Tripal v1.0 (6.x-1.0)
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00001 <?php 00007 function tripal_project_admin($form_state = NULL) { 00008 $form = array(); 00009 00010 // before proceeding check to see if we have any 00011 // currently processing jobs. If so, we don't want 00012 // to give the opportunity to sync libraries 00013 $active_jobs = FALSE; 00014 if (tripal_get_module_active_jobs('tripal_project')) { 00015 $active_jobs = TRUE; 00016 } 00017 00018 // add the field set for syncing libraries 00019 if (!$active_jobs) { 00020 get_tripal_project_admin_form_sync_set($form); 00021 get_tripal_project_admin_form_cleanup_set($form); 00022 // get_tripal_project_admin_form_reindex_set($form); 00023 00024 } 00025 else { 00026 $form['notice'] = array( 00027 '#type' => 'fieldset', 00028 '#title' => t('Project Management Temporarily Unavailable') 00029 ); 00030 $form['notice']['message'] = array( 00031 '#value' => t('Currently, project management jobs are waiting or are running. . Managemment features have been hidden until these jobs complete. Please check back later once these jobs have finished. You can view the status of pending jobs in the Tripal jobs page.'), 00032 ); 00033 } 00034 00035 return system_settings_form($form); 00036 } 00042 function get_tripal_project_admin_form_cleanup_set(&$form) { 00043 $form['cleanup'] = array( 00044 '#type' => 'fieldset', 00045 '#title' => t('Clean Up') 00046 ); 00047 $form['cleanup']['description'] = array( 00048 '#type' => 'item', 00049 '#value' => t("With Drupal and chado residing in different databases ". 00050 "it is possible that nodes in Drupal and projects in Chado become ". 00051 "\"orphaned\". This can occur if an project node in Drupal is ". 00052 "deleted but the corresponding chado project is not and/or vice ". 00053 "versa. Click the button below to resolve these discrepancies."), 00054 '#weight' => 1, 00055 ); 00056 $form['cleanup']['button'] = array( 00057 '#type' => 'submit', 00058 '#value' => t('Clean up orphaned projects'), 00059 '#weight' => 2, 00060 ); 00061 } 00066 function get_tripal_project_admin_form_sync_set(&$form) { 00067 // define the fieldsets 00068 $form['sync'] = array( 00069 '#type' => 'fieldset', 00070 '#title' => t('Sync Projects') 00071 ); 00072 00073 // before proceeding check to see if we have any 00074 // currently processing jobs. If so, we don't want 00075 // to give the opportunity to sync libraries 00076 $active_jobs = FALSE; 00077 if (tripal_get_module_active_jobs('tripal_project')) { 00078 $active_jobs = TRUE; 00079 } 00080 00081 if (!$active_jobs) { 00082 00083 // get the list of projects 00084 $sql = "SELECT * FROM {project} ORDER BY name"; 00085 $org_rset = chado_query($sql); 00086 00087 // if we've added any projects to the list that can be synced 00088 // then we want to build the form components to allow the user 00089 // to select one or all of them. Otherwise, just present 00090 // a message stating that all projects are currently synced. 00091 $proj_boxes = array(); 00092 $added = 0; 00093 while ($project = db_fetch_object($org_rset)) { 00094 // check to see if the project is already present as a node in drupal. 00095 // if so, then skip it. 00096 $sql = "SELECT * FROM {chado_project} WHERE project_id = %d"; 00097 if (!db_fetch_object(db_query($sql, $project->project_id))) { 00098 $proj_boxes[$project->project_id] = $project->name; 00099 $added++; 00100 } 00101 } 00102 00103 // if we have projects we need to add to the checkbox then 00104 // build that form element 00105 if ($added > 0) { 00106 $proj_boxes['all'] = "All Projects"; 00107 00108 $form['sync']['projects'] = array( 00109 '#title' => t('Available Projects'), 00110 '#type' => t('checkboxes'), 00111 '#description' => t("Check the projects you want to sync. Drupal content will be created for each of the projects listed above. Select 'All Projects' to sync all of them."), 00112 '#required' => FALSE, 00113 '#prefix' => '<div id="org_boxes">', 00114 '#suffix' => '</div>', 00115 '#options' => $proj_boxes, 00116 ); 00117 $form['sync']['button'] = array( 00118 '#type' => 'submit', 00119 '#value' => t('Submit Sync Job') 00120 ); 00121 } 00122 // we don't have any projects to select from 00123 else { 00124 $form['sync']['value'] = array( 00125 '#value' => t('All projects in Chado are currently synced with Drupal.') 00126 ); 00127 } 00128 } 00129 // we don't want to present a form since we have an active job running 00130 else { 00131 $form['sync']['value'] = array( 00132 '#value' => t('Currently, jobs exist related to chado projects. Please check back later for projects that can by synced once these jobs have finished. You can view the status of pending jobs in the Tripal jobs page.') 00133 ); 00134 } 00135 } 00140 function tripal_project_admin_validate($form, &$form_state) { 00141 global $user; // we need access to the user info 00142 $job_args = array(); 00143 00144 if ($form_state['values']['op'] == t('Submit Sync Job')) { 00145 00146 // check to see if the user wants to sync chado and drupal. If 00147 // so then we need to register a job to do so with tripal 00148 $projects = $form_state['values']['projects']; 00149 $do_all = FALSE; 00150 $to_sync = array(); 00151 00152 foreach ($projects as $project_id) { 00153 if (preg_match("/^all$/i" , $project_id)) { 00154 $do_all = TRUE; 00155 } 00156 if ($project_id and preg_match("/^\d+$/i" , $project_id)) { 00157 // get the list of projects 00158 $sql = "SELECT * FROM {Project} WHERE project_id = %d"; 00159 $project = db_fetch_object(chado_query($sql, $project_id)); 00160 $to_sync[$project_id] = "$project->genus $project->species"; 00161 } 00162 } 00163 00164 // submit the job the tripal job manager 00165 if ($do_all) { 00166 tripal_add_job('Sync all projects' , 'tripal_project', 00167 'tripal_project_sync_projects' , $job_args , $user->uid); 00168 } 00169 else{ 00170 foreach ($to_sync as $project_id => $name) { 00171 $job_args[0] = $project_id; 00172 tripal_add_job("Sync project: $name" , 'tripal_project', 00173 'tripal_project_sync_projects' , $job_args , $user->uid); 00174 } 00175 } 00176 } 00177 00178 // ------------------------------------- 00179 // Submit the Reindex Job if selected 00180 if ($form_state['values']['op'] == t('Reindex Features')) { 00181 $projects = $form_state['values']['re-projects']; 00182 foreach ($projects as $project_id) { 00183 if ($project_id and preg_match("/^\d+$/i" , $project_id)) { 00184 // get the project info 00185 $sql = "SELECT * FROM {project} WHERE project_id = %d"; 00186 $project = db_fetch_object(chado_query($sql , $project_id)); 00187 $job_args[0] = $project_id; 00188 tripal_add_job("Reindex features for project: $project->genus ". 00189 "$project->species", 'tripal_project' , 00190 'tripal_project_reindex_features', $job_args, $user->uid); 00191 } 00192 } 00193 } 00194 00195 // ------------------------------------- 00196 // Submit the taxonomy Job if selected 00197 if ($form_state['values']['op'] == t('Set Feature Taxonomy')) { 00198 $projects = $form_state['values']['tx-projects']; 00199 foreach ($projects as $project_id) { 00200 if ($project_id and preg_match("/^\d+$/i", $project_id)) { 00201 // get the project info 00202 $sql = "SELECT * FROM {project} WHERE project_id = %d"; 00203 $project = db_fetch_object(chado_query($sql , $project_id)); 00204 $job_args[0] = $project_id; 00205 tripal_add_job("Set taxonomy for features in project: ". 00206 "$project->genus $project->species" , 'tripal_project', 00207 'tripal_project_taxonify_features', $job_args, $user->uid); 00208 } 00209 } 00210 } 00211 00212 // ------------------------------------- 00213 // Submit the Cleanup Job if selected 00214 if ($form_state['values']['op'] == t('Clean up orphaned projects')) { 00215 tripal_add_job('Cleanup orphaned projects', 'tripal_project', 00216 'tripal_project_cleanup', $job_args, $user->uid); 00217 } 00218 } 00224 function tripal_project_sync_projects($project_id = NULL, $job_id = NULL) { 00225 global $user; 00226 $page_content = ''; 00227 00228 if (!$project_id) { 00229 $sql = "SELECT * FROM {project} P"; 00230 $results = chado_query($sql); 00231 } 00232 else { 00233 $sql = "SELECT * FROM {project} P WHERE project_id = %d"; 00234 $results = chado_query($sql, $project_id); 00235 } 00236 00237 // We'll use the following SQL statement for checking if the project 00238 // already exists as a drupal node. 00239 $sql = "SELECT * FROM {chado_project} ". 00240 "WHERE project_id = %d"; 00241 00242 while ($project = db_fetch_object($results)) { 00243 00244 // check if this project already exists in the drupal database. if it 00245 // does then skip this project and go to the next one. 00246 if (!db_fetch_object(db_query($sql, $project->project_id))) { 00247 00248 $new_node = new stdClass(); 00249 $new_node->type = 'chado_project'; 00250 $new_node->uid = $user->uid; 00251 $new_node->title = "$project->name"; 00252 $new_node->project_id = $project->project_id; 00253 $new_node->name = $project->name; 00254 $new_node->description = $project->description; 00255 node_validate($new_node); 00256 if (!form_get_errors()) { 00257 $node = node_submit($new_node); 00258 node_save($node); 00259 if ($node->nid) { 00260 print "Added $project->name\n"; 00261 } 00262 } 00263 else { 00264 print "Failed to insert project $project->name\n"; 00265 } 00266 } 00267 else { 00268 print "Skipped $project->name\n"; 00269 } 00270 } 00271 return $page_content; 00272 } 00273 /* 00274 * 00275 */ 00276 function tripal_project_sync_projects_form_submit($form, &$form_state) { 00277 global $user; 00278 00279 //sync'ing is done by a tripal_job that is added here 00280 $job_id = tripal_add_job('Sync Projects', 'tripal_project', 00281 'tripal_project_sync_all_projects', array(), $user->uid); 00282 00283 } 00284 00285 /* 00286 * 00287 */ 00288 function tripal_project_sync_all_projects() { 00289 00290 //retrieve all projects in drupal 00291 $resource = db_query('SELECT project_id FROM {chado_project}'); 00292 $drupal_projects = array(); 00293 while ($r = db_fetch_object($resource)) { 00294 $drupal_projects[$r->project_id] = $r->project_id; 00295 } 00296 00297 // retrieve all projects in chado 00298 $chado_projects = array(); 00299 $resource = chado_query('SELECT project_id FROM {project}'); 00300 while ($r = db_fetch_object($resource)) { 00301 // if not already in drupal add to list to be sync'd 00302 if (!isset($drupal_projects[$r->project_id])) { 00303 $chado_projects[$r->project_id] = $r->project_id; 00304 } 00305 } 00306 00307 print 'Number of Projects to Sync: ' . sizeof($chado_projects) . "\n"; 00308 00309 foreach ($chado_projects as $project_id) { 00310 $project = tripal_core_chado_select('project', array('name', 'description'), array('project_id' => $project_id)); 00311 00312 // create node 00313 $new_node = new stdClass(); 00314 $new_node->type = 'chado_project'; 00315 $new_node->uid = $user->uid; 00316 $new_node->title = $project[0]->name; 00317 $new_node->project_id = $project_id; 00318 $new_node->description = $project[0]->description; 00319 node_validate($new_node); 00320 $errors = form_get_errors(); 00321 if (!$errors) { 00322 $node = node_submit($new_node); 00323 node_save($node); 00324 if ($node->nid) { 00325 print "Added " . $project[0]->name . " (Node ID:" . $node->nid . ")\n"; 00326 } 00327 } 00328 else { 00329 print "Failed to insert project: " . $project[0]->name . "\n"; 00330 print "Errors: " . print_r($errors, TRUE) . "\n"; 00331 } 00332 00333 } 00334 00335 00336 } 00337 00348 function tripal_project_cleanup($dummy = NULL, $job_id = NULL) { 00349 00350 return tripal_core_clean_orphaned_nodes('project', $job_id); 00351 }