source: trunk/cleanup_gfac.php@ 34

Last change on this file since 34 was 25, checked in by gegorbet, 8 years ago

merge us3iab/airavata gridctl code
  • Property svn:keywords set to LastChangedDate Author
File size: 22.3 KB
RevLine 
[7]1<?php
2/*
3 * cleanup_gfac.php
4 *
5 * functions relating to copying results and cleaning up the gfac DB
6 *
7 */
8
[18]9$us3bin = exec( "ls -d ~us3/lims/bin" );
[7]10include_once "$us3bin/listen-config.php";
11$me = 'cleanup_gfac.php';
12$email_address = '';
13$queuestatus = '';
14$jobtype = '';
15$db = '';
16$editXMLFilename = '';
17$status = '';
18
19function gfac_cleanup( $us3_db, $reqID, $gfac_link )
20{
21 global $dbhost;
22 global $user;
23 global $passwd;
24 global $db;
25 global $guser;
26 global $gpasswd;
27 global $gDB;
28 global $me;
29 global $work;
30 global $email_address;
31 global $queuestatus;
32 global $jobtype;
33 global $editXMLFilename;
34 global $submittime;
35 global $status;
36 global $stdout;
37 global $requestID;
38
39 $requestID = $reqID;
40 $db = $us3_db;
41 write_log( "$me: debug db=$db; requestID=$requestID" );
42
43 $us3_link = mysql_connect( $dbhost, $user, $passwd );
44
45 if ( ! $us3_link )
46 {
47 write_log( "$me: could not connect: $dbhost, $user, $passwd" );
48 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" );
49 return( -1 );
50 }
51
52 $result = mysql_select_db( $db, $us3_link );
53
54 if ( ! $result )
55 {
56 write_log( "$me: could not select DB $db" );
57 mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" );
58 return( -1 );
59 }
60
61 // First get basic info for email messages
62 $query = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " .
63 "WHERE HPCAnalysisRequestID=$requestID";
64 $result = mysql_query( $query, $us3_link );
65
66 if ( ! $result )
67 {
68 write_log( "$me: Bad query: $query" );
69 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
70 return( -1 );
71 }
72
73 list( $email_address, $investigatorGUID, $editXMLFilename ) = mysql_fetch_array( $result );
74
75 $query = "SELECT personID FROM people " .
76 "WHERE personGUID='$investigatorGUID'";
77 $result = mysql_query( $query, $us3_link );
78
79 list( $personID ) = mysql_fetch_array( $result );
80
81 /*
82 $query = "SELECT clusterName, submitTime, queueStatus, method " .
83 "FROM HPCAnalysisRequest h LEFT JOIN HPCAnalysisResult " .
84 "ON h.HPCAnalysisRequestID=HPCAnalysisResult.HPCAnalysisRequestID " .
85 "WHERE h.HPCAnalysisRequestID=$requestID";
86 */
87 $query = "SELECT clusterName, submitTime, queueStatus, method " .
88 "FROM HPCAnalysisRequest h, HPCAnalysisResult r " .
89 "WHERE h.HPCAnalysisRequestID=$requestID " .
90 "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID";
91
92 $result = mysql_query( $query, $us3_link );
93
94 if ( ! $result )
95 {
96 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
97 return( -1 );
98 }
99
100 if ( mysql_num_rows( $result ) == 0 )
101 {
102 write_log( "$me: US3 Table error - No records for requestID: $requestID" );
103 return( -1 );
104 }
105
106 list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result );
107
108 // Get the GFAC ID
109 $query = "SELECT HPCAnalysisResultID, gfacID FROM HPCAnalysisResult " .
110 "WHERE HPCAnalysisRequestID=$requestID";
111
112 $result = mysql_query( $query, $us3_link );
113
114 if ( ! $result )
115 {
116 write_log( "$me: Bad query: $query" );
117 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
118 return( -1 );
119 }
120
121 list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result );
122
123 ////////
124 // Get data from global GFAC DB and insert it into US3 DB
125 // $gfac_link = mysql_connect( $dbhost, $guser, $gpasswd );
126
127 $result = mysql_select_db( $gDB, $gfac_link );
128
129 if ( ! $result )
130 {
131 write_log( "$me: Could not connect to DB $gDB" );
132 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" );
133 return( -1 );
134 }
135
136 $query = "SELECT status, cluster, id FROM analysis " .
137 "WHERE gfacID='$gfacID'";
138
139 $result = mysql_query( $query, $gfac_link );
140 if ( ! $result )
141 {
142 write_log( "$me: Could not select GFAC status for $gfacID" );
143 mail_to_user( "fail", "Could not select GFAC status for $gfacID" );
144 return( -1 );
145 }
146
147 $num_rows = mysql_num_rows( $result );
148 if ( $num_rows == 0 )
149 {
150 write_log( "$me: Cleanup analysis query found 0 entries for $gfacID" );
151 return( 0 );
152 }
153//else
154//{
155//write_log( "$me: db=$db; num_rows=$num_rows; queuestatus=$queuestatus" );
156//}
157
158 list( $status, $cluster, $id ) = mysql_fetch_array( $result );
159//write_log( "$me: db=$db; requestID=$requestID; status=$status; cluster=$cluster" );
160
[25]161// if ( $cluster == 'bcf-local' || $cluster == 'alamo-local' )
162 if ( preg_match( "/\-local/", $cluster ) ||
163 preg_match( "/us3iab/", $cluster ) )
[7]164 {
[25]165// $clushost = $cluster;
166// $clushost = preg_replace( "/\-local/", "", $clushost );
167 $parts = explode( "-", $cluster );
168 $clushost = $parts[ 0 ];
[7]169 get_local_files( $gfac_link, $clushost, $requestID, $id, $gfacID );
[25]170write_log( "$me: clushost=$clushost reqID=$requestID get_local_files() gfacID=$gfacID" );
[7]171 }
[25]172else
173write_log( "$me: NO get_local_files()" );
[7]174
175 $query = "SELECT id, stderr, stdout, tarfile FROM analysis " .
176 "WHERE gfacID='$gfacID'";
177
178 $result = mysql_query( $query, $gfac_link );
179
180 if ( ! $result )
181 {
182 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
183 mail_to_user( "fail", "Internal error " . mysql_error( $gfac_link ) );
184 return( -1 );
185 }
186
187 $num_rows = mysql_num_rows( $result );
188 if ( $num_rows == 0 )
189 {
190 write_log( "$me: Cleanup analysis query found 0 entries for $gfacID" );
191 return( 0 );
192 }
193
194 list( $analysisID, $stderr, $stdout, $tarfile ) = mysql_fetch_array( $result );
195
196 if ( strlen( $tarfile ) > 0 )
197 { // Log success at fetch attempt
198 write_log( "$me: Successful data fetch: $requestID $gfacID" );
199 }
200 else
201 { // Log failure at fetch attempt
202 write_log( "$me: Failed data fetch: $requestID $gfacID" );
203 if ( $analysisID == '' )
204 $analysisID = '0';
205 }
206
207 // Save queue messages for post-mortem analysis
208 $query = "SELECT message, time FROM queue_messages " .
209 "WHERE analysisID = $analysisID " .
210 "ORDER BY time ";
211 $result = mysql_query( $query, $gfac_link );
212
213 if ( ! $result )
214 {
215 // Just log it and continue
216 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
217 }
218
219 $now = date( 'Y-m-d H:i:s' );
220 $message_log = "US3 DB: $db\n" .
221 "RequestID: $requestID\n" .
222 "GFAC ID: $gfacID\n" .
223 "Processed: $now\n\n" .
224 "Queue Messages\n\n" ;
225
226 $need_finish = ( $status == 'COMPLETE' );
227
228 if ( mysql_num_rows( $result ) > 0 )
229 {
230 $time_msg = time();
231 while ( list( $message, $time ) = mysql_fetch_array( $result ) )
232 {
233//write_log( "$me: message=$message" );
234 $message_log .= "$time $message\n";
235 if ( preg_match( "/^Finished/i", $message ) )
236 $need_finish = false;
237 $time_msg = strtotime( $time );
238 }
239
240 if ( $need_finish )
241 { // No 'Finished' yet: forget if too much time has passed
242 $time_now = time();
243 $tdelta = $time_now - $time_msg;
244write_log( "$me: no-Finish time: tnow=$time_now, tmsg=$time_msg, tdelt=$tdelta" );
245 if ( $tdelta > 600 )
246 $need_finish = false;
247 }
248//write_log( "$me: no-Finish time: tnow=$time_now, tmsg=$time_msg, tdelt=$tdelta" );
249 }
250 else
251 {
252 write_log( "$me: No messages for analysisID=$analysisID ." );
253 $need_finish = false;
254 }
255
256 if ( $need_finish )
257 {
258 write_log( "$me: Cleanup has not yet found 'Finished' for $gfacID" );
259 return( 0 );
260 }
261
262 $query = "DELETE FROM queue_messages " .
263 "WHERE analysisID = $analysisID ";
264
265 $result = mysql_query( $query, $gfac_link );
266
267 if ( ! $result )
268 {
269 // Just log it and continue
270 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
271 }
272
273 // Save stdout, stderr, etc. for message log
274 $query = "SELECT stdout, stderr, status, queue_msg FROM analysis " .
275 "WHERE gfacID='$gfacID' ";
276 $result = mysql_query( $query, $gfac_link );
277 try
278 {
279 // What if this is too large?
280 list( $stdout, $stderr, $status, $queue_msg ) = mysql_fetch_array( $result );
281 }
282 catch ( Exception $e )
283 {
284 write_log( "$me: stdout + stderr larger than 128M - $gfacID\n" . mysql_error( $gfac_link ) );
285 // Just go ahead and clean up
286 }
287
288 // But let's allow for investigation of other large stdout and/or stderr
289 if ( strlen( $stdout ) > 20480000 ||
290 strlen( $stderr ) > 20480000 )
291 write_log( "$me: stdout + stderr larger than 20M - $gfacID\n" );
292
293 $message_log .= "\n\n\nStdout Contents\n\n" .
294 $stdout .
295 "\n\n\nStderr Contents\n\n" .
296 $stderr .
297 "\n\n\nGFAC Status: $status\n" .
298 "GFAC message field: $queue_msg\n";
299
300 // Delete data from GFAC DB
301 $query = "DELETE from analysis WHERE gfacID='$gfacID'";
302
303 $result = mysql_query( $query, $gfac_link );
304
305 if ( ! $result )
306 {
307 // Just log it and continue
308 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
309 }
310write_log( "$me: GFAC DB entry deleted" );
311
312 // Copy queue messages to LIMS submit directory (files there are deleted after 7 days)
313 global $submit_dir;
314
315 // Get the request guid (LIMS submit dir name)
316 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
317 "WHERE HPCAnalysisRequestID = $requestID ";
318 $result = mysql_query( $query, $us3_link );
319
320 if ( ! $result )
321 {
322 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
323 }
324
325 list( $requestGUID ) = mysql_fetch_array( $result );
326 $output_dir = "$submit_dir/$requestGUID";
327write_log( "$me: Output dir determined: $output_dir" );
328
329 // Try to create it if necessary, and write the file
330 // Let's use FILE_APPEND, in case this is the second time around and the
331 // GFAC job status was INSERTed, rather than UPDATEd
332 if ( ! is_dir( $output_dir ) )
333 mkdir( $output_dir, 0775, true );
334 $message_filename = "$output_dir/$db-$requestID-messages.txt";
335 file_put_contents( $message_filename, $message_log, FILE_APPEND );
336 // mysql_close( $gfac_link );
[25]337write_log( "$me: *messages.txt written" );
[7]338
339 /////////
340 // Insert data into HPCAnalysis
341
342 $query = "UPDATE HPCAnalysisResult SET " .
343 "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " .
344 "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "' " .
345 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
346
347 $result = mysql_query( $query, $us3_link );
348
349 if ( ! $result )
350 {
351 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
352 mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) );
353 return( -1 );
354 }
355
356 // Save the tarfile and expand it
357
358 if ( strlen( $tarfile ) == 0 )
359 {
360 write_log( "$me: No tarfile" );
361 mail_to_user( "fail", "No results" );
362 return( -1 );
363 }
364
365 // Shouldn't happen
366 if ( ! is_dir( "$work" ) )
367 {
368 write_log( "$me: $work directory does not exist" );
369 mail_to_user( "fail", "$work directory does not exist" );
370 return( -1 );
371 }
372
373 if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
374 chdir( "$work/$gfacID" );
375
[25]376 $f = fopen( "analysis-results.tar", "w" );
[7]377 fwrite( $f, $tarfile );
378 fclose( $f );
[25]379//write_log( "$me: analysis-results.tar file written to work dir" );
[7]380
381 $tar_out = array();
[25]382 exec( "tar -xf analysis-results.tar 2>&1", $tar_out, $err );
[7]383
384 if ( $err != 0 )
385 {
386 chdir( $work );
387 exec( "rm -r $gfacID" );
388 $output = implode( "\n", $tar_out );
389
390 write_log( "$me: Bad output tarfile: $output" );
391 mail_to_user( "fail", "Bad output file" );
392 return( -1 );
393 }
394//write_log( "$me: tar files extracted" );
395
396 // Insert the model files and noise files
397 $files = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES );
398 $noiseIDs = array();
399 $modelGUIDs = array();
400 $mrecsIDs = array();
401 $rmodlGUIDs = array();
402
403 foreach ( $files as $file )
404 {
405 $split = explode( ";", $file );
406
407 if ( count( $split ) > 1 )
408 {
409 list( $fn, $meniscus, $mc_iteration, $variance ) = explode( ";", $file );
410
411 list( $other, $mc_iteration ) = explode( "=", $mc_iteration );
412 list( $other, $variance ) = explode( "=", $variance );
413 list( $other, $meniscus ) = explode( "=", $meniscus );
414 }
415 else
416 $fn = $file;
417
418 if ( preg_match( "/mdl.tmp$/", $fn ) )
419 continue;
420
421 if ( filesize( $fn ) < 100 )
422 {
423 write_log( "$me:fn is invalid $fn" );
424 mail_to_user( "fail", "Internal error\n$fn is invalid" );
425 return( -1 );
426 }
427//write_log( "$me: handling file: $fn" );
428
429 if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file
430 {
431 $xml = file_get_contents( $fn );
432 $statistics = parse_xml( $xml, 'statistics' );
433 $otherdata = parse_xml( $xml, 'id' );
434
435 $query = "UPDATE HPCAnalysisResult SET " .
436 "wallTime = {$statistics['walltime']}, " .
437 "CPUTime = {$statistics['cputime']}, " .
438 "CPUCount = {$statistics['cpucount']}, " .
439 "max_rss = {$statistics['maxmemory']}, " .
440 "startTime = '{$otherdata['starttime']}', " .
441 "endTime = '{$otherdata['endtime']}', " .
442 "mgroupcount = {$otherdata['groupcount']} " .
443 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
444 $result = mysql_query( $query, $us3_link );
445
446 if ( ! $result )
447 {
448 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
449 }
450
451 file_put_contents( "$output_dir/$fn", $xml ); // Copy to submit dir
452 $file_type = "job_stats";
453//write_log( "$me: job_statistics file updated in Result and written" );
454
455 }
456
457 else if ( preg_match( "/\.noise/", $fn ) > 0 ) // It's a noise file
458 {
459 $xml = file_get_contents( $fn );
460 $noise_data = parse_xml( $xml, "noise" );
461 $type = ( $noise_data[ 'type' ] == "ri" ) ? "ri_noise" : "ti_noise";
462 $desc = $noise_data[ 'description' ];
463 $modelGUID = $noise_data[ 'modelGUID' ];
464 $noiseGUID = $noise_data[ 'noiseGUID' ];
465
466 $query = "INSERT INTO noise SET " .
467 "noiseGUID='$noiseGUID'," .
468 "modelGUID='$modelGUID'," .
[25]469 "editedDataID=2, " .
[7]470 "modelID=1, " .
471 "noiseType='$type'," .
472 "description='$desc'," .
473 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
474
475 // Add later after all files are processed: editDataID, modelID
476
477 $result = mysql_query( $query, $us3_link );
478
479 if ( ! $result )
480 {
481 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
482 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
483 return( -1 );
484 }
485
486 $id = mysql_insert_id( $us3_link );
487 $file_type = "noise";
488 $noiseIDs[] = $id;
489
490 // Keep track of modelGUIDs for later, when we replace them
491 $modelGUIDs[ $id ] = $modelGUID;
492//write_log( "$me: noise file inserted into DB : id=$id" );
493
494 }
495
496 else if ( preg_match( "/\.mrecs/", $fn ) > 0 ) // It's an mrecs file
497 {
498 $xml = file_get_contents( $fn );
499 $mrecs_data = parse_xml( $xml, "modelrecords" );
500 $desc = $mrecs_data[ 'description' ];
501 $editGUID = $mrecs_data[ 'editGUID' ];
502write_log( "$me: mrecs file editGUID=$editGUID" );
503 if ( strlen( $editGUID ) < 36 )
504 $editGUID = "12345678-0123-5678-0123-567890123456";
505 $mrecGUID = $mrecs_data[ 'mrecGUID' ];
506 $modelGUID = $mrecs_data[ 'modelGUID' ];
507
508 $query = "INSERT INTO pcsa_modelrecs SET " .
509 "editedDataID=" .
510 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
511 "modelID=0, " .
512 "mrecsGUID='$mrecGUID'," .
513 "description='$desc'," .
514 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
515
516 // Add later after all files are processed: editDataID, modelID
517
518 $result = mysql_query( $query, $us3_link );
519
520 if ( ! $result )
521 {
522 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
523 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
524 return( -1 );
525 }
526
527 $id = mysql_insert_id( $us3_link );
528 $file_type = "mrecs";
529 $mrecsIDs[] = $id;
530
531 // Keep track of modelGUIDs for later, when we replace them
532 $rmodlGUIDs[ $id ] = $modelGUID;
533//write_log( "$me: mrecs file inserted into DB : id=$id" );
534 }
535
[23]536 else if ( preg_match( "/\.model/", $fn ) > 0 ) // It's a model file
[7]537 {
538 $xml = file_get_contents( $fn );
539 $model_data = parse_xml( $xml, "model" );
540 $description = $model_data[ 'description' ];
541 $modelGUID = $model_data[ 'modelGUID' ];
542 $editGUID = $model_data[ 'editGUID' ];
543
544 if ( $mc_iteration > 1 )
545 {
546//write_log( "$me: MODELUpd: mc_iteration=$mc_iteration" );
547 $miter = sprintf( "_mcN%03d", $mc_iteration );
548//write_log( "$me: MODELUpd: miter=$miter" );
549//write_log( "$me: MODELUpd: I:description=$description" );
550 $description = preg_replace( "/_mc[0-9]+/", $miter, $description );
551write_log( "$me: MODELUpd: O:description=$description" );
552 }
553
554 $query = "INSERT INTO model SET " .
555 "modelGUID='$modelGUID'," .
556 "editedDataID=" .
557 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
558 "description='$description'," .
559 "MCIteration='$mc_iteration'," .
560 "meniscus='$meniscus'," .
561 "variance='$variance'," .
562 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
563
564 $result = mysql_query( $query, $us3_link );
565
566 if ( ! $result )
567 {
568 write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) );
569 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
570 return( -1 );
571 }
572
573 $modelID = mysql_insert_id( $us3_link );
574 $id = $modelID;
575 $file_type = "model";
576
577 $query = "INSERT INTO modelPerson SET " .
578 "modelID=$modelID, personID=$personID";
579 $result = mysql_query( $query, $us3_link );
580//write_log( "$me: model file inserted into DB : id=$id" );
581 }
582
583 $query = "INSERT INTO HPCAnalysisResultData SET " .
584 "HPCAnalysisResultID='$HPCAnalysisResultID', " .
585 "HPCAnalysisResultType='$file_type', " .
586 "resultID=$id";
587
588 $result = mysql_query( $query, $us3_link );
589
590 if ( ! $result )
591 {
592 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
593 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
594 return( -1 );
595 }
596//write_log( "$me: ResultData updated : file_type=$file_type" );
597 }
598
599 // Now fix up noise entries
600 // For noise files, there is, at most two: ti_noise and ri_noise
601 // In this case there will only be one modelID
602
603 foreach ( $noiseIDs as $noiseID )
604 {
605 $modelGUID = $modelGUIDs[ $noiseID ];
606 $query = "UPDATE noise SET " .
607 "editedDataID=" .
608 "(SELECT editedDataID FROM model WHERE modelGUID='$modelGUID')," .
609 "modelID=" .
610 "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
611 "WHERE noiseID=$noiseID";
612
613 $result = mysql_query( $query, $us3_link );
614
615 if ( ! $result )
616 {
617 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
618 mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
619 return( -1 );
620 }
621//write_log( "$me: noise entry updated : noiseID=$noiseID" );
622 }
623//write_log( "$me: noise entries updated" );
624
625 // Now possibly fix up mrecs entries
626
627 foreach ( $mrecsIDs as $mrecsID )
628 {
629 $modelGUID = $rmodlGUIDs[ $mrecsID ];
630 $query = "UPDATE pcsa_modelrecs SET " .
631 "modelID=" .
632 "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
633 "WHERE mrecsID=$mrecsID";
634
635 $result = mysql_query( $query, $us3_link );
636
637 if ( ! $result )
638 {
639 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
640 mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
641 return( -1 );
642 }
643//write_log( "$me: mrecs entry updated : mrecsID=$mrecsID" );
644 }
645//write_log( "$me: mrecs entries updated" );
646
647 // Copy results to LIMS submit directory (files there are deleted after 7 days)
648 global $submit_dir; // LIMS submit files dir
649
650 // Get the request guid (LIMS submit dir name)
651 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
652 "WHERE HPCAnalysisRequestID = $requestID ";
653 $result = mysql_query( $query, $us3_link );
654
655 if ( ! $result )
656 {
657 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
658 }
659
660 list( $requestGUID ) = mysql_fetch_array( $result );
661
662 chdir( "$submit_dir/$requestGUID" );
663 $f = fopen( "analysis.tar", "w" );
664 fwrite( $f, $tarfile );
665 fclose( $f );
666
667 // Clean up
668 chdir ( $work );
669 // exec( "rm -rf $gfacID" );
670
671 mysql_close( $us3_link );
672
673 /////////
674 // Send email
675
676 mail_to_user( "success", "" );
677}
678?>
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