/
Upload.pm
972 lines (875 loc) · 48.5 KB
/
Upload.pm
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
package MGRAST::WebPage::Upload;
use strict;
use warnings;
no warnings('once');
use Data::Dumper;
use Digest::MD5 qw(md5 md5_hex md5_base64);
use JSON;
use Encode;
use Conf;
use WebConfig;
use MGRAST::Metadata;
use base qw( WebPage );
1;
=pod
=head1 NAME
Upload - upload files and display uploaded files to user for creation of jobs
=head1 DESCRIPTION
Page used by user to upload files and create jobs from uploaded files
=head1 METHODS
=over 4
=item * B<init> ()
Called when the web page is instanciated.
=cut
sub init {
my $self = shift;
$self->title("Data Submission");
$self->{icon} = "<img src='./Html/mg-upload.png' style='width: 20px; height: 20px; padding-right: 5px; position: relative; top: -3px;'>";
$self->application->register_action($self, 'check_for_duplicates', 'check_for_duplicates');
$self->application->register_action($self, 'check_project_name', 'check_project_name');
$self->application->register_action($self, 'validate_metadata', 'validate_metadata');
$self->application->register_action($self, 'submit_to_mgrast', 'submit_to_mgrast');
$self->application->register_action($self, 'generate_webkey', 'generate_webkey');
$self->application->register_action($self, 'read_status_file', 'read_status_file');
$self->application->register_component('Table', 'sequence_table');
}
=item * B<output> ()
Returns the html output of the page.
=cut
sub output {
my ($self) = @_;
my $application = $self->application;
my $cgi = $application->cgi;
my $user = $application->session->user;
my $jobdb = $application->data_handle('MGRAST');
unless ($user) {
return "<p>You must be logged in to upload metagenome files and create jobs.</p><p>Please use the login box in the top right corner or return to the <a href='?page=Home'>start page</a>.</p>";
}
my $lock_file = $Conf::locks.'/upload.lock';
if (-e $lock_file) {
my $message = "We have temporarily suspended uploads for maintenance purposes, please try again later";
if (-s $lock_file) {
my @lines = `cat $lock_file`;
$message = join('', @lines);
}
$application->add_message('warning', $message);
$self->title("Upload suspended");
return '';
}
my $json = new JSON;
$json = $json->utf8();
my $ufo = { "login" => $user->login,
"auth" => $application->session->session_id };
my $html = qq~<style>h3 {margin-top: 0px;}</style><div style='display: none;' id='uifo'>~.$json->encode($ufo).qq~</div><div style="width: 960px;" id="upload_area">
<div>~;
if ($cgi->param('create_job')) {
my $success = $self->submit_to_mgrast();
if ($success && @$success) {
$html .= "<div class='well'><h4>Job submission successful</h4><p>Your data has been successfully submitted to the pipeline. You can view the status of your submitted jobs <a href='?page=MetagenomeSelect'>here</a> and click on the number next to 'In Progress'.</p><p>Your MG-RAST IDs: ".join(", ", @$success)."</p></div>";
}
}
my $user_project_ids = $user->has_right_to(undef, "edit", "project");
my $projects = [];
foreach my $pid (@$user_project_ids) {
next if ($pid eq '*');
my $p = $jobdb->Project->get_objects( { id => $pid } );
if (scalar($p)) {
push(@$projects, $p->[0]);
}
}
my $template_link = "ftp://".$Conf::ftp_download."/data/misc/metadata/".$Conf::mgrast_metadata_template;
$html .= qq~
<div class="well" style='width: 630px; float: left;'><h3>using the new mg-rast uploader:</h3>
<p>The new data uploader and submission site provides a more convenient way to upload and process your data! You can upload all of your sequence files and metadata at once and have the files modified and validated before submitting.</p>
<p>In short, use <b>Prepare Data</b> to upload any fasta, fastq or SFF files and GSC MIxS compliant metadata files into your inbox. While metadata is not required at submission, the priority for processing data without metadata is lower. Metadata can be modified on the project page after submission. The inbox is a temporary storage location allowing you to assemble all files required for submission. After manipulate the files in your inbox, use <b>Data Submission</b> to create and add to existing projects. When the submission process has been successfully completed, MG-RAST ID's ("Accession numbers") will be automatically assigned and the data will be removed from your inbox.<p>
<p>You can monitor the progress of your jobs in the My Data Summary, on the Browse Metagenomes page.</p>
<p>Questions? Check out our <a href='http://blog.metagenomics.anl.gov/upload-data-v3-2/' target='blank'>tutorial and instructional videos</a>. Still having trouble? <a href="mailto:mg-rast\@mcs.anl.gov">Email us!</a></p>
<p><b>Note: All numbered sections below expand on click to display additional information and options.</b></p>
</div>
<div class="well" style='width: 240px; float: right;'>
<h3>mini-faq</h3>
<ul class="unstyled">
<li><a href='http://blog.metagenomics.anl.gov/mg-rast-how-to-videos/#upload_single' target=_blank>Upload a single metagenome (Video)</a></li>
<li><a href='http://blog.metagenomics.anl.gov/mg-rast-how-to-videos/#upload_multiple' target=_blank>Upload multiple metagenomes (Video)</a></li>
<li><a href='http://blog.metagenomics.anl.gov/glossary-of-mg-rast-terms-and-concepts/#inbox' target=_blank>Inbox explained</a></li>
<li><a href='http://blog.metagenomics.anl.gov/mg-rast-v3-2-faq/#command_line_submission' target=_blank>Using cmd-line tools for submission</a></li>
<li><a href='http://blog.metagenomics.anl.gov/mg-rast-v3-2-faq/#api_submission' target=_blank>Automated submission via our API</a></li>
<li><a href='http://blog.metagenomics.anl.gov/mg-rast-v3-2-faq/#preparing_metadata' target=_blank>Preparing metadata</a></li>
<li><a href='http://blog.metagenomics.anl.gov/mg-rast-v3-2-faq/#job_priority' target=_blank>Priority assignments explained</a></li>
<li><a href='http://blog.metagenomics.anl.gov/glossary-of-mg-rast-terms-and-concepts/#accession_numbers' target=_blank>Obtaining Accession numbers</a></li>
<li><a href='http://blog.metagenomics.anl.gov/mg-rast-v3-2-faq/#projects_on_upload_page' target=_blank>Which projects are shown in the dialogue?</a></li>
<li><a href='http://blog.metagenomics.anl.gov/upload-data-v3-2/' target=_blank>How should barcode files be formatted?</a></li>
</ul>
</div>
<div class='clear'></div>
<h1>Prepare Data</h1>
<div class="row">
<div style="width: 960px; margin-left: 30px;">
<ul class="nav nav-pills nav-stacked">
<li><a onclick="toggle('sel_mddownload_div');" class="pill_incomplete" id="sel_mddownload_pill" style="font-size: 17px; font-weight: bold;">1. download metadata spreadsheet template</a></li>
<div id="sel_mddownload_div" style="display: none;" class="well">
<h3>download metadata spreadsheet template</h3>
<p>Metadata (or data about the data) has become a necessity as the community generates large quantities of data sets.</p>
<p>Using community generated questionnaires we capture this metadata. MG-RAST has implemented the use of <a href='http://gensc.org/gc_wiki/index.php/MIxS' target=_blank>Minimum Information about any (X) Sequence</a> developed by the <a href='http://gensc.org' target=_blank >Genomic Standards Consortium</a> (GSC).</p>
<p>The best form to capture metadata is via a simple spreadsheet with 12 mandatory terms. You can download the spreadsheet file here, fill in the required data fields later upload it to your inbox.</p>
<p>While the MIxS required data fields capture only the most minimal metadata, many areas of study have chosen to require more elaborate questionnaires ("environmental packages") to help with analysis and comparison. These are marked as optional in the spreadsheet. If the "environmental package" for your area of study has not been created yet, please <a href="mailto:mg-rast\@mcs.anl.gov">contact MG-RAST staff</a> and we will forward your inquiry to the appropriate GSC working group.</p>
<p>Once you have filled out the template, you can upload it below and it will be validated and appear in the metadata selection section.</p>
<p><a href="$template_link"><img title="download metadata spreadsheet template" style="width: 20px; height: 20px;" src="./Html/mg-download.png"> download metadata spreadsheet template</a></p>
</div>
<li><a onclick="toggle('sel_upload_div');" class="pill_incomplete" id="sel_upload_pill" style="font-size: 17px; font-weight: bold;">2. upload files</a></li>
<div id="sel_upload_div" style="display: none;" class="well">
<h3>upload files</h4>
<table>
<tr>
<td>
<form class="form-horizontal">
<input class="input-file" type="file" multiple size=40 id="file_upload">
</form>
</td>
<td style="padding-left: 240px;">
<p>Select one or more files to upload to your private inbox folder.</p>
<p>Sequence files must be fasta, fastq, or sff format.
Use vaild file extensions for the appropriate format: .fasta, .fa, .ffn, .frn, .fna, .fq, .fastq, .sff </p>
</td>
</tr>
</table>
<div id="upload_progress" style="display: none;">
<br><h3>upload progress</h3><br>
<div id="uploaded_files" style="display: none;" class="alert alert-info">
</div>
<div id="progress_display">
<table>
<tr>
<td colspan=2>
<div class="alert alert-success" id="upload_status"></div>
</td>
</tr>
<tr>
<td style="width: 150px;"><h5>total</h5></td>
<td>
<progress id="prog1" min="0" max="100" value="0" style="width: 400px;">0% complete</progress>
</td>
</tr>
<tr>
<td><h5>current file</h5></td>
<td>
<progress id="prog2" min="0" max="100" value="0" style="width: 400px;">0% complete</progress>
</td>
</tr>
<tr>
<td style="height: 50px;">
<a class="btn btn-danger" href="#" onclick="cancel_upload();" style="position: relative; top: 5px; left: 435px;"><i class="icon-ban-circle"></i> cancel upload</a>
</td>
</tr>
</table>
</div>
</div>
<p>In addition to using your web browser for uploads to the system the following alternatives are available:</p>
<table>
<tr style='display: none;'><td width="125px"><b>ftp</b></td><td>ftp://incoming.metagenomics.anl.gov/<span id="ftp_webkey">YOUR_PRIVATE_WEBKEY</span></td></tr>
<tr><td><b>http</b></td><td>http://api.metagenomics.anl.gov/inbox/<span id="http_webkey">YOUR_PRIVATE_WEBKEY</span></td></tr>
<tr><td colspan=2 style='padding-top: 10px; padding-bottom: 10px;'><div id='generate_key'><input type='button' class='btn' onclick='generate_webkey();' value='generate webkey'></div></td></tr>
</table>
<p><b>Note:</b> The <a href='http://blog.metagenomics.anl.gov/mg-rast-v3-2-faq/#command_line_submission' target=_blank>Blog</a> lists a number of examples for data transfer.</p>
</div>
<li><a onclick="toggle('sel_inbox_div');" class="pill_incomplete" id="sel_inbox_pill" style="font-size: 17px; font-weight: bold;">3. manage inbox</a></li>
<div id="sel_inbox_div" style="display: none;" class="well">
<p>You can unpack, delete, convert and demultiplex files from your inbox below. Metadata files will automatically appear in the <i>'select metadata file'</i> section below. Sequence files will automatically appear in the <i>'select sequence file(s)'</i> section below after sequence statistics are calculated (may take anywhere from seconds to hours depending on file size).</p>
<p>Filenames in gray in your Inbox are undergoing analysis and cannot be moved or submitted to a different process until analysis is complete. Filenames in red have encountered an error.</p>
<br>
<table border=0 cellpadding=4>
<tr >
<td colspan=2 style='font-size:14px;'><B>File Processing Operations</B></td>
</tr>
<tr>
<td><input type="button" class="btn" style='width:130px;' value="unpack selected" onclick="unpack_files();"></td>
<td width=250 style='vertical-align:middle;'>Unpacks selected zip, gzip, or tar files.</td>
<td><input type="button" class="btn" style='width:130px;' value="demultiplex" onclick="demultiplex_files();"></td>
<td width=250 style='vertical-align:middle;'>Demultiplexes selected files.</td>
</tr>
<tr>
<td><input type="button" class="btn" style='width:130px;' value="convert sff to fastq" onclick="convert_files();"></td>
<td width=250 style='vertical-align:middle;'>Converts selected sff files to fastq format.</td>
<td>
<form style='margin:0;'>
<div class="modal hide" id="mergeMatePairsModal" tabindex="-1" role="dialog" aria-labelledby="mergeMatePairsModalLabel" aria-hidden="true">
<button style="display: none;" onclick="merge_mate_pairs();" data-dismiss="modal" aria-hidden="true">Hidden merge mate-pairs button for enter key submission</button>
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">x</button>
<h3 id="mergeMatePairsModalLabel">create directory</h3>
</div>
<div class="modal-body">
<p>Please enter the desired name of your merge mate-pairs output file:</p>
<div id="merge_mate_pairs_input" style='margin-top: 10px;'><input type="text" id="merge_output_filename" /></div>
</div>
<div class="modal-footer">
<button class="btn" data-dismiss="modal" aria-hidden="true">Cancel</button>
<button class="btn btn-primary" style="background-color:#3A87AD;background-image:-moz-linear-gradient(center top , #3A87AD, #3A87AD);" onclick="merge_mate_pairs();" data-dismiss="modal" aria-hidden="true">Merge Mate-Pair Files</button>
</div>
</div>
</form>
<input type="button" class="btn" style='width:130px;' value="merge mate-pairs" data-toggle="modal" href="#mergeMatePairsModal"">
</td>
<td width=250 style='vertical-align:middle;'>Merges selected mate-pair files.</td>
</tr>
</table>
<br>
<table>
<tr>
<td rowspan=2 style="padding-right: 20px;">
<form class="form-horizontal">
<div id="inbox" style='margin-top: 10px;'><br><br><img src="./Html/ajax-loader.gif"> loading...</div>
</form>
<table border=0 cellpadding=4>
<tr>
<td colspan=2 style='font-size:14px;'><B>Directory Management Operations</B></td>
<tr>
<td><input type="button" class="btn" style='width:130px;' value="update inbox" onclick="update_inbox();"></td>
<td style='vertical-align:middle;'>Refreshes the contents of your inbox.</td>
</tr>
<tr>
<td>
<div class="modal hide" id="moveModal" tabindex="-1" role="dialog" aria-labelledby="moveModalLabel" aria-hidden="true">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">x</button>
<h3 id="moveModalLabel">move selected files</h3>
</div>
<div class="modal-body">
<p>Please select the directory where you would like to move your selected files:</p>
<div id="dir_list" style='margin-top: 10px;'><br><br><img src="./Html/ajax-loader.gif"> loading...</div>
</div>
<div class="modal-footer">
<button class="btn" data-dismiss="modal" aria-hidden="true">Cancel</button>
<button class="btn btn-primary" style="background-color:#3A87AD;background-image:-moz-linear-gradient(center top , #3A87AD, #3A87AD);" onclick="move_files();" data-dismiss="modal" aria-hidden="true">Move files</button>
</div>
</div>
<input type="button" class="btn" style='width:130px;' value="move selected" data-toggle="modal" href="#moveModal">
</td>
<td style='vertical-align:middle;'>Moves the selected files into or out of a directory.</td>
</tr>
<tr>
<td><input type="button" class="btn" style='width:130px;' value="delete selected" onclick="check_delete_files();"></td>
<td style='vertical-align:middle;'>Deletes the selected files.</td>
</tr>
<tr>
<td>
<form style='margin:0;'>
<div class="modal hide" id="createDirModal" tabindex="-1" role="dialog" aria-labelledby="createDirModalLabel" aria-hidden="true">
<button style="display: none;" onclick="create_dir();" data-dismiss="modal" aria-hidden="true">Hidden Create directory button for enter key submission</button>
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">x</button>
<h3 id="createDirModalLabel">create directory</h3>
</div>
<div class="modal-body">
<p>Please enter the name of the directory you would like to create:</p>
<div id="create_dir_input" style='margin-top: 10px;'><input type="text" id="create_dir_name" /></div>
</div>
<div class="modal-footer">
<button class="btn" data-dismiss="modal" aria-hidden="true">Cancel</button>
<button class="btn btn-primary" style="background-color:#3A87AD;background-image:-moz-linear-gradient(center top , #3A87AD, #3A87AD);" onclick="create_dir();" data-dismiss="modal" aria-hidden="true">Create directory</button>
</div>
</div>
</form>
<input type="button" class="btn" style='width:130px;' value="create directory" data-toggle="modal" href="#createDirModal">
</td>
<td style='vertical-align:middle;'>Creates a new directory in your inbox.</td>
</tr>
<tr>
<td>
<div class="modal hide" id="deleteDirModal" tabindex="-1" role="dialog" aria-labelledby="deleteDirModalLabel" aria-hidden="true">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">x</button>
<h3 id="deleteDirModalLabel">delete directory</h3>
</div>
<div class="modal-body">
<p>Please select the directory you would like to delete (only empty directories can be deleted):</p>
<div id="delete_dir_list" style='margin-top: 10px;'><br><br><img src="./Html/ajax-loader.gif"> loading...</div>
</div>
<div class="modal-footer">
<button class="btn" data-dismiss="modal" aria-hidden="true">Cancel</button>
<button class="btn btn-primary" style="background-color:#3A87AD;background-image:-moz-linear-gradient(center top , #3A87AD, #3A87AD);" onclick="delete_dir();" data-dismiss="modal" aria-hidden="true">Delete directory</button>
</div>
</div>
<input type="button" class="btn" style='width:130px;' value="delete directory" data-toggle="modal" href="#deleteDirModal">
</td>
<td style='vertical-align:middle;'>Allows you to select and delete an empty directory.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td><div id="inbox_feedback"></div><div id="inbox_file_info"></div></td>
</tr>
</table>
</div>
</ul>
</div>
</div>
<h1>Data Submission</h1>
<div class="row">
<div style="width: 960px; margin-left: 30px;">
<form class="form-horizontal" name="submission_form" method='post'>
<input type="hidden" name="page" value="Upload">
<input type="hidden" name="create_job" value="1">
<ul class="nav nav-pills nav-stacked">
<li><a onclick="toggle('sel_md_div');" class="pill_incomplete" id="sel_md_pill" style="font-size: 17px; font-weight: bold;">1. select metadata file <i id="icon_step_1" class="icon-ok icon-white" style="display: none;"></i></a></li>
<div id="sel_md_div" style="display: none;" class="well">
<div id="sel_mdfile_div" style='float:left;'></div><div style='float:left; margin-top: 25px; width: 350px;'>
<p>Select a spreadsheet with metadata for the project you want to submit. Uploaded spreedsheets will appear here after successful validation.</p>
<p>In order to map sequence files to metadata libraries, the names of the sequence files must exactly match the library <i>file_name</i> fields or match the library <i>metagenome_name</i> fields minus extension.</p>
<p><b>Note: While metadata is not required at submission, the priority for processing data without metadata is lower.</b></p>
</div><div class='clear'></div>
</div>
<li><a onclick="toggle('sel_project_div');" class="pill_incomplete" id="sel_project_pill" style="font-size: 17px; font-weight: bold;">2. select project <i id="icon_step_2" class="icon-ok icon-white" style="display: none;"></i></a></li>
<div id="sel_project_div" class="well" style="display: none;"><h3>select a project</h3><p>You have to specify a project to upload a job to MG-RAST. If you have a metadata file, the project must be specified in that file. If you choose to not use a metadata file, you can select a project here. You can either select an existing project or you can choose a new project.</p><select name="project" style="width: 420px; margin-bottom: 20px;" onchange="if(this.selectedIndex>0){document.getElementById('new_project').value='';document.getElementById('new_project').disabled=true;}else{document.getElementById('new_project').disabled=false;}" id='project'><option value=''>- new -</option>~;
foreach my $project (@$projects) {
next unless ($project->{name});
$html .= "<option value='".$project->{id}."'>".$project->{name}."</option>";
}
$html .= qq~</select> <input type='text' name='new_project' id='new_project' style='margin-bottom: 20px;'><br><input style='margin-bottom: 20px;' type='button' class='btn' value='select' onclick="check_project();">
<p>The projects shown in the list above are the ones you have write access to. Note that the owners of the projects can provide you with write access</p>
</div>
<li><a onclick="toggle('sel_seq_div');" class="pill_incomplete" id="sel_seq_pill" style="font-size: 17px; font-weight: bold;">3. select sequence file(s) <i id="icon_step_3" class="icon-ok icon-white" style="display: none;"></i></a></li>
<div id="sel_seq_div" style="display: none;"><div class='well'><div id='available_sequences'>
<h3>available sequence files</h3><p>Sequence files from your inbox will appear here. Please note, there is a delay between upload completion and appearing in the below table due to sequence statistics calculations. This may be on the order of seconds to hours depending on file size.</p>~;
my $seqtable = $self->application->component('sequence_table');
$seqtable->columns([ { name => "select<br><input type=\"checkbox\" onclick=\"table_select_all_checkboxes(0,0,this.checked,1);\"> all ", input_type => 'checkbox' },
{ name => 'directory', sortable => 1, filter => 1 },
{ name => 'filename', sortable => 1, filter => 1 },
{ name => 'format', sortable => 1, filter => 1 },
{ name => 'size', sortable => 1, filter => 1 },
{ name => 'upload date', sortable => 1, filter => 1 },
{ name => 'bp count', sortable => 1, filter => 1 },
{ name => 'sequencing method', sortable => 1, filter => 1, visible => 0 },
{ name => 'sequence type', sortable => 1, filter => 1, visible => 0 },
{ name => 'md5', sortable => 1, filter => 1, visible => 0 }]);
$seqtable->data([[0,"-","-","-","-","-","-","-","-","-"]]);
$seqtable->show_select_items_per_page(1);
$seqtable->show_top_browse(1);
$seqtable->show_bottom_browse(1);
$seqtable->items_per_page(10);
$seqtable->show_column_select(1);
$html .= $seqtable->output();
$html .= qq~<br><br><input type='button' class='btn' value='select' onclick='select_sequence_file();'></div><div id='selected_sequences'></div></div></div>
<li><a onclick="toggle('sel_pip_div');" class="pill_incomplete" id="sel_pip_pill" style="font-size: 17px; font-weight: bold;">4. choose pipeline options <i id="icon_step_4" class="icon-ok icon-white" style="display: none;"></i></a></li>
<div id="sel_pip_div" style="display: none;" class="well">
<h3>selected pipeline options</h3>
<div class="control-group">
<label class="control-label" for="dereplication"><b>dereplication</b></label>
<div class="controls">
<label class="checkbox">
<input id="dereplication" type="checkbox" value="dereplication" name="dereplication" checked>
Remove artificial replicate sequences produced by sequencing artifacts <a href='http://www.nature.com/ismej/journal/v3/n11/full/ismej200972a.html' target='blank'>Gomez-Alvarez, et al, The ISME Journal (2009)</a>.
</label>
</div>
<label class="control-label" for="screening"><b>screening</b></label>
<div class="controls">
<label class="select">
<select id="screening" name="screening">
<option value="h_sapiens_asm">H. sapiens, NCBI v36</option>
<option value="m_musculus_ncbi37">M. musculus, NCBI v37</option>
<option value="b_taurus">B. taurus, UMD v3.0</option>
<option value="d_melanogaster_fb5_22">D. melanogaster, Flybase, r5.22</option>
<option value="a_thaliana">A. thaliana, TAIR, TAIR9</option>
<option value="e_coli">E. coli, NCBI, st. 536</option>
<option value="s_scrofa_ncbi10.2">Sus scrofa, NCBI v10.2</option>
<option value="none">none</option>
</select>
<br>Remove any host specific species sequences (e.g. plant, human or mouse) using DNA level matching with bowtie <a href='http://genomebiology.com/2009/10/3/R25' target='blank'>Langmead et al., Genome Biol. 2009, Vol 10, issue 3</a>
</label>
</div>
<label class="control-label" for="dynamic_trim"><b>dynamic trimming</b><br>(fastq only)</label>
<div class="controls">
<label class="checkbox">
<input id="dynamic_trim" type="checkbox" value="dynamic_trim" name="dynamic_trim" checked>
Remove low quality sequences using a modified DynamicTrim <a href='http://www.biomedcentral.com/1471-2105/11/485' target='blank'>Cox et al., (BMC Bioinformatics, 2011, Vol. 11, 485)</a>.
</label>
<label class="text">
<input id="min_qual" type="text" value="15" name="min_qual">
Specify the lowest phred score that will be counted as a high-quality base.
</label>
<label class="text">
<input id="max_lqb" type="text" value="5" name="max_lqb">
Sequences will be trimmed to contain at most this many bases below the above-specified quality.
</label>
</div>
<label class="control-label" for="filter_ln"><b>length filtering</b><br>(fasta only)</label>
<div class="controls">
<label class="checkbox">
<input id="filter_ln" type="checkbox" value="filter_ln" name="filter_ln" checked>
Filter based on sequence length when no quality score information is available.
</label>
<label class="text">
<input id="deviation" type="text" value="2.0" name="deviation">
Specify the multiplicator of standard deviation for length cutoff.
</label>
</div>
<label class="control-label" for="filter_ambig"><b>ambiguous base filtering</b><br>(fasta only)</label>
<div class="controls">
<label class="checkbox">
<input id="filter_ambig" type="checkbox" value="filter_amibg" name="filter_ambig" checked>
Filter based on sequence ambiguity base (non-ACGT) count when no quality score information is available.
</label>
<label class="text">
<input id="max_ambig" type="text" value="5" name="max_ambig">
Specify the maximum allowed number of ambiguous basepairs.
</label>
</div>
</div>
<input type="button" class="btn" value="select" onclick="accept_pipeline_options();" id="accept_pipeline_options_button"><span style='margin-left: 20px;'><b>Warning: Comparison of datasets processed with different pipeline options may not be valid.</b></span>
</div>
<li><a onclick="toggle('sub_job_div');" class="pill_incomplete" id="sub_job_pill" style="font-size: 17px; font-weight: bold;">5. submit <i id="icon_step_4" class="icon-ok icon-white" style="display: none;"></i></a></li>
<div id="sub_job_div" style="display: none;" class="well">
<h3>Submit data to the MG-RAST pipeline.</h3>
<p>Data will be private (only visible to the submitter) unless you choose to share it with other users or make it public. If you decide to make data public your data will be given priority for the computational queue.</p>
<div class="control-group">
<div class="controls">
<label class="radio"><input id="priorityOption1" type="radio" value="immediately" name="priorityOption">Data will be publicly accessible <b> immediately </b> after processing completion - Highest Priority</label>
<label class="radio"><input id="priorityOption2" type="radio" value="3months" name="priorityOption">Data will be publicly accessible <b>after 3 months</b> - High Priority</label>
<label class="radio"><input id="priorityOption2" type="radio" value="6months" name="priorityOption">Data will be publicly accessible <b>after 6 months</b> - Medium Priority</label>
<label class="radio"><input id="priorityOption2" type="radio" value="date" name="priorityOption">Data will be publicly accessible <b>eventually</b> - Lower Priority</label>
<label class="radio"><input id="priorityOption2" type="radio" checked="" value="never" name="priorityOption"><b>Data will stay private </b> (DEFAULT) - Lowest Priority</label>
</div>
</div>
<p>Please note that only private data can be deleted.</p>
<div class='clear' style='height:10px;'></div>
<div style='margin-bottom: 20px;'><input type="button" class="btn" value="submit job" onclick="submit_job();" disabled id="submit_job_button"><span style='margin-left: 20px;'><b>Note: You must complete all previous steps to enable submission.</b></span></div>
<p>Upon successful submission MG-RAST ID's ("Accession numbers") will be automatically assigned and data files will be removed from your inbox. Progress through the system can be viewed via the <a href="metagenomics.cgi?page=MetagenomeSelect" target='blank'>Browse page <img title="Browse" style="width: 20px; height: 20px;" src="./Html/mgrast_globe.png"></a>.</p>
</div>
</ul>
</div>
</form>
</div>
</div>
</div>
</div>
<img src='./Html/clear.gif' onload='init_all();'>~;
}
sub require_javascript {
return [ "$Conf::cgi_url/Html/jquery.js",
"$Conf::cgi_url/Html/FileUploader.js",
"$Conf::cgi_url/Html/bootstrap.js",
"$Conf::cgi_url/Html/Upload.js",
"$Conf::cgi_url/Html/DataHandler.js" ];
}
sub require_css {
return [ "$Conf::cgi_url/Html/bootstrap-responsive.min.css",
"$Conf::cgi_url/Html/bootstrap.min.css",
"$Conf::cgi_url/Html/Upload.css" ];
}
sub submit_to_mgrast {
my ($self) = @_;
my $application = $self->application;
my $user = $self->application->session->user;
my $cgi = $self->application->cgi;
my $jobdbm = $self->application->data_handle('MGRAST');
my $mdata = $cgi->param('mdfile') || '';
my $project_name = $cgi->param('new_project') || '';
my $project_id = $cgi->param('project') || '';
my $base_dir = "$Conf::incoming";
my $udir = $base_dir."/".md5_hex($user->login);
my $lib_file_mgname = {};
my $project_obj = undef;
my $mddb = MGRAST::Metadata->new();
my ($is_valid, $data, $log);
# get project name from metadata
if ($mdata) {
($is_valid, $data, $log) = $mddb->validate_metadata($udir."/".$mdata);
if ($is_valid) {
$project_name = $data->{data}{project_name}{value};
foreach my $sample ( @{$data->{samples}} ) {
if ($sample->{libraries} && scalar(@{$sample->{libraries}})) {
foreach my $library (@{$sample->{libraries}}) {
next unless (exists($library->{data}) && exists($library->{data}{metagenome_name}));
if (exists $library->{data}{file_name}) {
my ($basename) = $library->{data}{file_name}{value} =~ /^(.*)\.(fasta|fa|ffn|frn|fna|fastq|fq)$/;
$lib_file_mgname->{$basename} = $library->{data}{metagenome_name}{value};
} else {
$lib_file_mgname->{$library->{data}{metagenome_name}{value}} = $library->{data}{metagenome_name}{value};
}
}
}
}
} else {
$self->application->add_message('warning', "Metadata file $mdata is invalid, aborting submission. Please re-run validation in Step 1.");
return undef;
}
}
# get project if exists from name or id
if ($project_name) {
my $projects = $jobdbm->Project->get_objects( { name => $project_name } );
if (scalar(@$projects) && $user->has_right(undef, 'view', 'project', $projects->[0]->id)) {
$project_obj = $projects->[0];
}
}
elsif ($project_id) {
my $projects = $jobdbm->Project->get_objects( { id => $project_id } );
if (scalar(@$projects) && $user->has_right(undef, 'view', 'project', $projects->[0]->id)) {
$project_obj = $projects->[0];
}
}
else {
$self->application->add_message('warning', "Unable to find project information, aborting submission. Please re-do Step 1 or 2.");
return undef;
}
# make project if no metadata
if ((! $mdata) && (! $project_obj) && $project_name) {
$project_obj = $jobdbm->Project->create_project($user, $project_name);
}
my $dereplicate = $cgi->param('dereplication');
my $bowtie = $cgi->param('screening') eq 'none' ? 0 : 1;
my $screen_indexes = $cgi->param('screening');
my $dynamic_trim = $cgi->param('dynamic_trim');
my $min_qual = $cgi->param('min_qual');
my $max_lqb = $cgi->param('max_lqb');
my $filter_ln = $cgi->param('filter_ln');
my $filter_ln_mult = $cgi->param('deviation');
my $filter_ambig = $cgi->param('filter_ambig');
my $max_ambig = $cgi->param('max_ambig');
my $priority = $cgi->param('priorityOption');
my $seqfiles = [];
@$seqfiles = split /\|/, $cgi->param('seqfiles');
my $infos = {};
foreach my $seqfile (@$seqfiles) {
if (open(FH, "<$udir/$seqfile.stats_info")) {
my ($filename_base, $filename_ending) = $seqfile =~ /^(.*)\.(fasta|fa|ffn|frn|fna|fastq|fq)$/;
my $subdir = "";
if ($filename_base =~ /\//) {
($subdir, $filename_base) = $filename_base =~ /^(.*\/)(.*)/;
}
if ($filename_ending ne 'fastq') {
if ($filename_ending eq 'fq') {
$filename_ending = 'fastq';
}
$filename_ending = 'fna';
`mv '$udir/$seqfile' '$udir/$subdir$filename_base.$filename_ending'`;
$seqfile = "$subdir$filename_base.$filename_ending";
}
my $name = $filename_base;
# die if using metadata and no filename-library match
if ($mdata) {
if (exists $lib_file_mgname->{$filename_base}) {
$name = $lib_file_mgname->{$filename_base};
}
else {
close FH;
$self->application->add_message('warning', "$seqfile has no matching library metagenome_name or file_name in metadata $mdata, aborting submission.");
return undef;
}
}
my $info = { 'dereplicate' => $dereplicate ? 1 : 0,
'bowtie' => $bowtie,
'screen_indexes' => $screen_indexes,
'dynamic_trim' => $dynamic_trim ? 1 : 0,
'min_qual' => $min_qual,
'max_lqb' => $max_lqb,
'filter_ln' => $filter_ln ? 1 : 0,
'filter_ambig' => $filter_ambig ? 1 : 0,
'max_ambig' => $max_ambig,
'file' => $seqfile,
'name' => $name,
'priority' => $priority
};
while (<FH>) {
chomp;
my ($key, $val) = split /\t/;
$info->{$key} = $val;
}
if ($filter_ln_mult) {
$info->{min_ln} = int($info->{average_length} - ($filter_ln_mult * $info->{standard_deviation_length}));
$info->{max_ln} = int($info->{average_length} + ($filter_ln_mult * $info->{standard_deviation_length}));
if ($info->{min_ln} < 1) { $info->{min_ln} = 1; }
}
if ($info->{file_type} eq 'fasta') { $info->{file_type} = 'fna'; }
$infos->{$seqfile} = $info;
close FH;
} else {
$self->application->add_message('warning', "Could not open information file for $seqfile, aborting submission.");
return undef;
}
}
my $jobs = [];
my $job2seq = {};
my $job2type = {};
# create jobs with providence data
foreach my $seqfile (@$seqfiles) {
my $job = $jobdbm->Job->initialize($user, $infos->{$seqfile});
$job2seq->{$job->{job_id}} = $seqfile;
$job2type->{$job->{job_id}} = $infos->{$seqfile}{file_type};
if (ref($job)) {
push(@$jobs, $job);
}
}
my $successfully_created_jobs = [];
my $err_msgs = [];
# create metadata collections
if ($mdata) {
($successfully_created_jobs, $err_msgs) = $mddb->add_valid_metadata($user, $data, $jobs, $project_obj);
}
# else just add to project
elsif ($project_obj) {
foreach my $job (@$jobs) {
my $msg = $project_obj->add_job($job);
if ($msg =~ /error/i) {
print STDERR $msg;
} else {
push @$successfully_created_jobs, $job;
}
}
}
else {
$self->application->add_message('warning', "Unable to find / create vaild project, aborting submission.");
return undef;
}
my $pid = fork();
# child
if ($pid == 0) {
close STDERR;
close STDOUT;
foreach my $job (@$successfully_created_jobs) {
my $create_job_script = $Conf::create_job;
my $seqfile = $job2seq->{$job->{job_id}};
my $jid = $job->{job_id};
my $is_fastq = ($job2type->{$job->{job_id}} eq 'fastq') ? " --fastq" : "";
my $options = $job->{options} ? ' -o "'.$job->{options}.'"' : "";
my $result = `$create_job_script -j $jid -f "$udir/$seqfile"$options$is_fastq`;
# check if the sequence file made it over to the jobdirectory, then delete it in the inbox
my $rawfile = $job->download_dir.$job->{job_id}.".";
if ($is_fastq) {
$rawfile .= "fastq";
} else {
$rawfile .= "fna";
}
if (-f $rawfile && (stat($rawfile))[7] == (stat("$udir/$seqfile"))[7]) {
`rm "$udir/$seqfile"`;
}
}
exit;
}
# parent
else {
my $mgids = [];
@$mgids = map { $_->{metagenome_id} } @$successfully_created_jobs;
return $mgids;
}
}
sub check_for_duplicates {
my ($self) = @_;
my $application = $self->application;
my $user = $self->application->session->user;
my $cgi = $self->application->cgi;
my $jobdbm = $self->application->data_handle('MGRAST');
my $seqfiles = [];
my $base_dir = "$Conf::incoming";
my $udir = $base_dir."/".md5_hex($user->login);
my $output = '';
@$seqfiles = split(/\|/, $cgi->param('seqfiles'));
my $dupes = [];
foreach my $seqfile (@$seqfiles) {
if (open(FH, "<$udir/$seqfile.stats_info")) {
my $info = {};
while (<FH>) {
chomp;
my ($key, $val) = split /\t/;
$info->{$key} = $val;
}
next unless (exists $info->{file_checksum});
my $dupe = $jobdbm->Job->has_checksum($info->{file_checksum}, $user);
if ($dupe) {
push @$dupes, [$dupe, $seqfile];
}
}
}
if (@$dupes > 0) {
$output = "WARNING: The following selected files already exist in MG-RAST:\n\nExisting ID\tYour File\n---------------\t---------------\n";
map { $output .= join("\t", @$_)."\n" } @$dupes;
$output .= "\nDo you really wish to continue with this submission and create ".scalar(@$dupes)." duplicate metagenomes?";
print $cgi->header;
print $output;
} else {
print $cgi->header;
print "unique";
}
exit 0;
}
sub check_project_name {
my ($self) = @_;
my $cgi = $self->application->cgi;
my $user = $self->application->session->user;
my $project_name = $cgi->param('new_project');
my $project_id = $cgi->param('project');
my $jobdb = $self->application->data_handle('MGRAST');
my $projects;
if ($project_name) {
$projects = $jobdb->Project->get_objects({ name => $project_name });
} else {
$projects = $jobdb->Project->get_objects({ id => $project_id });
}
if (scalar(@$projects) && ! $user->has_right(undef, 'edit', 'project', $projects->[0]->{id})) {
print $cgi->header();
print 0;
} else {
print $cgi->header();
print 1;
}
exit 0;
}
sub read_status_file {
my ($self) = @_;
my $application = $self->application;
my $user = $self->application->session->user;
my $cgi = $self->application->cgi;
my $type = $cgi->param('type');
my $filename = $cgi->param('filename');
my $base_dir = "$Conf::incoming";
my $udir = $base_dir."/".md5_hex($user->login);
my $status_file = "$udir/$filename.$type";
my $msg = "";
if (-f $status_file) {
$msg = `cat $status_file`;
chomp $msg;
}
print $cgi->header;
print $msg;
exit 0;
}
sub validate_metadata {
my ($self) = @_;
my $application = $self->application;
my $user = $self->application->session->user;
my $cgi = $self->application->cgi;
my $fn = $cgi->param('mdfn');
my $base_dir = "$Conf::incoming";
my $udir = $base_dir."/".md5_hex($user->login);
my $md_file = $udir."/".$fn;
my $project_name = 'none';
my ($is_valid, $data, $log) = MGRAST::Metadata->validate_metadata($md_file);
my $formatted_data = "<p>Your uploaded metadata did not pass validation. Please correct the file and upload again. The following errors were detected:</p>";
if ($is_valid) {
$formatted_data = "<p>Your metadata file successfully passed validation.</p>";
$project_name = $data->{data}->{project_name}->{value};
if ($project_name) {
my $jobdbm = $application->data_handle('MGRAST');
my $projects = $jobdbm->Project->get_objects( { name => $project_name } );
if (scalar(@$projects) && (! $user->has_right(undef, 'view', 'project', $projects->[0]->id))) {
print $cgi->header;
print "0||taken||The project name you have chosen is already taken and you do not have edit rights to this project.\nPlease choose a different project name or ask the owner of the project for edit rights.";
exit 0;
} else {
$formatted_data .= "<img src='./Html/clear.gif' onload='selected_project=".$project_name."'>";
}
}
my $barcodes = {};
my $lib_name_file = {};
foreach my $sample ( @{$data->{samples}} ) {
if ($sample->{libraries} && scalar(@{$sample->{libraries}})) {
foreach my $library (@{$sample->{libraries}}) {
next unless (exists($library->{data}) && exists($library->{data}{metagenome_name}));
if (exists $library->{data}{file_name}) {
my ($basename) = $library->{data}{file_name}{value} =~ /^(.*)\.(fasta|fa|ffn|frn|fna|fastq|fq)$/;
$lib_name_file->{$library->{data}{metagenome_name}{value}} = $basename;
} else {
$lib_name_file->{$library->{data}{metagenome_name}{value}} = $library->{data}{metagenome_name}{value};
}
if (exists $library->{data}{forward_barcodes}) {
$barcodes->{ $lib_name_file->{$library->{data}{metagenome_name}{value}} } = $library->{data}{forward_barcodes}{value};
}
}
}
}
if (scalar(keys(%$barcodes))) {
$fn =~ s/^(.*)\.xls(x)?$/$1/;
my $barname = $fn.".barcodes";
if (! -f $udir."/".$barname) {
open(FH, ">$udir/$barname") or die "could not open barcode file for writing ($udir/$barname): ".$!."\n";
foreach my $key (keys(%$barcodes)) {
print FH $barcodes->{$key}."\t".$key."\n";
}
close FH;
$formatted_data .= "<p>Barcodes were detected in your metadata file. A barcode file with the provided codes has been placed in your inbox. You can use this to demultiplex your sequence file below. Select the sequence file and the barcode file ($barname) and click 'demultiplex'.</p>";
}
}
$formatted_data .= "<p>You designated the administrative contact for the project <b>'".$project_name."'</b> to be ".$data->{data}->{PI_firstname}->{value}." ".$data->{data}->{PI_lastname}->{value}." (".$data->{data}->{PI_email}->{value}."). This project contains ".scalar(@{$data->{samples}})." samples with ".scalar(keys %$lib_name_file)." libraries having the following metagenome names:</p><p><table>";
my $example = '';
foreach my $name (sort keys %$lib_name_file) {
$example = $name;
$formatted_data .= "<tr><td>".$name."</td></tr>";
}
$formatted_data .= "</table></p>";
if (scalar(keys %$lib_name_file) > 1) {
$formatted_data .= "<p><b>Caution:</b> Since you have more than one library, the names of the sequence files must match the library <i>metagenome_name</i> fields minus extension (i.e. the filename for library metagenome_name $example must be $example.fastq or $example.fna) or exactly match the library <i>file_name</i> fields.<br><i><b>Note:</b> All FASTA files will automatically be renamed .fna</i></p>";
$formatted_data .= "||".join("@@", values %$lib_name_file);
}
} else {
$data = $data->{data};
if ($data && (@$data > 0)) {
$formatted_data .= "<table><tr><th>tab</th><th>column</th><th>row</th><th>value</th><th>error</th></tr>";
foreach my $row (@$data) {
$formatted_data .= "<tr><td>".$row->[0]."</td><td>".$row->[1]."</td><td>".$row->[2]."</td><td>".$row->[3]."</td><td>".$row->[4]."</td></tr>";
}
$formatted_data .= "</table>";
} else {
$formatted_data .= "<p><pre>$log</pre><p>";
}
$formatted_data .= "<input type='button' class='btn' value='select new metadata file' onclick='selected_metadata_file=null;update_inbox();'>";
}
print $cgi->header;
print $is_valid."||".$project_name."||".$formatted_data;
exit 0;
}
sub generate_webkey {
my ($self) = @_;
my $application = $self->application();
my $cgi = $application->cgi();
my $master = $application->dbmaster();
my $user = $application->session->user();
my $generated = "";
my $existing_key = $master->Preferences->get_objects( { 'user' => $user, 'name' => 'WebServicesKey' } );
my $existing_date = $master->Preferences->get_objects( { 'user' => $user, 'name' => 'WebServiceKeyTdate' } );
if (scalar(@$existing_key) && ! $cgi->param('generate_new_key')) {
$existing_key = $existing_key->[0]->{value};
$existing_date = $existing_date->[0]->{value};
} else {
my $possible = 'abcdefghijkmnpqrstuvwxyz23456789ABCDEFGHJKLMNPQRSTUVWXYZ';
while (length($generated) < 25) {
$generated .= substr($possible, (int(rand(length($possible)))), 1);
}
my $preference = $master->Preferences->get_objects( { value => $generated } );
while (scalar(@$preference)) {
$generated = "";
while (length($generated) < 25) {
$generated .= substr($possible, (int(rand(length($possible)))), 1);
}
$preference = $master->Preferences->get_objects( { value => $generated } );
}
my $timeout = 60 * 60 * 24 * 7; # one week
my $tdate = time + $timeout;
my $pref = $master->Preferences->get_objects( { 'user' => $user, 'name' => 'WebServiceKeyTdate' } );
if (scalar(@$pref)) {
$pref = $pref->[0];
} else {
$pref = $master->Preferences->create( { 'user' => $user, 'name' => 'WebServiceKeyTdate' } );
}
$pref->value($tdate);
$pref = $master->Preferences->get_objects( { 'user' => $user, 'name' => 'WebServicesKey' } );
if (scalar(@$pref)) {
$pref = $pref->[0];
} else {
$pref = $master->Preferences->create( { 'user' => $user, 'name' => 'WebServicesKey' } );
}
$pref->value($generated);
$existing_key = $generated;
$existing_date = $tdate;
# create a symlink
}
my $content = "<b>Your current WebKey:</b> <input type='text' readOnly=1 size=25 value='" . $existing_key . "'>";
my ($sec,$min,$hour,$mday,$mon,$year) = localtime($existing_date);
my $tdate_readable = ($year + 1900)." ".sprintf("%02d", $mon + 1)."-".sprintf("%02d", $mday)." ".sprintf("%02d", $hour).":".sprintf("%02d", $min).".".sprintf("%02d", $sec);
$content .= " <b>valid until</b>: <input type='text' readOnly=1 size=20 value='" . $tdate_readable . "'>";
$content .= " <input type='button' class='btn' value='generate new key' onclick='generate_webkey(1);'>";
$content .= "<img src='./Html/clear.gif' onload='document.getElementById(\"ftp_webkey\").innerHTML=\"" . $existing_key . "\";document.getElementById(\"http_webkey\").innerHTML=\"" . $existing_key . "\";'>";
print $cgi->header;
print $content;
exit 0;
}
sub TO_JSON { return { %{ shift() } }; }