Changeset 10 for trunk/cleanup_aira.php

Timestamp:

Jun 4, 2015, 9:48:05 PM (9 years ago)

Author:

gegorbet

Message:

fixes to allow simultaneous production/development jobs

File:

• trunk/cleanup_aira.php (modified) (2 diffs)

trunk/cleanup_aira.php

@@ -4 +4 @@
  *
  * functions relating to copying results and cleaning up the gfac DB
- *  where the job used an Airavata interface.
+ *  where the job used an Airavata interface (production version).
  *
  */
@@ -10 +10 @@
 $us3bin = exec( "ls -d ~us3/bin" );
 include_once "$us3bin/listen-config.php";
-include "/srv/www/htdocs/common/class/experiment_status.php";
-include "/srv/www/htdocs/common/class/experiment_errors.php";
+include $class_dir_p . "experiment_status.php";
+include $class_dir_p . "experiment_errors.php";
 $me              = 'cleanup_aira.php';
-$email_address   = '';
-$queuestatus     = '';
-$jobtype         = '';
-$db              = '';
-$editXMLFilename = '';
-$status          = '';
+$class_dir       = $class_dir_p;
+include_once "cleanup.php";
 
-function aira_cleanup( $us3_db, $reqID, $gfac_link )
-{
-   global $dbhost;
-   global $user;
-   global $passwd;
-   global $db;
-   global $guser;
-   global $gpasswd;
-   global $gDB;
-   global $me;
-   global $work;
-   global $email_address;
-   global $queuestatus;
-   global $jobtype;
-   global $editXMLFilename;
-   global $submittime;
-   global $status;
-   global $stderr;
-   global $stdout;
-   global $tarfile;
-   global $requestID;
-   global $submit_dir;
-   $me        = 'cleanup_aira.php';
-
-   $requestID = $reqID;
-   $db = $us3_db;
-   write_log( "$me: debug db=$db; requestID=$requestID" );
-
-   $us3_link = mysql_connect( $dbhost, $user, $passwd );
-
-   if ( ! $us3_link )
-   {
-      write_log( "$me: could not connect: $dbhost, $user, $passwd" );
-      mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" );
-      return( -1 );
-   }
-
-   $result = mysql_select_db( $db, $us3_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: could not select DB $db" );
-      mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" );
-      return( -1 );
-   }
-
-   // First get basic info for email messages
-   $query  = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " .
-             "WHERE HPCAnalysisRequestID=$requestID";
-   $result = mysql_query( $query, $us3_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query: $query" );
-      mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
-      return( -1 );
-   }
-
-   list( $email_address, $investigatorGUID, $editXMLFilename ) =  mysql_fetch_array( $result );
-
-   $query  = "SELECT personID FROM people " .
-             "WHERE personGUID='$investigatorGUID'";
-   $result = mysql_query( $query, $us3_link );
-
-   list( $personID ) = mysql_fetch_array( $result );
-
-   $query  = "SELECT clusterName, submitTime, queueStatus, method "              .
-             "FROM HPCAnalysisRequest h, HPCAnalysisResult r "                   .
-             "WHERE h.HPCAnalysisRequestID=$requestID "                          .
-             "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID";
-
-   $result = mysql_query( $query, $us3_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-      return( -1 );
-   }
-
-   if ( mysql_num_rows( $result ) == 0 )
-   {
-      write_log( "$me: US3 Table error - No records for requestID: $requestID" );
-      return( -1 );
-   }
-
-   list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result );
-
-   // Get the GFAC ID
-   $query = "SELECT HPCAnalysisResultID, gfacID FROM HPCAnalysisResult " .
-            "WHERE HPCAnalysisRequestID=$requestID";
-
-   $result = mysql_query( $query, $us3_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query: $query" );
-      mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
-      return( -1 );
-   }
-
-   list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result ); 
-
-   // Get data from global GFAC DB then insert it into US3 DB
-
-   $result = mysql_select_db( $gDB, $gfac_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Could not connect to DB $gDB" );
-      mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" );
-      return( -1 );
-   }
-
-   $query = "SELECT status, cluster, id FROM analysis " .
-            "WHERE gfacID='$gfacID'";
-
-   $result = mysql_query( $query, $gfac_link );
-   if ( ! $result )
-   {
-      write_log( "$me: Could not select GFAC status for $gfacID" );
-      mail_to_user( "fail", "Could not select GFAC status for $gfacID" );
-      return( -1 );
-   }
-   
-   list( $status, $cluster, $id ) = mysql_fetch_array( $result );
-
-   if ( $cluster == 'bcf-local'  || $cluster == 'alamo-local' )
-   {
-         $clushost = $cluster;
-         $clushost = preg_replace( "/\-local/", "", $clushost );
-         get_local_files( $gfac_link, $clushost, $requestID, $id, $gfacID );
-   }
-
-
-   $query = "SELECT id FROM analysis " .
-            "WHERE gfacID='$gfacID'";
-
-   $result = mysql_query( $query, $gfac_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
-      mail_to_user( "fail", "Internal error " . mysql_error( $gfac_link ) );
-      return( -1 );
-   }
-
-   list( $analysisID ) = mysql_fetch_array( $result );
-
-   // Get the request guid (LIMS submit dir name)
-   $query  = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
-             "WHERE HPCAnalysisRequestID = $requestID ";
-   $result = mysql_query( $query, $us3_link );
-   
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-   }
-
-   list( $requestGUID ) = mysql_fetch_array( $result );
-   $output_dir = "$submit_dir/$requestGUID";
-
-   // Get stderr,stdout,tarfile from work directory
-   if ( ! is_dir( "$output_dir" ) ) mkdir( "$output_dir", 0770 );
-   chdir( "$output_dir" );
-//write_log( "$me: gfacID=$gfacID" );
-//write_log( "$me: submit_dir=$submit_dir" );
-//write_log( "$me: requestGUID=$requestGUID" );
-write_log( "$me: output_dir=$output_dir" );
-
-   $stderr     = "";
-   $stdout     = "";
-   $tarfile    = "";
-   $fn_stderr  = "Ultrascan.stderr";
-   $fn_stdout  = "Ultrascan.stdout";
-   $fn_tarfile = "analysis-results.tar";
-   $num_try    = 0;
-   while ( ! file_exists( $fn_tarfile ) && $num_try < 3 )
-   {
-      sleep( 10 );
-      $num_try++;
-   }
-
-   $ofiles     = scandir( $output_dir );
-   foreach ( $ofiles as $ofile )
-   {
-      if ( preg_match( "/^" . $gfacID . ".*stderr$/", $ofile ) )
-         $fn_stderr  = $ofile;
-      if ( preg_match( "/^" . $gfacID . ".*stdout$/", $ofile ) )
-         $fn_stdout  = $ofile;
-//write_log( "$me:    ofile=$ofile" );
-   }
-write_log( "$me: fn_stderr=$fn_stderr" );
-write_log( "$me: fn_stdout=$fn_stdout" );
-if (file_exists($fn_tarfile)) write_log( "$me: fn_tarfile=$fn_tarfile" );
-else                          write_log( "$me: NOT FOUND: $fn_tarfile" );
-
-   if ( file_exists( $fn_stderr  ) ) $stderr   = file_get_contents( $fn_stderr  );
-   if ( file_exists( $fn_stdout  ) ) $stdout   = file_get_contents( $fn_stdout  );
-   if ( file_exists( $fn_tarfile ) ) $tarfile  = file_get_contents( $fn_tarfile );
-
-   if ( $cluster == 'alamo'  || $cluster == 'alamo-local' )
-   {  // Filter "ipath_userinit" lines out of alamo stdout lines
-      $prefln = strlen( $stdout );
-      $output = array();
-      exec( "grep -v 'ipath_userinit' $fn_stdout 2>&1", $output, $err );
-      $stdout = implode( "\n", $output );
-      $posfln = strlen( $stdout );
-write_log( "$me: fn_stdout : filtered. Length $prefln -> $posfln ." );
-   }
-
-   // Save queue messages for post-mortem analysis
-   $query = "SELECT message, time FROM queue_messages " .
-            "WHERE analysisID = $analysisID " .
-            "ORDER BY time ";
-   $result = mysql_query( $query, $gfac_link );
-
-   if ( ! $result )
-   {
-      // Just log it and continue
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
-   }
-
-   $now = date( 'Y-m-d H:i:s' );
-   $message_log = "US3 DB: $db\n" .
-                  "RequestID: $requestID\n" .
-                  "GFAC ID: $gfacID\n" .
-                  "Processed: $now\n\n" .
-                  "Queue Messages\n\n" ;
-   if ( mysql_num_rows( $result ) > 0 )
-   {
-      while ( list( $message, $time ) = mysql_fetch_array( $result ) )
-         $message_log .= "$time $message\n";
-   }
-
-   $query = "DELETE FROM queue_messages " .
-            "WHERE analysisID = $analysisID ";
-
-   $result = mysql_query( $query, $gfac_link );
-
-   if ( ! $result )
-   {
-      // Just log it and continue
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
-   }
-
-   $query = "SELECT queue_msg FROM analysis " .
-            "WHERE gfacID='$gfacID' ";
-
-   $result = mysql_query( $query, $gfac_link );
-   list( $queue_msg ) = mysql_fetch_array( $result );
-
-   // But let's allow for investigation of other large stdout and/or stderr
-   if ( strlen( $stdout ) > 20480000 ||
-        strlen( $stderr ) > 20480000 )
-      write_log( "$me: stdout + stderr larger than 20M - $gfacID\n" );
-
-   $message_log .= "\n\n\nStdout Contents\n\n" .
-                   $stdout .
-                   "\n\n\nStderr Contents\n\n" .
-                   $stderr .
-                   "\n\n\nGFAC Status: $status\n" .
-                   "GFAC message field: $queue_msg\n";
-
-   // Delete data from GFAC DB
-   $query = "DELETE from analysis WHERE gfacID='$gfacID'";
-
-   $result = mysql_query( $query, $gfac_link );
-
-   if ( ! $result )
-   {
-      // Just log it and continue
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
-   }
-
-
-   // Try to create it if necessary, and write the file
-   // Let's use FILE_APPEND, in case this is the second time around and the 
-   //  GFAC job status was INSERTed, rather than UPDATEd
-   if ( ! is_dir( $output_dir ) )
-      mkdir( $output_dir, 0775, true );
-   $message_filename = "$output_dir/$db-$requestID-messages.txt";
-   file_put_contents( $message_filename, $message_log, FILE_APPEND );
-  // mysql_close( $gfac_link );
-
-   /////////
-   // Insert data into HPCAnalysis
-
-   $query = "UPDATE HPCAnalysisResult SET "                              .
-            "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " .
-            "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "', " .
-            "queueStatus='completed' " .
-            "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
-
-   $result = mysql_query( $query, $us3_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-      mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) );
-      return( -1 );
-   }
-
-   // Delete data from GFAC DB
-   $query = "DELETE from analysis WHERE gfacID='$gfacID'";
-
-   $result = mysql_query( $query, $gfac_link );
-
-   if ( ! $result )
-   {
-      // Just log it and continue
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
-   }
-
-   // Expand the tar file
-
-   if ( strlen( $tarfile ) == 0 )
-   {
-      write_log( "$me: No tarfile" );
-      mail_to_user( "fail", "No results" );
-      return( -1 );
-   }
-
-   $tar_out = array();
-   exec( "tar -xf analysis-results.tar 2>&1", $tar_out, $err );
-
-   // Insert the model files and noise files
-   $files      = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES );
-   $noiseIDs   = array();
-   $modelGUIDs = array();
-
-   foreach ( $files as $file )
-   {
-      $split = explode( ";", $file );
-
-      if ( count( $split ) > 1 )
-      {
-         list( $fn, $meniscus, $mc_iteration, $variance ) = explode( ";", $file );
-      
-         list( $other, $mc_iteration ) = explode( "=", $mc_iteration );
-         list( $other, $variance     ) = explode( "=", $variance );
-         list( $other, $meniscus     ) = explode( "=", $meniscus );
-      }
-      else
-         $fn = $file;
-
-      if ( preg_match( "/mdl.tmp$/", $fn ) )
-         continue;
-
-      if ( filesize( $fn ) < 100 )
-      {
-         write_log( "$me:fn is invalid $fn size filesize($fn)" );
-         mail_to_user( "fail", "Internal error\n$fn is invalid" );
-         return( -1 );
-      }
-
-      if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file
-      {
-         $xml         = file_get_contents( $fn );
-         $statistics  = parse_xml( $xml, 'statistics' );
-//         $ntries      = 0;
-//
-//         while ( $statistics['cpucount'] < 1  &&  $ntries < 3 )
-//         {  // job_statistics file not totally copied, so retry
-//            sleep( 10 );
-//            $xml         = file_get_contents( $fn );
-//            $statistics  = parse_xml( $xml, 'statistics' );
-//            $ntries++;
-//write_log( "$me:jobstats retry $ntries" );
-//         }
-//write_log( "$me:cputime=$statistics['cputime']" );
-
-         $otherdata   = parse_xml( $xml, 'id' );
-
-         $query = "UPDATE HPCAnalysisResult SET "   .
-                  "wallTime = {$statistics['walltime']}, " .
-                  "CPUTime = {$statistics['cputime']}, " .
-                  "CPUCount = {$statistics['cpucount']}, " .
-                  "max_rss = {$statistics['maxmemory']}, " .
-                  "startTime = '{$otherdata['starttime']}', " .
-                  "endTime = '{$otherdata['endtime']}', " .
-                  "mgroupcount = {$otherdata['groupcount']} " .
-                  "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
-         $result = mysql_query( $query, $us3_link );
-
-         if ( ! $result )
-         {
-            write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-         }
-
-         file_put_contents( "$output_dir/$fn", $xml );    // Copy to submit dir
-
-      }
-
-      else if ( preg_match( "/\.noise/", $fn ) > 0 ) // It's a noise file
-      {
-         $xml        = file_get_contents( $fn );
-         $noise_data = parse_xml( $xml, "noise" );
-         $type       = ( $noise_data[ 'type' ] == "ri" ) ? "ri_noise" : "ti_noise";
-         $desc       = $noise_data[ 'description' ];
-         $modelGUID  = $noise_data[ 'modelGUID' ];
-         $noiseGUID  = $noise_data[ 'noiseGUID' ];
-
-         $query = "INSERT INTO noise SET "  .
-                  "noiseGUID='$noiseGUID'," .
-                  "modelGUID='$modelGUID'," .
-                  "editedDataID=1, "        .
-                  "modelID=1, "             .
-                  "noiseType='$type',"      .
-                  "description='$desc',"    .
-                  "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
-
-         // Add later after all files are processed: editDataID, modelID
-
-         $result = mysql_query( $query, $us3_link );
-
-         if ( ! $result )
-         {
-            write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-            mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
-            return( -1 );
-         }
-
-         $id        = mysql_insert_id( $us3_link );
-         $file_type = "noise";
-         $noiseIDs[] = $id;
-
-         // Keep track of modelGUIDs for later, when we replace them
-         $modelGUIDs[ $id ] = $modelGUID;
-         
-      }
-
-      else if ( preg_match( "/\.mrecs/", $fn ) > 0 )  // It's an mrecs file
-      {
-         $xml         = file_get_contents( $fn );
-         $mrecs_data  = parse_xml( $xml, "modelrecords" );
-         $desc        = $mrecs_data[ 'description' ];
-         $editGUID    = $mrecs_data[ 'editGUID' ];
-write_log( "$me:   mrecs file editGUID=$editGUID" );
-         if ( strlen( $editGUID ) < 36 )
-            $editGUID    = "12345678-0123-5678-0123-567890123456";
-         $mrecGUID    = $mrecs_data[ 'mrecGUID' ];
-         $modelGUID   = $mrecs_data[ 'modelGUID' ];
-
-         $query = "INSERT INTO pcsa_modelrecs SET "  .
-                  "editedDataID="                .
-                  "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
-                  "modelID=0, "             .
-                  "mrecsGUID='$mrecGUID'," .
-                  "description='$desc',"    .
-                  "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
-
-         // Add later after all files are processed: editDataID, modelID
-
-         $result = mysql_query( $query, $us3_link );
-
-         if ( ! $result )
-         {
-            write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-            mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
-            return( -1 );
-         }
-
-         $id         = mysql_insert_id( $us3_link );
-         $file_type  = "mrecs";
-         $mrecsIDs[] = $id;
-
-         // Keep track of modelGUIDs for later, when we replace them
-         $rmodlGUIDs[ $id ] = $modelGUID;
-//write_log( "$me:   mrecs file inserted into DB : id=$id" );
-      }
-
-      else                                           // It's a model file
-      {
-         $xml         = file_get_contents( $fn );
-         $model_data  = parse_xml( $xml, "model" );
-         $description = $model_data[ 'description' ];
-         $modelGUID   = $model_data[ 'modelGUID' ];
-         $editGUID    = $model_data[ 'editGUID' ];
-
-         if ( $mc_iteration > 1 )
-         {
-            $miter       = sprintf( "_mcN%03d", $mc_iteration );
-            $description = preg_replace( "/_mc[0-9]+/", $miter, $description );
-write_log( "$me:   MODELUpd: O:description=$description" );
-         }
-
-         $query = "INSERT INTO model SET "       .
-                  "modelGUID='$modelGUID',"      .
-                  "editedDataID="                .
-                  "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
-                  "description='$description',"  .
-                  "MCIteration='$mc_iteration'," .
-                  "meniscus='$meniscus'," .
-                  "variance='$variance'," .
-                  "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
-
-         $result = mysql_query( $query, $us3_link );
-
-         if ( ! $result )
-         {
-            write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) );
-            mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
-            return( -1 );
-         }
-
-         $modelID   = mysql_insert_id( $us3_link );
-         $id        = $modelID;
-         $file_type = "model";
-
-         $query = "INSERT INTO modelPerson SET " .
-                  "modelID=$modelID, personID=$personID";
-         $result = mysql_query( $query, $us3_link );
-      }
-
-      $query = "INSERT INTO HPCAnalysisResultData SET "       .
-               "HPCAnalysisResultID='$HPCAnalysisResultID', " .
-               "HPCAnalysisResultType='$file_type', "         .
-               "resultID=$id";
-
-      $result = mysql_query( $query, $us3_link );
-
-      if ( ! $result )
-      {
-         write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-         mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
-         return( -1 );
-      }
-   }
-
-   // Now fix up noise entries
-   // For noise files, there is, at most two: ti_noise and ri_noise
-   // In this case there will only be one modelID
-
-   foreach ( $noiseIDs as $noiseID )
-   {
-      $modelGUID = $modelGUIDs[ $noiseID ];
-      $query = "UPDATE noise SET "                                                 .
-               "editedDataID="                                                     .
-               "(SELECT editedDataID FROM model WHERE modelGUID='$modelGUID'),"    .
-               "modelID="                                                          .
-               "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')"          .
-               "WHERE noiseID=$noiseID";
-
-      $result = mysql_query( $query, $us3_link );
-
-      if ( ! $result )
-      {
-         write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-         mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
-         return( -1 );
-      }
-   }
-
-   // Copy results to LIMS submit directory (files there are deleted after 7 days)
-   global $submit_dir; // LIMS submit files dir
-   
-   // Get the request guid (LIMS submit dir name)
-   $query  = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
-             "WHERE HPCAnalysisRequestID = $requestID ";
-   $result = mysql_query( $query, $us3_link );
-   
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-   }
-   
-//   list( $requestGUID ) = mysql_fetch_array( $result );
-//   
-//   chdir( "$submit_dir/$requestGUID" );
-//   $f = fopen( "analysis-results.tar", "w" );
-//   fwrite( $f, $tarfile );
-//   fclose( $f );
-
-   // Clean up
-//   chdir ( $work );
-   // exec( "rm -rf $gfacID" );
-
-   mysql_close( $us3_link );
-
-   /////////
-   // Send email 
-
-   mail_to_user( "success", "" );
-}
-
-function mail_to_user( $type, $msg )
-{
-   // Note to me. Just changed subject line to include a modified $status instead 
-   // of the $type variable passed. More informative than just "fail" or "success." 
-   // See how it works for awhile and then consider removing $type parameter from 
-   // function.
-   global $email_address;
-   global $submittime;
-   global $queuestatus;
-   global $status;
-   global $cluster;
-   global $jobtype;
-   global $org_name;
-   global $admin_email;
-   global $db;
-   global $dbhost;
-   global $requestID;
-   global $gfacID;
-   global $editXMLFilename;
-   global $stdout;
-
-global $me;
-write_log( "$me mail_to_user(): sending email to $email_address for $gfacID" );
-
-   // Get GFAC status and message
-   // function get_gfac_message() also sets global $status
-   $gfac_message = get_gfac_message( $gfacID );
-   if ( $gfac_message === false ) $gfac_message = "Job Finished";
-      
-   // Create a status to put in the subject line
-   switch ( $status )
-   {
-      case "COMPLETE":
-         $subj_status = 'completed';
-         break;
-
-      case "CANCELLED":
-      case "CANCELED":
-         $subj_status = 'canceled';
-         break;
-
-      case "FAILED":
-         $subj_status = 'failed';
-         if ( preg_match( "/^US3-AIRA/i", $gfacID ) )
-         {  // For A/Thrift FAIL, get error message
-            $gfac_message = getExperimentErrors( $gfacID );
-//$gfac_message .= "Test ERROR MESSAGE";
-         }
-         break;
-
-      case "ERROR":
-         $subj_status = 'unknown error';
-         break;
-
-      default:
-         $subj_status = $status;       // For now
-         break;
-
-   }
-
-   $queuestatus = $subj_status;
-   $limshost    = $dbhost;
-   if ( $limshost == 'localhost' )
-      $limshost    = gethostname();
-
-   // Parse the editXMLFilename
-   list( $runID, $editID, $dataType, $cell, $channel, $wl, $ext ) =
-      explode( ".", $editXMLFilename );
-
-   $headers  = "From: $org_name Admin<$admin_email>"     . "\n";
-   $headers .= "Cc: $org_name Admin<$admin_email>"       . "\n";
-
-   // Set the reply address
-   $headers .= "Reply-To: $org_name<$admin_email>"      . "\n";
-   $headers .= "Return-Path: $org_name<$admin_email>"   . "\n";
-
-   // Try to avoid spam filters
-   $now = time();
-   $headers .= "Message-ID: <" . $now . "cleanup@$dbhost>\n";
-   $headers .= "X-Mailer: PHP v" . phpversion()         . "\n";
-   $headers .= "MIME-Version: 1.0"                      . "\n";
-   $headers .= "Content-Transfer-Encoding: 8bit"        . "\n";
-
-   $subject       = "UltraScan Job Notification - $subj_status - " . substr( $gfacID, 0, 16 );
-   $message       = "
-   Your UltraScan job is complete:
-
-   Submission Time : $submittime
-   LIMS Host       : $limshost
-   Analysis ID     : $gfacID
-   Request ID      : $requestID  ( $db )
-   RunID           : $runID
-   EditID          : $editID
-   Data Type       : $dataType
-   Cell/Channel/Wl : $cell / $channel / $wl
-   Status          : $queuestatus
-   Cluster         : $cluster
-   Job Type        : $jobtype
-   GFAC Status     : $status
-   GFAC Message    : $gfac_message
-   Stdout          : $stdout
-   ";
-
-   if ( $type != "success" ) $message .= "Grid Ctrl Error :  $msg\n";
-
-   // Handle the error case where an error occurs before fetching the
-   // user's email address
-   if ( $email_address == "" ) $email_address = $admin_email;
-
-   mail( $email_address, $subject, $message, $headers );
-}
-
-function parse_xml( $xml, $type )
-{
-   $parser = new XMLReader();
-   $parser->xml( $xml );
-
-   $results = array();
-
-   while ( $parser->read() )
-   {
-      if ( $parser->name == $type )
-      {
-         while ( $parser->moveToNextAttribute() ) 
-         {
-            $results[ $parser->name ] = $parser->value;
-         }
-
-         break;
-      }
-   }
-
-   $parser->close();
-   return $results;
-}
-
-// Function to get information about the current job GFAC
-function get_gfac_message( $gfacID )
-{
-  global $serviceURL;
-  global $me;
-
-  $hex = "[0-9a-fA-F]";
-  if ( ! preg_match( "/^US3-Experiment/i", $gfacID ) &&
-       ! preg_match( "/^US3-$hex{8}-$hex{4}-$hex{4}-$hex{4}-$hex{12}$/", $gfacID ) )
-   {
-      // Then it's not a GFAC job
-      return false;
-   }
-
-   $url = "$serviceURL/jobstatus/$gfacID";
-   try
-   {
-      $post = new HttpRequest( $url, HttpRequest::METH_GET );
-      $http = $post->send();
-      $xml  = $post->getResponseBody();      
-   }
-   catch ( HttpException $e )
-   {
-      write_log( "$me: Job status not available - $gfacID" );
-      return false;
-   }
-
-   // Parse the result
-   $gfac_message = parse_message( $xml );
-
-   return $gfac_message;
-}
-
-function parse_message( $xml )
-{
-   global $status;
-   $status       = "";
-   $gfac_message = "";
-
-   $parser = new XMLReader();
-   $parser->xml( $xml );
-
-   $results = array();
-
-   while( $parser->read() )
-   {
-      $type = $parser->nodeType;
-
-      if ( $type == XMLReader::ELEMENT )
-         $name = $parser->name;
-
-      else if ( $type == XMLReader::TEXT )
-      {
-         if ( $name == "status" ) 
-            $status       = $parser->value;
-         else 
-            $gfac_message = $parser->value; 
-      }
-   }
-      
-   $parser->close();
-   return $gfac_message;
-}
-
-function get_local_files( $gfac_link, $cluster, $requestID, $id, $gfacID )
-{
-   global $work;
-   global $work_remote;
-   global $me;
-   global $db;
-   global $status;
-
-   // Figure out local working directory
-   if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
-   $pwd = chdir( "$work/$gfacID" );
-
-   // Figure out remote directory
-   $remoteDir = sprintf( "$work_remote/$db-%06d", $requestID );
-
-   // Get stdout, stderr, output/analysis-results.tar
-   $output = array();
-//   $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
-//
-//   exec( $cmd, $output, $stat );
-//   if ( $stat != 0 ) 
-//      write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
-//     
-//   $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
-//   exec( $cmd, $output, $stat );
-//   if ( $stat != 0 ) 
-//      write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
-
-   $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/output/analysis-results.tar . 2>&1";
-   exec( $cmd, $output, $stat );
-   if ( $stat != 0 ) 
-      write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
-
-   $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
-   exec( $cmd, $output, $stat );
-   if ( $stat != 0 ) 
-   {
-      write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
-      sleep( 10 );
-      write_log( "$me: RETRY" );
-      exec( $cmd, $output, $stat );
-      if ( $stat != 0 ) 
-         write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
-   }
-     
-   $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
-   exec( $cmd, $output, $stat );
-   if ( $stat != 0 ) 
-   {
-      write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
-      sleep( 10 );
-      write_log( "$me: RETRY" );
-      exec( $cmd, $output, $stat );
-      if ( $stat != 0 ) 
-         write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
-   }
-
-   // Write the files to gfacDB
-
-   if ( file_exists( "stderr" ) ) $stderr  = file_get_contents( "stderr" );
-   if ( file_exists( "stdout" ) ) $stdout  = file_get_contents( "stdout" );
-   if ( file_exists( "analysis-results.tar" ) ) 
-      $tarfile = file_get_contents( "analysis-results.tar" );
-
-   $query = "UPDATE analysis SET " .
-            "stderr='"  . mysql_real_escape_string( $stderr,  $gfac_link ) . "'," .
-            "stdout='"  . mysql_real_escape_string( $stdout,  $gfac_link ) . "'," .
-            "tarfile='" . mysql_real_escape_string( $tarfile, $gfac_link ) . "'";
-
-   $result = mysql_query( $query, $gfac_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
-      echo "Bad query\n";
-      return( -1 );
-   }
-}
 ?>