192 'description' => 'Materialized views are used to improve speed of large or complex queries.', 00193 'page callback' => 'tripal_mviews_report', 00194 'access arguments' => array('access administration pages'), 00195 'type' => MENU_NORMAL_ITEM, 00196 ); 00197 $items['admin/tripal/mviews/report/%'] = array( 00198 'title' => 'Materialized View', 00199 'description' => 'Materialized views are used to improve speed of large or complex queries.', 00200 'page callback' => 'tripal_mview_report', 00201 'page arguments' => array(4), 00202 'access arguments' => array('access administration pages'), 00203 'type' => MENU_NORMAL_ITEM, 00204 ); 00205 $items['admin/tripal/mviews/new'] = array( 00206 'title' => 'Create MView', 00207 'description' => 'Materialized views are used to improve speed of large or complex queries.', 00208 'page callback' => 'drupal_get_form', 00209 'page arguments' => array('tripal_mviews_form'), 00210 'access arguments' => array('access administration pages'), 00211 'type' => MENU_CALLBACK, 00212 ); 00213 $items['admin/tripal/mviews/edit/%'] = array( 00214 'title' => 'Edit MView', 00215 'page callback' => 'drupal_get_form', 00216 'page arguments' => array('tripal_mviews_form', 4), 00217 'access arguments' => array('access administration pages'), 00218 'type' => MENU_NORMAL_ITEM, 00219 ); 00220 $items['admin/tripal/mviews/action/%/%'] = array( 00221 'title' => 'Create MView', 00222 'description' => 'Materialized views are used to improve speed of large or complex queries.', 00223 'page callback' => 'tripal_mviews_action', 00224 'page arguments' => array(4, 5, "1"), 00225 'access arguments' => array('access administration pages'), 00226 'type' => MENU_CALLBACK, 00227 ); 00228 00229 // Custom Tables 00230 $items['admin/tripal/custom_tables'] = array( 00231 'title' => 'Custom Tables', 00232 'description' => 'Custom tables are added to Chado.', 00233 'page callback' => 'tripal_custom_tables_list', 00234 'access arguments' => array('access administration pages'), 00235 'type' => MENU_NORMAL_ITEM, 00236 ); 00237 $items['admin/tripal/custom_tables/view/%'] = array( 00238 'title' => 'Custom Tables', 00239 'description' => 'Custom tables are added to Chado.', 00240 'page callback' => 'tripal_custom_table_view', 00241 'page arguments' => array(4), 00242 'access arguments' => array('access administration pages'), 00243 'type' => MENU_NORMAL_ITEM, 00244 ); 00245 $items['admin/tripal/custom_tables/new'] = array( 00246 'title' => 'Create Custom Table', 00247 'description' => 'Custom tables are added to Chado.', 00248 'page callback' => 'drupal_get_form', 00249 'page arguments' => array('tripal_custom_tables_form'), 00250 'access arguments' => array('access administration pages'), 00251 'type' => MENU_CALLBACK, 00252 ); 00253 $items['admin/tripal/custom_tables/edit/%'] = array( 00254 'title' => 'Edit Custom Table', 00255 'page callback' => 'drupal_get_form', 00256 'page arguments' => array('tripal_custom_tables_form', 4), 00257 'access arguments' => array('access administration pages'), 00258 'type' => MENU_NORMAL_ITEM, 00259 ); 00260 $items['admin/tripal/custom_tables/action/%/%'] = array( 00261 'title' => 'Create Custom TAble', 00262 'description' => 'Custom tables are added to Chado.', 00263 'page callback' => 'tripal_custom_tables_action', 00264 'page arguments' => array(4, 5, "1"), 00265 'access arguments' => array('access administration pages'), 00266 'type' => MENU_CALLBACK, 00267 ); 00268 00269 return $items; 00270 } 00271 00279 function tripal_core_perm() { 00280 return array('install chado'); 00281 } 00282 00289 function tripal_core_theme() { 00290 return array( 00291 'tripal_core_job_view' => array( 00292 'arguments' => array('job_id' => NULL), 00293 'template' => 'tripal_core_job_view', 00294 ), 00295 'tripal_core_customize' => array( 00296 'arguments' => array('job_id' => NULL), 00297 'template' => 'tripal_core_customize', 00298 'path' => drupal_get_path('module', 'tripal_core') . '/theme' 00299 ), 00300 ); 00301 } 00302 00319 function tripal_core_job_describe_args($callback, $args) { 00320 $new_args = array(); 00321 if ($callback == 'tripal_update_mview') { 00322 // get this mview details 00323 $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d "; 00324 $mview = db_fetch_object(db_query($sql, $args[0])); 00325 $new_args['View Name'] = $mview->name; 00326 } 00327 00328 elseif ($callback == 'tripal_core_install_chado') { 00329 $new_args['Action'] = $args[0]; 00330 } 00331 return $new_args; 00332 } 00333 00340 function tripal_core_load_gff3($gff_file, $organism_id, $analysis_id, $add_only = 0, 00341 $update = 0, $refresh = 0, $remove = 0, $job = NULL) { 00342 00343 tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id, $add_only, 00344 $update, $refresh, $remove, $job); 00345 } 00346 00351 function tripal_core_coder_ignore() { 00352 return array( 00353 'path' => drupal_get_path('module', 'tripal_core'), 00354 'line prefix' => drupal_get_path('module', 'tripal_core'), 00355 ); 00356 }