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Revision 1.4 - (view) (download) (as text)
| 1 : | jared | 1.1 | package PRAST::WebPage::Jobs; |
| 2 : | |||
| 3 : | use strict; | ||
| 4 : | use warnings; | ||
| 5 : | |||
| 6 : | use base qw( WebPage ); | ||
| 7 : | |||
| 8 : | use WebComponent::WebGD; | ||
| 9 : | use RAST::MGRAST; | ||
| 10 : | use WebConfig; | ||
| 11 : | use Data::Dumper; | ||
| 12 : | |||
| 13 : | 1; | ||
| 14 : | |||
| 15 : | |||
| 16 : | =pod | ||
| 17 : | |||
| 18 : | =head1 NAME | ||
| 19 : | |||
| 20 : | Jobs - an instance of WebPage which displays an overview over all jobs | ||
| 21 : | |||
| 22 : | =head1 DESCRIPTION | ||
| 23 : | |||
| 24 : | Job overview page | ||
| 25 : | |||
| 26 : | =head1 METHODS | ||
| 27 : | |||
| 28 : | =over 4 | ||
| 29 : | |||
| 30 : | =item * B<init> () | ||
| 31 : | |||
| 32 : | Called when the web page is instanciated. | ||
| 33 : | |||
| 34 : | =cut | ||
| 35 : | |||
| 36 : | sub init { | ||
| 37 : | my $self = shift; | ||
| 38 : | |||
| 39 : | $self->title("Jobs Overview"); | ||
| 40 : | $self->application->register_component('Table', 'Jobs'); | ||
| 41 : | |||
| 42 : | |||
| 43 : | } | ||
| 44 : | |||
| 45 : | |||
| 46 : | =item * B<output> () | ||
| 47 : | |||
| 48 : | Returns the html output of the page. | ||
| 49 : | |||
| 50 : | =cut | ||
| 51 : | |||
| 52 : | sub output { | ||
| 53 : | my ($self) = @_; | ||
| 54 : | |||
| 55 : | my $content = '<h1>Jobs Overview</h1>'; | ||
| 56 : | |||
| 57 : | jared | 1.3 | $content .= '<p>The overview below list all genomes currently processed and the progress on the annotation. '. |
| 58 : | 'To get a more detailed report on an annotation job, please click on the progress bar graphic in the overview.</p>'; | ||
| 59 : | $content .= '<p>In case of questions or problems using this service, please contact: '.(($WebConfig::RAST_TYPE eq 'metagenome') ? '<a href="mailto:mg-rast@mcs.anl.gov">mg-rast@mcs.anl.gov</a>' : '<a href="mailto:rast@mcs.anl.gov">rast@mcs.anl.gov</a>').'.</p>'; | ||
| 60 : | jared | 1.1 | |
| 61 : | $content .= $self->get_color_key(); | ||
| 62 : | |||
| 63 : | $content .= '<h2>Jobs you have access to :</h2>'; | ||
| 64 : | |||
| 65 : | my $data = []; | ||
| 66 : | my @job_list; | ||
| 67 : | my $users; | ||
| 68 : | my $pjobs; | ||
| 69 : | my %admins; | ||
| 70 : | |||
| 71 : | eval { | ||
| 72 : | |||
| 73 : | @job_list = $self->app->data_handle('RAST')->Job->get_jobs_for_user_fast($self->application->session->user); | ||
| 74 : | |||
| 75 : | # | ||
| 76 : | # Gather the user ids from the job list, and query for them. | ||
| 77 : | # | ||
| 78 : | |||
| 79 : | my $udbh = $self->application->session->user->_master->db_handle; | ||
| 80 : | |||
| 81 : | my %users = map { $_->{owner} => 1 } @job_list; | ||
| 82 : | |||
| 83 : | if (scalar(keys(%users))) { | ||
| 84 : | my $user_cond = join(", ", keys %users); | ||
| 85 : | $users = $udbh->selectall_hashref(qq(SELECT _id, firstname, lastname, email | ||
| 86 : | FROM User | ||
| 87 : | WHERE _id IN ($user_cond)), '_id'); | ||
| 88 : | |||
| 89 : | # | ||
| 90 : | # Create display names for users, with email addresses if we're an admin. | ||
| 91 : | # | ||
| 92 : | |||
| 93 : | my $user = $self->app->session->user; | ||
| 94 : | my $app = $self->application->backend; | ||
| 95 : | |||
| 96 : | for my $val (values (%$users)) | ||
| 97 : | { | ||
| 98 : | if ( $val->{email} and $user and $user->is_admin($app) ) | ||
| 99 : | { | ||
| 100 : | $val->{name_display} = qq(<a href="mailto:$val->{email}, mg-rast\@mcs.anl.gov">$val->{lastname}, $val->{firstname}</a>); | ||
| 101 : | } else { | ||
| 102 : | $val->{name_display} = "$val->{lastname}, $val->{firstname}"; | ||
| 103 : | |||
| 104 : | } | ||
| 105 : | } | ||
| 106 : | |||
| 107 : | if ($WebConfig::RAST_TYPE eq 'metagenome'){ | ||
| 108 : | $pjobs = RAST::MGRAST::get_public_metagenomes($self->application->dbmaster); | ||
| 109 : | } | ||
| 110 : | } else { | ||
| 111 : | @job_list = (); | ||
| 112 : | } | ||
| 113 : | }; | ||
| 114 : | |||
| 115 : | if (ref $pjobs and scalar (@$pjobs) ){ | ||
| 116 : | $content .= "<p>You currently have access to ".scalar @$pjobs." public jobs.</p>"; | ||
| 117 : | } | ||
| 118 : | elsif ($WebConfig::RAST_TYPE eq 'metagenome'){ | ||
| 119 : | $content .= "<p>There are no public jobs.</p>"; | ||
| 120 : | } | ||
| 121 : | |||
| 122 : | my $user = $self->app->session->user->_id; | ||
| 123 : | my $is_admin = $admins{$user}; | ||
| 124 : | |||
| 125 : | if (scalar(@job_list)) { | ||
| 126 : | @job_list = sort { $b->{id} <=> $a->{id} } @job_list; | ||
| 127 : | foreach my $job (@job_list) { | ||
| 128 : | push @$data, $self->genome_entry_fast($job, $users, $is_admin); | ||
| 129 : | } | ||
| 130 : | # create table | ||
| 131 : | my $table = $self->application->component('Jobs'); | ||
| 132 : | $table->width(800); | ||
| 133 : | if (scalar(@$data) > 50) { | ||
| 134 : | $table->show_top_browse(1); | ||
| 135 : | $table->show_bottom_browse(1); | ||
| 136 : | $table->items_per_page(50); | ||
| 137 : | $table->show_select_items_per_page(1); | ||
| 138 : | } | ||
| 139 : | $table->columns([ { name => 'Job', filter => 1, sortable => 1 }, | ||
| 140 : | paczian | 1.4 | { name => 'Owner', filter => 1, sortable => 1 }, |
| 141 : | { name => 'ID', filter => 1, sortable => 1 }, | ||
| 142 : | { name => 'Name', filter => 1, sortable => 1 }, | ||
| 143 : | { name => 'Num contigs', sortable => 1 }, | ||
| 144 : | { name => 'Size (bp)', sortable => 1 }, | ||
| 145 : | { name => 'Creation Date' }, | ||
| 146 : | { name => 'Annotation Progress' }, | ||
| 147 : | { name => 'Current Stage', filter => 1, operator => 'combobox' } | ||
| 148 : | ]); | ||
| 149 : | jared | 1.1 | $table->data($data); |
| 150 : | $content .= $table->output(); | ||
| 151 : | } | ||
| 152 : | else { | ||
| 153 : | $content .= "<p>You currently have no jobs.</p>"; | ||
| 154 : | $content .= "<p> » <a href='?page=Upload'>Upload a new genome</a></p>"; | ||
| 155 : | } | ||
| 156 : | |||
| 157 : | return $content; | ||
| 158 : | } | ||
| 159 : | |||
| 160 : | sub output_old { | ||
| 161 : | my ($self) = @_; | ||
| 162 : | |||
| 163 : | my $content = '<h1>Jobs Overview</h1>'; | ||
| 164 : | |||
| 165 : | $content .= '<p>The overview below list all genomes currently processed and the progress on the annotation. '. | ||
| 166 : | 'To get a more detailed report on an annotation job, please click on the progress bar graphic in the overview.</p>'; | ||
| 167 : | $content .= '<p>In case of questions or problems using this service, please contact: '.(($WebConfig::RAST_TYPE eq 'metagenome') ? '<a href="mailto:mg-rast@mcs.anl.gov">mg-rast@mcs.anl.gov</a>' : '<a href="mailto:rast@mcs.anl.gov">rast@mcs.anl.gov</a>').'.</p>'; | ||
| 168 : | |||
| 169 : | $content .= $self->get_color_key(); | ||
| 170 : | |||
| 171 : | $content .= '<h2>Jobs you have access to :</h2>'; | ||
| 172 : | |||
| 173 : | my $data = []; | ||
| 174 : | my $jobs; | ||
| 175 : | my $pjobs; | ||
| 176 : | eval { | ||
| 177 : | $jobs = $self->app->data_handle('RAST')->Job->get_jobs_for_user($self->application->session->user); | ||
| 178 : | if ($WebConfig::RAST_TYPE eq 'metagenome'){ | ||
| 179 : | $pjobs = RAST::MGRAST::get_public_metagenomes($self->application->dbmaster); | ||
| 180 : | } | ||
| 181 : | }; | ||
| 182 : | unless (defined $jobs) { | ||
| 183 : | $self->app->error("Unable to retrieve the job overview."); | ||
| 184 : | return ''; | ||
| 185 : | } | ||
| 186 : | if (ref $pjobs and scalar (@$pjobs) ){ | ||
| 187 : | $content .= "<p>You currently have access to ".scalar @$pjobs." public jobs.</p>"; | ||
| 188 : | } | ||
| 189 : | elsif ($WebConfig::RAST_TYPE eq 'metagenome'){ | ||
| 190 : | $content .= "<p>There are no public jobs.</p>"; | ||
| 191 : | } | ||
| 192 : | |||
| 193 : | if (scalar(@$jobs)) { | ||
| 194 : | $jobs->[0]->resolve('owner', $jobs); | ||
| 195 : | @$jobs = sort { $b->id <=> $a->id } @$jobs; | ||
| 196 : | foreach my $job (@$jobs) { | ||
| 197 : | push @$data, $self->genome_entry($job); | ||
| 198 : | } | ||
| 199 : | # create table | ||
| 200 : | my $table = $self->application->component('Jobs'); | ||
| 201 : | $table->width(800); | ||
| 202 : | if (scalar(@$data) > 50) { | ||
| 203 : | $table->show_top_browse(1); | ||
| 204 : | $table->show_bottom_browse(1); | ||
| 205 : | $table->items_per_page(50); | ||
| 206 : | $table->show_select_items_per_page(1); | ||
| 207 : | } | ||
| 208 : | $table->columns([ { name => 'Job', filter => 1, sortable => 1 }, | ||
| 209 : | { name => 'Owner', filter => 1, }, | ||
| 210 : | { name => 'ID', filter => 1 }, | ||
| 211 : | { name => 'Name', filter => 1 }, | ||
| 212 : | { name => 'Size (bp)', sortable => 1 }, | ||
| 213 : | { name => 'Creation Date' }, | ||
| 214 : | { name => 'Annotation Progress' }, | ||
| 215 : | ]); | ||
| 216 : | $table->data($data); | ||
| 217 : | $content .= $table->output(); | ||
| 218 : | } | ||
| 219 : | else { | ||
| 220 : | $content .= "<p>You currently have no jobs.</p>"; | ||
| 221 : | $content .= "<p> » <a href='?page=Upload'>Upload a new genome</a></p>"; | ||
| 222 : | } | ||
| 223 : | |||
| 224 : | return $content; | ||
| 225 : | } | ||
| 226 : | |||
| 227 : | |||
| 228 : | =pod | ||
| 229 : | |||
| 230 : | =item * B<genome_entry> (I<job>) | ||
| 231 : | |||
| 232 : | Returns one entry row for the overview table, containing job id, user, | ||
| 233 : | genome info and the progress bar graphic. I<job> has to be the reference | ||
| 234 : | to a RAST::Job object. | ||
| 235 : | |||
| 236 : | =cut | ||
| 237 : | |||
| 238 : | sub genome_entry_fast { | ||
| 239 : | my ($self, $job, $users, $is_admin) = @_; | ||
| 240 : | |||
| 241 : | my $stages; | ||
| 242 : | if ($job->{type} eq 'Metagenome') | ||
| 243 : | { | ||
| 244 : | $stages = $job->{server_version} == 1 ? RAST::Job::stages_for_mgrast_1() : RAST::Job::stages_for_mgrast_(); | ||
| 245 : | } | ||
| 246 : | else | ||
| 247 : | { | ||
| 248 : | jared | 1.3 | print STDERR "attempting PRAST::Job::stages_for_prast()\n"; |
| 249 : | arodri7 | 1.2 | $stages = PRAST::Job::stages_for_prast(); |
| 250 : | jared | 1.1 | } |
| 251 : | |||
| 252 : | # create a new image | ||
| 253 : | my $height = 14; my $box_width = 12; | ||
| 254 : | my $image = WebGD->new(scalar(@$stages)*$box_width,$height); | ||
| 255 : | |||
| 256 : | # allocate some colors | ||
| 257 : | my $colors = $self->get_colors($image); | ||
| 258 : | |||
| 259 : | # make the background transparent and interlaced | ||
| 260 : | $image->transparent($colors->{'white'}); | ||
| 261 : | $image->interlaced('true'); | ||
| 262 : | my $info = ''; | ||
| 263 : | |||
| 264 : | my $index = 0; | ||
| 265 : | paczian | 1.4 | my $cs = ''; |
| 266 : | jared | 1.1 | foreach my $stage (@$stages) |
| 267 : | { | ||
| 268 : | my $s = $job->{status}->{$stage}; | ||
| 269 : | my $status = $s ne '' ? $s : 'not_started'; | ||
| 270 : | if (exists($colors->{$status})) { | ||
| 271 : | $image->filledRectangle($index*$box_width,0,10+$index*$box_width,$height,$colors->{$status}); | ||
| 272 : | } | ||
| 273 : | else { | ||
| 274 : | die "Found unknown status for stage '$stage' in job ".$job->{id}."\n"; | ||
| 275 : | } | ||
| 276 : | |||
| 277 : | if ($status ne 'not_started') { | ||
| 278 : | $status =~ s/_/ /g; | ||
| 279 : | paczian | 1.4 | $cs = $status; |
| 280 : | jared | 1.1 | my $steps = $index + 1; |
| 281 : | $info = "$steps of ".scalar(@$stages)." steps, current step: $status "; | ||
| 282 : | } | ||
| 283 : | $index++; | ||
| 284 : | } | ||
| 285 : | |||
| 286 : | my $id = $job->{id}; | ||
| 287 : | my $progress = '<img style="border: none;" src="'.$image->image_src.'"/>'; | ||
| 288 : | my $link_img = "<a title='$info' href='?page=JobDetails&job=".$id."'>$progress</a>"; | ||
| 289 : | my $link_text = "[ <a href='?page=JobDetails&job=".$id."'><em> view details </em></a> ]"; | ||
| 290 : | |||
| 291 : | my $owner = $users->{$job->{owner}}; | ||
| 292 : | |||
| 293 : | my $creation_date = $job->{created_on}; | ||
| 294 : | #my $size = $job->metaxml->get_metadata('preprocess.count_raw.total') || 0; | ||
| 295 : | my $size = $job->{bp_count}; | ||
| 296 : | |||
| 297 : | return [ $job->{id}, $owner->{name_display}, $job->{genome_id}, $job->{genome_name}, | ||
| 298 : | paczian | 1.4 | $job->{contig_count}, $size, $creation_date, $link_img.'<br/>'.$link_text, $cs ]; |
| 299 : | jared | 1.1 | } |
| 300 : | |||
| 301 : | sub genome_entry { | ||
| 302 : | my ($self, $job) = @_; | ||
| 303 : | |||
| 304 : | # create a new image | ||
| 305 : | my $height = 14; my $box_width = 12; | ||
| 306 : | my $image = WebGD->new(scalar(@{$job->stages})*$box_width,$height); | ||
| 307 : | |||
| 308 : | # allocate some colors | ||
| 309 : | my $colors = $self->get_colors($image); | ||
| 310 : | |||
| 311 : | # make the background transparent and interlaced | ||
| 312 : | $image->transparent($colors->{'white'}); | ||
| 313 : | $image->interlaced('true'); | ||
| 314 : | my $info = ''; | ||
| 315 : | |||
| 316 : | my $index = 0; | ||
| 317 : | foreach my $stage (@{$job->stages}) { | ||
| 318 : | my $s = $job->status($stage); | ||
| 319 : | my $status = (ref $s) ? $s->status : 'not_started'; | ||
| 320 : | if (exists($colors->{$status})) { | ||
| 321 : | $image->filledRectangle($index*$box_width,0,10+$index*$box_width,$height,$colors->{$status}); | ||
| 322 : | } | ||
| 323 : | else { | ||
| 324 : | die "Found unknown status for stage '$stage' in job ".$job->id."\n"; | ||
| 325 : | } | ||
| 326 : | |||
| 327 : | if ($status ne 'not_started') { | ||
| 328 : | $status =~ s/_/ /g; | ||
| 329 : | my $steps = $index + 1; | ||
| 330 : | $info = "$steps of ".scalar(@{$job->stages})." steps, current step: $status "; | ||
| 331 : | } | ||
| 332 : | $index++; | ||
| 333 : | } | ||
| 334 : | |||
| 335 : | my $progress = '<img style="border: none;" src="'.$image->image_src.'"/>'; | ||
| 336 : | my $link_img = "<a title='$info' href='?page=JobDetails&job=".$job->id."'>$progress</a>"; | ||
| 337 : | my $link_text = "[ <a href='?page=JobDetails&job=".$job->id."'><em> view details </em></a> ]"; | ||
| 338 : | my $email = $job->owner->email if (ref $job->owner); | ||
| 339 : | my $firstname = $job->owner->firstname if (ref $job->owner); | ||
| 340 : | my $lastname = $job->owner->lastname if (ref $job->owner); | ||
| 341 : | |||
| 342 : | my $name_display; | ||
| 343 : | |||
| 344 : | my $user = $self->app->session->user; | ||
| 345 : | my $app = $self->application->backend; | ||
| 346 : | |||
| 347 : | if ( $firstname and $lastname ) { | ||
| 348 : | if ( $email and $user and $user->is_admin($app) ) { | ||
| 349 : | $name_display = qq(<a href="mailto:$email, mg-rast\@mcs.anl.gov">$lastname, $firstname</a>); | ||
| 350 : | } else { | ||
| 351 : | $name_display = "$lastname, $firstname"; | ||
| 352 : | } | ||
| 353 : | } else { | ||
| 354 : | $name_display = 'unknown'; | ||
| 355 : | } | ||
| 356 : | |||
| 357 : | my $creation_date = $job->created_on; | ||
| 358 : | my $size = 0; | ||
| 359 : | if ($WebConfig::RAST_TYPE eq 'metagenome') | ||
| 360 : | { | ||
| 361 : | $size = $job->metaxml->get_metadata('preprocess.count_raw.total') || 0; | ||
| 362 : | } | ||
| 363 : | |||
| 364 : | return [ $job->id, $name_display, $job->genome_id, $job->genome_name, $size, $creation_date, $link_img.'<br/>'.$link_text ]; | ||
| 365 : | } | ||
| 366 : | |||
| 367 : | =pod | ||
| 368 : | |||
| 369 : | =item * B<get_color_key> () | ||
| 370 : | |||
| 371 : | Returns the html of the color key used in the progress bars. | ||
| 372 : | |||
| 373 : | =cut | ||
| 374 : | |||
| 375 : | sub get_color_key { | ||
| 376 : | my ($self) = @_; | ||
| 377 : | |||
| 378 : | my $keys = [ [ 'not_started', 'not started' ], | ||
| 379 : | [ 'queued', 'queued for computation' ], | ||
| 380 : | [ 'in_progress', 'in progress' ], | ||
| 381 : | [ 'requires_intervention' => 'requires user input' ], | ||
| 382 : | [ 'error', 'failed with an error' ], | ||
| 383 : | [ 'complete', 'successfully completed' ] ]; | ||
| 384 : | |||
| 385 : | my $html = "<h4>Progress bar color key:</h4>"; | ||
| 386 : | foreach my $k (@$keys) { | ||
| 387 : | |||
| 388 : | my $image = WebGD->new(10, 14); | ||
| 389 : | my $colors = $self->get_colors($image); | ||
| 390 : | $image->filledRectangle(0,0,10,14,$colors->{$k->[0]}); | ||
| 391 : | $html .= '<img style="border: none;" src="'.$image->image_src.'"/> '.$k->[1].'<br>'; | ||
| 392 : | |||
| 393 : | } | ||
| 394 : | |||
| 395 : | return $html; | ||
| 396 : | } | ||
| 397 : | |||
| 398 : | |||
| 399 : | =pod | ||
| 400 : | |||
| 401 : | =item * B<get_colors> (I<gd_image>) | ||
| 402 : | |||
| 403 : | Returns the reference to the hash of allocated colors. I<gd_image> is mandatory and | ||
| 404 : | has to be a GD Image object reference. | ||
| 405 : | |||
| 406 : | =cut | ||
| 407 : | |||
| 408 : | sub get_colors { | ||
| 409 : | my ($self, $image) = @_; | ||
| 410 : | return { 'white' => $image->colorResolve(255,255,255), | ||
| 411 : | 'black' => $image->colorResolve(0,0,0), | ||
| 412 : | 'not_started' => $image->colorResolve(185,185,185), | ||
| 413 : | 'queued' => $image->colorResolve(30,120,220), | ||
| 414 : | 'in_progress' => $image->colorResolve(255,190,30), | ||
| 415 : | 'requires_intervention' => $image->colorResolve(255,30,30), | ||
| 416 : | 'error' => $image->colorResolve(175,45,45), | ||
| 417 : | 'complete' => $image->colorResolve(60,165,60), | ||
| 418 : | }; | ||
| 419 : | } | ||
| 420 : | |||
| 421 : | |||
| 422 : | =pod | ||
| 423 : | |||
| 424 : | =item * B<required_rights>() | ||
| 425 : | |||
| 426 : | Returns a reference to the array of required rights | ||
| 427 : | |||
| 428 : | =cut | ||
| 429 : | |||
| 430 : | sub required_rights { | ||
| 431 : | return [ [ 'login' ], | ||
| 432 : | ]; | ||
| 433 : | } |
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