cgi-bin/cview/map.pl

   1
   2 use strict;
   3 use warnings;
   4
   5 use CXGN::Page;
   6 use CXGN::DB::Connection;
   7
   8 my $page = CXGN::Page->new();
   9 my ($map_id, $map_version_id, $size, $hilite, $physical, $force) = $page->get_encoded_arguments("map_id", "map_version_id", "size", "hilite", "physical", "force");
  10
  11 my $dbh = CXGN::DB::Connection->new();
  12
  13
  14 my $referer = ($page->get_request()->uri()) ."?". ($page->get_request->args());
  15
  16
  17 my $tempdir = $c->path_to($c->tempfiles_subdir('cview'));
  18
  19
  20 $c->forward_to_mason_view('/cview/map/index.mas', dbh=>$dbh, map_version_id=>$map_version_id, map_id=>$map_id, hilite=>$hilite, physical=>$physical, size=>$size, referer=>$referer, force=>$force, tempdir=>$tempdir);
  21
  22 =head1 NAME
  23
  24 map.pl - display top level map web page
  25
  26 =head1 DESCRIPTION
  27
  28 A script that displays a web page with an overview graph of a map, an abstract and some statistics about the map, using map_id or map_version_id as a parameter.
  29
  30 Older versions of this script accepted other parameters, such as the mysterious legacy_id or the more cumbersome map short name. Support for these has been scrapped. Sorry!
  31
  32 As well, older versions supported a parameter called "physical", which then, through some inextricable hack displayed a physical map. This parameter has been deprecated but is still supported.
  33
  34 On the other hand, a new parameter was added, called "force", which, if set to true, will force the cached images and stats to be re-calculated. Normally, the map overview image and associated image map and the map statistics are cached.
  35
  36 Parameters summary:
  37
  38 =over 15
  39
  40 =item map_id
  41
  42 The map_id of the map to display.
  43
  44 =item map_version_id
  45
  46 the map_version_id of the map to display. Note that map_id and map_version_id are mutually exclusive.
  47
  48 =item hilite
  49
  50 a space separated, url-encoded string that gives the markers to be highlighted.
  51
  52 =item size
  53
  54 the size of the map to display. 0 denotes the standard size (smallest), 10 denotes the largest size.
  55
  56 =item force
  57
  58 if set to true, force the image and map stats caches to be re-calculated.
  59
  60 =back
  61
  62 =head1 AUTHOR(S)
  63
  64 Early versions were written by Robert Ahrens, with later additions by Lukas Mueller and John Binns <zombieite@gmail.com>.
  65
  66 Currently maintained by Lukas Mueller <lam87@cornell.edu>.
  67
  68 =cut
  69
  70 # use strict;
  71
  72 # use Cache::File;
  73 # use File::Spec;
  74 # use URI::Escape;
  75
  76 # use CXGN::DB::Connection;
  77 # use CXGN::Page;
  78 # use CXGN::Page::FormattingHelpers qw(page_title_html blue_section_html tooltipped_text);
  79 # use CXGN::Cview::Map_overviews::Generic;
  80 # use CXGN::People::PageComment;
  81 # use CXGN::VHost;
  82 # use CXGN::Map::Tools;
  83 # use CXGN::Cview::MapFactory;
  84 # use CXGN::Cview::Map::Tools;
  85
  86
  87 # my %marker_info;
  88 # my $vh = CXGN::VHost->new();
  89
  90 # # set up a cache for the map statistics, using Cache::File
  91 # #
  92 # my $cache_file_dir = File::Spec->catfile($vh->get_conf("basepath"), $vh->get_conf("tempfiles_subdir"), "cview", "cache_file");
  93
  94 # tie %marker_info, 'Cache::File', { cache_root => $cache_file_dir };
  95
  96 # # report some unusual conditions to the user.
  97 # #
  98 # my $message = "";
  99
 100 # our $page = CXGN::Page -> new( "SGN map", "Lukas");
 101
 102 # $page->jsan_use('MochiKit.Base', 'MochiKit.Async');
 103
 104 # my ($map_id, $map_version_id, $size, $hilite, $physical, $force) = $page->get_encoded_arguments("map_id", "map_version_id", "size", "hilite", "physical", "force");
 105
 106 # my $dbh = CXGN::DB::Connection->new();
 107
 108
 109 # # maintain some backwards compatibility. The physical parameter is deprecated, but
 110 # # we still support it...
 111 # #
 112 # if ($physical==1) { $map_id= "p".$map_id; }
 113
 114 # # if the map_id was supplied, convert immediately to map_version_id
 115 # #
 116 # if ($map_id && !$map_version_id) {
 117 #     $map_version_id = CXGN::Cview::Map::Tools::find_current_version($dbh, $map_id);
 118 # }
 119
 120
 121 # # get the map data using the CXGN::Map API.
 122 # #
 123 # my $map_factory = CXGN::Cview::MapFactory->new($dbh);
 124 # my $map = $map_factory ->create({ map_version_id => $map_version_id });
 125
 126 # if (!$map) { missing_map_page(); }
 127
 128 # # adjust the size parameter, which scales the size of the map overview image.
 129 # #
 130 # my $enlarge_button_disabled = "";
 131 # my $shrink_button_disabled = "";
 132 # my $smaller_size = 0;
 133 # my $larger_size = 0;
 134
 135 # $size ||=0;
 136
 137 # if ($size <= 0) {
 138 #     $size = 0;
 139 #     $shrink_button_disabled = qq { disabled="1" };
 140 #     $smaller_size = $size;
 141 # }
 142 # else {
 143 #     $smaller_size = $size - 1;
 144 # }
 145
 146 # if ($size>=10) {
 147 #     $size=10;
 148 #     $enlarge_button_disabled = qq { disabled="1" };
 149 #     $larger_size = $size;
 150 # }
 151 # else {
 152 #     $larger_size = $size+ 1;
 153 # }
 154 # $larger_size = 10 if $larger_size > 10;
 155
 156 # my $image_height = 160;
 157 # my $image_width = 820;
 158
 159 # $image_height = $image_height + $image_height * $size /2;
 160
 161 # my $map_fullname = $map->get_long_name();
 162 # my $abstract     = $map->get_abstract();
 163 # my $short_name   = $map->get_short_name();
 164
 165 # my @chr_names = $map->get_chromosome_names();
 166
 167 # my $abstract = $map->get_abstract();
 168
 169 # my $map_image_file="";
 170 # my $image_map = "";
 171
 172 # my $map_overview;
 173
 174
 175 # # create an appropriate overview diagram - physical or generic
 176 # # (the generic will also provide an appropriate overview for the fish map).
 177 # #
 178 # $map_overview = CXGN::Cview::Map_overviews::Generic -> new($map, $force);
 179
 180 # $map_overview->set_image_height($image_height);
 181 # $map_overview->set_image_width($image_width);
 182
 183 # # deal with marker names to be highlighted on the overview diagram
 184 # # (the ones to be requested to be hilited using the hilite feature)
 185 # #
 186 # my @hilite_markers = split /\s+|\,\s*|\;s*/, $hilite;
 187
 188 # foreach my $hm (@hilite_markers) {
 189 #     #print STDERR "Hilite marker $hm...\n";
 190 #     $map_overview -> hilite_marker($hm);
 191 # }
 192
 193 # # generate the marker list for use in the URL links
 194 # #
 195 # my $hilite_encoded = URI::Escape::uri_escape(join (" ", @hilite_markers));
 196
 197 # # render the map and get the imagemap
 198 # #
 199 # $map_overview -> render_map();
 200
 201 # my $map_overview_html = $map_overview->get_image_html();
 202
 203 # # get the markers that could not be hilited
 204 # #
 205 # my @markers_not_found = $map_overview -> get_markers_not_found();
 206 # if (@markers_not_found) {
 207 #         $message .= "The following markers requested for hiliting were not found on this map (click to search on other maps):<br />";
 208 #     foreach my $m (@markers_not_found) {
 209 #       $message .= "&nbsp;&nbsp;<a href=\"/search/markers/markersearch.pl?searchtype=exactly&amp;name=$m\">$m</a>";
 210 #     }
 211 #     $message .= "<br />\n";
 212 # }
 213
 214 # # start displaying the page
 215 # #
 216 # $page -> header();
 217
 218 # print page_title_html($short_name);
 219 # print "<div id=\"pagetitle2\"><center><h3>$map_fullname</h3></center></div>";
 220
 221 # if ($message) {
 222 #     print "<div class=\"boxbgcolor5\"><b>NOTE:</b><br />$message</div>\n";
 223 # }
 224
 225 # print <<HTML;
 226
 227 #     <table summary="outer table" width="100%" border="0"><tr>
 228 #     <td width="10%"><br /></td>
 229 #     <td width="80%">
 230 #     <center>
 231 #     $map_overview_html
 232 #     </center>
 233 #     </td></tr></table>
 234
 235 # HTML
 236
 237
 238 # #
 239 # # add the input box and form for the hilite marker feature
 240 # #
 241 #     my $hilite_tooltip = tooltipped_text("Highlight marker(s)", "You can highlight markers on the overview graphic by entering them here, separated by spaces");
 242 # my $size_tooltip = tooltipped_text("Image size", "You can increase the size of the overview graph by clicking on the (+) button and decrease it by clicking on (-).");
 243
 244 # print <<HTML;
 245
 246 # <table><tr><td align="left">
 247 #     <div class="indentedcontent">
 248
 249 #     <form action="/cview/map.pl?map_version_id=$map_version_id&amp;physical=$physical">
 250
 251 #       $hilite_tooltip: <input type="text" name="hilite" value="$hilite" size="10" />
 252 #       <input type="hidden" name="physical" value="$physical" />
 253 #       <input type="hidden" name="map_version_id" value="$map_version_id" />
 254 #         <input type="hidden" name="size" value="$size" />
 255 #       <input type="submit" value="Highlight" />
 256 #     </form>
 257 #     </div>
 258 #     </td><td width=400 align="right">$size_tooltip:
 259 # </td><td align="right">
 260 #     <form>
 261 #     <input type="hidden" name="physical" value="$physical" />
 262 #     <input type="hidden" name="map_version_id" value="$map_version_id" />
 263 #     <input type="hidden" name="size" value="$smaller_size" />
 264 #     <input type="hidden" name="hilite" value="$hilite" />
 265 #     <input type="submit" value="-" $shrink_button_disabled />
 266 #     </form>
 267 # </td><td>
 268 #     <form>
 269 #     <input type="hidden" name="physical" value="$physical" />
 270 #     <input type="hidden" name="map_version_id" value="$map_version_id" />
 271 #     <input type="hidden" name="hilite" value="$hilite" />
 272 #     <input type="hidden" name="size" value="$larger_size" />
 273 #     <input type="submit" value="+" $enlarge_button_disabled />
 274 #     </form>
 275 # </td></tr></table>
 276
 277
 278 # HTML
 279
 280
 281 # #
 282 # # print the abstract
 283 # #
 284 #     print blue_section_html("Abstract", "<div class=\"indentedcontent\">$abstract</div><br />") if ($abstract);
 285 # #
 286 # # print a list of links, one per chromosome, and some marker stats
 287 # #
 288
 289
 290 # my $map_stats = qq |
 291
 292 #       <table summary="map stats" align="center" border="0">
 293 #       <tr>
 294 #       <td valign="middle"><b>Click to view a given chromosome<br /><br /></b></td>
 295 #       <td width="70">&nbsp;</td>
 296 #       <td><b>Marker collections:</b><br /><br /></td>
 297 #       </tr>
 298
 299
 300 #       <tr><td>
 301
 302 #     <table summary="marker stats table" >
 303 #     <tr><td>&nbsp;</td><td>\# markers</td></tr>
 304
 305 # |;
 306
 307 # if (!$map_id) {
 308 #     $map_id = CXGN::Cview::Map::Tools::find_map_id_with_version($dbh, $map_version_id);
 309 # }
 310
 311 # my $total_markers=0;
 312 # for (my $i=0; $i<@chr_names; $i++) {
 313 #     my $hash_key = $map_version_id."-".$i;
 314 #     if (!exists($marker_info{$hash_key}) || $force) {
 315 #       $marker_info{$hash_key} = $map->get_marker_count($chr_names[$i]);
 316 #     }
 317 #     $map_stats .= "<tr><td><a href=\"/cview/view_chromosome.pl?map_version_id=$map_version_id&amp;chr_nr=$chr_names[$i]&amp;hilite=$hilite_encoded\"><b>Chromosome $chr_names[$i]</b></a></td><td align=\"right\"><a href=\"/search/markers/markersearch.pl?w822_nametype=starts+with&w822_marker_name=&w822_mapped=on&w822_species=Any&w822_protos=Any&w822_colls=Any&w822_pos_start=&w822_pos_end=&w822_confs=Any&w822_submit=Search&w822_chromos=$chr_names[$i]&w822_maps=$map_id\">$marker_info{$hash_key}</a></td></tr>\n";
 318 #     $total_markers += $marker_info{$hash_key};
 319 # }
 320 # $map_stats .= qq { <tr><td colspan="2">&nbsp;</td></tr><tr><td><b>Total mapped:</b></td><td align=\"right\"><b>$total_markers</b></td></tr>\n };
 321 # $map_stats .=  "</table>\n";
 322 # my $marker_type_table = "";
 323 # if (!exists($marker_info{$map_version_id}) || $force) {
 324 #     $marker_info{$map_version_id} = $map->get_map_stats();
 325 # }
 326
 327 # $map_stats .= qq |
 328
 329 #     </td><td>&nbsp;</td><td valign="middle">$marker_info{$map_version_id}</td></tr>
 330 #     </table>
 331 #     <br /><br />
 332
 333
 334
 335 # |;
 336
 337 # print blue_section_html("Map statistics", $map_stats);
 338
 339 # # add the page comment feature. Only show for maps that have completely
 340 # # numeric identifiers.
 341 # #
 342 #  if ($map_overview->get_map()->get_id=~/^\d+$/) {
 343
 344 #      my $referer = $page->{request}->uri()."?".$page->{request}->args();
 345 #      my $comment_map_id=0;
 346 #      if ($map_id=~/(\d+)/) {
 347 #        $comment_map_id=$1;
 348 #      }
 349
 350 #      print $page->comments_html('map', $comment_map_id, $referer);
 351 #  }
 352
 353
 354 # #print "</td></tr>\n";
 355 # #print "</table>";
 356
 357
 358 # # end page
 359 # #
 360 # $page -> footer();
 361
 362
 363 # sub missing_map_page {
 364 #     $page->header();
 365
 366 #     my $title = page_title_html("The requested map could not be found.");
 367
 368 #     print <<HTML;
 369
 370 #     $title
 371
 372 #     <p>
 373 #     All available maps on SGN are listed on the <a href="/cview/">map index page</a>.
 374 #     </p>
 375 #     <p>
 376 #     Please contact <a href="mailto:sgn-feedback\@sgn.cornell.edu">SGN</a> if you think there is a problem.
 377 #     </p>
 378
 379 # HTML
 380
 381 #     $page->footer();
 382
 383
 384 #     exit();
 385 # }
 386
 387 # # sub hack_abstract ($$$) {
 388 # #     # Look.  This is a total hack and that's that.  Let's make no
 389 # #     # bones about it. There is doubtlessly a good way to handle this,
 390 # #     # but in the meantime this sub will allow us to swap in a decent
 391 # #     # abstract for the physical mapping project w/o having to redesign
 392 # #     # code.
 393 # #     my ($abstract, $map, $physical) = @_;
 394 # #     my $vhost_conf=CXGN::VHost->new();
 395 # #     my $physabstractfile = $vhost_conf->get_conf('basepath').$vhost_conf->get_conf('support_data_subdir')."/mapviewer/physicalabstract";
 396 # #     my $overgo_stats_page = '/maps/physical/overgo_stats.pl';
 397 # #     my $overgo_plate_browser = '/maps/physical/list_bacs_by_plate.pl';
 398 # #     my $overgo_explanation = '/maps/physical/overgo_process_explained.pl';
 399
 400 # #     my $map_id = $map->map_id();
 401 # #     my $map_fullname = $map->long_name();
 402 # #     if (! $physical) { $physical = 0; }
 403
 404 # #     if (($map_id==9) && ($physical==1)) {
 405 # #     open PHYSABSTRACT, "<$physabstractfile"
 406 # #         or die( "<i>ERROR: Unable to read from $physabstractfile</i>.\n" );
 407 # #     my @phys_abst = <PHYSABSTRACT>;
 408 # #     close PHYSABSTRACT;
 409 # #     $abstract = join("", @phys_abst);
 410 # #         $abstract =~ s/MAPID/$map_id/;
 411 # #     }
 412
 413 # #     if ( $map->has_physical() ) {
 414
 415 # #     if ($physical) {
 416
 417 # #         $abstract .= <<PHYSICAL;
 418
 419 # #         <p>
 420 # #             <b>Genetic Map:</b> This map is extracted from the
 421 # #             <a href="/cview/map.pl?map_id=$map_id&physical=0">$map_fullname</a>.
 422 # #             </p>
 423
 424 # #             <p>
 425 # #             <b>Overgo Data</b>
 426 # #             <ul>
 427 # #             <li>Statistics on the <a href="$overgo_stats_page">Overgo Plating Process</a></li>
 428 # #             <li><a href="$overgo_explanation">Explanation of the Overgo Plating process</a></li>
 429 # #             </ul>
 430
 431 # # PHYSICAL
 432
 433 # #     }
 434 # #     else {
 435 # #         $abstract .= <<PHYSICAL;
 436
 437 # #         <p>
 438 # #             <b><a href="/cview/map.pl?map_id=$map_id&amp;physical=1">The physical Map</a></b> -- a combined genetic and physical map, showing the association of BACs and BAC contigs to this genetic map
 439 # #             </p>
 440
 441 # # PHYSICAL
 442
 443 # #         }
 444
 445
 446 # #     }
 447 # #     return $abstract;
 448 # # }
 449