source: trunk/cleanup.php@ 28

Last change on this file since 28 was 28, checked in by gegorbet, 7 years ago

fixes for alamo-local and airavata EXECUTING status
File size: 30.9 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 $secwait = 10;
197 $num_try = 0;
198write_log( "$me: fn_tarfile=$fn_tarfile" );
199 while ( ! file_exists( $fn_tarfile ) && $num_try < 3 )
200 {
201 sleep( $secwait );
202 $num_try++;
203 $secwait *= 2;
204write_log( "$me: tar-exists: num_try=$num_try" );
205 }
206
207 $ofiles = scandir( $output_dir );
208 foreach ( $ofiles as $ofile )
209 {
210 if ( preg_match( "/^.*stderr$/", $ofile ) )
211 $fn_stderr = $ofile;
212 if ( preg_match( "/^.*stdout$/", $ofile ) )
213 $fn_stdout = $ofile;
214//write_log( "$me: ofile=$ofile" );
215 }
216write_log( "$me: fn_stderr=$fn_stderr" );
217write_log( "$me: fn_stdout=$fn_stdout" );
218if (file_exists($fn_tarfile)) write_log( "$me: fn_tarfile=$fn_tarfile" );
219else write_log( "$me: NOT FOUND: $fn_tarfile" );
220
221 $stderr = '';
222 $stdout = '';
223 $tarfile = '';
224 if ( file_exists( $fn_stderr ) ) $stderr = file_get_contents( $fn_stderr );
225 if ( file_exists( $fn_stdout ) ) $stdout = file_get_contents( $fn_stdout );
226 if ( file_exists( $fn_tarfile ) ) $tarfile = file_get_contents( $fn_tarfile );
227 // If stdout,stderr have no content, retry after delay
228 if ( strlen( $stdout ) == 0 || strlen( $stderr ) == 0 )
229 {
230 sleep( 20 );
231 if ( file_exists( $fn_stderr ) )
232 $stderr = file_get_contents( $fn_stderr );
233 if ( file_exists( $fn_stdout ) )
234 $stdout = file_get_contents( $fn_stdout );
235 }
236
237write_log( "$me: length contents stderr,stdout,tarfile -- "
238 . strlen($stderr) . "," . strlen($stdout) . "," . strlen($tarfile) );
239
240 if ( $cluster == 'alamo' || $cluster == 'alamo-local' )
241 { // Filter "ipath_userinit" lines out of alamo stdout lines
242 $prefln = strlen( $stdout );
243 $output = array();
244 exec( "grep -v 'ipath_userinit' $fn_stdout 2>&1", $output, $err );
245 $stdout = implode( "\n", $output );
246 $posfln = strlen( $stdout );
247write_log( "$me: fn_stdout : filtered. Length $prefln -> $posfln ." );
248 }
249
250 // Save queue messages for post-mortem analysis
251 $query = "SELECT message, time FROM queue_messages " .
252 "WHERE analysisID = $analysisID " .
253 "ORDER BY time ";
254 $result = mysql_query( $query, $gfac_link );
255
256 if ( ! $result )
257 {
258 // Just log it and continue
259 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
260 }
261
262 $now = date( 'Y-m-d H:i:s' );
263 $message_log = "US3 DB: $db\n" .
264 "RequestID: $requestID\n" .
265 "GFAC ID: $gfacID\n" .
266 "Processed: $now\n\n" .
267 "Queue Messages\n\n" ;
268 if ( mysql_num_rows( $result ) > 0 )
269 {
270 while ( list( $message, $time ) = mysql_fetch_array( $result ) )
271 $message_log .= "$time $message\n";
272 }
273
274 $query = "DELETE FROM queue_messages " .
275 "WHERE analysisID = $analysisID ";
276
277 $result = mysql_query( $query, $gfac_link );
278
279 if ( ! $result )
280 {
281 // Just log it and continue
282 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
283 }
284
285 $query = "SELECT queue_msg FROM analysis " .
286 "WHERE gfacID='$gfacID' ";
287
288 $result = mysql_query( $query, $gfac_link );
289 list( $queue_msg ) = mysql_fetch_array( $result );
290
291 // But let's allow for investigation of other large stdout and/or stderr
292 if ( strlen( $stdout ) > 20480000 ||
293 strlen( $stderr ) > 20480000 )
294 write_log( "$me: stdout + stderr larger than 20M - $gfacID\n" );
295
296 $message_log .= "\n\n\nStdout Contents\n\n" .
297 $stdout .
298 "\n\n\nStderr Contents\n\n" .
299 $stderr .
300 "\n\n\nGFAC Status: $status\n" .
301 "GFAC message field: $queue_msg\n";
302
303 // Delete data from GFAC DB
304 $query = "DELETE from analysis WHERE gfacID='$gfacID'";
305
306 $result = mysql_query( $query, $gfac_link );
307
308 if ( ! $result )
309 {
310 // Just log it and continue
311 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
312 }
313
314
315 // Try to create it if necessary, and write the file
316 // Let's use FILE_APPEND, in case this is the second time around and the
317 // GFAC job status was INSERTed, rather than UPDATEd
318 if ( ! is_dir( $output_dir ) )
319 mkdir( $output_dir, 0775, true );
320 $message_filename = "$output_dir/$db-$requestID-messages.txt";
321 file_put_contents( $message_filename, $message_log, FILE_APPEND );
322 // mysql_close( $gfac_link );
323
324 /////////
325 // Insert data into HPCAnalysis
326
327 $query = "UPDATE HPCAnalysisResult SET " .
328 "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " .
329 "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "', " .
330 "queueStatus='completed' " .
331 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
332
333 $result = mysql_query( $query, $us3_link );
334
335 if ( ! $result )
336 {
337 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
338 mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) );
339 return( -1 );
340 }
341
342 // Delete data from GFAC DB
343 $query = "DELETE from analysis WHERE gfacID='$gfacID'";
344
345 $result = mysql_query( $query, $gfac_link );
346
347 if ( ! $result )
348 {
349 // Just log it and continue
350 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
351 }
352
353 // Expand the tar file
354
355 if ( strlen( $tarfile ) == 0 )
356 {
357 write_log( "$me: No tarfile" );
358 mail_to_user( "fail", "No results" );
359 return( -1 );
360 }
361
362 $tar_out = array();
363 exec( "tar -xf analysis-results.tar 2>&1", $tar_out, $err );
364
365 // Insert the model files and noise files
366 $files = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES );
367 $noiseIDs = array();
368 $modelGUIDs = array();
369 $mrecsIDs = array();
370 $fns_used = array();
371
372 foreach ( $files as $file )
373 {
374 $split = explode( ";", $file );
375
376 if ( count( $split ) > 1 )
377 {
378 list( $fn, $meniscus, $mc_iteration, $variance ) = explode( ";", $file );
379
380 list( $other, $mc_iteration ) = explode( "=", $mc_iteration );
381 list( $other, $variance ) = explode( "=", $variance );
382 list( $other, $meniscus ) = explode( "=", $meniscus );
383 }
384 else
385 $fn = $file;
386
387 if ( preg_match( "/mdl.tmp$/", $fn ) )
388 continue;
389
390 if ( in_array( $fn, $fns_used ) )
391 continue;
392
393 $fns_used[] = $fn;
394
395 if ( filesize( $fn ) < 100 )
396 {
397 write_log( "$me:fn is invalid $fn size filesize($fn)" );
398 mail_to_user( "fail", "Internal error\n$fn is invalid" );
399 return( -1 );
400 }
401
402 if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file
403 {
404 $xml = file_get_contents( $fn );
405 $statistics = parse_xml( $xml, 'statistics' );
406// $ntries = 0;
407//
408// while ( $statistics['cpucount'] < 1 && $ntries < 3 )
409// { // job_statistics file not totally copied, so retry
410// sleep( 10 );
411// $xml = file_get_contents( $fn );
412// $statistics = parse_xml( $xml, 'statistics' );
413// $ntries++;
414//write_log( "$me:jobstats retry $ntries" );
415// }
416//write_log( "$me:cputime=$statistics['cputime']" );
417
418 $otherdata = parse_xml( $xml, 'id' );
419
420 $query = "UPDATE HPCAnalysisResult SET " .
421 "wallTime = {$statistics['walltime']}, " .
422 "CPUTime = {$statistics['cputime']}, " .
423 "CPUCount = {$statistics['cpucount']}, " .
424 "max_rss = {$statistics['maxmemory']}, " .
425 "startTime = '{$otherdata['starttime']}', " .
426 "endTime = '{$otherdata['endtime']}', " .
427 "mgroupcount = {$otherdata['groupcount']} " .
428 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
429 $result = mysql_query( $query, $us3_link );
430
431 if ( ! $result )
432 {
433 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
434 }
435
436 file_put_contents( "$output_dir/$fn", $xml ); // Copy to submit dir
437
438 $file_type = "job_stats";
439 $id = 1;
440 }
441
442 else if ( preg_match( "/\.noise/", $fn ) > 0 ) // It's a noise file
443 {
444 $xml = file_get_contents( $fn );
445 $noise_data = parse_xml( $xml, "noise" );
446 $type = ( $noise_data[ 'type' ] == "ri" ) ? "ri_noise" : "ti_noise";
447 $desc = $noise_data[ 'description' ];
448 $modelGUID = $noise_data[ 'modelGUID' ];
449 $noiseGUID = $noise_data[ 'noiseGUID' ];
450
451 $query = "INSERT INTO noise SET " .
452 "noiseGUID='$noiseGUID'," .
453 "modelGUID='$modelGUID'," .
454 "editedDataID=1, " .
455 "modelID=1, " .
456 "noiseType='$type'," .
457 "description='$desc'," .
458 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
459
460 // Add later after all files are processed: editDataID, modelID
461
462 $result = mysql_query( $query, $us3_link );
463
464 if ( ! $result )
465 {
466 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
467 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
468 return( -1 );
469 }
470
471 $id = mysql_insert_id( $us3_link );
472 $file_type = "noise";
473 $noiseIDs[] = $id;
474
475 // Keep track of modelGUIDs for later, when we replace them
476 $modelGUIDs[ $id ] = $modelGUID;
477
478 }
479
480 else if ( preg_match( "/\.mrecs/", $fn ) > 0 ) // It's an mrecs file
481 {
482 $xml = file_get_contents( $fn );
483 $mrecs_data = parse_xml( $xml, "modelrecords" );
484 $desc = $mrecs_data[ 'description' ];
485 $editGUID = $mrecs_data[ 'editGUID' ];
486write_log( "$me: mrecs file editGUID=$editGUID" );
487 if ( strlen( $editGUID ) < 36 )
488 $editGUID = "12345678-0123-5678-0123-567890123456";
489 $mrecGUID = $mrecs_data[ 'mrecGUID' ];
490 $modelGUID = $mrecs_data[ 'modelGUID' ];
491
492 $query = "INSERT INTO pcsa_modelrecs SET " .
493 "editedDataID=" .
494 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
495 "modelID=0, " .
496 "mrecsGUID='$mrecGUID'," .
497 "description='$desc'," .
498 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
499
500 // Add later after all files are processed: editDataID, modelID
501
502 $result = mysql_query( $query, $us3_link );
503
504 if ( ! $result )
505 {
506 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
507 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
508 return( -1 );
509 }
510
511 $id = mysql_insert_id( $us3_link );
512 $file_type = "mrecs";
513 $mrecsIDs[] = $id;
514
515 // Keep track of modelGUIDs for later, when we replace them
516 $rmodlGUIDs[ $id ] = $modelGUID;
517//write_log( "$me: mrecs file inserted into DB : id=$id" );
518 }
519
520 else if ( preg_match( "/\.model/", $fn ) > 0 ) // It's a model file
521 {
522 $xml = file_get_contents( $fn );
523 $model_data = parse_xml( $xml, "model" );
524 $description = $model_data[ 'description' ];
525 $modelGUID = $model_data[ 'modelGUID' ];
526 $editGUID = $model_data[ 'editGUID' ];
527
528 if ( $mc_iteration > 1 )
529 {
530 $miter = sprintf( "_mcN%03d", $mc_iteration );
531 $description = preg_replace( "/_mc[0-9]+/", $miter, $description );
532write_log( "$me: MODELUpd: O:description=$description" );
533 }
534
535 $query = "INSERT INTO model SET " .
536 "modelGUID='$modelGUID'," .
537 "editedDataID=" .
538 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
539 "description='$description'," .
540 "MCIteration='$mc_iteration'," .
541 "meniscus='$meniscus'," .
542 "variance='$variance'," .
543 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
544
545 $result = mysql_query( $query, $us3_link );
546
547 if ( ! $result )
548 {
549 write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) );
550 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
551 return( -1 );
552 }
553
554 $modelID = mysql_insert_id( $us3_link );
555 $id = $modelID;
556 $file_type = "model";
557
558 $query = "INSERT INTO modelPerson SET " .
559 "modelID=$modelID, personID=$personID";
560 $result = mysql_query( $query, $us3_link );
561 }
562
563 else // Undetermined type: skip result data update
564 continue;
565
566 $query = "INSERT INTO HPCAnalysisResultData SET " .
567 "HPCAnalysisResultID='$HPCAnalysisResultID', " .
568 "HPCAnalysisResultType='$file_type', " .
569 "resultID=$id";
570
571 $result = mysql_query( $query, $us3_link );
572
573 if ( ! $result )
574 {
575 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
576 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
577 return( -1 );
578 }
579 }
580
581 // Now fix up noise entries
582 // For noise files, there is, at most two: ti_noise and ri_noise
583 // In this case there will only be one modelID
584
585 foreach ( $noiseIDs as $noiseID )
586 {
587 $modelGUID = $modelGUIDs[ $noiseID ];
588 $query = "UPDATE noise SET " .
589 "editedDataID=" .
590 "(SELECT editedDataID FROM model WHERE modelGUID='$modelGUID')," .
591 "modelID=" .
592 "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
593 "WHERE noiseID=$noiseID";
594
595 $result = mysql_query( $query, $us3_link );
596
597 if ( ! $result )
598 {
599 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
600 mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
601 return( -1 );
602 }
603 }
604
605 // Now possibly fix up mrecs entries
606
607 foreach ( $mrecsIDs as $mrecsID )
608 {
609 $modelGUID = $rmodlGUIDs[ $mrecsID ];
610 $query = "UPDATE pcsa_modelrecs SET " .
611 "modelID=" .
612 "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
613 "WHERE mrecsID=$mrecsID";
614
615 $result = mysql_query( $query, $us3_link );
616
617 if ( ! $result )
618 {
619 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
620 mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
621 return( -1 );
622 }
623write_log( "$me: mrecs entry updated : mrecsID=$mrecsID" );
624 }
625//write_log( "$me: mrecs entries updated" );
626
627 // Copy results to LIMS submit directory (files there are deleted after 7 days)
628 global $submit_dir; // LIMS submit files dir
629
630 // Get the request guid (LIMS submit dir name)
631 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
632 "WHERE HPCAnalysisRequestID = $requestID ";
633 $result = mysql_query( $query, $us3_link );
634
635 if ( ! $result )
636 {
637 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
638 }
639
640// list( $requestGUID ) = mysql_fetch_array( $result );
641//
642// chdir( "$submit_dir/$requestGUID" );
643// $f = fopen( "analysis-results.tar", "w" );
644// fwrite( $f, $tarfile );
645// fclose( $f );
646
647 // Clean up
648// chdir ( $work );
649 // exec( "rm -rf $gfacID" );
650
651 mysql_close( $us3_link );
652
653 /////////
654 // Send email
655
656 mail_to_user( "success", "" );
657}
658
659function mail_to_user( $type, $msg )
660{
661 // Note to me. Just changed subject line to include a modified $status instead
662 // of the $type variable passed. More informative than just "fail" or "success."
663 // See how it works for awhile and then consider removing $type parameter from
664 // function.
665 global $email_address;
666 global $submittime;
667 global $queuestatus;
668 global $status;
669 global $cluster;
670 global $jobtype;
671 global $org_name;
672 global $admin_email;
673 global $db;
674 global $dbhost;
675 global $requestID;
676 global $gfacID;
677 global $editXMLFilename;
678 global $stdout;
679 global $org_domain;
680
681global $me;
682write_log( "$me mail_to_user(): sending email to $email_address for $gfacID" );
683
684 // Get GFAC status and message
685 // function get_gfac_message() also sets global $status
686 $gfac_message = get_gfac_message( $gfacID );
687 if ( $gfac_message === false ) $gfac_message = "Job Finished";
688
689 // Create a status to put in the subject line
690 switch ( $status )
691 {
692 case "COMPLETE":
693 $subj_status = 'completed';
694 break;
695
696 case "CANCELLED":
697 case "CANCELED":
698 $subj_status = 'canceled';
699 break;
700
701 case "FAILED":
702 $subj_status = 'failed';
703 if ( preg_match( "/^US3-A/i", $gfacID ) )
704 { // For A/Thrift FAIL, get error message
705 $gfac_message = getExperimentErrors( $gfacID );
706//$gfac_message .= "Test ERROR MESSAGE";
707 }
708 break;
709
710 case "ERROR":
711 $subj_status = 'unknown error';
712 break;
713
714 default:
715 $subj_status = $status; // For now
716 break;
717
718 }
719
720 $queuestatus = $subj_status;
721 $limshost = $dbhost;
722 if ( $limshost == 'localhost' )
723 {
724 $limshost = gethostname();
725 if ( ! preg_match( "/\./", $limshost ) )
726 $limshost = $limshost . $org_domain;
727 }
728
729 // Parse the editXMLFilename
730 list( $runID, $editID, $dataType, $cell, $channel, $wl, $ext ) =
731 explode( ".", $editXMLFilename );
732
733 $headers = "From: $org_name Admin<$admin_email>" . "\n";
734 $headers .= "Cc: $org_name Admin<$admin_email>" . "\n";
735
736 // Set the reply address
737 $headers .= "Reply-To: $org_name<$admin_email>" . "\n";
738 $headers .= "Return-Path: $org_name<$admin_email>" . "\n";
739
740 // Try to avoid spam filters
741 $now = time();
742 $headers .= "Message-ID: <" . $now . "cleanup@$dbhost>\n";
743 $headers .= "X-Mailer: PHP v" . phpversion() . "\n";
744 $headers .= "MIME-Version: 1.0" . "\n";
745 $headers .= "Content-Transfer-Encoding: 8bit" . "\n";
746
747 $subject = "UltraScan Job Notification - $subj_status - " . substr( $gfacID, 0, 16 );
748 $message = "
749 Your UltraScan job is complete:
750
751 Submission Time : $submittime
752 LIMS Host : $limshost
753 Analysis ID : $gfacID
754 Request ID : $requestID ( $db )
755 RunID : $runID
756 EditID : $editID
757 Data Type : $dataType
758 Cell/Channel/Wl : $cell / $channel / $wl
759 Status : $queuestatus
760 Cluster : $cluster
761 Job Type : $jobtype
762 GFAC Status : $status
763 GFAC Message : $gfac_message
764 Stdout : $stdout
765 ";
766
767 if ( $type != "success" ) $message .= "Grid Ctrl Error : $msg\n";
768
769 // Handle the error case where an error occurs before fetching the
770 // user's email address
771 if ( $email_address == "" ) $email_address = $admin_email;
772
773 mail( $email_address, $subject, $message, $headers );
774}
775
776function parse_xml( $xml, $type )
777{
778 $parser = new XMLReader();
779 $parser->xml( $xml );
780
781 $results = array();
782
783 while ( $parser->read() )
784 {
785 if ( $parser->name == $type )
786 {
787 while ( $parser->moveToNextAttribute() )
788 {
789 $results[ $parser->name ] = $parser->value;
790 }
791
792 break;
793 }
794 }
795
796 $parser->close();
797 return $results;
798}
799
800// Function to get information about the current job GFAC
801function get_gfac_message( $gfacID )
802{
803 global $serviceURL;
804 global $me;
805
806 $hex = "[0-9a-fA-F]";
807 if ( ! preg_match( "/^US3-Experiment/i", $gfacID ) &&
808 ! preg_match( "/^US3-$hex{8}-$hex{4}-$hex{4}-$hex{4}-$hex{12}$/", $gfacID ) )
809 {
810 // Then it's not a GFAC job
811 return false;
812 }
813
814 $url = "$serviceURL/jobstatus/$gfacID";
815 try
816 {
817 $post = new HttpRequest( $url, HttpRequest::METH_GET );
818 $http = $post->send();
819 $xml = $post->getResponseBody();
820 }
821 catch ( HttpException $e )
822 {
823 write_log( "$me: Job status not available - $gfacID" );
824 return false;
825 }
826
827 // Parse the result
828 $gfac_message = parse_message( $xml );
829
830 return $gfac_message;
831}
832
833function parse_message( $xml )
834{
835 global $status;
836 $status = "";
837 $gfac_message = "";
838
839 $parser = new XMLReader();
840 $parser->xml( $xml );
841
842 $results = array();
843
844 while( $parser->read() )
845 {
846 $type = $parser->nodeType;
847
848 if ( $type == XMLReader::ELEMENT )
849 $name = $parser->name;
850
851 else if ( $type == XMLReader::TEXT )
852 {
853 if ( $name == "status" )
854 $status = $parser->value;
855 else
856 $gfac_message = $parser->value;
857 }
858 }
859
860 $parser->close();
861 return $gfac_message;
862}
863
864function get_local_files( $gfac_link, $cluster, $requestID, $id, $gfacID )
865{
866 global $work;
867 global $work_remote;
868 global $me;
869 global $db;
870 global $status;
871 $is_us3iab = preg_match( "/us3iab/", $cluster );
872
873 // Figure out remote directory
874 $remoteDir = sprintf( "$work_remote/$db-%06d", $requestID );
875//write_log( "$me: is_us3iab=$is_us3iab remoteDir=$remoteDir" );
876
877 // Get stdout, stderr, output/analysis-results.tar
878 $output = array();
879
880 if ( $is_us3iab == 0 )
881 {
882 // For "-local", recompute remote work directory
883 $cmd = "ssh us3@$cluster.uthscsa.edu 'ls -d ~us3/lims/work/local' 2/dev/null";
884 exec( $cmd, $output, $stat );
885 $work_remote = $output[ 0 ];
886 $remoteDir = sprintf( "$work_remote/$db-%06d", $requestID );
887write_log( "$me: -LOCAL: remoteDir=$remoteDir" );
888
889 // Figure out local working directory
890 if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
891 $pwd = chdir( "$work/$gfacID" );
892
893 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/output/analysis-results.tar . 2>&1";
894
895 exec( $cmd, $output, $stat );
896 if ( $stat != 0 )
897 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
898
899 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
900
901 exec( $cmd, $output, $stat );
902 if ( $stat != 0 )
903 {
904 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
905 sleep( 10 );
906 write_log( "$me: RETRY" );
907 exec( $cmd, $output, $stat );
908 if ( $stat != 0 )
909 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
910 }
911
912 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
913
914 exec( $cmd, $output, $stat );
915 if ( $stat != 0 )
916 {
917 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
918 sleep( 10 );
919 write_log( "$me: RETRY" );
920 exec( $cmd, $output, $stat );
921 if ( $stat != 0 )
922 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
923 }
924 }
925 else
926 {
927 $pwd = chdir( "$remoteDir" );
928write_log( "$me: IS US3IAB: pwd=$pwd $remoteDir");
929 }
930
931
932 // Write the files to gfacDB
933
934 if ( file_exists( "stderr" ) )
935 { // Filter stderr to not have libnnls debug lines
936// exec( "mv stderr stderr+nnls", $output, $stat );
937// exec( "grep -vi nnls stderr+nnls >stderr", $output, $stat );
938 $stderr = file_get_contents( "stderr" );
939 }
940 else
941 $stderr = "";
942 if ( file_exists( "stdout" ) ) $stdout = file_get_contents( "stdout" );
943 $fn1_tarfile = "analysis-results.tar";
944 $fn2_tarfile = "output/" . $fn1_tarfile;
945 if ( file_exists( $fn1_tarfile ) )
946 $tarfile = file_get_contents( $fn1_tarfile );
947 else if ( file_exists( $fn2_tarfile ) )
948 $tarfile = file_get_contents( $fn2_tarfile );
949
950 $lense = strlen( $stderr );
951 if ( $lense > 1000000 )
952 { // Replace exceptionally large stderr with smaller version
953 exec( "mv stderr stderr-orig", $output, $stat );
954 exec( "head -n 5000 stderr-orig >stderr-h", $output, $stat );
955 exec( "tail -n 5000 stderr-orig >stderr-t", $output, $stat );
956 exec( "cat stderr-h stderr-t >stderr", $output, $stat );
957 $stderr = file_get_contents( "stderr" );
958 }
959$lent = strlen( $tarfile );
960write_log( "$me: tarfile size: $lent");
961$lene = strlen( $stderr );
962write_log( "$me: stderr size: $lene (was $lense)");
963$leno = strlen( $stdout );
964write_log( "$me: stdout size: $leno");
965$estarf=mysql_real_escape_string($tarfile,$gfac_link);
966$lenf = strlen($estarf);
967write_log( "$me: es-tarfile size: $lenf");
968$esstdo=mysql_real_escape_string($stdout,$gfac_link);
969$leno = strlen($esstdo);
970write_log( "$me: es-stdout size: $leno");
971$esstde=mysql_real_escape_string($stderr,$gfac_link);
972$lene = strlen($esstde);
973write_log( "$me: es-stderr size: $lene");
974 $query = "UPDATE analysis SET " .
975 "stderr='" . mysql_real_escape_string( $stderr, $gfac_link ) . "'," .
976 "stdout='" . mysql_real_escape_string( $stdout, $gfac_link ) . "'," .
977 "tarfile='" . mysql_real_escape_string( $tarfile, $gfac_link ) . "'";
978
979 $result = mysql_query( $query, $gfac_link );
980
981 if ( ! $result )
982 {
983 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
984 echo "Bad query\n";
985 return( -1 );
986 }
987}
988?>
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