Index: trunk/cleanup_aira.php =================================================================== --- trunk/cleanup_aira.php (revision 7) +++ trunk/cleanup_aira.php (revision 7) @@ -0,0 +1,844 @@ +&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 // 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( $gfac_link ) ); + echo "Bad query\n"; + return( -1 ); + } +} +?> Index: trunk/cleanup_gfac.php =================================================================== --- trunk/cleanup_gfac.php (revision 7) +++ trunk/cleanup_gfac.php (revision 7) @@ -0,0 +1,673 @@ + 0 ) + { // Log success at fetch attempt + write_log( "$me: Successful data fetch: $requestID $gfacID" ); + } + else + { // Log failure at fetch attempt + write_log( "$me: Failed data fetch: $requestID $gfacID" ); + if ( $analysisID == '' ) + $analysisID = '0'; + } + + // 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" ; + + $need_finish = ( $status == 'COMPLETE' ); + + if ( mysql_num_rows( $result ) > 0 ) + { + $time_msg = time(); + while ( list( $message, $time ) = mysql_fetch_array( $result ) ) + { +//write_log( "$me: message=$message" ); + $message_log .= "$time $message\n"; + if ( preg_match( "/^Finished/i", $message ) ) + $need_finish = false; + $time_msg = strtotime( $time ); + } + + if ( $need_finish ) + { // No 'Finished' yet: forget if too much time has passed + $time_now = time(); + $tdelta = $time_now - $time_msg; +write_log( "$me: no-Finish time: tnow=$time_now, tmsg=$time_msg, tdelt=$tdelta" ); + if ( $tdelta > 600 ) + $need_finish = false; + } +//write_log( "$me: no-Finish time: tnow=$time_now, tmsg=$time_msg, tdelt=$tdelta" ); + } + else + { + write_log( "$me: No messages for analysisID=$analysisID ." ); + $need_finish = false; + } + + if ( $need_finish ) + { + write_log( "$me: Cleanup has not yet found 'Finished' for $gfacID" ); + return( 0 ); + } + + $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 ) ); + } + + // Save stdout, stderr, etc. for message log + $query = "SELECT stdout, stderr, status, queue_msg FROM analysis " . + "WHERE gfacID='$gfacID' "; + $result = mysql_query( $query, $gfac_link ); + try + { + // What if this is too large? + list( $stdout, $stderr, $status, $queue_msg ) = mysql_fetch_array( $result ); + } + catch ( Exception $e ) + { + write_log( "$me: stdout + stderr larger than 128M - $gfacID\n" . mysql_error( $gfac_link ) ); + // Just go ahead and clean up + } + + // 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( $gfac_link ) ); + } +write_log( "$me: GFAC DB entry deleted" ); + + // Copy queue messages to LIMS submit directory (files there are deleted after 7 days) + global $submit_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 ); + $output_dir = "$submit_dir/$requestGUID"; +write_log( "$me: Output dir determined: $output_dir" ); + + // 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( $gfac_link ); +//write_log( "$me: *messages.txt written" ); + + ///////// + // Insert data into HPCAnalysis + + $query = "UPDATE HPCAnalysisResult SET " . + "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " . + "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "' " . + "WHERE HPCAnalysisResultID=$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( $us3_link ) ); + return( -1 ); + } +//write_log( "$me: HPCAnalysisResult stderr,stdout updated" ); + + // Save the tarfile and expand it + + if ( strlen( $tarfile ) == 0 ) + { + write_log( "$me: No tarfile" ); + mail_to_user( "fail", "No results" ); + return( -1 ); + } + + // Shouldn't happen + if ( ! is_dir( "$work" ) ) + { + write_log( "$me: $work directory does not exist" ); + mail_to_user( "fail", "$work directory does not exist" ); + return( -1 ); + } + + if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 ); + chdir( "$work/$gfacID" ); + + $f = fopen( "analysis.tar", "w" ); + fwrite( $f, $tarfile ); + fclose( $f ); +write_log( "$me: analysis.tar file written to work dir" ); + + $tar_out = array(); + exec( "tar -xf analysis.tar 2>&1", $tar_out, $err ); + + if ( $err != 0 ) + { + chdir( $work ); + exec( "rm -r $gfacID" ); + $output = implode( "\n", $tar_out ); + + write_log( "$me: Bad output tarfile: $output" ); + mail_to_user( "fail", "Bad output file" ); + return( -1 ); + } +//write_log( "$me: tar files extracted" ); + + // Insert the model files and noise files + $files = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES ); + $noiseIDs = array(); + $modelGUIDs = array(); + $mrecsIDs = array(); + $rmodlGUIDs = 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 $fn" ); + mail_to_user( "fail", "Internal error\n$fn is invalid" ); + return( -1 ); + } +//write_log( "$me: handling file: $fn" ); + + if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file + { + $xml = file_get_contents( $fn ); + $statistics = parse_xml( $xml, 'statistics' ); + $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 + $file_type = "job_stats"; +//write_log( "$me: job_statistics file updated in Result and written" ); + + } + + 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 ] = $modelGUID; +//write_log( "$me: noise file inserted into DB : id=$id" ); + + } + + 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 ( $mc_iteration > 1 ) + { +//write_log( "$me: MODELUpd: mc_iteration=$mc_iteration" ); + $miter = sprintf( "_mcN%03d", $mc_iteration ); +//write_log( "$me: MODELUpd: miter=$miter" ); +//write_log( "$me: MODELUpd: I:description=$description" ); + $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, $us3_link ); +//write_log( "$me: model file inserted into DB : id=$id" ); + } + + $query = "INSERT INTO HPCAnalysisResultData SET " . + "HPCAnalysisResultID='$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( $us3_link ) ); + return( -1 ); + } +//write_log( "$me: ResultData updated : file_type=$file_type" ); + } + + // 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( $us3_link ) ); + return( -1 ); + } +//write_log( "$me: noise entry updated : noiseID=$noiseID" ); + } +//write_log( "$me: noise entries updated" ); + + // Now possibly fix up mrecs entries + + foreach ( $mrecsIDs as $mrecsID ) + { + $modelGUID = $rmodlGUIDs[ $mrecsID ]; + $query = "UPDATE pcsa_modelrecs SET " . + "modelID=" . + "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" . + "WHERE mrecsID=$mrecsID"; + + $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( $us3_link ) ); + return( -1 ); + } +//write_log( "$me: mrecs entry updated : mrecsID=$mrecsID" ); + } +//write_log( "$me: mrecs entries updated" ); + + // 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.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", "" ); +} + +?> Index: trunk/runID_info.php =================================================================== --- trunk/runID_info.php (revision 7) +++ trunk/runID_info.php (revision 7) @@ -0,0 +1,805 @@ + + +
+ +

Info by Run ID

+ + + +
+ + 2 ) ? "" : "AND people.personID = $myID "; + + $query = "SELECT experimentID, runID, lname " . + "FROM experiment, projectPerson, people " . + "WHERE experiment.projectID = projectPerson.projectID " . + "AND projectPerson.personID = people.personID " . + $users_clause . + "ORDER BY lname, runID "; + $result = mysql_query( $query ) + or die( "Query failed : $query
" . mysql_error() ); + + if ( mysql_num_rows( $result ) == 0 ) return ""; + + $text = "
\n" . + " \n" . + "
\n"; + + return $text; +} + +// A function to retrieve information about that runID +function runID_info( $experimentID ) +{ + $query = "SELECT people.personID, personGUID, lname, fname, email " . + "FROM experiment, projectPerson, people " . + "WHERE experiment.experimentID = $experimentID " . + "AND experiment.projectID = projectPerson.projectID " . + "AND projectPerson.personID = people.personID "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + list( $ID, $GUID, $lname, $fname, $email ) = mysql_fetch_array( $result ); + + $text = << + Investigator Information + ID: + $ID + + GUID: + $GUID + + Name: + $fname $lname + + Email: + $email + + +HTML; + + $query = "SELECT experimentGUID, coeff1, coeff2, type, runType " . + "FROM experiment, rotorCalibration " . + "WHERE experimentID = $experimentID " . + "AND experiment.rotorCalibrationID = rotorCalibration.rotorCalibrationID "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + list( $GUID, $coeff1, $coeff2, $type, $runType ) = mysql_fetch_array( $result ); + $text .= << + Run Information + GUID: + $GUID + + Rotor stretch coeff 1: + $coeff1 + + Rotor stretch coeff 2: + $coeff2 + + Experiment type: + $type + + Run Type: + $runType + + +HTML; + + $query = "SELECT rawDataID, rawDataGUID, filename, solutionID " . + "FROM rawData " . + "WHERE experimentID = $experimentID " . + "ORDER BY filename "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + + if ( mysql_num_rows( $result ) == 0 ) + return $text; + + $rawIDs = array(); + $solutionIDs = array(); + $text .= << + Raw Data + + ID + GUID + Filename + Solution + + + + +HTML; + + while ( list( $ID, $GUID, $filename, $solutionID ) = mysql_fetch_array( $result ) ) + { + $rawIDs[] = $ID; + $solutionIDs[] = $solutionID; + + $text .= <<$ID + $GUID + $filename + $solutionID + + +HTML; + + } + + $text .= "\n\n" . + "\n"; + + $rawIDs_csv = implode( ", ", $rawIDs ); + $query = "SELECT editedDataID, rawDataID, editGUID, filename " . + "FROM editedData " . + "WHERE rawDataID IN ( $rawIDs_csv ) " . + "ORDER BY editedDataID, filename "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + + if ( mysql_num_rows( $result ) == 0 ) + return $text; + + $text .= << + Edit Profiles + + ID + GUID + Filename + Raw ID + + + + + +HTML; + + $editIDs = array(); + while ( list ( $editID, $rawID, $GUID, $filename ) = mysql_fetch_array( $result ) ) + { + $editIDs[] = $editID; + + $text .= <<$editID + $GUID + $filename + $rawID + + +HTML; + } + + $text .= "\n\n" . + "\n"; + + $editIDs_csv = implode( ", ", $editIDs ); + $query = "SELECT model.modelID, editedDataID, modelGUID, variance, meniscus, personID " . + "FROM model LEFT JOIN modelPerson " . + "ON ( model.modelID = modelPerson.modelID ) " . + "WHERE editedDataID IN ( $editIDs_csv ) " . + "ORDER BY modelID "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + + if ( mysql_num_rows( $result ) != 0 ) + { + $text .= << + Models + + ID + GUID + Edit ID + Variance + Meniscus + Owner ID + + + + + +HTML; + + $modelIDs = array(); + while ( list ( $modelID, $editID, $GUID, $variance, $meniscus, $personID ) = mysql_fetch_array( $result ) ) + { + $modelIDs[] = $modelID; + + $text .= <<$modelID + $GUID + $editID + $variance + $meniscus + $personID + + +HTML; + } + + $text .= "\n\n" . + "\n"; + } + + if ( count( $modelIDs ) > 0 ) + { + $modelIDs_csv = implode( ", ", $modelIDs ); + $query = "SELECT noiseID, noiseGUID, editedDataID, modelID, modelGUID, noiseType " . + "FROM noise " . + "WHERE modelID IN ( $modelIDs_csv ) " . + "ORDER BY noiseID "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + + if ( mysql_num_rows( $result ) != 0 ) + { + $text .= << + Noise Linked to Models + + ID + GUID + Edit ID + Model ID + Model GUID + Type + + + + + +HTML; + + while ( list ( $noiseID, $GUID, $editID, $modelID, $modelGUID, $type ) = mysql_fetch_array( $result ) ) + { + $text .= <<$noiseID + $GUID + $editID + $modelID + $modelGUID + $type + + +HTML; + } + + $text .= "\n\n" . + "\n"; + } + } + + $query = "SELECT noiseID, noiseGUID, editedDataID, modelID, modelGUID, noiseType " . + "FROM noise " . + "WHERE editedDataID IN ( $editIDs_csv ) " . + "ORDER BY noiseID "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + + if ( mysql_num_rows( $result ) != 0 ) + { + $text .= << + Noise Linked to Edit Profiles + + ID + GUID + Edit ID + Model ID + Model GUID + Type + + + + + +HTML; + + while ( list ( $noiseID, $GUID, $editID, $modelID, $modelGUID, $type ) = mysql_fetch_array( $result ) ) + { + $text .= <<$noiseID + $GUID + $editID + $modelID + $modelGUID + $type + + +HTML; + } + + $text .= "\n\n" . + "\n"; + } + + $reportIDs = array(); + $query = "SELECT reportID, reportGUID, title " . + "FROM report " . + "WHERE experimentID = $experimentID " . + "ORDER BY reportID "; + + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + + if ( mysql_num_rows( $result ) != 0 ) + { + $text .= << + Reports Related to This Experiment + + ID + GUID + Title + + + + + +HTML; + + while ( list ( $reportID, $GUID, $title ) = mysql_fetch_array( $result ) ) + { + $reportIDs[] = $reportID; + $text .= <<$reportID + $GUID + $title + + +HTML; + } + + $text .= "\n\n" . + "\n"; + } + + $reportTripleIDs = array(); + if ( ! empty( $reportIDs ) ) + { + $reportIDs_csv = implode( ",", $reportIDs ); + $query = "SELECT reportTripleID, reportTripleGUID, resultID, triple, dataDescription, reportID " . + "FROM reportTriple " . + "WHERE reportID IN ( $reportIDs_csv ) " . + "ORDER BY reportID, reportTripleID "; + + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + + if ( mysql_num_rows( $result ) != 0 ) + { + $text .= << + Report Triples Related to Reports + + ID + GUID + Result ID + Triple + Description + Report ID + + + + + +HTML; + + while ( list ( $reportTripleID, $GUID, $resultID, $triple, $dataDesc, $rptID ) + = mysql_fetch_array( $result ) ) + { + $reportTripleIDs[] = $reportTripleID; + $text .= <<$reportTripleID + $GUID + $resultID + $triple + $dataDesc + $rptID + + +HTML; + } + + $text .= "\n\n" . + "\n"; + } + } + + if ( ! empty( $reportTripleIDs ) ) + { + $reportTripleIDs_csv = implode( ",", $reportTripleIDs ); + $query = "SELECT d.reportDocumentID, reportDocumentGUID, editedDataID, label, " . + "filename, analysis, subAnalysis, documentType, l.reportTripleID " . + "FROM documentLink l, reportDocument d " . + "WHERE reportTripleID IN ( $reportTripleIDs_csv ) " . + "AND l.reportDocumentID = d.reportDocumentID " . + "ORDER BY reportTripleID, reportDocumentID "; + + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + + if ( mysql_num_rows( $result ) != 0 ) + { + $text .= << + Report Documents Related to Triples + + ID + GUID + Edit ID + Label/Filename + Anal/Sub/DocType + Trip ID + + + + + +HTML; + + while ( list ( $reportDocumentID, $GUID, $editID, $label, $filename, + $analysis, $subAnal, $docType, $tripID ) + = mysql_fetch_array( $result ) ) + { + $text .= <<$reportDocumentID + $GUID + $editID + $label/$filename + $analysis/$subAnal/$docType + $tripID + + +HTML; + } + + $text .= "\n\n" . + "\n"; + } + } + + $query = "SELECT HPCAnalysisRequestID, HPCAnalysisRequestGUID, editXMLFilename, " . + "submitTime, clusterName, method " . + "FROM HPCAnalysisRequest " . + "WHERE experimentID = $experimentID " . + "ORDER BY HPCAnalysisRequestID "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + + if ( mysql_num_rows( $result ) == 0 ) + return $text; + + $requestIDs = array(); + $text .= << + HPC Requests + + ID + GUID + XML Filename + Submit + Cluster + Method + + + + +HTML; + + while ( list( $ID, $GUID, $filename, $submit, $cluster, $method ) = mysql_fetch_array( $result ) ) + { + $requestIDs[] = $ID; + + $text .= <<$ID + $GUID + $filename + $submit + $cluster + $method + + +HTML; + + } + + $text .= "\n\n" . + "\n"; + + $requestIDs_csv = implode( ", ", $requestIDs ); + $query = "SELECT HPCAnalysisResultID, HPCAnalysisRequestID, gfacID, queueStatus, updateTime " . + "FROM HPCAnalysisResult " . + "WHERE HPCAnalysisRequestID IN ( $requestIDs_csv ) " . + "ORDER BY HPCAnalysisResultID "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + + if ( mysql_num_rows( $result ) != 0 ) + { + $text .= << + HPC Results + + ID + Request ID + gfac ID + Status + Updated + + + + +HTML; + + $incomplete = array(); + while ( list( $ID, $requestID, $gfacID, $status, $updated ) = mysql_fetch_array( $result ) ) + { + if ( $status != 'completed' ) + $incomplete[] = $gfacID; + + $text .= <<$ID + $requestID + $gfacID + $status + $updated + + +HTML; + + } + + $text .= "\n\n" . + "\n"; + + } + + if ( empty( $incomplete ) ) + return $text; + + // Now switch over to the global db + global $globaldbhost, $globaldbuser, $globaldbpasswd, $globaldbname; + + $globaldb = mysql_connect( $globaldbhost, $globaldbuser, $globaldbpasswd ); + + if ( ! $globaldb ) + { + $text .= "

Cannot open global database on $globaldbhost

\n"; + return $text; + } + + if ( ! mysql_select_db( $globaldbname, $globaldb ) ) + { + $text .= "

Cannot change to global database $globaldbname

\n"; + return $text; + } + + $text .= << + GFAC Status + + gfacID + Cluster + DB + Status + Message + Updated + + + + +HTML; + + $in_queue = 0; + foreach ( $incomplete as $gfacID ) + { + + $query = "SELECT cluster, us3_db, status, queue_msg, time " . + "FROM analysis " . + "WHERE gfacID = '$gfacID' "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error() ); + + if ( mysql_num_rows( $result ) == 1 ) + { + $in_queue++; + list( $cluster, $db, $status, $msg, $time ) = mysql_fetch_array( $result ); + $text .= <<$gfacID + $cluster + $db + $status + $msg + $time + + +HTML; + } + } + + if ( $in_queue == 0 ) + $text .= "No local jobs currently in the queue\n"; + + $text .= "\n\n" . + "\n"; + + mysql_close( $globaldb ); + + return $text; +} + +function HPCDetail( $requestID ) +{ + $query = "SELECT * FROM HPCAnalysisRequest WHERE HPCAnalysisRequestID=$requestID"; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error()); + $row = mysql_fetch_assoc( $result ); + $row['requestXMLFile'] = '
' . htmlentities( $row['requestXMLFile'] ) . '
'; + + // Save for later + $requestGUID = $row['HPCAnalysisRequestGUID']; + $cluster = $row['clusterName']; + #var_dump($cluster); + $text = << + HPC Request Detail + +HTML; + + foreach ($row as $key => $value) + { + $text .= " $key$value\n"; + } + + $text .= "\n"; + + $query = "SELECT * FROM HPCAnalysisResult WHERE HPCAnalysisRequestID=$requestID"; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error()); + $row = mysql_fetch_assoc( $result ); + $row['jobfile'] = '
' . htmlentities( $row['jobfile'] ) . '
'; + + // Get GFAC job status + global $uses_airavata; + + if ( $uses_airavata === true && $cluster != 'juropa.fz-juelich.de' ) + { + $row['gfacStatus'] = nl2br( getExperimentStatus( $row['gfacID'] ) ); + } + else + { + $row['gfacStatus'] = nl2br( getJobstatus( $row['gfacID'] ) ); + } + + // Get queue messages from disk directory, if it still exists + global $submit_dir; + global $dbname; + + $msg_filename = "$submit_dir$requestGUID/$dbname-$requestID-messages.txt"; + $queue_msgs = false; + if ( file_exists( $msg_filename ) ) + { + $queue_msgs = file_get_contents( $msg_filename ); + $len_msgs = strlen( $queue_msgs ); + $queue_msgs = '
' . $queue_msgs . '
'; + } + + // Get resulting model and noise information + if ( ! empty( $resultID ) ) + { + $resultID = $row['HPCAnalysisResultID']; + $models = array(); + $noise = array(); + $query = "SELECT resultID FROM HPCAnalysisResultData " . + "WHERE HPCAnalysisResultID = $resultID " . + "AND HPCAnalysisResultType = 'model' "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error()); + $models = mysql_fetch_row( $result ); // An array with all of them + if ( $models !== false ) + $row['modelIDs'] = implode( ", ", $models ); + + $query = "SELECT resultID FROM HPCAnalysisResultData " . + "WHERE HPCAnalysisResultID = $resultID " . + "AND HPCAnalysisResultType = 'noise' "; + $result = mysql_query( $query ) + or die( "Query failed : $query
\n" . mysql_error()); + $noise = mysql_fetch_row( $result ); // An array with all of them + if ( $noise !== false ) + $row['noiseIDs'] = implode( ", ", $noise ); + } + + $text .= << + + + +HTML; + + foreach ($row as $key => $value) + { + $text .= " \n"; + } + + if ( $queue_msgs !== false ) + { + $linkmsg = "Length Messages"; + + $text .= " \n"; + if ( isset( $_GET[ 'msgs' ] ) ) + $text .= " \n"; + } + + $text .= "
HPC Result Detail
$key$value
$linkmsg$len_msgs
Queue Messages$queue_msgs
\n"; + + return $text; +} + +?> Index: trunk/save-jobstats.sh =================================================================== --- trunk/save-jobstats.sh (revision 7) +++ trunk/save-jobstats.sh (revision 7) @@ -0,0 +1,67 @@ +#!/bin/sh +# save-jobstats.sh -- save uslims3_data job_statistics.xml files + +BASEDIR=/srv/www/htdocs/uslims3/uslims3_data +SAVEDIR=/srv/www/htdocs/uslims3/job_stats +STATFILE=job_statistics.xml +if [ ! -d ${SAVEDIR} ]; then + mkdir ${SAVEDIR} +fi +HOSTNAME=`uname -n` +echo "HOSTNAME=${HOSTNAME}" + +##JSTIME=`stat ${SAVEDIR} -c %Y` +JSTIME=`date +%s` +##echo "JSTIME=${JSTIME}" +NCFILE=0 +NMFILE=0 +ONEDAY=86400 # 24-hours worth of seconds + +# Get uslims3_data subdirectories +cd ${BASEDIR} +DATADIRS=`ls -rtF|tail -500|grep '/'` +##DATADIRS=`ls -rtF|tail -200|grep '/'` + +for D in $DATADIRS ; do + # Change to job subdirectory + JDTIME=`stat ${D} -c %Y` + AGE=`expr ${JSTIME} - ${JDTIME}` +##echo "D=${D}" +##echo " JDTIME=${JDTIME}" +##echo " AGE=${AGE}" + + # Only process directories less than a day old + if [ ${AGE} -lt ${ONEDAY} ]; then + JDDATE=`stat ${D} -c %y | cut -d: -f1-2 | sed -e 's/ /-/' -e 's/://g'` + cd ${BASEDIR}/${D} +##echo " +++Less than 1 day old+++" + + if [ -f ${STATFILE} ]; then + # Build job stats if job_statistics.xml exists + PART1A=`grep cluster= ${STATFILE}|sed -e 's/^.*cluster=\"//'|cut -d'"' -f1` + PART1A=`echo ${PART1A} | sed -e 's@-@_@'` + PART1B=`echo ${D} | cut -d'-' -f1` + PART1=${PART1A}-${PART1B} + PART2=`grep submittime= ${STATFILE}|sed -e 's/^.*submittime=\"//'|cut -d' ' -f1` + PART2=`echo ${PART2}|sed -e 's/\-//g'` + SOUTFILE=${SAVEDIR}/${PART1}-${PART2}-${STATFILE} +##echo "we can build: ${SOUTFILE}" + if [ ! -f ${SOUTFILE} ]; then + echo "cp -p ${STATFILE} ${SOUTFILE}" + cp -p ${STATFILE} ${SOUTFILE} + NCFILE=`expr ${NCFILE} + 1` + fi + else + CLUST=`grep shortname ${BASEDIR}/${D}hpcr*xml|cut -d'"' -f4` + echo "job_statistics.xml in ${D} [ ${JDDATE} ${CLUST} ] does not exist!" + NMFILE=`expr ${NMFILE} + 1` + fi + fi + + # Change back to ./uslims3_data + cd ${BASEDIR} +done + +echo "job_stats+++ Files Created: ${NCFILE}" +echo "jobxml/stats Files Missing: ${NMFILE} (aborted,running jobs?)" + Index: trunk/update_notice.php =================================================================== --- trunk/update_notice.php (revision 7) +++ trunk/update_notice.php (revision 7) @@ -0,0 +1,198 @@ + $s_rev2 ) + $sysrev = $s_rev1; +$sysrev = "3.3." . $sysrev; + +// Global variables +$notice_db = "us3_notice"; +$dbhost = "localhost"; +$dbuser = "root"; +//$dbpassw = exec( "cat ~us3/.sec/.pwsq" ); +$dbpassw = exec( "cat ~/.sec/.pwsq" ); + +// Produce some output temporarily, so cron will send me message +$now = time(); +echo "Time started: " . date( 'Y-m-d H:i:s', $now ) . "\n"; + +// Read and parse the local notice file + +$n_fname = "$us3etc/us3-notice.xml"; +$fh = fopen( $n_fname, "r" ); +$xml = fread( $fh, filesize( $n_fname ) ); + +$parser = new XMLReader(); +$parser->xml( $xml ); + +$notices = array(); +$keys = array(); + +echo "=====START of PARSE LOOP===== \n"; +while( $parser->read() ) +{ + $n_type = $parser->nodeType; +//echo "n_type=$n_type \n"; + + if ( $n_type == XMLReader::ELEMENT ) + { + $name = $parser->name; +//echo "name=$name \n"; + + if ( $name == "notice" ) + { + $type = $parser->getAttribute( "type" ); +//echo " type=$type \n"; + $parser->moveToAttribute( "revision" ); + $rev = $parser->value; +//echo " rev=$rev \n"; + if ( $rev == "latest" ) + $rev = $sysrev; +//echo " rev=$rev \n"; + + $key = $type . $rev; + $notices[ $key ] = array(); +//echo " key=$key \n"; + } + } + + else if ( $n_type == XMLReader::TEXT ) + { + $msg = $parser->readString(); +//echo " msg=+++$msg+++ \n"; + $len = strlen( $msg ); + + if ( $len > 0 ) + { // Only add if not an empty message + $msg = preg_replace( "/\@revision/", $rev, $msg ); + $msg = preg_replace( "/'/", "\\'", $msg ); + $notices[ $key ][ 'type' ] = $type; + $notices[ $key ][ 'rev' ] = $rev; + $notices[ $key ][ 'msg' ] = $msg; + $notices[ $key ][ 'act' ] = 'add'; + $notices[ $key ][ 'id' ] = '0'; + + $keys[] = $key; + } + } +} + +$parser->close(); +echo "=====END of PARSE LOOP===== \n"; + +// Get data from notice DB. Update the action field to +// reflect which action is required on each entry: +// "add" - is only present in file (add to DB); +// "del" - is only present in DB (delete from DB); +// "upd" - present in both, but messages differ (update in DB); +// "none" - present in both and messages identical (no DB update). + +$noteLink = mysql_connect( $dbhost, $dbuser, $dbpassw ); + +if ( ! mysql_select_db( $notice_db, $noteLink ) ) +{ + echo "Could not select DB $notice_db - " . mysql_error() . "\n"; + exit(); +} + +$query = "SELECT id, type, revision, message FROM notice"; + +$result = mysql_query( $query, $noteLink ) + or die( "Query failed : $query
" . mysql_error() ); + +echo "=====START of DB QUERY LOOP===== \n"; +$num_rows = mysql_num_rows( $result ); + +echo " numrows = $num_rows \n"; +while ( list( $id, $type, $rev, $msg ) = mysql_fetch_array( $result ) ) +{ + $key = $type . $rev; + $msgf = $notices[ $key ][ 'msg' ]; + + if ( in_array( $key, $keys ) ) + { // Entry is in both file and DB + $notices[ $key ][ 'id' ] = $id; + $notices[ $key ][ 'type' ] = $type; + $notices[ $key ][ 'rev' ] = $rev; + + if ( strcmp( $msg, $msgf ) == 0 ) + { // Messages match, so no update is needed + $notices[ $key ][ 'act' ] = 'none'; + } + else + { // Messages differ, so DB entry must be updated + $notices[ $key ][ 'act' ] = 'upd'; + $notices[ $key ][ 'msg' ] = $msgf; +echo " msg = ++$msg++\n"; +echo " msgf = ++$msgf++\n"; + } + } + + else + { // Entry is only in DB, so a delete is needed + $notices[ $key ] = array(); + $notices[ $key ][ 'id' ] = $id; + $notices[ $key ][ 'type' ] = $type; + $notices[ $key ][ 'rev' ] = $rev; + $notices[ $key ][ 'act' ] = 'del'; + $notices[ $key ][ 'msg' ] = $msg; + $keys[] = $key; + } +} +echo "=====END of DB QUERY LOOP===== \n"; + +echo "=====START of DB Update LOOP===== \n"; +foreach ( $keys as $key ) +{ + $type = $notices[ $key ][ 'type' ]; + $rev = $notices[ $key ][ 'rev' ]; + $act = $notices[ $key ][ 'act' ]; + $id = $notices[ $key ][ 'id' ]; + $msg = $notices[ $key ][ 'msg' ]; + $len = strlen( $msg ); + echo "-- key=$key --\n"; + echo " type: $type \n"; + echo " rev: $rev \n"; + echo " act: $act \n"; + echo " id: $id \n"; +// echo " msg: $msg \n"; + echo " msg: ( $len characters ) \n"; + + if ( $act == "add" ) + { // Must add the entry to the database + $query = "INSERT INTO notice " . + "SET type='$type', revision='$rev', message='$msg'"; + } + else if ( $act == "del" ) + { // Must delete the entry from the database + $query = "DELETE FROM notice WHERE id='$id'"; + } + else if ( $act == "upd" ) + { // Must update an existing entry in the database + $query = "UPDATE notice " . + "SET message='$msg' " . + "WHERE id='$id'"; + } + echo " query: [ $query ] \n"; + + $result = mysql_query( $query, $noteLink ) + or die( "Query failed : $query
" . mysql_error() ); + +} +echo "=====END of DB Update LOOP===== \n"; + +?> Index: trunk/us3-listen =================================================================== --- trunk/us3-listen (revision 7) +++ trunk/us3-listen (revision 7) @@ -0,0 +1,47 @@ +#!/bin/sh +######################################################################## +# Begin $rc_base/init.d/ +# +# Description : gridctl us3-listen daemons (listen, manage-us3-pipe) +# +# Authors : Gary Gorbet +# +# Version : 01.01 +# +# Notes : Goes in /etc/rc.d/init.d +# +######################################################################## + +. /etc/init.d/functions + +case "${1}" in + start) + echo -n "Starting us3-listen daemons ..." + /usr/bin/php ~us3/bin/listen.php & + echo "" + sleep 1 + ${0} status + ;; + + stop) + echo -n "Stopping us3-listen daemons ..." + killproc /usr/bin/php + ;; + + restart) + ${0} stop + sleep 1 + ${0} start + ;; + + status) + ps -aef|grep -v grep|egrep 'listen.php|us3-pipe' + ;; + + *) + echo "Usage: ${0} {start|stop|restart|status}" + exit 1 + ;; +esac + +# End $rc_base/init.d/ Index: trunk/us3-notice.php =================================================================== --- trunk/us3-notice.php (revision 7) +++ trunk/us3-notice.php (revision 7) @@ -0,0 +1,4 @@ +$us3bin = exec( "ls -d ~us3/bin" ); +include_once "$us3bin/listen-config.php"; +include "$us3bin/cleanup_aira.php"; +include "$us3bin/cleanup_gfac.php";