tripal_core/jobs.php

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<?php

/** 
 * @defgroup tripal_jobs_api Core Module Jobs API
 * @{
 * Tripal offers a job management subsystem for managing tasks that may require an extended period of time for 
 * completion.  Drupal uses a UNIX-based cron job to handle tasks such as  checking  the  availability of updates, 
 * indexing new nodes for searching, etc.   Drupal's cron uses the web interface for launching these tasks, however, 
 * Tripal provides several administrative tasks that may time out and not complete due to limitations of the web 
 * server.  Examples including syncing of a large number of features between chado and Drupal.  To circumvent this, 
 * as well as provide more fine-grained control and monitoring, Tripal uses a jobs management sub-system built into 
 * the Tripal Core module.   It is anticipated that this functionality will be used for managing analysis jobs provided by 
 * future tools, with eventual support for distributed computing.   
 *
 * The  Tripal jobs management system allows administrators to submit tasks to be performed which can then  be 
 * launched through a UNIX command-line PHP script or cron job.  This command-line script can be added to a cron 
 * entry along-side the Drupal cron entry for automatic, regular launching of Tripal jobs.  The order of execution of 
 * waiting jobs is determined first by priority and second by the order the jobs were entered.  
 *
 * The API functions described below provide a programmatic interface for adding, checking and viewing jobs.
 * @}
 * @ingroup tripal_api
 */
 
/**
 * Adds a job to the Tripal Jbo queue
 *
 * @param $job_name
 *    The human readable name for the job
 * @param $modulename
 *    The name of the module adding the job
 * @param $callback
 *    The name of a function to be called when the job is executed
 * @param $arguments
 *    An array of arguements to be passed on to the callback
 * @param $uid
 *    The uid of the user adding the job
 * @param $priority
 *    The priority at which to run the job where the highest priority is 10 and the lowest priority 
 *    is 1. The default priority is 10.
 *
 * @return
 *    The job_id of the registered job
 *
 * @ingroup tripal_jobs_api
 */
function tripal_add_job ($job_name,$modulename,$callback,$arguments,$uid,$priority = 10){

   # convert the arguments into a string for storage in the database
   $args = implode("::",$arguments);

   $record = new stdClass();
   $record->job_name = $job_name;
   $record->modulename = $modulename;
   $record->callback = $callback;
   $record->status = 'Waiting';
   $record->submit_date = time();
   $record->uid = $uid;
   $record->priority = $priority;  # the lower the number the higher the priority
   if($args){
      $record->arguments = $args;
   }
   if(drupal_write_record('tripal_jobs',$record)){
      $jobs_url = url("admin/tripal/tripal_jobs");
      drupal_set_message(t("Job '$job_name' submitted.  Check the <a href='$jobs_url'>jobs page</a> for status"));
   } else {
      drupal_set_message("Failed to add job $job_name.");
   }

   return $record->job_id;
}

/**
 * An internal function for setting the progress for a current job
 *
 * @param $job_id
 *   The job_id to set the progress for
 * @param $percentage
 *   The progress to set the job to
 *
 * @return
 *   True on success and False otherwise
 *
 * @ingroup tripal_core
 */
function tripal_job_set_progress($job_id,$percentage){

   if(preg_match("/^(\d\d|100)$/",$percentage)){
      $record = new stdClass();
      $record->job_id = $job_id; 
      $record->progress = $percentage;
    if(drupal_write_record('tripal_jobs',$record,'job_id')){
       return 1;
    }
   }
   return 0;
}

/**
 * Returns a list of jobs associated with the given module
 *
 * @param $modulename
 *    The module to return a list of jobs for
 *
 * @return
 *    An array of objects where each object describes a tripal job
 *
 * @ingroup tripal_jobs_api
 */
function tripal_get_module_active_jobs ($modulename){
   $sql =  "SELECT * FROM {tripal_jobs} TJ ".
           "WHERE TJ.end_time IS NULL and TJ.modulename = '%s' ";
  return db_fetch_object(db_query($sql,$modulename));

}
/**
 * Returns the Tripal Job Report
 *
 * @return
 *   The HTML to be rendered which describes the job report
 *
 * @ingroup tripal_core
 */
function tripal_jobs_report () {
   //$jobs = db_query("SELECT * FROM {tripal_jobs} ORDER BY job_id DESC");
   $jobs = pager_query(
      "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
       FROM {tripal_jobs} TJ 
         INNER JOIN users U on TJ.uid = U.uid 
       ORDER BY job_id DESC", 10,0,"SELECT count(*) FROM {tripal_jobs}");
  
   // create a table with each row containig stats for 
   // an individual job in the results set.
   $output .= "Waiting jobs are executed first by priority level (the lower the ".
              "number the higher the priority) and second by the order they ".
              "were entered";
   $output .= "<table class=\"tripal-table tripal-table-horz\">". 
              "  <tr>".
              "    <th>Job ID</th>".
              "    <th>User</th>".
              "    <th>Job Name</th>".
              "    <th nowrap>Dates</th>".             
           "    <th>Priority</th>".
           "    <th>Progress</th>".
              "    <th>Status</th>".
              "    <th>Actions</th>".
              "  </tr>";
   $i = 0;
   while($job = db_fetch_object($jobs)){
      $class = 'tripal-table-odd-row';
      if($i % 2 == 0 ){
         $class = 'tripal-table-even-row';
      }
      $submit = tripal_jobs_get_submit_date($job);
      $start = tripal_jobs_get_start_time($job);
      $end = tripal_jobs_get_end_time($job);

      $cancel_link = '';
      if($job->start_time == 0 and $job->end_time == 0){
         $cancel_link = "<a href=\"".url("admin/tripal/tripal_jobs/cancel/".$job->job_id)."\">Cancel</a><br>";
      }
      $rerun_link = "<a href=\"".url("admin/tripal/tripal_jobs/rerun/".$job->job_id)."\">Re-run</a><br>";
      $view_link ="<a href=\"".url("admin/tripal/tripal_jobs/view/".$job->job_id)."\">View</a>";
      $output .= "  <tr class=\"$class\">";
      $output .= "    <td>$job->job_id</td>".
                 "    <td>$job->username</td>".
                 "    <td>$job->job_name</td>".
                 "    <td nowrap>Submit Date: $submit".
                 "    <br>Start Time: $start".
                 "    <br>End Time: $end</td>".
                 "    <td>$job->priority</td>".
             "    <td>$job->progress%</td>".
                 "    <td>$job->job_status</td>".
                 "    <td>$cancel_link $rerun_link $view_link</td>".
                 "  </tr>";
      $i++;
   }
   $output .= "</table>";
  $output .= theme_pager();
   return $output;
}

/**
 * Returns the start time for a given job
 * 
 * @param $job
 *   An object describing the job
 *
 * @return
 *   The start time of the job if it was already run and either "Cancelled" or "Not Yet Started" otherwise
 *
 * @ingroup tripal_jobs_api
 */
function tripal_jobs_get_start_time($job){
   if($job->start_time > 0){
      $start = format_date($job->start_time);
   } else {
      if(strcmp($job->job_status,'Cancelled')==0){
         $start = 'Cancelled';
      } else {
         $start = 'Not Yet Started';
      }
   }
   return $start;
}

/**
 * Returns the end time for a given job
 * 
 * @param $job
 *   An object describing the job
 *
 * @return
 *   The end time of the job if it was already run and empty otherwise
 *
 * @ingroup tripal_jobs_api
 */
function tripal_jobs_get_end_time($job){
   if($job->end_time > 0){
      $end = format_date($job->end_time);
   } else {
      $end = '';
   }
   return $end;
}

/**
 * Returns the date the job was added to the queue
 *
 * @param $job
 *   An object describing the job
 *
 * @return
 *   The date teh job was submitted
 *
 * @ingroup tripal_jobs_api
 */
function tripal_jobs_get_submit_date($job){
   return format_date($job->submit_date);
}

/**
 * A function used to manually launch all queued tripal jobs
 *
 * @param $do_parallel
 *   A boolean indicating whether jobs should be attempted to run in parallel
 *
 * @ingroup tripal_jobs_api
 */
function tripal_jobs_launch ($do_parallel = 0){
   
   // first check if any jobs are currently running
   // if they are, don't continue, we don't want to have
   // more than one job script running at a time
   if(!$do_parallel and tripal_jobs_check_running()){
      return;
   }
   
   // get all jobs that have not started and order them such that
   // they are processed in a FIFO manner. 
   $sql =  "SELECT * FROM {tripal_jobs} TJ ".
           "WHERE TJ.start_time IS NULL and TJ.end_time IS NULL ".
           "ORDER BY priority ASC,job_id ASC";
   $job_res = db_query($sql);
   while($job = db_fetch_object($job_res)){

    // set the start time for this job
    $record = new stdClass();
    $record->job_id = $job->job_id;
    $record->start_time = time();
    $record->status = 'Running';
    $record->pid = getmypid();
    drupal_write_record('tripal_jobs',$record,'job_id');

    // call the function provided in the callback column.
    // Add the job_id as the last item in the list of arguments. All
    // callback functions should support this argument.
    $callback = $job->callback;
    $args = split("::",$job->arguments);
    $args[] = $job->job_id;
    print "Calling: $callback(" . implode(", ",$args) . ")\n";   
    call_user_func_array($callback,$args);
    
    // set the end time for this job
    $record->end_time = time();
    $record->status = 'Completed';
    $record->progress = '100';
    drupal_write_record('tripal_jobs',$record,'job_id');
    
    // send an email to the user advising that the job has finished
   }
}

/**
 * Returns a list of running tripal jobs
 *
 * @return
 *    and array of objects where each object describes a running job or false if no jobs are running
 *
 * @ingroup tripal_jobs_api
 */
function tripal_jobs_check_running () {
   // iterate through each job that has not ended
   // and see if it is still running. If it is not
   // running but does not have an end_time then
   // set the end time and set the status to 'Error'
   $sql =  "SELECT * FROM {tripal_jobs} TJ ".
           "WHERE TJ.end_time IS NULL and NOT TJ.start_time IS NULL ";
   $jobs = db_query($sql);
   while($job = db_fetch_object($jobs)){
      if($job->pid and posix_kill($job->pid, 0)) {
         // the job is still running so let it go
       // we return 1 to indicate that a job is running
       print "Job is still running (pid $job->pid)\n";
       return 1;
      } else {
        // the job is not running so terminate it
        $record = new stdClass();
         $record->job_id = $job->job_id;
        $record->end_time = time();
         $record->status = 'Error';
        $record->error_msg = 'Job has terminated unexpectedly.';
         drupal_write_record('tripal_jobs',$record,'job_id');
     }
   }
   // return 1 to indicate that no jobs are currently running.
   return 0;
}

/**
 * Returns the HTML code to display a given job
 *
 * @param $job_id
 *   The job_id of the job to display
 * 
 * @return
 *   The HTML describing the indicated job
 * @ingroup tripal_core
 */
function tripal_jobs_view ($job_id){
   return theme('tripal_core_job_view',$job_id);
}

/**
 * Registers variables for the tripal_core_job_view themeing function
 *
 * @param $variables
 *   An array containing all variables supplied to this template
 *
 * @ingroup tripal_core
 */
function tripal_core_preprocess_tripal_core_job_view (&$variables){
   // get the job record
   $job_id = $variables['job_id'];
   $sql = 
      "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,TJ.arguments,
              TJ.callback,TJ.error_msg,TJ.pid
       FROM {tripal_jobs} TJ 
         INNER JOIN users U on TJ.uid = U.uid 
       WHERE TJ.job_id = %d";
   $job = db_fetch_object(db_query($sql,$job_id));

   // we do not know what the arguments are for and we want to provide a 
   // meaningful description to the end-user. So we use a callback function
   // deinfed in the module that created the job to describe in an array
   // the arguments provided.  If the callback fails then just use the 
   // arguments as they are
   $args = preg_split("/::/",$job->arguments);
   $arg_hook = $job->modulename."_job_describe_args";
   if(is_callable($arg_hook)){
      $new_args = call_user_func_array($arg_hook,array($job->callback,$args));
      if(is_array($new_args) and count($new_args)){
         $job->arguments = $new_args;
      } else {
         $job->arguments = $args;
      }
   } else {
      $job->arguments = $args;
   }

   // make our start and end times more legible
   $job->submit_date = tripal_jobs_get_submit_date($job);
   $job->start_time = tripal_jobs_get_start_time($job);
   $job->end_time = tripal_jobs_get_end_time($job);

   // add the job to the variables that get exported to the template
   $variables['job'] = $job;
}
/**
 * Set a job to be re-ran (ie: add it back into the job queue)
 * 
 * @param $job_id
 *   The job_id of the job to be re-ran
 * 
 * @ingroup tripal_jobs_api
 */
function tripal_jobs_rerun ($job_id){
   global $user;

   $sql = "select * from {tripal_jobs} where job_id = %d";
   $job = db_fetch_object(db_query($sql,$job_id));

   $args = explode("::",$job->arguments);
   tripal_add_job ($job->job_name,$job->modulename,$job->callback,$args,$user->uid,
      $job->priority);

   drupal_goto("admin/tripal/tripal_jobs");
}

/**
 * Cancel a Tripal Job currently waiting in the job queue
 *
 * @param $job_id
 *   The job_id of the job to be cancelled
 *
 * @ingroup tripal_jobs_api
 */
function tripal_jobs_cancel ($job_id){
   $sql = "select * from {tripal_jobs} where job_id = %d";
   $job = db_fetch_object(db_query($sql,$job_id));

   // set the end time for this job
   if($job->start_time == 0){
      $record = new stdClass();
      $record->job_id = $job->job_id;
     $record->end_time = time();
     $record->status = 'Cancelled';
     $record->progress = '0';
     drupal_write_record('tripal_jobs',$record,'job_id');
      drupal_set_message("Job #$job_id cancelled");
   } else {
      drupal_set_message("Job #$job_id cannot be cancelled. It is in progress or has finished.");
   }
   drupal_goto("admin/tripal/tripal_jobs");
}