source: trunk/cleanup.php@ 26

Last change on this file since 26 was 26, checked in by gegorbet, 7 years ago

various minor fixes/mods to gridctl
File size: 30.5 KB
Line 
1<?php
2/*
3 * cleanup.php
4 *
5 * functions relating to copying results and cleaning up the gfac DB
6 * where the job used an Airavata interface.
7 *
8 */
9
10$email_address = '';
11$queuestatus = '';
12$jobtype = '';
13$db = '';
14$editXMLFilename = '';
15$status = '';
16
17function aira_cleanup( $us3_db, $reqID, $gfac_link )
18{
19 global $org_domain;
20 global $dbhost;
21 global $user;
22 global $passwd;
23 global $db;
24 global $guser;
25 global $gpasswd;
26 global $gDB;
27 global $me;
28 global $work;
29 global $email_address;
30 global $queuestatus;
31 global $jobtype;
32 global $editXMLFilename;
33 global $submittime;
34 global $status;
35 global $stderr;
36 global $stdout;
37 global $tarfile;
38 global $requestID;
39 global $submit_dir;
40 $me = 'cleanup_aira.php';
41
42 $requestID = $reqID;
43 $db = $us3_db;
44 write_log( "$me: debug db=$db; requestID=$requestID" );
45
46 $us3_link = mysql_connect( $dbhost, $user, $passwd );
47
48 if ( ! $us3_link )
49 {
50 write_log( "$me: could not connect: $dbhost, $user, $passwd" );
51 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" );
52 return( -1 );
53 }
54
55 $result = mysql_select_db( $db, $us3_link );
56
57 if ( ! $result )
58 {
59 write_log( "$me: could not select DB $db" );
60 mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" );
61 return( -1 );
62 }
63
64 // First get basic info for email messages
65 $query = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " .
66 "WHERE HPCAnalysisRequestID=$requestID";
67 $result = mysql_query( $query, $us3_link );
68
69 if ( ! $result )
70 {
71 write_log( "$me: Bad query: $query" );
72 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
73 return( -1 );
74 }
75
76 list( $email_address, $investigatorGUID, $editXMLFilename ) = mysql_fetch_array( $result );
77
78 $query = "SELECT personID FROM people " .
79 "WHERE personGUID='$investigatorGUID'";
80 $result = mysql_query( $query, $us3_link );
81
82 list( $personID ) = mysql_fetch_array( $result );
83
84 $query = "SELECT clusterName, submitTime, queueStatus, method " .
85 "FROM HPCAnalysisRequest h, HPCAnalysisResult r " .
86 "WHERE h.HPCAnalysisRequestID=$requestID " .
87 "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID";
88
89 $result = mysql_query( $query, $us3_link );
90
91 if ( ! $result )
92 {
93 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
94 return( -1 );
95 }
96
97 if ( mysql_num_rows( $result ) == 0 )
98 {
99 write_log( "$me: US3 Table error - No records for requestID: $requestID" );
100 return( -1 );
101 }
102
103 list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result );
104
105 // Get the GFAC ID
106 $query = "SELECT HPCAnalysisResultID, gfacID FROM HPCAnalysisResult " .
107 "WHERE HPCAnalysisRequestID=$requestID";
108
109 $result = mysql_query( $query, $us3_link );
110
111 if ( ! $result )
112 {
113 write_log( "$me: Bad query: $query" );
114 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
115 return( -1 );
116 }
117
118 list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result );
119
120 // Get data from global GFAC DB then insert it into US3 DB
121
122 $result = mysql_select_db( $gDB, $gfac_link );
123
124 if ( ! $result )
125 {
126 write_log( "$me: Could not connect to DB $gDB" );
127 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" );
128 return( -1 );
129 }
130
131 $query = "SELECT status, cluster, id FROM analysis " .
132 "WHERE gfacID='$gfacID'";
133
134 $result = mysql_query( $query, $gfac_link );
135 if ( ! $result )
136 {
137 write_log( "$me: Could not select GFAC status for $gfacID" );
138 mail_to_user( "fail", "Could not select GFAC status for $gfacID" );
139 return( -1 );
140 }
141
142 list( $status, $cluster, $id ) = mysql_fetch_array( $result );
143
144 $is_us3iab = preg_match( "/us3iab/", $cluster );
145 $is_local = preg_match( "/-local/", $cluster );
146
147 if ( $is_us3iab || $is_local )
148 {
149 $clushost = $cluster;
150 $clushost = preg_replace( "/\-local/", "", $clushost );
151 get_local_files( $gfac_link, $clushost, $requestID, $id, $gfacID );
152 }
153
154
155 $query = "SELECT id FROM analysis " .
156 "WHERE gfacID='$gfacID'";
157
158 $result = mysql_query( $query, $gfac_link );
159
160 if ( ! $result )
161 {
162 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
163 mail_to_user( "fail", "Internal error " . mysql_error( $gfac_link ) );
164 return( -1 );
165 }
166
167 list( $analysisID ) = mysql_fetch_array( $result );
168
169 // Get the request guid (LIMS submit dir name)
170 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
171 "WHERE HPCAnalysisRequestID = $requestID ";
172 $result = mysql_query( $query, $us3_link );
173
174 if ( ! $result )
175 {
176 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
177 }
178
179 list( $requestGUID ) = mysql_fetch_array( $result );
180 $output_dir = "$submit_dir/$requestGUID";
181
182 // Get stderr,stdout,tarfile from work directory
183 if ( ! is_dir( "$output_dir" ) ) mkdir( "$output_dir", 0770 );
184 chdir( "$output_dir" );
185//write_log( "$me: gfacID=$gfacID" );
186//write_log( "$me: submit_dir=$submit_dir" );
187//write_log( "$me: requestGUID=$requestGUID" );
188write_log( "$me: output_dir=$output_dir" );
189
190 $stderr = "";
191 $stdout = "";
192 $tarfile = "";
193 $fn_stderr = "Ultrascan.stderr";
194 $fn_stdout = "Ultrascan.stdout";
195 $fn_tarfile = "analysis-results.tar";
196 $num_try = 0;
197write_log( "$me: fn_tarfile=$fn_tarfile" );
198 while ( ! file_exists( $fn_tarfile ) && $num_try < 3 )
199 {
200 sleep( 10 );
201 $num_try++;
202write_log( "$me: tar-exists: num_try=$num_try" );
203 }
204
205 $ofiles = scandir( $output_dir );
206 foreach ( $ofiles as $ofile )
207 {
208 if ( preg_match( "/^" . $gfacID . ".*stderr$/", $ofile ) )
209 $fn_stderr = $ofile;
210 if ( preg_match( "/^" . $gfacID . ".*stdout$/", $ofile ) )
211 $fn_stdout = $ofile;
212//write_log( "$me: ofile=$ofile" );
213 }
214write_log( "$me: fn_stderr=$fn_stderr" );
215write_log( "$me: fn_stdout=$fn_stdout" );
216if (file_exists($fn_tarfile)) write_log( "$me: fn_tarfile=$fn_tarfile" );
217else write_log( "$me: NOT FOUND: $fn_tarfile" );
218
219 $stderr = '';
220 $stdout = '';
221 $tarfile = '';
222 if ( file_exists( $fn_stderr ) ) $stderr = file_get_contents( $fn_stderr );
223 if ( file_exists( $fn_stdout ) ) $stdout = file_get_contents( $fn_stdout );
224 if ( file_exists( $fn_tarfile ) ) $tarfile = file_get_contents( $fn_tarfile );
225 // If stdout,stderr have no content, retry after delay
226 if ( strlen( $stdout ) == 0 || strlen( $stderr ) == 0 )
227 {
228 sleep( 20 );
229 if ( file_exists( $fn_stderr ) )
230 $stderr = file_get_contents( $fn_stderr );
231 if ( file_exists( $fn_stdout ) )
232 $stdout = file_get_contents( $fn_stdout );
233 }
234
235write_log( "$me: length contents stderr,stdout,tarfile -- "
236 . strlen($stderr) . "," . strlen($stdout) . "," . strlen($tarfile) );
237
238 if ( $cluster == 'alamo' || $cluster == 'alamo-local' )
239 { // Filter "ipath_userinit" lines out of alamo stdout lines
240 $prefln = strlen( $stdout );
241 $output = array();
242 exec( "grep -v 'ipath_userinit' $fn_stdout 2>&1", $output, $err );
243 $stdout = implode( "\n", $output );
244 $posfln = strlen( $stdout );
245write_log( "$me: fn_stdout : filtered. Length $prefln -> $posfln ." );
246 }
247
248 // Save queue messages for post-mortem analysis
249 $query = "SELECT message, time FROM queue_messages " .
250 "WHERE analysisID = $analysisID " .
251 "ORDER BY time ";
252 $result = mysql_query( $query, $gfac_link );
253
254 if ( ! $result )
255 {
256 // Just log it and continue
257 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
258 }
259
260 $now = date( 'Y-m-d H:i:s' );
261 $message_log = "US3 DB: $db\n" .
262 "RequestID: $requestID\n" .
263 "GFAC ID: $gfacID\n" .
264 "Processed: $now\n\n" .
265 "Queue Messages\n\n" ;
266 if ( mysql_num_rows( $result ) > 0 )
267 {
268 while ( list( $message, $time ) = mysql_fetch_array( $result ) )
269 $message_log .= "$time $message\n";
270 }
271
272 $query = "DELETE FROM queue_messages " .
273 "WHERE analysisID = $analysisID ";
274
275 $result = mysql_query( $query, $gfac_link );
276
277 if ( ! $result )
278 {
279 // Just log it and continue
280 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
281 }
282
283 $query = "SELECT queue_msg FROM analysis " .
284 "WHERE gfacID='$gfacID' ";
285
286 $result = mysql_query( $query, $gfac_link );
287 list( $queue_msg ) = mysql_fetch_array( $result );
288
289 // But let's allow for investigation of other large stdout and/or stderr
290 if ( strlen( $stdout ) > 20480000 ||
291 strlen( $stderr ) > 20480000 )
292 write_log( "$me: stdout + stderr larger than 20M - $gfacID\n" );
293
294 $message_log .= "\n\n\nStdout Contents\n\n" .
295 $stdout .
296 "\n\n\nStderr Contents\n\n" .
297 $stderr .
298 "\n\n\nGFAC Status: $status\n" .
299 "GFAC message field: $queue_msg\n";
300
301 // Delete data from GFAC DB
302 $query = "DELETE from analysis WHERE gfacID='$gfacID'";
303
304 $result = mysql_query( $query, $gfac_link );
305
306 if ( ! $result )
307 {
308 // Just log it and continue
309 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
310 }
311
312
313 // Try to create it if necessary, and write the file
314 // Let's use FILE_APPEND, in case this is the second time around and the
315 // GFAC job status was INSERTed, rather than UPDATEd
316 if ( ! is_dir( $output_dir ) )
317 mkdir( $output_dir, 0775, true );
318 $message_filename = "$output_dir/$db-$requestID-messages.txt";
319 file_put_contents( $message_filename, $message_log, FILE_APPEND );
320 // mysql_close( $gfac_link );
321
322 /////////
323 // Insert data into HPCAnalysis
324
325 $query = "UPDATE HPCAnalysisResult SET " .
326 "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " .
327 "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "', " .
328 "queueStatus='completed' " .
329 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
330
331 $result = mysql_query( $query, $us3_link );
332
333 if ( ! $result )
334 {
335 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
336 mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) );
337 return( -1 );
338 }
339
340 // Delete data from GFAC DB
341 $query = "DELETE from analysis WHERE gfacID='$gfacID'";
342
343 $result = mysql_query( $query, $gfac_link );
344
345 if ( ! $result )
346 {
347 // Just log it and continue
348 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
349 }
350
351 // Expand the tar file
352
353 if ( strlen( $tarfile ) == 0 )
354 {
355 write_log( "$me: No tarfile" );
356 mail_to_user( "fail", "No results" );
357 return( -1 );
358 }
359
360 $tar_out = array();
361 exec( "tar -xf analysis-results.tar 2>&1", $tar_out, $err );
362
363 // Insert the model files and noise files
364 $files = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES );
365 $noiseIDs = array();
366 $modelGUIDs = array();
367 $mrecsIDs = array();
368 $fns_used = array();
369
370 foreach ( $files as $file )
371 {
372 $split = explode( ";", $file );
373
374 if ( count( $split ) > 1 )
375 {
376 list( $fn, $meniscus, $mc_iteration, $variance ) = explode( ";", $file );
377
378 list( $other, $mc_iteration ) = explode( "=", $mc_iteration );
379 list( $other, $variance ) = explode( "=", $variance );
380 list( $other, $meniscus ) = explode( "=", $meniscus );
381 }
382 else
383 $fn = $file;
384
385 if ( preg_match( "/mdl.tmp$/", $fn ) )
386 continue;
387
388 if ( in_array( $fn, $fns_used ) )
389 continue;
390
391 $fns_used[] = $fn;
392
393 if ( filesize( $fn ) < 100 )
394 {
395 write_log( "$me:fn is invalid $fn size filesize($fn)" );
396 mail_to_user( "fail", "Internal error\n$fn is invalid" );
397 return( -1 );
398 }
399
400 if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file
401 {
402 $xml = file_get_contents( $fn );
403 $statistics = parse_xml( $xml, 'statistics' );
404// $ntries = 0;
405//
406// while ( $statistics['cpucount'] < 1 && $ntries < 3 )
407// { // job_statistics file not totally copied, so retry
408// sleep( 10 );
409// $xml = file_get_contents( $fn );
410// $statistics = parse_xml( $xml, 'statistics' );
411// $ntries++;
412//write_log( "$me:jobstats retry $ntries" );
413// }
414//write_log( "$me:cputime=$statistics['cputime']" );
415
416 $otherdata = parse_xml( $xml, 'id' );
417
418 $query = "UPDATE HPCAnalysisResult SET " .
419 "wallTime = {$statistics['walltime']}, " .
420 "CPUTime = {$statistics['cputime']}, " .
421 "CPUCount = {$statistics['cpucount']}, " .
422 "max_rss = {$statistics['maxmemory']}, " .
423 "startTime = '{$otherdata['starttime']}', " .
424 "endTime = '{$otherdata['endtime']}', " .
425 "mgroupcount = {$otherdata['groupcount']} " .
426 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
427 $result = mysql_query( $query, $us3_link );
428
429 if ( ! $result )
430 {
431 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
432 }
433
434 file_put_contents( "$output_dir/$fn", $xml ); // Copy to submit dir
435
436 $file_type = "job_stats";
437 $id = 1;
438 }
439
440 else if ( preg_match( "/\.noise/", $fn ) > 0 ) // It's a noise file
441 {
442 $xml = file_get_contents( $fn );
443 $noise_data = parse_xml( $xml, "noise" );
444 $type = ( $noise_data[ 'type' ] == "ri" ) ? "ri_noise" : "ti_noise";
445 $desc = $noise_data[ 'description' ];
446 $modelGUID = $noise_data[ 'modelGUID' ];
447 $noiseGUID = $noise_data[ 'noiseGUID' ];
448
449 $query = "INSERT INTO noise SET " .
450 "noiseGUID='$noiseGUID'," .
451 "modelGUID='$modelGUID'," .
452 "editedDataID=1, " .
453 "modelID=1, " .
454 "noiseType='$type'," .
455 "description='$desc'," .
456 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
457
458 // Add later after all files are processed: editDataID, modelID
459
460 $result = mysql_query( $query, $us3_link );
461
462 if ( ! $result )
463 {
464 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
465 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
466 return( -1 );
467 }
468
469 $id = mysql_insert_id( $us3_link );
470 $file_type = "noise";
471 $noiseIDs[] = $id;
472
473 // Keep track of modelGUIDs for later, when we replace them
474 $modelGUIDs[ $id ] = $modelGUID;
475
476 }
477
478 else if ( preg_match( "/\.mrecs/", $fn ) > 0 ) // It's an mrecs file
479 {
480 $xml = file_get_contents( $fn );
481 $mrecs_data = parse_xml( $xml, "modelrecords" );
482 $desc = $mrecs_data[ 'description' ];
483 $editGUID = $mrecs_data[ 'editGUID' ];
484write_log( "$me: mrecs file editGUID=$editGUID" );
485 if ( strlen( $editGUID ) < 36 )
486 $editGUID = "12345678-0123-5678-0123-567890123456";
487 $mrecGUID = $mrecs_data[ 'mrecGUID' ];
488 $modelGUID = $mrecs_data[ 'modelGUID' ];
489
490 $query = "INSERT INTO pcsa_modelrecs SET " .
491 "editedDataID=" .
492 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
493 "modelID=0, " .
494 "mrecsGUID='$mrecGUID'," .
495 "description='$desc'," .
496 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
497
498 // Add later after all files are processed: editDataID, modelID
499
500 $result = mysql_query( $query, $us3_link );
501
502 if ( ! $result )
503 {
504 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
505 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
506 return( -1 );
507 }
508
509 $id = mysql_insert_id( $us3_link );
510 $file_type = "mrecs";
511 $mrecsIDs[] = $id;
512
513 // Keep track of modelGUIDs for later, when we replace them
514 $rmodlGUIDs[ $id ] = $modelGUID;
515//write_log( "$me: mrecs file inserted into DB : id=$id" );
516 }
517
518 else if ( preg_match( "/\.model/", $fn ) > 0 ) // It's a model file
519 {
520 $xml = file_get_contents( $fn );
521 $model_data = parse_xml( $xml, "model" );
522 $description = $model_data[ 'description' ];
523 $modelGUID = $model_data[ 'modelGUID' ];
524 $editGUID = $model_data[ 'editGUID' ];
525
526 if ( $mc_iteration > 1 )
527 {
528 $miter = sprintf( "_mcN%03d", $mc_iteration );
529 $description = preg_replace( "/_mc[0-9]+/", $miter, $description );
530write_log( "$me: MODELUpd: O:description=$description" );
531 }
532
533 $query = "INSERT INTO model SET " .
534 "modelGUID='$modelGUID'," .
535 "editedDataID=" .
536 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
537 "description='$description'," .
538 "MCIteration='$mc_iteration'," .
539 "meniscus='$meniscus'," .
540 "variance='$variance'," .
541 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
542
543 $result = mysql_query( $query, $us3_link );
544
545 if ( ! $result )
546 {
547 write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) );
548 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
549 return( -1 );
550 }
551
552 $modelID = mysql_insert_id( $us3_link );
553 $id = $modelID;
554 $file_type = "model";
555
556 $query = "INSERT INTO modelPerson SET " .
557 "modelID=$modelID, personID=$personID";
558 $result = mysql_query( $query, $us3_link );
559 }
560
561 else // Undetermined type: skip result data update
562 continue;
563
564 $query = "INSERT INTO HPCAnalysisResultData SET " .
565 "HPCAnalysisResultID='$HPCAnalysisResultID', " .
566 "HPCAnalysisResultType='$file_type', " .
567 "resultID=$id";
568
569 $result = mysql_query( $query, $us3_link );
570
571 if ( ! $result )
572 {
573 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
574 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
575 return( -1 );
576 }
577 }
578
579 // Now fix up noise entries
580 // For noise files, there is, at most two: ti_noise and ri_noise
581 // In this case there will only be one modelID
582
583 foreach ( $noiseIDs as $noiseID )
584 {
585 $modelGUID = $modelGUIDs[ $noiseID ];
586 $query = "UPDATE noise SET " .
587 "editedDataID=" .
588 "(SELECT editedDataID FROM model WHERE modelGUID='$modelGUID')," .
589 "modelID=" .
590 "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
591 "WHERE noiseID=$noiseID";
592
593 $result = mysql_query( $query, $us3_link );
594
595 if ( ! $result )
596 {
597 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
598 mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
599 return( -1 );
600 }
601 }
602
603 // Now possibly fix up mrecs entries
604
605 foreach ( $mrecsIDs as $mrecsID )
606 {
607 $modelGUID = $rmodlGUIDs[ $mrecsID ];
608 $query = "UPDATE pcsa_modelrecs SET " .
609 "modelID=" .
610 "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
611 "WHERE mrecsID=$mrecsID";
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( $us3_link ) );
619 return( -1 );
620 }
621write_log( "$me: mrecs entry updated : mrecsID=$mrecsID" );
622 }
623//write_log( "$me: mrecs entries updated" );
624
625 // Copy results to LIMS submit directory (files there are deleted after 7 days)
626 global $submit_dir; // LIMS submit files dir
627
628 // Get the request guid (LIMS submit dir name)
629 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
630 "WHERE HPCAnalysisRequestID = $requestID ";
631 $result = mysql_query( $query, $us3_link );
632
633 if ( ! $result )
634 {
635 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
636 }
637
638// list( $requestGUID ) = mysql_fetch_array( $result );
639//
640// chdir( "$submit_dir/$requestGUID" );
641// $f = fopen( "analysis-results.tar", "w" );
642// fwrite( $f, $tarfile );
643// fclose( $f );
644
645 // Clean up
646// chdir ( $work );
647 // exec( "rm -rf $gfacID" );
648
649 mysql_close( $us3_link );
650
651 /////////
652 // Send email
653
654 mail_to_user( "success", "" );
655}
656
657function mail_to_user( $type, $msg )
658{
659 // Note to me. Just changed subject line to include a modified $status instead
660 // of the $type variable passed. More informative than just "fail" or "success."
661 // See how it works for awhile and then consider removing $type parameter from
662 // function.
663 global $email_address;
664 global $submittime;
665 global $queuestatus;
666 global $status;
667 global $cluster;
668 global $jobtype;
669 global $org_name;
670 global $admin_email;
671 global $db;
672 global $dbhost;
673 global $requestID;
674 global $gfacID;
675 global $editXMLFilename;
676 global $stdout;
677 global $org_domain;
678
679global $me;
680write_log( "$me mail_to_user(): sending email to $email_address for $gfacID" );
681
682 // Get GFAC status and message
683 // function get_gfac_message() also sets global $status
684 $gfac_message = get_gfac_message( $gfacID );
685 if ( $gfac_message === false ) $gfac_message = "Job Finished";
686
687 // Create a status to put in the subject line
688 switch ( $status )
689 {
690 case "COMPLETE":
691 $subj_status = 'completed';
692 break;
693
694 case "CANCELLED":
695 case "CANCELED":
696 $subj_status = 'canceled';
697 break;
698
699 case "FAILED":
700 $subj_status = 'failed';
701 if ( preg_match( "/^US3-A/i", $gfacID ) )
702 { // For A/Thrift FAIL, get error message
703 $gfac_message = getExperimentErrors( $gfacID );
704//$gfac_message .= "Test ERROR MESSAGE";
705 }
706 break;
707
708 case "ERROR":
709 $subj_status = 'unknown error';
710 break;
711
712 default:
713 $subj_status = $status; // For now
714 break;
715
716 }
717
718 $queuestatus = $subj_status;
719 $limshost = $dbhost;
720 if ( $limshost == 'localhost' )
721 {
722 $limshost = gethostname();
723 if ( ! preg_match( "/\./", $limshost ) )
724 $limshost = $limshost . $org_domain;
725 }
726
727 // Parse the editXMLFilename
728 list( $runID, $editID, $dataType, $cell, $channel, $wl, $ext ) =
729 explode( ".", $editXMLFilename );
730
731 $headers = "From: $org_name Admin<$admin_email>" . "\n";
732 $headers .= "Cc: $org_name Admin<$admin_email>" . "\n";
733
734 // Set the reply address
735 $headers .= "Reply-To: $org_name<$admin_email>" . "\n";
736 $headers .= "Return-Path: $org_name<$admin_email>" . "\n";
737
738 // Try to avoid spam filters
739 $now = time();
740 $headers .= "Message-ID: <" . $now . "cleanup@$dbhost>\n";
741 $headers .= "X-Mailer: PHP v" . phpversion() . "\n";
742 $headers .= "MIME-Version: 1.0" . "\n";
743 $headers .= "Content-Transfer-Encoding: 8bit" . "\n";
744
745 $subject = "UltraScan Job Notification - $subj_status - " . substr( $gfacID, 0, 16 );
746 $message = "
747 Your UltraScan job is complete:
748
749 Submission Time : $submittime
750 LIMS Host : $limshost
751 Analysis ID : $gfacID
752 Request ID : $requestID ( $db )
753 RunID : $runID
754 EditID : $editID
755 Data Type : $dataType
756 Cell/Channel/Wl : $cell / $channel / $wl
757 Status : $queuestatus
758 Cluster : $cluster
759 Job Type : $jobtype
760 GFAC Status : $status
761 GFAC Message : $gfac_message
762 Stdout : $stdout
763 ";
764
765 if ( $type != "success" ) $message .= "Grid Ctrl Error : $msg\n";
766
767 // Handle the error case where an error occurs before fetching the
768 // user's email address
769 if ( $email_address == "" ) $email_address = $admin_email;
770
771 mail( $email_address, $subject, $message, $headers );
772}
773
774function parse_xml( $xml, $type )
775{
776 $parser = new XMLReader();
777 $parser->xml( $xml );
778
779 $results = array();
780
781 while ( $parser->read() )
782 {
783 if ( $parser->name == $type )
784 {
785 while ( $parser->moveToNextAttribute() )
786 {
787 $results[ $parser->name ] = $parser->value;
788 }
789
790 break;
791 }
792 }
793
794 $parser->close();
795 return $results;
796}
797
798// Function to get information about the current job GFAC
799function get_gfac_message( $gfacID )
800{
801 global $serviceURL;
802 global $me;
803
804 $hex = "[0-9a-fA-F]";
805 if ( ! preg_match( "/^US3-Experiment/i", $gfacID ) &&
806 ! preg_match( "/^US3-$hex{8}-$hex{4}-$hex{4}-$hex{4}-$hex{12}$/", $gfacID ) )
807 {
808 // Then it's not a GFAC job
809 return false;
810 }
811
812 $url = "$serviceURL/jobstatus/$gfacID";
813 try
814 {
815 $post = new HttpRequest( $url, HttpRequest::METH_GET );
816 $http = $post->send();
817 $xml = $post->getResponseBody();
818 }
819 catch ( HttpException $e )
820 {
821 write_log( "$me: Job status not available - $gfacID" );
822 return false;
823 }
824
825 // Parse the result
826 $gfac_message = parse_message( $xml );
827
828 return $gfac_message;
829}
830
831function parse_message( $xml )
832{
833 global $status;
834 $status = "";
835 $gfac_message = "";
836
837 $parser = new XMLReader();
838 $parser->xml( $xml );
839
840 $results = array();
841
842 while( $parser->read() )
843 {
844 $type = $parser->nodeType;
845
846 if ( $type == XMLReader::ELEMENT )
847 $name = $parser->name;
848
849 else if ( $type == XMLReader::TEXT )
850 {
851 if ( $name == "status" )
852 $status = $parser->value;
853 else
854 $gfac_message = $parser->value;
855 }
856 }
857
858 $parser->close();
859 return $gfac_message;
860}
861
862function get_local_files( $gfac_link, $cluster, $requestID, $id, $gfacID )
863{
864 global $work;
865 global $work_remote;
866 global $me;
867 global $db;
868 global $status;
869 $is_us3iab = preg_match( "/us3iab/", $cluster );
870
871 // Figure out remote directory
872 $remoteDir = sprintf( "$work_remote/$db-%06d", $requestID );
873write_log( "$me: is_us3iab=$is_us3iab remoteDir=$remoteDir" );
874
875 // Get stdout, stderr, output/analysis-results.tar
876 $output = array();
877
878 if ( $is_us3iab == 0 )
879 {
880 // Figure out local working directory
881 if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
882 $pwd = chdir( "$work/$gfacID" );
883
884 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/output/analysis-results.tar . 2>&1";
885
886 exec( $cmd, $output, $stat );
887 if ( $stat != 0 )
888 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
889
890 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
891
892 exec( $cmd, $output, $stat );
893 if ( $stat != 0 )
894 {
895 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
896 sleep( 10 );
897 write_log( "$me: RETRY" );
898 exec( $cmd, $output, $stat );
899 if ( $stat != 0 )
900 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
901 }
902
903 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
904
905 exec( $cmd, $output, $stat );
906 if ( $stat != 0 )
907 {
908 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
909 sleep( 10 );
910 write_log( "$me: RETRY" );
911 exec( $cmd, $output, $stat );
912 if ( $stat != 0 )
913 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
914 }
915 }
916 else
917 {
918 $pwd = chdir( "$remoteDir" );
919write_log( "$me: IS US3IAB: pwd=$pwd $remoteDir");
920 }
921
922
923 // Write the files to gfacDB
924
925 if ( file_exists( "stderr" ) )
926 { // Filter stderr to not have libnnls debug lines
927 exec( "mv stderr stderr+nnls", $output, $stat );
928 exec( "grep -vi nnls stderr+nnls >stderr", $output, $stat );
929 $stderr = file_get_contents( "stderr" );
930 }
931 else
932 $stderr = "";
933 if ( file_exists( "stdout" ) ) $stdout = file_get_contents( "stdout" );
934 $fn1_tarfile = "analysis-results.tar";
935 $fn2_tarfile = "output/" . $fn1_tarfile;
936 if ( file_exists( $fn1_tarfile ) )
937 $tarfile = file_get_contents( $fn1_tarfile );
938 else if ( file_exists( $fn2_tarfile ) )
939 $tarfile = file_get_contents( $fn2_tarfile );
940
941 $lense = strlen( $stderr );
942 if ( $lense > 1000000 )
943 { // Replace exceptionally large stderr with smaller version
944 exec( "mv stderr stderr-orig", $output, $stat );
945 exec( "head -n 5000 stderr-orig >stderr-h", $output, $stat );
946 exec( "tail -n 5000 stderr-orig >stderr-t", $output, $stat );
947 exec( "cat stderr-h stderr-t >stderr", $output, $stat );
948 $stderr = file_get_contents( "stderr" );
949 }
950$lent = strlen( $tarfile );
951write_log( "$me: tarfile size: $lent");
952$lene = strlen( $stderr );
953write_log( "$me: stderr size: $lene (was $lense)");
954$leno = strlen( $stdout );
955write_log( "$me: stdout size: $leno");
956$estarf=mysql_real_escape_string($tarfile,$gfac_link);
957$lenf = strlen($estarf);
958write_log( "$me: es-tarfile size: $lenf");
959$esstdo=mysql_real_escape_string($stdout,$gfac_link);
960$leno = strlen($esstdo);
961write_log( "$me: es-stdout size: $leno");
962$esstde=mysql_real_escape_string($stderr,$gfac_link);
963$lene = strlen($esstde);
964write_log( "$me: es-stderr size: $lene");
965 $query = "UPDATE analysis SET " .
966 "stderr='" . mysql_real_escape_string( $stderr, $gfac_link ) . "'," .
967 "stdout='" . mysql_real_escape_string( $stdout, $gfac_link ) . "'," .
968 "tarfile='" . mysql_real_escape_string( $tarfile, $gfac_link ) . "'";
969
970 $result = mysql_query( $query, $gfac_link );
971
972 if ( ! $result )
973 {
974 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
975 echo "Bad query\n";
976 return( -1 );
977 }
978}
979?>
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