Added drush functions for bulk loader: tripal-loader-view, tripal-loader-cancel, tripal-loader-submit, tripal-loader-revert

tripal_bulk_loader/tripal_bulk_loader.drush.inc

@@ -14,6 +14,51 @@ function tripal_bulk_loader_drush_command() {
     'description' => dt('Display the progress of any running tripal bulk loading job.'),
     'aliases' => array('trpload-%'),
   );
+  $items['tripal-loader-view'] = array(
+    // used by drush help
+    'description' => dt('Returns the status/details of the specified bulk loading job.'),
+    'arguments' => array(
+      'nid' => dt('The Node ID of the bulk Loading Job')
+    ),
+    'examples' => array(
+      'Standard Example' => 'drush tripal-loader-view 5433',
+    ),
+    'aliases' => array('trpload-view')
+  );
+  $items['tripal-loader-cancel'] = array(
+    // used by drush help
+    'description' => dt('Cancels the specified bulk loading job.'),
+    'arguments' => array(
+      'nid' => dt('The Node ID of the bulk Loading Job')
+    ),
+    'examples' => array(
+      'Standard Example' => 'drush tripal-loader-cancel 5433',
+    ),
+    'aliases' => array('trpload-cncl')
+  );
+  $items['tripal-loader-submit'] = array(
+    // used by drush help
+    'description' => dt('Submit or Re-submit the given bulk loading job.'),
+    'arguments' => array(
+      'nid' => dt('The Node ID of the bulk Loading Job')
+    ),
+    'examples' => array(
+      'Standard Example' => 'drush tripal-loader-submit 5433',
+    ),
+    'aliases' => array('trpload-sbmt')
+  );
+  $items['tripal-loader-revert'] = array(
+    // used by drush help
+    'description' => dt('Revert the records loaded by the last run of the specified loading job. This is only available if the specified loading job is keeping track of inserted IDs.'),
+    'arguments' => array(
+      'nid' => dt('The Node ID of the bulk Loading Job')
+    ),
+    'examples' => array(
+      'Standard Example' => 'drush tripal-loader-revert 5433',
+    ),
+    'aliases' => array('trpload-revert')
+  );
+
   return $items;
 }
 
@@ -46,3 +91,98 @@ function drush_tripal_bulk_loader_tripal_loader_progress() {
     }
   }
 }
+
+/**
+ * Returns the status/details of the specified bulk loading job.
+ *
+ * @param $nid
+ *   The Node ID of the bulk Loading Job
+ */
+function drush_tripal_bulk_loader_tripal_loader_view ($nid) {
+  $node = node_load($nid);
+  $author = user_load($node->uid);
+
+  drush_print("Job Name: ".$node->loader_name);
+  drush_print("Submitted By: ".$author->name);
+  drush_print("Job Creation Date: ".format_date($node->created));
+  drush_print("Last Updated: ".format_date($node->changed));
+  drush_print("Template Name: ".$node->template->name);
+  drush_print("Data File: ".$node->file);
+  drush_print("Job Status: ".$node->job_status);
+}
+
+/**
+ * Cancels the specified bulk loading job.
+ *
+ * @param $nid
+ *   The Node ID of the bulk Loading Job
+ */
+function drush_tripal_bulk_loader_tripal_loader_cancel ($nid) {
+  $node = node_load($nid);
+  db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", 'Job Cancelled', $node->nid);
+  tripal_jobs_cancel($node->job_id,FALSE);
+}
+
+/**
+ * Submit or Re-submit the given bulk loading job.
+ *
+ * @param $nid
+ *   The Node ID of the bulk Loading Job
+ */
+function drush_tripal_bulk_loader_tripal_loader_submit ($nid) {
+  global $user;
+
+  if ($node->job_id) {
+    //Re-submit Tripal Job
+    tripal_jobs_rerun($node->job_id);
+    db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", 'Submitted to Queue', $nid);
+  }
+  else {
+    //Submit Tripal Job
+    $node= node_load($nid);
+    $job_args[1] = $nid;
+    if (is_readable($node->file)) {
+      $fname = basename($node->file);
+      $job_id = tripal_add_job("Bulk Loading Job: $fname", 'tripal_bulk_loader', 'tripal_bulk_loader_load_data', $job_args, $user->uid);
+
+      // add job_id to bulk_loader node
+      $success = db_query("UPDATE {tripal_bulk_loader} SET job_id=%d WHERE nid=%d", $job_id, $nid);
+
+      // change status
+      db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", 'Submitted to Queue', $nid);
+    }
+    else {
+      drupal_set_message(t("Can not open %file. Job not scheduled.", array('%file' => $node->file)));
+    }
+  }
+
+}
+
+/**
+ * Revert the records loaded by the last run of the specified loading job. This is only
+ * available if the specified loading job is keeping track of inserted IDs.
+ *
+ * @param $nid
+ *   The Node ID of the bulk Loading Job
+ */
+function drush_tripal_bulk_loader_tripal_loader_revert ($nid) {
+
+  // Remove the records from the database that were already inserted
+  $resource = db_query('SELECT * FROM {tripal_bulk_loader_inserted} WHERE nid=%d ORDER BY tripal_bulk_loader_inserted_id DESC', $node->nid);
+  while ($r = db_fetch_object($resource)) {
+    $ids = preg_split('/,/', $r->ids_inserted);
+    db_query('DELETE FROM %s WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted);
+    $result = db_fetch_object(db_query('SELECT true as present FROM %s WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted));
+    if (!$result->present) {
+      drupal_set_message(t('Successfully Removed data Inserted into the %tableto table.', array('%tableto' => $r->table_inserted_into)));
+      db_query('DELETE FROM {tripal_bulk_loader_inserted} WHERE tripal_bulk_loader_inserted_id=%d', $r->tripal_bulk_loader_inserted_id);
+    }
+    else {
+      drupal_set_message(t('Unable to remove data Inserted into the %tableto table!', array('%tableto' => $r->table_inserted_into)), 'error');
+    }
+  }
+
+  // reset status
+  db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", 'Reverted -Data Deleted', $node->nid);
+
+}

tripal_core/includes/jobs.php

@@ -137,14 +137,14 @@ function tripal_get_module_active_jobs($modulename) {
  */
 function tripal_jobs_report_form($form, &$form_state = NULL) {
   $form = array();
-	
+
   // set the default values
   $default_status = $form_state['values']['job_status'];
-  
+
   if (!$default_status) {
     $default_status = $_SESSION['tripal_job_status_filter'];
-  }    
-  
+  }
+
   $form['job_status'] = array(
     '#type'          => 'select',
     '#title'         => t('Filter by Job Status'),
@@ -153,17 +153,17 @@ function tripal_jobs_report_form($form, &$form_state = NULL) {
 	    0           => 'All Jobs',
 	    'Running'   => 'Running',
 	    'Waiting'   => 'Waiting',
-	    'Completed' => 'Completed',    
-	    'Cancelled' => 'Cancelled', 
-	    'Error'     => 'Error',  
+	    'Completed' => 'Completed',
+	    'Cancelled' => 'Cancelled',
+	    'Error'     => 'Error',
 	  ),
   );
-  
+
   $form['submit'] = array(
     '#type'         => 'submit',
     '#value'        => t('Filter'),
   );
-  return $form;  
+  return $form;
 }
 /**
  *
@@ -171,7 +171,7 @@ function tripal_jobs_report_form($form, &$form_state = NULL) {
  */
 function tripal_jobs_report_form_submit($form, &$form_state = NULL) {
   $job_status = $form_state['values']['job_status'];
-  $_SESSION['tripal_job_status_filter'] = $job_status;    
+  $_SESSION['tripal_job_status_filter'] = $job_status;
 }
 /**
  * Returns the Tripal Job Report
@@ -183,14 +183,14 @@ function tripal_jobs_report_form_submit($form, &$form_state = NULL) {
  */
 function tripal_jobs_report() {
 
-  // run the following function which will 
+  // run the following function which will
   // change the status of jobs that have errored out
   tripal_jobs_check_running();
-  
+
 	$jobs_status_filter = $_SESSION['tripal_job_status_filter'];
-  
+
   $sql = "
-    SELECT 
+    SELECT
       TJ.job_id,TJ.uid,TJ.job_name,TJ.modulename,TJ.progress,
       TJ.status as job_status, TJ,submit_date,TJ.start_time,
       TJ.end_time,TJ.priority,U.name as username
@@ -200,19 +200,19 @@ function tripal_jobs_report() {
     $sql .= "WHERE TJ.status = '%s' ";
   }
   $sql .= "ORDER BY job_id DESC";
-  
+
   $jobs = pager_query($sql, 25, 0, "SELECT count(*) FROM ($sql) as t1", $jobs_status_filter);
   $header = array(
-    'Job ID', 
-    'User', 
-    'Job Name', 
-    array('data' => 'Dates', 'style'=> "white-space: nowrap"), 
-    'Priority', 
-    'Progress', 
-    'Status', 
+    'Job ID',
+    'User',
+    'Job Name',
+    array('data' => 'Dates', 'style'=> "white-space: nowrap"),
+    'Priority',
+    'Progress',
+    'Status',
     'Action');
-  $rows = array();  
-  
+  $rows = array();
+
   // iterate through the jobs
   while ($job = db_fetch_object($jobs)) {
     $submit = tripal_jobs_get_submit_date($job);
@@ -235,7 +235,7 @@ function tripal_jobs_report() {
       "$cancel_link $rerun_link $view_link",
     );
   }
-  
+
   // create the report page
   $output .= "Waiting jobs are executed first by priority level (the lower the ".
              "number the higher the priority) and second by the order they ".
@@ -321,7 +321,7 @@ function tripal_jobs_get_submit_date($job) {
  *   To launch a specific job provide the job id.  This option should be
  *   used sparingly as the jobs queue managment system should launch jobs
  *   based on order and priority.  However there are times when a specific
- *   job needs to be launched and this argument will allow it.  Only jobs 
+ *   job needs to be launched and this argument will allow it.  Only jobs
  *   which have not been run previously will run.
  *
  * @ingroup tripal_jobs_api
@@ -343,7 +343,7 @@ function tripal_jobs_launch($do_parallel = 0, $job_id = NULL) {
             "WHERE TJ.start_time IS NULL and TJ.end_time IS NULL and TJ.job_id = %d ".
             "ORDER BY priority ASC,job_id ASC";
     $job_res = db_query($sql,$job_id);
-  } 
+  }
   else {
     $sql =  "SELECT * FROM {tripal_jobs} TJ ".
             "WHERE TJ.start_time IS NULL and TJ.end_time IS NULL ".
@@ -496,13 +496,13 @@ function tripal_jobs_rerun($job_id, $goto_jobs_page = TRUE) {
   $job = db_fetch_object(db_query($sql, $job_id));
   $args = explode("::", $job->arguments);
   $job_id = tripal_add_job(
-    $job->job_name, 
-    $job->modulename, 
-    $job->callback, 
-    $args, 
+    $job->job_name,
+    $job->modulename,
+    $job->callback,
+    $args,
     $user->uid,
     $job->priority);
-    
+
   if ($goto_jobs_page) {
     drupal_goto("admin/tripal/tripal_jobs");
   }
@@ -517,7 +517,7 @@ function tripal_jobs_rerun($job_id, $goto_jobs_page = TRUE) {
  *
  * @ingroup tripal_jobs_api
  */
-function tripal_jobs_cancel($job_id) {
+function tripal_jobs_cancel($job_id, $redirect = TRUE) {
   $sql = "SELECT * FROM {tripal_jobs} WHERE job_id = %d";
   $job = db_fetch_object(db_query($sql, $job_id));
 
@@ -534,5 +534,7 @@ function tripal_jobs_cancel($job_id) {
   else {
     drupal_set_message(t("Job %job_id cannot be cancelled. It is in progress or has finished.", array('%job_id' => $job_id)));
   }
-  drupal_goto("admin/tripal/tripal_jobs");
+  if ($redirect) {
+    drupal_goto("admin/tripal/tripal_jobs");
+  }
 }