cgi-bin/phenome/recent_annotated_loci.pl

   1 #!usr/bin/perl
   2 use warnings;
   3 use strict;
   4
   5 use CXGN::Page;
   6 use CXGN::Login;
   7 use CXGN::People;
   8 use CXGN::Page::WebForm;
   9
  10 use CXGN::Phenome::Locus;
  11 use CXGN::Page::FormattingHelpers qw/info_section_html
  12                                      page_title_html
  13                                      columnar_table_html
  14                                      info_table_html
  15                                      html_optional_show
  16                                      html_alternate_show
  17                                     /;
  18 #use base qw /CXGN::Page::WebForm/;
  19 my $dbh= CXGN::DB::Connection->new('phenome');
  20 my $logged_sp_person_id = CXGN::Login->new($dbh)->verify_session();
  21
  22 my $page = CXGN::Page->new("Recently annotated loci","Naama");
  23 #$page->jsan_use("Dynarch.Calendar");
  24 $page->jsan_use("CXGN.Calendar");
  25
  26 $page->header();
  27 #$page->jsan_use("CXGN.Calendar", "CXGN.Phenome.Locus");
  28
  29
  30 my $form = CXGN::Page::WebForm->new();
  31
  32 $form->set_data(date =>'');
  33 $form->template(<<HTML);
  34      <input type="text" name="date"  id="cal_target" />
  35     <input type="submit" id="submit_button" value="Submit" />
  36
  37 HTML
  38 print '<form action="" method="get">',
  39     '<h3 align="center">Find recently annotated loci</h3>',
  40
  41     $form->to_html,
  42
  43     '</form>'; #now print the auto-filled-in form
  44 my $cal=get_calendar();
  45 print $cal;
  46
  47 ######Javascript calendar: this stuff is not working. I guess the Calendar object is not called correctly.#####
  48 print <<EOT;
  49
  50         <script language="javascript" type="text/javascript"  >
  51         <!--
  52
  53     var c = new Calendar;
  54     c.showFlatCalendar('');
  55     c.showCalendar('cal_target', '%m/%d/%Y', '24', '1');
  56     -->
  57         </script>
  58 EOT
  59
  60
  61
  62 my %params= $page->cgi_params();
  63 $form->from_request( \%params );
  64
  65 my $date = $params{date};
  66
  67
  68 if ($date) { print_results($dbh, $date) } ;
  69
  70
  71 $page->footer();
  72
  73 sub get_calendar {
  74     my $c=qq|
  75
  76         <a href="javascript:Calendar.showCalendar('cal_id')">[Calendar]</a><br>
  77
  78         <div id='popUpCal' style="display: none">
  79         <div id='cal_id'>
  80         <input type="hidden"
  81         value=""
  82         id="">
  83         </div>
  84         </div>
  85         |;
  86 }
  87
  88 sub print_results {
  89     my $dbh =shift;
  90     my $date = shift;
  91
  92     my %locus_edits = CXGN::Phenome::Locus::get_recent_annotated_loci($dbh, $date);
  93
  94     ####################
  95     #locus updates and creates section
  96     ###################
  97     my @locus_updates;
  98     my $action;
  99     foreach my $locus(@{$locus_edits{loci} }) {
 100         my $locus_id = $locus->get_locus_id();
 101         my $locus_name=$locus->get_common_name() . " " . $locus->get_locus_name();
 102         my $updated_by= $locus->get_updated_by() || ($locus->get_owners())[0];
 103         my $person= get_person_info($dbh, $updated_by);
 104         my $udate = $locus->get_modification_date();
 105         $action='Updated';
 106         if (!$udate ) { #&& $locus->get_create_date() > $date) {
 107             $action= 'Created';
 108             $udate = $locus->get_create_date() ;
 109         }
 110         if ($locus->get_obsolete() eq 't') { $action= 'Obsoleted'; }
 111         push @locus_updates, [map {$_} (qq|<a href="locus_display.pl?locus_id=$locus_id">$locus_name</a>|, $person,$udate, $action)];
 112     }
 113     my $updated_loci= columnar_table_html(headings => ['Locus name',
 114                                                        'Updated by',
 115                                                        "Date",
 116                                                        ],
 117                                           data=>\@locus_updates, __align=>'llc') if @locus_updates;
 118
 119
 120     print info_section_html(title   => "Updated loci (" . scalar(@locus_updates) . ")",
 121                             contents =>$updated_loci,
 122                             collapsible=>1,
 123                             collapsed=>0,
 124                             );
 125
 126     ####################
 127     #Locus alias section
 128     ####################
 129
 130     my @alias_updates;;
 131     foreach my $alias(@{$locus_edits{aliases} } ) {
 132         my $locus_id=$alias->get_locus_id();
 133         my $locus_name=$alias->get_common_name() ." " . $alias->get_locus_name();
 134         my $alias_name= $alias->get_locus_alias();
 135         my $alias_person_id=  $alias->get_sp_person_id();
 136         my $udate= $alias->get_modification_date() || $alias->get_create_date();
 137         my $alias_obsoleted =  $alias->get_obsolete();
 138         $action='Created';
 139         my $person= get_person_info($dbh, $alias_person_id);
 140         if ($alias_obsoleted eq 't' ) { $action= 'Obsoleted'; }
 141         push @alias_updates, [map {$_} (qq|<a href="locus_display.pl?locus_id=$locus_id">$locus_name</a>|, $alias_name, $person, $udate, $action)];
 142     }
 143
 144     my $aliases;
 145     if (@alias_updates) { $aliases= columnar_table_html(headings => ['Locus name',
 146                                                                      'Synonym',
 147                                                                      'Submitted by',
 148                                                                      'Date',
 149                                                                      ],
 150                                                         data=>\@alias_updates, __align=>'llc'); }
 151
 152     print info_section_html(title   => "Locus synonyms (" . scalar(@alias_updates) . ")",
 153                             contents => $aliases ,
 154                             collapsible=>1,
 155                             );
 156
 157     ####################
 158     #alleles section
 159     ####################
 160
 161     my @allele_updates;
 162
 163     foreach my $allele(@{$locus_edits{alleles} } ) {
 164         my $allele_id=$allele->get_allele_id();
 165         my $locus_name=$allele->get_locus()->get_common_name() ." " . $allele->get_locus_name();
 166         my $allele_name= $allele->get_allele_name();
 167         my $allele_symbol=$allele->get_allele_symbol();
 168         my $allele_owner=  $allele->get_sp_person_id();
 169         my $udate= $allele->get_modification_date() ;
 170         my $allele_obsoleted =  $allele->get_obsolete();
 171         $action='Updated';
 172         if (!$udate) {
 173             $udate=$allele->get_create_date();
 174             $action='Created';
 175         }
 176         my $person= get_person_info($dbh, $allele_owner);
 177         if ($allele_obsoleted eq 't' ) { $action= 'Obsoleted'; }
 178         push @allele_updates, [map {$_} ($locus_name, qq|<a href="allele.pl?allele_id=$allele_id">$allele_symbol</a>|, $person, $udate, $action)];
 179     }
 180
 181     my $alleles;
 182     if (@allele_updates) {
 183         $alleles= columnar_table_html(headings => ['Locus name',
 184                                                    'Allele symbol',
 185                                                    'Submitted by',
 186                                                    'Date',
 187                                                    ],
 188                                       data=>\@allele_updates, __align=>'llc');}
 189
 190
 191     print info_section_html(title   => "Alleles (" . scalar(@allele_updates) . ")",
 192                             contents => $alleles ,
 193                             collapsible=>1,
 194                             );
 195
 196     ####################
 197     #locus dbxrefs
 198     ####################
 199
 200     my @ld_updates;
 201
 202     foreach my $ld(@{$locus_edits{locus_dbxrefs} } ) {
 203         my $locus_id=$ld->get_locus_id();
 204         my $locus=CXGN::Phenome::Locus->new($dbh, $locus_id);
 205         my $dbxref=CXGN::Chado::Dbxref->new($dbh, $ld->get_dbxref_id());
 206         my $annotation= get_annotation($dbxref);
 207         my $locus_symbol=$locus->get_common_name() ." " . $locus->get_locus_symbol();
 208         my $ld_owner=  $ld->get_sp_person_id();
 209         my $udate= $ld->get_modification_date() ;
 210         my $ld_obsoleted =  $ld->get_obsolete();
 211         $action='Updated';
 212         if (!$udate) {
 213             $udate=$ld->get_create_date();
 214             $action='Created';
 215         }
 216         my $person= get_person_info($dbh, $ld_owner);
 217         if ($ld_obsoleted eq 't' ) { $action= 'Obsoleted'; }
 218         push @ld_updates, [map {$_} (qq|<a href="locus_display.pl?locus_id=$locus_id">$locus_symbol</a>|, $annotation, $person, $udate, $action)];
 219     }
 220
 221     my $lds;
 222     if (@ld_updates) {
 223         $lds= columnar_table_html(headings => ['Locus',
 224                                                'Annotation',
 225                                                'Updated by',
 226                                                'Date',
 227                                                ],
 228                                       data=>\@ld_updates, __align=>'llc');}
 229
 230
 231     print info_section_html(title   => "Locus Annotations (" . scalar(@ld_updates) . ")",
 232                             contents => $lds ,
 233                             collapsible=>1,
 234                             collapsed=>1,
 235                             );
 236
 237
 238     ####################
 239     #locus images
 240     ####################
 241
 242     my @locus_images;
 243
 244     foreach my $list(@{$locus_edits{locus_images} } ) {
 245         #[$locus, $image, $person_id, $cdate, $mdate, $obsolete];
 246         my $locus=$list->[0];
 247         my $image_id=$list->[1];
 248 #       my $image_id=$image->get_image_id();
 249 #       my $image_name= $image->get_name() || "image: $image_id";
 250         my $locus_id=$locus->get_locus_id();
 251         my $locus_symbol=$locus->get_common_name() ." " . $locus->get_locus_symbol();
 252         my $owner=  $list->[2];
 253         my $person= get_person_info($dbh, $owner);
 254
 255         my $udate= $list->[4];
 256         $action='Updated';
 257         if (!$udate) {
 258             $udate=$list->[3];
 259             $action='Created';
 260         }
 261         my $obsoleted =  $list->[5];
 262         if ($obsoleted eq 't' ) { $action= 'Obsoleted'; }
 263         push @locus_images, [map {$_} (qq|<a href="locus_display.pl?locus_id=$locus_id">$locus_symbol</a>|, qq|<a href="/image/index.pl?image_id=$image_id">image: $image_id</a>|, $person, $udate, $action)];
 264     }
 265
 266     my $lis;
 267     if (@locus_images) {
 268         $lis= columnar_table_html(headings => ['Locus',
 269                                                'Image',
 270                                                'Updated by',
 271                                                'Date',
 272                                                ],
 273                                       data=>\@locus_images, __align=>'llc');}
 274
 275
 276     print info_section_html(title   => "Locus images (" . scalar(@locus_images) . ")",
 277                             contents => $lis ,
 278                             collapsible=>1,
 279                             collapsed=>1,
 280                             );
 281
 282     ####################
 283     #individuals
 284     ####################
 285
 286     my @individuals;
 287
 288     foreach my $list(@{$locus_edits{individuals} } ) {
 289         my $ind=$list->[0];
 290         my $allele=$list->[1];
 291         my $ind_id=$ind->get_individual_id();
 292         my $ind_name= $ind->get_name() ;
 293         my $locus_name=$allele->get_locus()->get_common_name() ." " . $allele->get_locus_name();
 294         my $locus_id=$allele->get_locus_id();
 295         my $owner=  $list->[2];
 296         my $person= get_person_info($dbh, $owner);
 297
 298         my $udate= $list->[4];
 299         $action='Updated';
 300         if (!$udate) {
 301             $udate=$list->[3];
 302             $action='Created';
 303         }
 304         my $obsoleted =  $list->[5];
 305         if ($obsoleted eq 't' ) { $action= 'Obsoleted'; }
 306         push @individuals, [map {$_} (qq|<a href="locus_display.pl?locus_id=$locus_id">$locus_name</a>|, qq|<a href="individual.pl?individual_id=$ind_id">$ind_name</a>|, $person, $udate, $action)];
 307     }
 308
 309     my $ias;
 310     if (@individuals) {
 311         $ias= columnar_table_html(headings => ['Locus',
 312                                                'Accessions',
 313                                                'Updated by',
 314                                                'Date',
 315                                                ],
 316                                       data=>\@individuals, __align=>'llc');}
 317
 318
 319     print info_section_html(title   => "Locus accessions (" . scalar(@individuals) . ")",
 320                             contents => $ias ,
 321                             collapsible=>1,
 322                             collapsed=>1,
 323                             );
 324
 325     ####################
 326     #locus unigenes
 327     ####################
 328
 329     my @locus_unigenes;
 330
 331     foreach my $list(@{$locus_edits{locus_unigenes} } ) {
 332         my $unigene=$list->[0];
 333         my $locus=$list->[1];
 334         my $unigene_id='SGN-U' . $unigene->get_unigene_id();
 335         my $locus_name=$locus->get_common_name() ." " . $locus->get_locus_name();
 336         my $locus_id=$locus->get_locus_id();
 337         my $owner=  $list->[2];
 338         my $person= get_person_info($dbh, $owner);
 339
 340         my $udate= $list->[4];
 341         $action='Updated';
 342         if (!$udate) {
 343             $udate=$list->[3];
 344             $action='Created';
 345         }
 346         my $obsoleted =  $list->[5];
 347         if ($obsoleted eq 't' ) { $action= 'Obsoleted'; }
 348         push @locus_unigenes, [map {$_} (qq|<a href="locus_display.pl?locus_id=$locus_id">$locus_name</a>|, qq|<a href="/search/unigene.pl?unigene_id=$unigene_id">$unigene_id</a>|, $person, $udate, $action)];
 349     }
 350
 351     my $uls;
 352     if (@locus_unigenes) {
 353         $uls= columnar_table_html(headings => ['Locus',
 354                                                'Unigene',
 355                                                'Updated by',
 356                                                'Date',
 357                                                ],
 358                                       data=>\@locus_unigenes, __align=>'llc');}
 359
 360
 361     print info_section_html(title   => "Locus-unigenes (" . scalar(@locus_unigenes) . ")",
 362                             contents => $uls ,
 363                             collapsible=>1,
 364                             collapsed=>1,
 365                             );
 366
 367
 368     ####################
 369     #locus markers
 370     ####################
 371
 372     my @lm_updates;
 373
 374     foreach my $lm(@{$locus_edits{locus_markers} } ) {
 375         my $locus_id=$lm->get_locus_id();
 376         my $locus=CXGN::Phenome::Locus->new($dbh, $locus_id);
 377         my $marker_id= $lm->get_marker_id();
 378         my $marker=CXGN::Marker->new($dbh, $lm->get_marker_id());
 379         my $marker_name=$marker->name_that_marker();
 380         my $locus_symbol=$locus->get_common_name() ." " . $locus->get_locus_symbol();
 381         my $lm_owner=  $lm->get_sp_person_id();
 382         my $udate= $lm->get_modification_date() ;
 383         my $lm_obsoleted =  $lm->get_obsolete();
 384         $action='Updated';
 385         if (!$udate) {
 386             $udate=$lm->get_create_date();
 387             $action='Created';
 388         }
 389         my $person= get_person_info($dbh, $lm_owner);
 390         if ($lm_obsoleted eq 't' ) { $action= 'Obsoleted'; }
 391         push @lm_updates, [map {$_} (qq|<a href="locus_display.pl?locus_id=$locus_id">$locus_symbol</a>|, qq|<a href="/markers/marker_info.pl?marker_id=$marker_id">$marker_name</a>|, $person, $udate, $action)];
 392     }
 393
 394     my $lms;
 395     if (@lm_updates) {
 396         $lms= columnar_table_html(headings => ['Locus',
 397                                                'Marker',
 398                                                'Updated by',
 399                                                'Date',
 400                                                ],
 401                                       data=>\@lm_updates, __align=>'llc');}
 402
 403
 404     print info_section_html(title   => "Locus markers (" . scalar(@lm_updates) . ")",
 405                             contents => $lms ,
 406                             collapsible=>1,
 407                             collapsed=>1,
 408                             );
 409
 410 }
 411
 412
 413
 414 sub get_person_info {
 415     my $dbh=shift;
 416     my $sp_person_id=shift;
 417     my $user = CXGN::People::Person -> new($dbh, $sp_person_id);
 418     my $username=$user->get_first_name()." ".$user->get_last_name();
 419     my $person= qq| <a href="../solpeople/personal_info.pl?sp_person_id=$sp_person_id">$username</a> | ;
 420     return $person;
 421 }
 422
 423 sub get_annotation {
 424     my $dbxref=shift;
 425     my $acc=$dbxref->get_full_accession();
 426     my $accession= $dbxref->get_accession();
 427     my $db=$dbxref->get_db_name();
 428     if ($db eq 'SGN_ref') {
 429         $accession= $dbxref->get_publication()->get_pub_id();
 430     }
 431     my $url=$dbxref->get_urlprefix() . $dbxref->get_url() . $accession;
 432     return qq |<a href="$url">$acc</a>|;
 433 }