source: trunk/cleanup_gfac.php

Last change on this file was 40, checked in by gegorbet, 6 years ago

more time information in error,completion emails
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[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;
[40]35 global $endtime;
[7]36 global $status;
37 global $stdout;
38 global $requestID;
39
40 $requestID = $reqID;
41 $db = $us3_db;
42 write_log( "$me: debug db=$db; requestID=$requestID" );
43
[35]44 $us3_link = mysqli_connect( $dbhost, $user, $passwd, $db );
[7]45
46 if ( ! $us3_link )
47 {
[35]48 write_log( "$me: could not connect: $dbhost, $user, $passwd, $db" );
49 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $db" );
[7]50 return( -1 );
51 }
52
53 // First get basic info for email messages
54 $query = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " .
55 "WHERE HPCAnalysisRequestID=$requestID";
[35]56 $result = mysqli_query( $us3_link, $query );
[7]57
58 if ( ! $result )
59 {
60 write_log( "$me: Bad query: $query" );
[35]61 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysqli_error( $us3_link ) );
[7]62 return( -1 );
63 }
64
[35]65 list( $email_address, $investigatorGUID, $editXMLFilename ) = mysqli_fetch_array( $result );
[7]66
67 $query = "SELECT personID FROM people " .
68 "WHERE personGUID='$investigatorGUID'";
[35]69 $result = mysqli_query( $us3_link, $query );
[7]70
[35]71 list( $personID ) = mysqli_fetch_array( $result );
[7]72
73 /*
74 $query = "SELECT clusterName, submitTime, queueStatus, method " .
75 "FROM HPCAnalysisRequest h LEFT JOIN HPCAnalysisResult " .
76 "ON h.HPCAnalysisRequestID=HPCAnalysisResult.HPCAnalysisRequestID " .
77 "WHERE h.HPCAnalysisRequestID=$requestID";
78 */
[40]79 $query = "SELECT clusterName, submitTime, queueStatus, analType " .
[7]80 "FROM HPCAnalysisRequest h, HPCAnalysisResult r " .
81 "WHERE h.HPCAnalysisRequestID=$requestID " .
82 "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID";
83
[35]84 $result = mysqli_query( $us3_link, $query );
[7]85
86 if ( ! $result )
87 {
[35]88 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
[7]89 return( -1 );
90 }
91
[35]92 if ( mysqli_num_rows( $result ) == 0 )
[7]93 {
94 write_log( "$me: US3 Table error - No records for requestID: $requestID" );
95 return( -1 );
96 }
97
[35]98 list( $cluster, $submittime, $queuestatus, $jobtype ) = mysqli_fetch_array( $result );
[7]99
100 // Get the GFAC ID
[40]101 $query = "SELECT HPCAnalysisResultID, gfacID, endTime FROM HPCAnalysisResult " .
[7]102 "WHERE HPCAnalysisRequestID=$requestID";
103
[35]104 $result = mysqli_query( $us3_link, $query );
[7]105
106 if ( ! $result )
107 {
108 write_log( "$me: Bad query: $query" );
[35]109 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysqli_error( $us3_link ) );
[7]110 return( -1 );
111 }
112
[40]113 list( $HPCAnalysisResultID, $gfacID, $endtime ) = mysqli_fetch_array( $result );
[7]114
115 ////////
116 // Get data from global GFAC DB and insert it into US3 DB
[35]117 $gfac_link = mysqli_connect( $dbhost, $guser, $gpasswd, $gDB );
[7]118
[35]119 if ( ! $gfac_link )
[7]120 {
[35]121 write_log( "$me: Could not connect to DB $dbhost : $gDB" );
[7]122 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" );
123 return( -1 );
124 }
125
126 $query = "SELECT status, cluster, id FROM analysis " .
127 "WHERE gfacID='$gfacID'";
128
[35]129 $result = mysqli_query( $gfac_link, $query );
[7]130 if ( ! $result )
131 {
132 write_log( "$me: Could not select GFAC status for $gfacID" );
133 mail_to_user( "fail", "Could not select GFAC status for $gfacID" );
134 return( -1 );
135 }
136
[35]137 $num_rows = mysqli_num_rows( $result );
[7]138 if ( $num_rows == 0 )
139 {
140 write_log( "$me: Cleanup analysis query found 0 entries for $gfacID" );
141 return( 0 );
142 }
143//else
144//{
145//write_log( "$me: db=$db; num_rows=$num_rows; queuestatus=$queuestatus" );
146//}
147
[35]148 list( $status, $cluster, $id ) = mysqli_fetch_array( $result );
[7]149//write_log( "$me: db=$db; requestID=$requestID; status=$status; cluster=$cluster" );
150
[25]151// if ( $cluster == 'bcf-local' || $cluster == 'alamo-local' )
152 if ( preg_match( "/\-local/", $cluster ) ||
153 preg_match( "/us3iab/", $cluster ) )
[7]154 {
[25]155// $clushost = $cluster;
156// $clushost = preg_replace( "/\-local/", "", $clushost );
157 $parts = explode( "-", $cluster );
158 $clushost = $parts[ 0 ];
[7]159 get_local_files( $gfac_link, $clushost, $requestID, $id, $gfacID );
[25]160write_log( "$me: clushost=$clushost reqID=$requestID get_local_files() gfacID=$gfacID" );
[7]161 }
[25]162else
163write_log( "$me: NO get_local_files()" );
[7]164
165 $query = "SELECT id, stderr, stdout, tarfile FROM analysis " .
166 "WHERE gfacID='$gfacID'";
167
[35]168 $result = mysqli_query( $gfac_link, $query );
[7]169
170 if ( ! $result )
171 {
[35]172 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) );
173 mail_to_user( "fail", "Internal error " . mysqli_error( $gfac_link ) );
[7]174 return( -1 );
175 }
176
[35]177 $num_rows = mysqli_num_rows( $result );
[7]178 if ( $num_rows == 0 )
179 {
180 write_log( "$me: Cleanup analysis query found 0 entries for $gfacID" );
181 return( 0 );
182 }
183
[35]184 list( $analysisID, $stderr, $stdout, $tarfile ) = mysqli_fetch_array( $result );
[7]185
186 if ( strlen( $tarfile ) > 0 )
187 { // Log success at fetch attempt
188 write_log( "$me: Successful data fetch: $requestID $gfacID" );
189 }
190 else
191 { // Log failure at fetch attempt
192 write_log( "$me: Failed data fetch: $requestID $gfacID" );
193 if ( $analysisID == '' )
194 $analysisID = '0';
195 }
196
197 // Save queue messages for post-mortem analysis
198 $query = "SELECT message, time FROM queue_messages " .
199 "WHERE analysisID = $analysisID " .
200 "ORDER BY time ";
[35]201 $result = mysqli_query( $gfac_link, $query );
[7]202
203 if ( ! $result )
204 {
205 // Just log it and continue
[35]206 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) );
[7]207 }
208
209 $now = date( 'Y-m-d H:i:s' );
210 $message_log = "US3 DB: $db\n" .
211 "RequestID: $requestID\n" .
212 "GFAC ID: $gfacID\n" .
213 "Processed: $now\n\n" .
214 "Queue Messages\n\n" ;
215
216 $need_finish = ( $status == 'COMPLETE' );
217
[35]218 if ( mysqli_num_rows( $result ) > 0 )
[7]219 {
220 $time_msg = time();
[35]221 while ( list( $message, $time ) = mysqli_fetch_array( $result ) )
[7]222 {
223//write_log( "$me: message=$message" );
224 $message_log .= "$time $message\n";
225 if ( preg_match( "/^Finished/i", $message ) )
226 $need_finish = false;
227 $time_msg = strtotime( $time );
228 }
229
230 if ( $need_finish )
231 { // No 'Finished' yet: forget if too much time has passed
232 $time_now = time();
233 $tdelta = $time_now - $time_msg;
234write_log( "$me: no-Finish time: tnow=$time_now, tmsg=$time_msg, tdelt=$tdelta" );
235 if ( $tdelta > 600 )
236 $need_finish = false;
237 }
238//write_log( "$me: no-Finish time: tnow=$time_now, tmsg=$time_msg, tdelt=$tdelta" );
239 }
240 else
241 {
242 write_log( "$me: No messages for analysisID=$analysisID ." );
243 $need_finish = false;
244 }
245
246 if ( $need_finish )
247 {
248 write_log( "$me: Cleanup has not yet found 'Finished' for $gfacID" );
249 return( 0 );
250 }
251
252 $query = "DELETE FROM queue_messages " .
253 "WHERE analysisID = $analysisID ";
254
[35]255 $result = mysqli_query( $gfac_link, $query );
[7]256
257 if ( ! $result )
258 {
259 // Just log it and continue
[35]260 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) );
[7]261 }
262
263 // Save stdout, stderr, etc. for message log
264 $query = "SELECT stdout, stderr, status, queue_msg FROM analysis " .
265 "WHERE gfacID='$gfacID' ";
[35]266 $result = mysqli_query( $gfac_link, $query );
[7]267 try
268 {
269 // What if this is too large?
[35]270 list( $stdout, $stderr, $status, $queue_msg ) = mysqli_fetch_array( $result );
[7]271 }
272 catch ( Exception $e )
273 {
[35]274 write_log( "$me: stdout + stderr larger than 128M - $gfacID\n" . mysqli_error( $gfac_link ) );
[7]275 // Just go ahead and clean up
276 }
277
278 // But let's allow for investigation of other large stdout and/or stderr
279 if ( strlen( $stdout ) > 20480000 ||
280 strlen( $stderr ) > 20480000 )
281 write_log( "$me: stdout + stderr larger than 20M - $gfacID\n" );
282
283 $message_log .= "\n\n\nStdout Contents\n\n" .
284 $stdout .
285 "\n\n\nStderr Contents\n\n" .
286 $stderr .
287 "\n\n\nGFAC Status: $status\n" .
288 "GFAC message field: $queue_msg\n";
289
290 // Delete data from GFAC DB
291 $query = "DELETE from analysis WHERE gfacID='$gfacID'";
292
[35]293 $result = mysqli_query( $gfac_link, $query );
[7]294
295 if ( ! $result )
296 {
297 // Just log it and continue
[35]298 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) );
[7]299 }
300write_log( "$me: GFAC DB entry deleted" );
301
302 // Copy queue messages to LIMS submit directory (files there are deleted after 7 days)
303 global $submit_dir;
304
305 // Get the request guid (LIMS submit dir name)
306 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
307 "WHERE HPCAnalysisRequestID = $requestID ";
[35]308 $result = mysqli_query( $us3_link, $query );
[7]309
310 if ( ! $result )
311 {
[35]312 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
[7]313 }
314
[35]315 list( $requestGUID ) = mysqli_fetch_array( $result );
[7]316 $output_dir = "$submit_dir/$requestGUID";
317write_log( "$me: Output dir determined: $output_dir" );
318
319 // Try to create it if necessary, and write the file
320 // Let's use FILE_APPEND, in case this is the second time around and the
321 // GFAC job status was INSERTed, rather than UPDATEd
322 if ( ! is_dir( $output_dir ) )
323 mkdir( $output_dir, 0775, true );
324 $message_filename = "$output_dir/$db-$requestID-messages.txt";
325 file_put_contents( $message_filename, $message_log, FILE_APPEND );
[35]326 // mysqli_close( $gfac_link );
[25]327write_log( "$me: *messages.txt written" );
[7]328
329 /////////
330 // Insert data into HPCAnalysis
331
332 $query = "UPDATE HPCAnalysisResult SET " .
[35]333 "stderr='" . mysqli_real_escape_string( $us3_link, $stderr ) . "', " .
334 "stdout='" . mysqli_real_escape_string( $us3_link, $stdout ) . "' " .
[7]335 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
336
[35]337 $result = mysqli_query( $us3_link, $query );
[7]338
339 if ( ! $result )
340 {
[35]341 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
342 mail_to_user( "fail", "Bad query:\n$query\n" . mysqli_error( $us3_link ) );
[7]343 return( -1 );
344 }
345
346 // Save the tarfile and expand it
347
348 if ( strlen( $tarfile ) == 0 )
349 {
350 write_log( "$me: No tarfile" );
351 mail_to_user( "fail", "No results" );
352 return( -1 );
353 }
354
355 // Shouldn't happen
356 if ( ! is_dir( "$work" ) )
357 {
358 write_log( "$me: $work directory does not exist" );
359 mail_to_user( "fail", "$work directory does not exist" );
360 return( -1 );
361 }
362
363 if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
364 chdir( "$work/$gfacID" );
365
[25]366 $f = fopen( "analysis-results.tar", "w" );
[7]367 fwrite( $f, $tarfile );
368 fclose( $f );
[25]369//write_log( "$me: analysis-results.tar file written to work dir" );
[7]370
371 $tar_out = array();
[25]372 exec( "tar -xf analysis-results.tar 2>&1", $tar_out, $err );
[7]373
374 if ( $err != 0 )
375 {
376 chdir( $work );
377 exec( "rm -r $gfacID" );
378 $output = implode( "\n", $tar_out );
379
380 write_log( "$me: Bad output tarfile: $output" );
381 mail_to_user( "fail", "Bad output file" );
382 return( -1 );
383 }
384//write_log( "$me: tar files extracted" );
385
386 // Insert the model files and noise files
387 $files = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES );
388 $noiseIDs = array();
389 $modelGUIDs = array();
390 $mrecsIDs = array();
391 $rmodlGUIDs = array();
392
393 foreach ( $files as $file )
394 {
395 $split = explode( ";", $file );
396
397 if ( count( $split ) > 1 )
398 {
399 list( $fn, $meniscus, $mc_iteration, $variance ) = explode( ";", $file );
400
401 list( $other, $mc_iteration ) = explode( "=", $mc_iteration );
402 list( $other, $variance ) = explode( "=", $variance );
403 list( $other, $meniscus ) = explode( "=", $meniscus );
404 }
405 else
406 $fn = $file;
407
408 if ( preg_match( "/mdl.tmp$/", $fn ) )
409 continue;
410
411 if ( filesize( $fn ) < 100 )
412 {
413 write_log( "$me:fn is invalid $fn" );
414 mail_to_user( "fail", "Internal error\n$fn is invalid" );
415 return( -1 );
416 }
417//write_log( "$me: handling file: $fn" );
418
419 if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file
420 {
421 $xml = file_get_contents( $fn );
422 $statistics = parse_xml( $xml, 'statistics' );
423 $otherdata = parse_xml( $xml, 'id' );
424
425 $query = "UPDATE HPCAnalysisResult SET " .
426 "wallTime = {$statistics['walltime']}, " .
427 "CPUTime = {$statistics['cputime']}, " .
428 "CPUCount = {$statistics['cpucount']}, " .
429 "max_rss = {$statistics['maxmemory']}, " .
430 "startTime = '{$otherdata['starttime']}', " .
431 "endTime = '{$otherdata['endtime']}', " .
432 "mgroupcount = {$otherdata['groupcount']} " .
433 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
[35]434 $result = mysqli_query( $us3_link, $query );
[7]435
436 if ( ! $result )
437 {
[35]438 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
[7]439 }
440
441 file_put_contents( "$output_dir/$fn", $xml ); // Copy to submit dir
442 $file_type = "job_stats";
443//write_log( "$me: job_statistics file updated in Result and written" );
444
445 }
446
447 else if ( preg_match( "/\.noise/", $fn ) > 0 ) // It's a noise file
448 {
449 $xml = file_get_contents( $fn );
450 $noise_data = parse_xml( $xml, "noise" );
451 $type = ( $noise_data[ 'type' ] == "ri" ) ? "ri_noise" : "ti_noise";
452 $desc = $noise_data[ 'description' ];
453 $modelGUID = $noise_data[ 'modelGUID' ];
454 $noiseGUID = $noise_data[ 'noiseGUID' ];
[35]455 $editGUID = '00000000-0000-0000-0000-000000000000';
456 if ( isset( $model_data[ 'editGUID' ] ) )
457 $editGUID = $model_data[ 'editGUID' ];
[7]458
459 $query = "INSERT INTO noise SET " .
460 "noiseGUID='$noiseGUID'," .
461 "modelGUID='$modelGUID'," .
[35]462 "editedDataID=" .
463 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
[7]464 "modelID=1, " .
465 "noiseType='$type'," .
466 "description='$desc'," .
[35]467 "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'";
[7]468
469 // Add later after all files are processed: editDataID, modelID
470
[35]471 $result = mysqli_query( $us3_link, $query );
[7]472
473 if ( ! $result )
474 {
[35]475 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
476 mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) );
[7]477 return( -1 );
478 }
479
[35]480 $id = mysqli_insert_id( $us3_link );
[7]481 $file_type = "noise";
482 $noiseIDs[] = $id;
483
484 // Keep track of modelGUIDs for later, when we replace them
485 $modelGUIDs[ $id ] = $modelGUID;
[35]486//write_log( "$me: noise file inserted into DB : id=$id modelGUID=$modelGUID" );
[7]487
488 }
489
490 else if ( preg_match( "/\.mrecs/", $fn ) > 0 ) // It's an mrecs file
491 {
492 $xml = file_get_contents( $fn );
493 $mrecs_data = parse_xml( $xml, "modelrecords" );
494 $desc = $mrecs_data[ 'description' ];
495 $editGUID = $mrecs_data[ 'editGUID' ];
496write_log( "$me: mrecs file editGUID=$editGUID" );
497 if ( strlen( $editGUID ) < 36 )
498 $editGUID = "12345678-0123-5678-0123-567890123456";
499 $mrecGUID = $mrecs_data[ 'mrecGUID' ];
500 $modelGUID = $mrecs_data[ 'modelGUID' ];
501
502 $query = "INSERT INTO pcsa_modelrecs SET " .
503 "editedDataID=" .
504 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
505 "modelID=0, " .
506 "mrecsGUID='$mrecGUID'," .
507 "description='$desc'," .
[35]508 "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'";
[7]509
510 // Add later after all files are processed: editDataID, modelID
511
[35]512 $result = mysqli_query( $us3_link, $query );
[7]513
514 if ( ! $result )
515 {
[35]516 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
517 mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) );
[7]518 return( -1 );
519 }
520
[35]521 $id = mysqli_insert_id( $us3_link );
[7]522 $file_type = "mrecs";
523 $mrecsIDs[] = $id;
524
525 // Keep track of modelGUIDs for later, when we replace them
526 $rmodlGUIDs[ $id ] = $modelGUID;
527//write_log( "$me: mrecs file inserted into DB : id=$id" );
528 }
529
[23]530 else if ( preg_match( "/\.model/", $fn ) > 0 ) // It's a model file
[7]531 {
532 $xml = file_get_contents( $fn );
533 $model_data = parse_xml( $xml, "model" );
534 $description = $model_data[ 'description' ];
535 $modelGUID = $model_data[ 'modelGUID' ];
536 $editGUID = $model_data[ 'editGUID' ];
537
538 if ( $mc_iteration > 1 )
539 {
540//write_log( "$me: MODELUpd: mc_iteration=$mc_iteration" );
541 $miter = sprintf( "_mcN%03d", $mc_iteration );
542//write_log( "$me: MODELUpd: miter=$miter" );
543//write_log( "$me: MODELUpd: I:description=$description" );
544 $description = preg_replace( "/_mc[0-9]+/", $miter, $description );
545write_log( "$me: MODELUpd: O:description=$description" );
546 }
547
548 $query = "INSERT INTO model SET " .
549 "modelGUID='$modelGUID'," .
550 "editedDataID=" .
551 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
552 "description='$description'," .
553 "MCIteration='$mc_iteration'," .
554 "meniscus='$meniscus'," .
555 "variance='$variance'," .
[35]556 "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'";
[7]557
[35]558 $result = mysqli_query( $us3_link, $query );
[7]559
560 if ( ! $result )
561 {
[35]562 write_log( "$me: Bad query:\n$query " . mysqli_error( $us3_link ) );
563 mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) );
[7]564 return( -1 );
565 }
566
[35]567 $modelID = mysqli_insert_id( $us3_link );
[7]568 $id = $modelID;
569 $file_type = "model";
570
571 $query = "INSERT INTO modelPerson SET " .
572 "modelID=$modelID, personID=$personID";
[35]573 $result = mysqli_query( $us3_link, $query );
[7]574//write_log( "$me: model file inserted into DB : id=$id" );
575 }
576
577 $query = "INSERT INTO HPCAnalysisResultData SET " .
578 "HPCAnalysisResultID='$HPCAnalysisResultID', " .
579 "HPCAnalysisResultType='$file_type', " .
580 "resultID=$id";
581
[35]582 $result = mysqli_query( $us3_link, $query );
[7]583
584 if ( ! $result )
585 {
[35]586 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
587 mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) );
[7]588 return( -1 );
589 }
590//write_log( "$me: ResultData updated : file_type=$file_type" );
591 }
592
593 // Now fix up noise entries
594 // For noise files, there is, at most two: ti_noise and ri_noise
595 // In this case there will only be one modelID
596
597 foreach ( $noiseIDs as $noiseID )
598 {
599 $modelGUID = $modelGUIDs[ $noiseID ];
600 $query = "UPDATE noise SET " .
601 "editedDataID=" .
602 "(SELECT editedDataID FROM model WHERE modelGUID='$modelGUID')," .
603 "modelID=" .
604 "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
605 "WHERE noiseID=$noiseID";
606
[35]607 $result = mysqli_query( $us3_link, $query );
[7]608
609 if ( ! $result )
610 {
[35]611 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
612 mail_to_user( "fail", "Bad query\n$query\n" . mysqli_error( $us3_link ) );
[7]613 return( -1 );
614 }
615//write_log( "$me: noise entry updated : noiseID=$noiseID" );
616 }
617//write_log( "$me: noise entries updated" );
618
619 // Now possibly fix up mrecs entries
620
621 foreach ( $mrecsIDs as $mrecsID )
622 {
623 $modelGUID = $rmodlGUIDs[ $mrecsID ];
624 $query = "UPDATE pcsa_modelrecs SET " .
625 "modelID=" .
626 "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
627 "WHERE mrecsID=$mrecsID";
628
[35]629 $result = mysqli_query( $us3_link, $query );
[7]630
631 if ( ! $result )
632 {
[35]633 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
634 mail_to_user( "fail", "Bad query\n$query\n" . mysqli_error( $us3_link ) );
[7]635 return( -1 );
636 }
637//write_log( "$me: mrecs entry updated : mrecsID=$mrecsID" );
638 }
639//write_log( "$me: mrecs entries updated" );
640
641 // Copy results to LIMS submit directory (files there are deleted after 7 days)
642 global $submit_dir; // LIMS submit files dir
643
644 // Get the request guid (LIMS submit dir name)
645 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
646 "WHERE HPCAnalysisRequestID = $requestID ";
[35]647 $result = mysqli_query( $us3_link, $query );
[7]648
649 if ( ! $result )
650 {
[35]651 write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
[7]652 }
653
[35]654 list( $requestGUID ) = mysqli_fetch_array( $result );
[7]655
656 chdir( "$submit_dir/$requestGUID" );
657 $f = fopen( "analysis.tar", "w" );
658 fwrite( $f, $tarfile );
659 fclose( $f );
660
661 // Clean up
662 chdir ( $work );
663 // exec( "rm -rf $gfacID" );
664
[35]665 mysqli_close( $us3_link );
[7]666
667 /////////
668 // Send email
669
670 mail_to_user( "success", "" );
671}
672?>
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