cgi-bin/sequencing/itag/status_html.pl

   1 use CatalystX::GlobalContext qw( $c );
   2 use strict;
   3 use warnings;
   4
   5 use File::Basename;
   6
   7 use JSON;
   8
   9 use CXGN::Page;
  10 use CXGN::Page::FormattingHelpers qw( info_section_html
  11                                       modesel
  12                                       hierarchical_selectboxes_html
  13                                       columnar_table_html
  14                                       info_table_html
  15                                     );
  16 use CXGN::Tools::Identifiers qw/link_identifier/;
  17 use CXGN::ITAG::Pipeline;
  18 use CXGN::Tools::List qw/all/;
  19
  20 my $itag_feature = $c->enabled_feature('itag')
  21     or $c->forward_to_mason_view('/itag/not_enabled.mas');
  22
  23 my $page = CXGN::Page->new('ITAG Pipeline Status Viewer','Robert Buels');
  24 $page->jsan_use('MochiKit.Base','MochiKit.Async');
  25
  26 my ($mode,$pipe,$batch) = $page->get_encoded_arguments(qw( mode pipe batch ));
  27 if( $mode && $mode eq 'async' ) {
  28   $ENV{CXGNITAGPIPELINEANALYSISTESTING}=1 unless $c->get_conf('production_server');
  29   my $pipe_obj = $itag_feature->pipeline( version => $pipe );
  30   my $s = get_status( $pipe_obj, $batch+0 );
  31   print "Content-type: text/html\n\n$s";
  32   exit;
  33 } elsif( $mode && $mode eq 'async_ainfo' ) {
  34   my ($aname) = $page->get_encoded_arguments('aname');
  35   my $ainfo = get_analysis_info($pipe,$aname);
  36   print "Content-type: text/html\n\n$ainfo";
  37   exit;
  38 }
  39
  40 $page->header(('ITAG Pipeline Status Viewer') x 2);
  41
  42 #now load styles and javascript specific to this script
  43 print <<EOHTML;
  44 <style>
  45 div#loading_indicator {
  46   background: #eee;
  47   font-weight: bold;
  48   color: black;
  49   padding: 3px;
  50   display: inline;
  51   visibility: hidden;
  52 }
  53 div#loading_indicator > img {
  54   position: relative;
  55   top: 2px;
  56 }
  57
  58 ul.errlist {
  59   margin-top: 0.1em;
  60   max-height: 12em;
  61   overflow: auto;
  62 }
  63 hr.depgroup {
  64   border: 0;
  65   border-top: 1px solid black;
  66 }
  67 span.owner {
  68   white-space: nowrap;
  69 }
  70 span.depends,span.produces, span.tagname, span.owner {
  71  font-family: monospace;
  72 }
  73
  74 #viewer {
  75  border: 1px solid #888;
  76 }
  77
  78 </style>
  79 EOHTML
  80
  81 print <<EOHTML;
  82 <div style="margin-bottom: 1.5em;">This page provides continuously updated information on the running status of the <a href="http://www.ab.wur.nl/TomatoWiki">ITAG Distributed Annotation Pipeline</a>.</div>
  83 EOHTML
  84
  85
  86 my @pipelines = $itag_feature->list_pipelines;
  87 print <<EOH
  88   <table id="viewer" align="center" cellspacing="0" width="100%" ><tr><td style="padding: 0.3em; background: #ccc;">
  89     <form name="batch_selector">
  90 EOH
  91       .hierarchical_selectboxes_html(
  92                                    parentsel => { label => '<b>Pipeline version: </b>',
  93                                                   choices => \@pipelines,
  94                                                   name => 'pipever',
  95                                                   params => {onchange => qq|updateStatusContents()|,
  96                                                             },
  97                                                   selected => $pipe,
  98                                                 },
  99                                    childsel => { label => '<b>Batch: </b>',
 100                                                  name => 'batchnum',
 101                                                  params => {onchange => qq|updateStatusContents()|,
 102                                                            },
 103                                                  selected => $batch,
 104                                                },
 105                                    childchoices => [
 106                                                     map {
 107                                                       my $p = $itag_feature->pipeline( version => $_ );
 108                                                       [sort {$b+0 <=> $a+0} $p->list_batches]
 109                                                     } @pipelines
 110                                                    ],
 111                                   )
 112     .<<EOH
 113     <input type="button" style="background: url(/documents/img/refresh.png); width: 22px; height: 21px" name="refresh" value="" onclick="this.blur(); updateStatusContents()" />
 114     <div id="loading_indicator">Loading... <img src="/documents/img/spinner.gif" /></div>
 115     </form>
 116   </td></tr>
 117   <tr><td id="pipestatus_contents" style="border: 2px solid #bbb; padding: 0.5em;">
 118   </td></tr>
 119   </table>
 120 EOH
 121   ;
 122
 123 print <<EOS;
 124 <script type="text/javascript">
 125   var refresh_bg = document.batch_selector.refresh.style.background;
 126
 127   var updateStatusContents = function() {
 128     var loading_ind = document.getElementById('loading_indicator');
 129
 130     var pipesel = document.batch_selector.pipever;
 131     var batchsel = document.batch_selector.batchnum;
 132     var refresh_button = document.batch_selector.refresh
 133
 134     var controls_disabled = function(disabled) {
 135         pipesel.disabled =
 136           batchsel.disabled =
 137              refresh_button.disabled = disabled;
 138         if( disabled ) {
 139           refresh_button.style.background = null;
 140         } else {
 141           refresh_button.style.background = refresh_bg;
 142         }
 143     };
 144
 145     var set_loading = function(is_on) {
 146       if(is_on) {
 147         loading_ind.style.visibility = 'visible';
 148         controls_disabled(true);
 149       } else {
 150         loading_ind.style.visibility = 'hidden';
 151         controls_disabled(false);
 152       }
 153     };
 154
 155     var contentarea = document.getElementById('pipestatus_contents');
 156
 157     // don't update if we don't have any pipeline or batches
 158     if( !pipesel.options.length ) {
 159       controls_disabled(true);
 160       contentarea.innerHTML = 'no pipelines available';
 161       return;
 162     }
 163     if( !batchsel.options.length ) {
 164       batchsel.disabled = refresh_button.disabled = true;
 165       contentarea.innerHTML = 'no batches available in pipeline ' + pipesel.value
 166       return;
 167     }
 168
 169     set_loading(true);
 170
 171     var set = function(req) {
 172       contentarea.innerHTML = req.responseText;
 173       set_loading(false);
 174     };
 175     var err = function() {
 176        contentarea.innerHTML = 'Error retrieving pipeline status';
 177        set_loading(false);
 178     }
 179     var res = MochiKit.Async.doSimpleXMLHttpRequest( "status_html.pl",
 180                                                      { mode: 'async',
 181                                                        pipe: pipesel.value,
 182                                                        batch: batchsel.value,
 183                                                        t: Math.random()
 184                                                      }
 185                                                    );
 186     res.addCallbacks(set,err);
 187
 188   };
 189
 190   updateStatusContents();
 191 </script>
 192 EOS
 193
 194 $page->footer;
 195
 196
 197
 198
 199 ###################### SUBROUTINES ######################
 200
 201 #given a pipeline version and batch number, return a bunch of html showing its status
 202 sub get_status {
 203   my ( $pipe, $batchnum ) = @_;
 204
 205   my $retstring;
 206   my $batch = $pipe->batch($batchnum);
 207   my %errstrings; #< hash of tag name => error message
 208
 209   my @analyses = map { $pipe->analysis($_) } $pipe->list_analyses;
 210   my %existing_analyses = map {$_->tagname =>1} @analyses;
 211   #now sort the analyses by their dependencies
 212   my @sorted_analyses;
 213   my %already_processed;
 214   while( @analyses ) {
 215     my @ans_this_level;
 216     foreach my $an (@analyses) {
 217       next unless $an;
 218       my @existing_dependencies = grep $existing_analyses{$_}, $an->dependencies;
 219       if( all @already_processed{ @existing_dependencies } ) {
 220         push @ans_this_level, $an;
 221         $an = undef;
 222       }
 223     }
 224     last unless @ans_this_level;
 225     $already_processed{$_} = 1 foreach map {$_->tagname} @ans_this_level;
 226     push @sorted_analyses,\@ans_this_level;
 227   }
 228   if( my @other_analyses = grep $_,@analyses ) {
 229     push @sorted_analyses,\@other_analyses;
 230   }
 231
 232   #now sorted_analyses is an array like ( [an,an,...], [an,an,...] ),
 233   #where each set of analyses is dependent on the ones before it
 234
 235   my $rowcount = 0;
 236   my $statuses =  columnar_table_html( headings => ['Status','Analysis Tag','Owner','Produces',],
 237                                        __alt_freq => 2,
 238                                       #__align => 'cl',
 239                                        __tableattrs => 'width="100%" summary="" cellspacing="0" align="center"',
 240                                        data =>
 241                                       [
 242                                        map {
 243                                          (($rowcount++) ? ([('<hr class="depgroup" />')x4]) : ()),
 244                                          map {
 245                                            my $an = $_;
 246                                            my $st = $an->status($batchnum);
 247                                            my %t = ( ready => 'inputs ready',
 248                                                      not_ready => 'not ready',
 249                                                    );
 250                                            my %c = ( ready   => '#6666ff',
 251                                                      error   => '#ff0000',
 252                                                      done    => '#00ff00',
 253                                                      running => '#00ffff',
 254                                                      validating => '#dd00dd',
 255                                                    );
 256                                            my $c = $c{$st};
 257                                            my $t = $t{$st} || $st;
 258                                            if ($st eq 'error') {
 259                                              my @errors = $an->errors($batchnum);
 260                                              #TODO: MAKE THIS NOT BE SUCH A HACK
 261                                              my $atag = $an->tagname;
 262                                              foreach (@errors) {
 263                                                my ($valname,$filename) = /^(\S+) validation failed for file (\S+),/
 264                                                  or next;
 265                                                $_ =~ s|\[report file\]|<a href="report_download.pl?pipe=&batch=$batchnum&atag=$atag&filename=$filename&valname=$valname">report file</a>|;
 266                                              }
 267                                              $errstrings{$atag} = join '',map "<li>$_</li>",@errors;
 268                                              $errstrings{$atag} &&= '<ul class="errlist">'.$errstrings{$atag}.'</ul>';
 269                                            }
 270                                            $st = $c ? qq|<div style="background: $c; padding: 2px 2em 2px 2em;">$t</div>| : $t;
 271                                            my $owner_info = $an->owner_info;
 272                                            my $name = $owner_info->{contact_name};
 273                                            $name .= ',' if $name;
 274                                            $owner_info->{email} = obfuscate_email($owner_info->{email});
 275                                            [ mkspans(
 276                                                      status => $st,
 277                                                      tagname => $an->tagname,
 278                                                      owner => qq|$name $owner_info->{email}|,
 279                                                      produces => join(', ', $an->output_files_specs ),
 280                                                     )
 281                                            ],
 282                                          } grep {
 283                                            $_->status($batchnum) ne 'disabled'
 284                                          } @$_
 285                                        } @sorted_analyses
 286                                       ],
 287                                      );
 288
 289   my $errs = do {
 290     if(%errstrings) {
 291       info_section_html( title => 'Errors',
 292                          contents =>
 293                          join('',
 294                               map {
 295                                 "<b>$_</b>$errstrings{$_}"
 296                               } sort keys %errstrings
 297                              ),
 298                          is_subsection => 1,
 299                        );
 300       } else {
 301         ''
 302       }
 303   };
 304
 305   my @seqlist = sort $batch->seqlist;
 306   my $seqlist_html = join('',
 307                           '<div style="height: 20em; width: 10em; overflow: auto; border: 1px solid #cccccc; padding: 6px">',
 308                           ( map {
 309                               (link_identifier($_)||$_).'<br />'
 310                             } @seqlist
 311                           ),
 312                           '</div>',
 313                          );
 314   my $seq_cnt = scalar @seqlist;
 315   return <<EOH;
 316 <table align="center" style="margin-bottom: 0.5em">
 317   <tr>
 318     <td><b>Sequences ($seq_cnt)</b> $seqlist_html</td>
 319     <td>$statuses</td>
 320   </tr>
 321 </table>
 322 $errs
 323 EOH
 324 }
 325
 326 ########## UTILITY FUNCTIONS
 327
 328 sub obfuscate_email {
 329   my $email = shift;
 330   my ($emailuser,$emaildomain) = split /@/, $email;
 331   $emaildomain =~ s/\./ /g;
 332   return "$emailuser _ $emaildomain";
 333 }
 334
 335 sub mkspans(@) {
 336   my @ret;
 337   while(my ($class,$html) = splice @_,0,2) {
 338     push @ret,qq|<span class="$class">$html</span>|;
 339   }
 340   return @ret;
 341 }