[Bio] / FigKernelPackages / HTML.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/HTML.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.6, Sun Mar 21 02:20:55 2004 UTC revision 1.115, Fri Aug 24 12:13:15 2007 UTC
# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package HTML;  package HTML;
19    
20    use strict;
21    use Tracer;
22    use FIG;
23  use Carp;  use Carp;
24  use Data::Dumper;  use Data::Dumper;
25  use LWP::UserAgent;  use LWP::UserAgent;
26  use LWP::Simple;  use LWP::Simple;
27    use URI::Escape;  # uri_escape()
28  use URI::URL;  use URI::URL;
29  use HTTP::Request::Common;  use HTTP::Request::Common;
30    use POSIX;
31    use CGI;
32    
33  sub show_page {  #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
34      my($cgi,$html,$no_home) = @_;  my $raelib;
35      my $i;  
36    
37    my $top_link_cache;
38    
39    
40    sub new
41    {
42        my($class) = @_;
43    
44        my $self = {};
45    
46        return bless $self, $class;
47    }
48    
49    sub top_link
50    {
51    
52      #      #
53      # Find the HTML header      # Determine if this is a toplevel cgi or one in one of the subdirs (currently
54        # just /p2p).
55      #      #
56    
57      my $html_hdr_file = "./Html/html.hdr";      return $top_link_cache if ($top_link_cache);
58    
59        my @parts = split(/\//, $ENV{SCRIPT_NAME});
60        my $top;
61        if (defined $parts[-2] && $parts[-2] eq 'FIG')
62        {
63            $top = '.';
64    #       warn "toplevel @parts\n";
65        }
66        elsif (defined $parts[-3] && $parts[-3] eq 'FIG')
67        {
68            $top = '..';
69    #       warn "subdir @parts\n";
70        }
71        else
72        {
73            $top = $FIG_Config::cgi_base;
74    #       warn "other @parts\n";
75        }
76    
77        $top_link_cache = $top;
78        return $top;
79    }
80    
81    sub compute_html_header
82    {
83        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
84        my($additional_insert, $user, %options ) = @_;
85    
86        local $/ = "\n";
87    
88        my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
89        my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
90    
91        my $html_hdr_file = "./Html/$header_name";
92      if (! -f $html_hdr_file)      if (! -f $html_hdr_file)
93      {      {
94          $html_hdr_file = "$FIG_Config::fig/CGI/Html/html.hdr";          $html_hdr_file = "$FIG_Config::fig/CGI/Html/$header_name";
95      }      }
96        my @html_hdr = &FIG::file_read($html_hdr_file);
97    
98      my $html_tail_file = "./Html/html.tail";      # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
99      if (! -f $html_tail_file)  
100        #
101        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
102        # just /p2p).
103        #
104    
105        my @parts = split(/\//, $ENV{SCRIPT_NAME});
106        my $top;
107        if ($parts[-2] eq 'FIG')
108        {
109            $top = '.';
110    #       warn "toplevel @parts\n";
111        }
112        elsif ($parts[-3] eq 'FIG')
113        {
114            $top = '..';
115    #       warn "subdir @parts\n";
116        }
117        else
118        {
119            $top = $FIG_Config::cgi_base;
120    #       warn "other @parts\n";
121        }
122    
123        $options{no_fig_search} or push( @html_hdr, "<br><a href=\"$top/index.cgi?user=$user\">FIG search</a>\n" );
124    
125        if (@html_hdr)
126      {      {
127          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          my $insert_stuff;
128    
129            if (not $options{no_release_info})
130            {
131                my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
132                my $ver = $ver[0];
133                chomp $ver;
134                if ($ver =~ /^cvs\.(\d+)$/)
135                {
136                    my $d = asctime(localtime($1));
137                    chomp($d);
138                    $ver .=  " ($d)";
139                }
140                my $host = &FIG::get_local_hostname();
141                $insert_stuff = "SEED version <b>$ver</b> on $host";
142            }
143    
144            if ($additional_insert)
145            {
146                $insert_stuff .= "<br>" . $additional_insert;
147            }
148    
149            for $_ (@html_hdr)
150            {
151                s,(href|img\s+src)="/FIG/,$1="$top/,g;
152                    s,(\?user\=)\",$1$user",;
153                if ($_ eq "<!-- HEADER_INSERT -->\n")
154                {
155                    $_ = $insert_stuff;
156                }
157      }      }
158        }
159    
160        return @html_hdr;
161    }
162    
163    sub show_page {
164        #warn "SHOWPAGE: cgi=", Dumper(@_);
165        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
166        my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
167        my $i;
168        Trace("Setting top link.") if T(3);
169        my $top = top_link();
170    
171        # ARGUMENTS:
172        #     $cgi is the CGI method
173        #     $html is an array with all the html in it. It is just joined by "\n" (and not <br> or <p>
174        #     $no_home eliminates ONLY the bottom FIG search link in a page
175        #     $alt_header is a reference to an array for an alternate header banner that you can replace the standard one with
176        #     $css is a reference to a hash. The key is the name of the CSS sheet and the value is the URL of that sheet. Note the usual rules about relative css urls
177        #               the sheet named "Default" is considered to be the default style sheet, and if this is not set it points at $FIG_Config::HTML/css/default.css
178        #               the sheet named "Sans Serif" is considered to the the first alternate, and if this is not set it points at $FIG_Config::HTML/css/sanserif.css
179        #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")
180        #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
181        #     $options is a reference to a hash of options that you can pass around the pages
182        #
183        # Find the HTML header
184        #
185        Trace("Reading tail.") if T(3);
186        my $tail_name = $options->{tail_name} ? $options->{tail_name} : "html.tail";
187        my $html_tail_file = "./Html/$tail_name";
188        if (! -f $html_tail_file)
189        {
190            $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
191        }
192        Trace("Extracting user name and header data.") if T(3);
193        my $user = $cgi->param('user') || "";
194        my @html_hdr;
195        if ($alt_header && ref($alt_header) eq "ARRAY")
196        {
197           @html_hdr = @$alt_header;
198        }
199        else
200        {
201            @html_hdr = compute_html_header(undef,$user,%$options);
202        }
203    
204      print $cgi->header;      # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.
205        # This modification adds the cookies if necessary
206    
207        # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about
208        # to add cookies back in replace these two header lines with each other
209        #my $hdr_thing = $cgi->header(-cookie=>$cookie);
210        my $hdr_thing = $cgi->header();
211        Trace("Printing HTML header: $hdr_thing.") if T(3);
212        print $hdr_thing;
213        Trace("Header printed.") if T(3);
214      #      #
215      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
216      #  what parts of the HTML document skeleton are there, and fill in      #  what parts of the HTML document skeleton are there, and fill in
# Line 46  Line 227 
227                       meta     => 1,                       meta     => 1,
228                       nextid   => 1,                       nextid   => 1,
229                       style    => 1,                       style    => 1,
230                       title    => 1                       title    => 1,
231                     );                     );
232    
233      #      #
# Line 74  Line 255 
255      my $body_line = -1;      my $body_line = -1;
256      my $last_head_line = -1;  #  If no head tags are found, text goes at top.      my $last_head_line = -1;  #  If no head tags are found, text goes at top.
257      my $done = 0;      my $done = 0;
258        Trace("Processing special cases.") if T(3);
259      for ( $i = 0; $i < @$html; $i++ )      for ( $i = 0; $i < @$html; $i++ )
260      {      {
261          #  Some special cases:          #  Some special cases:
# Line 89  Line 270 
270          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )
271          {          {
272              $body_line = $i;              $body_line = $i;
273              $last;              last;
274          }          }
275    
276          #  Now the general case.          #  Now the general case.
# Line 120  Line 301 
301    
302      if ( 1 )      if ( 1 )
303      {      {
304            Trace("Sanity checks in progress.") if T(3);
305          if ( $html_line >= 0 )          if ( $html_line >= 0 )
306          {          {
307              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )
308              {              {
309                  print STDERR "<HTML> tag follows <HEAD> tag\n";                  Trace("<HTML> tag follows <HEAD> tag.") if T(1);
310              }              }
311              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )
312              {              {
313                  print STDERR "<HTML> tag follows </HEAD> tag\n";                  Trace("<HTML> tag follows </HEAD> tag.") if T(1);
314              }              }
315          }          }
316          if ( $head_line >= 0 )          if ( $head_line >= 0 )
317          {          {
318              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )
319              {              {
320                  print STDERR "<HEAD> tag follows </HEAD> tag\n";                  Trace("<HEAD> tag follows </HEAD> tag.") if T(1);
321              }              }
322          }          }
323      }      }
324        Trace("Sanity checks complete.") if T(3);
325      #      #
326      #  Okay.  Let's put in the html header file, and missing tags:      #  Okay.  Let's put in the html header file, and missing tags:
327      #      #
328      #  <BODY> goes after last head line      #  <BODY> goes after last head line
329      #      #
330        #  RAE:
331        #  Added the javascript for the buttons immediately after body.
332        #  Note if no buttons are added we still (at the moment) add the script,
333        #  but it only adds a little text (495 characters) to the html and noone will notice!
334        #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
335      if ( $body_line < 0 )      if ( $body_line < 0 )
336      {      {
337          $body_line = $last_head_line + 1;          $body_line = $last_head_line + 1;
338            Trace("Splicing body line at $body_line.") if T(3);
339          splice( @$html, $body_line, 0, "<BODY>\n" );          splice( @$html, $body_line, 0, "<BODY>\n" );
340      }      }
341    
# Line 156  Line 343 
343      #  Seed page header (if it exists) goes after <BODY>      #  Seed page header (if it exists) goes after <BODY>
344      #      #
345    
346      if ( -f $html_hdr_file )      if (@html_hdr)
347      {      {
348          splice( @$html, $body_line + 1, 0, `cat $html_hdr_file` );          Trace("Splicing SEED page header after $body_line.") if T(3);
349            splice( @$html, $body_line + 1, 0, @html_hdr );
350      }      }
351    
352      #      #
# Line 168  Line 356 
356      if ( $head_end_line < 0 )      if ( $head_end_line < 0 )
357      {      {
358          $head_end_line = $body_line;          $head_end_line = $body_line;
359            Trace("Splicing header terminater at $body_line.") if T(3);
360          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
361      }      }
362    
363        # RAE:
364        # Add css here
365        # Note that at the moment I define these two sheets here. I think this should
366        # be moved out, but I want to try it and see what happens.  css has the format:
367        #
368        # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
369        Trace("Formatting CSS.") if T(3);
370        # convert the default key to the right case. and eliminate dups
371        foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
372    
373        if (!$css || !$css->{'Default'})
374        {
375           $css->{'Default'} = "Html/css/default.css";
376        }
377        if (!$css->{"Sans Serif"})
378        {
379           $css->{'Sans Serif'} = "Html/css/sanserif.css";
380        }
381    
382        my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";
383        $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";
384    
385        foreach my $k (keys %$css)
386        {
387           next if (lc($k) eq "default" || lc($k) eq "sans serif");
388           $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
389        }
390    
391        $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='Html/rss/SEED.rss' type='application/rss+xml'>\n";
392    
393        # RAE: also added support for external javascripts here.
394        # we are cluttering the HTML code with all the javascripts when they could easily be in external files
395        # this solution allows us to source other files
396    
397        # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
398        # it will reduce our overhead.
399        Trace("Formatting javascript.") if T(3);
400        # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
401        push @$javasrc, "Html/css/FIG.js";
402        foreach my $script (@$javasrc) {
403            $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
404        }
405    
406        Trace("Re-splicing the header terminator at $head_end_line.") if T(3);
407        splice( @$html, $head_end_line, 1, "$csstext</HEAD>\n" );  # note here I am replacing the </head> line. Could be bad...? But it doesn't increment everything else.
408    
409      #      #
410      #  <BASE ...> goes before </HEAD>      #  <BASE ...> goes before </HEAD>
411      #      #
# Line 183  Line 418 
418          #  only, or every update?), I provide an alternative derivation          #  only, or every update?), I provide an alternative derivation
419          #  from $cgi_url. -- GJO          #  from $cgi_url. -- GJO
420          #          #
421            # BASE href needs to be absolute. RDO.
422          my $base_url = $FIG_Config::cgi_base;          #
423          if ( ! $base_url )                      # if cgi_base was not defined          #
424          {  #        $base_url = &FIG::cgi_url;
425              $base_url = $FIG_Config::cgi_url;   # get the full cgi url  #       my $base_url = $FIG_Config::cgi_base;
426              $base_url =~ s~^http://[^/]*~~;     # remove protocol and host  #       if ( ! $base_url )                      # if cgi_base was not defined
427              $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash  #       {
428          }  #           $base_url = $FIG_Config::cgi_url;   # get the full cgi url
429    #           $base_url =~ s~^http://[^/]*~~;     # remove protocol and host
430    #           $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash
431    #       }
432    
433          $base_line = $head_end_line;          $base_line = $head_end_line;
434          splice( @$html, $base_line, 0, "<BASE href=\"$base_url\">\n" );          #
435            # RDO 2005-1006. Remove this so proxying works better.
436            #
437    #        splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );
438      }      }
439    
440      #      #
# Line 203  Line 444 
444      if ( $html_line < 0 )      if ( $html_line < 0 )
445      {      {
446          $html_line = 0;          $html_line = 0;
447            Trace("Splicing the HTML tag at $html_line.") if T(3);
448          splice( @$html, $html_line, 0, "<HTML>\n" );          splice( @$html, $html_line, 0, "<HTML>\n" );
449      }      }
450    
# Line 213  Line 455 
455      if ( $head_line < 0 )      if ( $head_line < 0 )
456      {      {
457          $head_line = $html_line + 1;          $head_line = $html_line + 1;
458            Trace("Splicing the HEAD tag at $head_line.") if T(3);
459          splice( @$html, $head_line, 0, "<HEAD>\n" );          splice( @$html, $head_line, 0, "<HEAD>\n" );
460      }      }
461    
462      #      #
463      #  Place FIG search link at bottom of page      #  Place FIG search link at bottom of page
464      #      #
465        Trace("Placing FIG search link.") if T(3);
466      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();
467      if (! $no_home)      if (! $no_home)
468      {      {
# Line 228  Line 471 
471      }      }
472    
473      #      #
474        # See if we have a site-specific tail (for disclaimers, etc).
475        #
476        Trace("Placing site tail.") if T(3);
477        my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
478        my $site_fh;
479        if (open($site_fh, "<$site_tail"))
480        {
481            push(@tail, <$site_fh>);
482            close($site_fh);
483        }
484    
485        #
486      #  Figure out where to insert The SEED tail.  Before </body>,      #  Figure out where to insert The SEED tail.  Before </body>,
487      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
488      #      #
   
489      my @tags = ();      my @tags = ();
490        Trace("Processing closing tags.") if T(3);
491      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
492      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
493      {      {
# Line 248  Line 502 
502    
503      if ( @tail )      if ( @tail )
504      {      {
505            Trace("Splicing tail.") if T(3);
506          splice( @$html, $i, 0, @tail, @tags );          splice( @$html, $i, 0, @tail, @tags );
507      }      }
508      elsif ( @tags )      elsif ( @tags )
509      {      {
510            Trace("Splicing tags.") if T(3);
511          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
512      }      }
513    
514      print @$html;      Trace("Printing the HTML array.") if T(3);
515        # RAE the chomp will return any new lines at the ends of elements in the array,
516        # and then we can join  with a "\n". This is because somethings put newlines in,
517        # and others don't. This should make nicer looking html
518        #
519        # chomp(@$html);
520        # print join "\n", @$html;
521        #
522        # Apparently the above still breaks things. This is the correct code:
523        foreach $_ (@$html)
524        {
525            my $line = $_;
526            if (T(4)) {
527                my $escapedLine = CGI::escapeHTML($line);
528                Trace("Printing:\n$escapedLine") if T(4);
529            }
530            print $line;
531        }
532    
533  }  }
534    
535    
536    =head1 make_table
537    
538    The main method to convert an array into a table.
539    
540    The col_hdrs are set to the <th> headers, the $tab is an array of arrays. The first is the rows, and the second is the columns. The title is the title of the table.
541    
542    The options define the settings for the table such as border, width, and class for css formatting. If the option "excelfile" is set to a filename that will be created in FIG_Config::temp, and the link included that allows the user to download the file as an excel file.
543    
544    =cut
545    
546  sub make_table {  sub make_table {
547      my($col_hdrs,$tab,$title,$instr) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
548      my(@tab);      my(@tab);
549    
550      push( @tab, "\n<table border>\n",      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
551        my $width = defined $options{width} ? "width=\"$options{width}\"" : "";
552        my $class = defined $options{class} ? "class=\"$options{class}\"" : "";
553        push( @tab, "\n<table $border $width $class>\n",
554                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
555                  "\t<tr>\n\t\t<th>"                  "\t<tr>\n\t\t"
556                . join( "</th>\n\t\t<th>", @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
557                . "</th>\n\t</tr>\n"                . "\n\t</tr>\n"
558          );          );
559      my($i,$nowrap);      my($i);
   
     for ($i=0; ($i < @$instr) && ($instr->[$i] !~ /nowrap/); $i++) {}  
     $nowrap = ($i == @$instr) ? "" : " nowrap";  
560    
561      my $row;      my $row;
562      foreach $row (@$tab)      foreach $row (@$tab)
563      {      {
564          push( @tab, "\t<tr>\n"          push( @tab, "\t<tr>\n"
565                    . join( "\n", map { &expand($_,$nowrap) } @$row )                    . join( "\n", map { &expand($_) } @$row )
566                    . "\n\t</tr>\n"                    . "\n\t</tr>\n"
567              );              );
568      }      }
569      push(@tab,"</table>\n");      push(@tab,"</table>\n");
570    
571        # excelfile should be appropriate for a filename (no spaces/special characters)
572        if (defined $options{"excelfile"}) {
573            if (! defined($raelib)) {
574                require raelib;
575                $raelib = new raelib;
576            }
577            push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
578    
579      return join("",@tab);      return join("",@tab);
580  }  }
581    
582    sub abstract_coupling_table {
583        my($cgi,$prot,$coupling) = @_;
584        my %fc;
585    
586        my $col_hdrs = ["coupled to","Score","Type of Coupling", "Type-specific Data"];
587        my $tab = [];
588        my %by_peg;
589        foreach my $x (@$coupling)
590        {
591            my($peg2,$psc,$type,$extra) = @$x;
592            if (($type !~ /^[ID]FC$/) || (! $fc{$peg2}))
593            {
594                if ($type =~  /^[ID]FC$/)
595                {
596                    $fc{$peg2} = 1;
597                }
598    
599                $by_peg{$peg2} += $psc;
600            }
601        }
602    
603        foreach my $x (sort { ($by_peg{$b->[0]} <=> $by_peg{$a->[0]})
604                              or ($a->[0] cmp $b->[0])
605                              or ($b->[1] <=> $a->[1])
606                              or ($a->[2] cmp $b->[2]) } @$coupling)
607        {
608            my($peg2,$psc,$type,$extra) = @$x;
609            push(@$tab,[&fid_link($cgi,$peg2,1),$psc,$type,&set_prot_links($cgi,join(", ",@$extra))]);
610        }
611    
612    
613         my $help = "<a href=\"Html/abstract_coupling.html\" target=\"SEED_or_SPROUT_help\">for help</a>";
614    #    my @html = &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot");
615    #    push(@html,"<hr>\n",$cgi->h3($help),"<br>");
616    #    return @html;
617    
618        return &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot [$help]");
619    }
620    
621  sub expand {  sub expand {
622      my($x,$nowrap) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
623        my( $x, $tag ) = @_;
624    
625        $tag = "td" unless $tag;
626        my $endtag = $tag;
627    
628        # RAE modified this so that you can pass in a reference to an array where
629        # the first element is the data to display and the second element is optional
630        # things like colspan and align. Note that in this case you need to include the td
631        # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
632    
633      if ($x =~ /^\@([^:]+)\:([^:]+)\:(.*)$/)      # per GJO's request modified this line so it can take any tag.
634        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
635    
636        if ( $x =~ /^\@([^:]+)\:(.*)$/ )
637      {      {
638          return "\t\t<td$nowrap $1=\"$2\">$3</td>";          return "\t\t<$tag $1>$2</$endtag>";
639      }      }
640      else      else
641      {      {
642          return "\t\t<td$nowrap>$x</td>";          return "\t\t<$tag>$x</$endtag>";
643        }
644    }
645    
646    
647    =head2 merge_table_rows()
648    
649    Merge table rows together. This will merge a table so that adjacent cells with the same content will only be shown once.
650    
651    Something like this:
652    
653        -----------------------
654        |    1     |    a     |
655        -----------------------
656        |    1     |    b     |
657        -----------------------
658        |    2     |    c     |
659        -----------------------
660        |    3     |    d     |
661        -----------------------
662        |    4     |    d     |
663        -----------------------
664        |    5     |    d     |
665        -----------------------
666    
667    Will become:
668    
669        -----------------------
670        |          |    a     |
671        |    1     |-----------
672        |          |    b     |
673        -----------------------
674        |    2     |    c     |
675        -----------------------
676        |    3     |          |
677        ------------          |
678        |    4     |    5     |
679        ------------          |
680        |    5     |          |
681        -----------------------
682    
683    
684    The method takes two arguments. The reference to the array that is the table ($tab). This is the standard table that is created for HTML.pm to draw, and a reference to a hash of columns that you don't want to merge together. The reference to the hash is optional, and if not included, everything will be merged.
685    
686     $tab=&HTML::merge_table_rows($tab);
687    
688     or
689    
690     $skip=(1=>1, 3=>1, 5=>1);
691     $tab=&HTML::merge_table_rows($tab, $skip);  # will merge all columns except 1, 3 and 5. Note the first column in the table is #0
692    
693    
694    =cut
695    
696    
697    
698    
699    sub merge_table_rows {
700     # RAE:
701     # Experimental piece of code. We often want to have rows or columns were cells are merged. It just looks so much nicer
702     # this block should merge adjacent rows that have the same text in them.
703     # use like this:
704     #      $tab=&HTML::merge_table_rows($tab);
705     # before you do a make_table call
706    
707     my $self=shift if UNIVERSAL::isa($_[0],__PACKAGE__);
708     my ($tab, $skip)=@_;
709    
710     my $newtable;
711     my $lastrow;
712     my $rowspan;
713     my $refs;
714    
715     for (my $y=0; $y <= $#$tab; $y++) {
716     #$y is the row in the table;
717      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
718       # this is the user definable columns not to merge
719       if ($skip->{$x})
720       {
721        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
722        next;
723       }
724    
725       #$x is the column in the table
726       # if the column in the row we are looking at is the same as the column in the previous row, we don't add
727       # this cell to $newtable. Instead we increment the rowspan of the previous row by one
728    
729       # handle cells that are references to arrays
730       if (ref($tab->[$y]->[$x]) eq "ARRAY") {$refs->[$y]->[$x]=$tab->[$y]->[$x]->[1]; $tab->[$y]->[$x]=$tab->[$y]->[$x]->[0]}
731    
732       # now we go back through the table looking where to draw the merge line:
733       my $lasty=$y;
734       while ($lasty >= 0 && $tab->[$y]->[$x] eq $tab->[$lasty]->[$x]) {$lasty--}
735       $lasty++; # this is the last identical cell. If lasty==y it is the current cell, so we just save the data. Otherwise we increment the rowspan
736       if ($lasty == $y) {
737        # we always want to have something in rows that may otherwise be empty but should be there (see below)
738        unless ($tab->[$y]->[$x]) {$tab->[$y]->[$x]=" &nbsp; "}
739        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
740       }
741       else {$rowspan->[$lasty]->[$x]++}
742      }
743     }
744    
745     # now just join everything back together
746     for (my $y=0; $y <= $#$tab; $y++) {
747      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
748       if ($rowspan->[$y]->[$x]) {
749        if ($refs->[$y]->[$x]) {$refs->[$y]->[$x] .= " rowspan=". ($rowspan->[$y]->[$x]+1)}
750        else {$refs->[$y]->[$x] = "td rowspan=". ($rowspan->[$y]->[$x]+1)}
751        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
752       }
753       elsif ($newtable->[$y]->[$x] && $refs->[$y]->[$x]) {
754        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
755       }
756      }
757     }
758    
759    
760     # finally we have to remove any completely empty cells that have been added by the array mechanism
761     # (e.g. if you define $a->[2] then $a->[0] and $a->[1] are now undef).
762     # that is why in the loop above I replace empty cells with nbsp. They are now not undef!
763     # I am sure that Gary can do this in one line, but I am hacking.
764     my @trimmed;
765     foreach my $a (@$newtable) {
766      my @row;
767      foreach my $b (@$a) {
768       push @row, $b if ($b);
769      }
770      push @trimmed, \@row;
771     }
772    
773     return \@trimmed;
774    }
775    
776    
777    
778    
779    sub set_ec_links {
780        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
781        my($cgi,$x) = @_;
782        my($before,$match,$after);
783    
784        if ($x =~ /^(.*)(EC \d+\.\d+\.\d+\.\d+)(.*)/s)
785        {
786            $before = $1;
787            $match = $2;
788            $after = $3;
789            return &set_ec_links($cgi,$before) . &HTML::ec_link($match) . &set_ec_links($cgi,$after);
790      }      }
791        return $x;
792  }  }
793    
794  sub ec_link {  sub ec_link {
795        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
796      my($role) = @_;      my($role) = @_;
797    
798      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)
# Line 312  Line 806 
806  }  }
807    
808  sub role_link {  sub role_link {
809        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
810      my($cgi,$role) = @_;      my($cgi,$role) = @_;
811    
812      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;
# Line 322  Line 817 
817      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
818  }  }
819    
820    =head2 fid_link
821    
822    Get a link to a fid.
823    
824    use: my $html=&HTML::fid_link($cgi, $fid, Local, Just_URL, Full_Path);
825    
826    Local is a boolean means to eliminate the fig|org.peg from the text of the link.
827    
828    Just_URL will only return the URL and not the HTML code. The default is to return the full code.
829    
830    Full_Path is a boolean that will get the full path to the URL not just a relative path. This is required in pages where the base href changes (e.g. if an image is imported like on the metabolic pages).
831    
832    =cut
833    
834    
835  sub fid_link {  sub fid_link {
836      my($cgi,$fid,$local,$just_url) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
837        my($cgi,$fid,$local,$just_url,$fullpath) = @_;
838        Trace("Creating link for feature $fid.") if T(4);
839        my $err=join(" ", $cgi,$fid,$local,$just_url,$fullpath);
840    
841      my($n);      my($n);
842    
843      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      my $top = top_link();
844        if ($fullpath) {$top=$FIG_Config::cgi_url}
845    
846        if ($fid =~ /^fig\|\d+\.\d+\.([a-zA-Z]+)\.(\d+)/)
847      {      {
848          if ($local)          if ($local)
849          {          {
# Line 343  Line 860 
860          {          {
861              $n = $fid;              $n = $fid;
862          }          }
863          if ($1 ne "peg") { return $n }  
864            my $link;
865            my $new_framework = $cgi->param('new_framework') ? 1 : 0;
866            #added to format prophage and path island links to feature.cgi
867            my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
868            my $virt = "&48hr_job=" . $cgi->param("48hr_job");
869            Trace("Sprout mode is \"$sprout\".") if T(4);
870            if ($1 ne "peg" && ! $sprout)
871            {
872               Trace("Creating feature link for $fid.") if T(4);
873               my $user = $cgi->param('user');
874               if (! $user) { $user = "" }
875               $link = "$top/feature.cgi?feature=$fid&user=$user$sprout$virt";
876               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
877            }
878            else
879            {
880                Trace("Creating protein link for $fid.") if T(4);
881          my $user = $cgi->param('user');          my $user = $cgi->param('user');
882          if (! $user) { $user = "" }          if (! $user) { $user = "" }
883          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
884          my $link = $cgi->url() . "?prot=$fid&user=$user$trans";              my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
885          $link =~ s/[a-z_A-Z]+\.cgi\?/protein.cgi?/;  ###a
886    
887    ### This used to be
888    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
889    ###
890    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
891    ###
892    ### RAO
893    
894                #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
895                #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
896                $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout$virt\&new_framework=$new_framework";
897                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
898            }
899          if ($just_url)          if ($just_url)
900          {          {
901              return $link;              return $link;
902          }          }
903          else          else
904          {          {
905              return "<a href=$link>$n</a>";              return "<a href='$link'>$n</a>";
906          }          }
907      }      }
908      return $fid;      return $fid;
909  }  }
910    
911  sub family_link {  sub family_link {
912        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
913      my($family,$user) = @_;      my($family,$user) = @_;
914    
915      return $family;      return $family;
916  }  }
917    
918  use URI::Escape;  =head2 evidence_codes_explain
919    
920    Given an evidence code, returns a string that explains this eveidence code.
921    
922    =cut
923    
924    sub evidence_codes_explain {
925     my($ec)=@_;
926     return unless ($ec);
927    
928     $ec=uc($ec);
929     return "IDA: Inferred from Direct Assay" if ($ec =~ /IDA/);
930     return "IGI: Inferred from Genetic Interaction" if ($ec =~ /IGI/);
931     return "TAS: Traceable Author Statement" if ($ec =~ /TAS/);
932     return "ISU: in subsystem unique" if ($ec =~ /ISU/);
933     return "$ec: in subsystem duplicates" if ($ec =~ /IDU/);
934     return "$ec: in cluster with" if ($ec =~ /ICW/);
935     return "FF: in FIGfam" if ($ec =~ /FF/);
936     return "CWN: clustered with nonhypothetical" if ($ec =~ /CWN/);
937     return "CWH: clustered, but only with hypotheticals" if ($ec =~ /CWH/);
938     return "DLIT: literature references to this gene exist" if ($ec =~ /DLIT/);
939     return "ILIT: no references to this gene exist, but they do to other genes with the same functional role" if ($ec =~ /ILIT/);
940     return "$ec: unknown!";
941    }
942    
943  sub get_html {  sub get_html {
944        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
945      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
946      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
947    
948      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
949      $ua->timeout( 900 );      $ua->timeout( 900 );
   
950      if ($type =~/post/i)      if ($type =~/post/i)
951      {      {
952          $args = [];          $args = [];
# Line 387  Line 958 
958          my $response = $ua->request($request);          my $response = $ua->request($request);
959          $out = $response->content;          $out = $response->content;
960      }      }
961      else  
962        if ($type =~/get/i)
963      {      {
964          @args = ();          @args = ();
965          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 399  Line 971 
971          {          {
972              $url .= "?" . join("&",@args);              $url .= "?" . join("&",@args);
973          }          }
974          $request = new HTTP::Request('GET', $url);          my $request = new HTTP::Request('GET', $url);
975          my $response = $ua->request($request);          my $response = $ua->request($request);
976    
977          if ($response->is_success)          if ($response->is_success)
# Line 417  Line 989 
989    
990  #   Now splice in a line of the form <base href=URL> to cause all relative links to work  #   Now splice in a line of the form <base href=URL> to cause all relative links to work
991  #   properly.  Remove the header.  #   properly.  Remove the header.
992        my $i;
993      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}
994      if ($i < @output)      if ($i < @output) {
     {  
   
995          splice(@output,0,$i);          splice(@output,0,$i);
996      }      }
997    
# Line 435  Line 1005 
1005  }  }
1006    
1007  sub trim_output {  sub trim_output {
1008        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1009      my($out) = @_;      my($out) = @_;
1010      my $i;      my ($i, $j);
1011    
1012      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}
1013      splice(@$out,0,$i);      splice(@$out,0,$i);
# Line 465  Line 1036 
1036      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}
1037      if ($j > 0)      if ($j > 0)
1038      {      {
1039            #
1040            # Hm. We would have tried using the options here:
1041            # my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
1042            # but they're not passed in. So use the default html.tail.
1043            #
1044            my $html_tail_file = "./Html/html.tail";
1045          my @tmp = `cat $html_tail_file`;          my @tmp = `cat $html_tail_file`;
1046          my $n = @tmp;          my $n = @tmp;
1047          splice(@$out,$j-$n,$n+1);          splice(@$out,$j-$n,$n+1);
# Line 472  Line 1049 
1049  }  }
1050    
1051  sub set_prot_links {  sub set_prot_links {
1052        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1053      my($cgi,$x) = @_;      my($cgi,$x) = @_;
1054      my($before,$match,$after);      my($before,$match,$after);
1055    
1056      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
1057      {      {
1058          $before = $1;          $before = $1;
1059          $match = $2;          $match = $2;
1060          $after = $3;          $after = $3;
1061          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);
1062      }      }
1063      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)      elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
1064      {      {
1065          $before = $1;          $before = $1;
1066          $match = $2;          $match = $2;
1067          $after = $3;          $after = $3;
1068          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::refseq_link($cgi,$match) . &set_prot_links($cgi,$after);
1069      }      }
1070      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
1071      {      {
1072          $before = $1;          $before = $1;
1073          $match = $2;          $match = $2;
1074          $after = $3;          $after = $3;
1075          return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);
1076      }      }
1077      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~ /^(.*)(img\|\d+)(.*)/s)
1078      {      {
1079          $before = $1;          $before = $1;
1080          $match = $2;          $match = $2;
1081          $after = $3;          $after = $3;
1082          return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::img_link($cgi,$match) . &set_prot_links($cgi,$after);
     }  
     return $x;  
1083  }  }
1084        elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
 sub gi_link {  
     my($cgi,$gi) = @_;  
   
     if ($gi =~ /^gi\|(\d+)$/)  
1085      {      {
1086          return "<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept>$gi</a>";          $before = $1;
1087            $match = $2;
1088            $after = $3;
1089            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1090      }      }
1091      return $gi;      elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1092        {
1093            $before = $1;
1094            $match = $2;
1095            $after = $3;
1096            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1097  }  }
1098    
1099  sub sp_link {      elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
     my($cgi,$sp) = @_;  
   
     if ($sp =~ /^sp\|(\S+)$/)  
1100      {      {
1101          return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";          $before = $1;
1102            $match = $2;
1103            $after = $3;
1104            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1105        }
1106    
1107        elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1108        {
1109            $before = $1;
1110            $match = $2;
1111            $after = $3;
1112            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1113        }
1114    
1115        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1116        {
1117            $before = $1;
1118            $match = $2;
1119            $after = $3;
1120            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1121        }
1122    
1123        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1124        {
1125            $before = $1;
1126            $match = $2;
1127            $after = $3;
1128            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1129        }
1130    
1131        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1132        {
1133            $before = $1;
1134            $match = $2;
1135            $after = $3;
1136            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1137        }
1138        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1139        {
1140            $before = $1;
1141            $match = $2;
1142            $after = $3;
1143            return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
1144        }
1145        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
1146        {
1147            $before = $1;
1148            $match = $2;
1149            $after = $3;
1150            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
1151        }
1152        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
1153        {
1154            $before = $1;
1155            $match = $2;
1156            $after = $3;
1157            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
1158        }
1159        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
1160        {
1161            $before = $1;
1162            $match = $2;
1163            $after = $3;
1164            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1165        }
1166        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1167        {
1168            $before = $1;
1169            $match = $2;
1170            $after = $3;
1171            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1172        }
1173        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1174        {
1175            $before = $1;
1176            $match = $2;
1177            $after = $3;
1178            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1179        }
1180        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1181        {
1182            $before = $1;
1183            $match = $2;
1184            $after = $3;
1185            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1186        }
1187        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1188        {
1189            $before = $1;
1190            $match = $2;
1191            $after = $3;
1192            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1193        }
1194        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1195        {
1196            $before = $1;
1197            $match = $2;
1198            $after = $3;
1199            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1200        }
1201    # IPI stopped working. turn off for now.
1202    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1203    #    {
1204    #        $before = $1;
1205    #        $match = $2;
1206    #        $after = $3;
1207    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1208    #    }
1209        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1210        {
1211            #wormbase
1212    
1213            $before = $1;
1214            $match = $2;
1215            $after = $3;
1216            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1217        }
1218        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1219        {
1220            #flybase
1221    
1222            $before = $1;
1223            $match = $2;
1224            $after = $3;
1225            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1226        }
1227        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1228        {
1229            #flybase
1230    
1231            $before = $1;
1232            $match = $2;
1233            $after = $3;
1234            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1235        }
1236        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1237        {
1238            #flybase
1239    
1240            $before = $1;
1241            $match = $2;
1242            $after = $3;
1243            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1244        }
1245        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1246        {
1247    
1248          $before = $1;
1249          $match = $2;
1250          $after = $3;
1251    
1252          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1253        }
1254        return $x;
1255    }
1256    
1257    sub trembl_link {
1258        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1259        my($cgi,$id) = @_;
1260    
1261        if ($id =~ /^tr\|(.*)/) {
1262          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1263        } else {
1264          return "invalid call to trembl link";
1265        }
1266    }
1267    
1268    sub refseq_link {
1269        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1270        my($cgi,$id) = @_;
1271    
1272        if ($id =~ /^[NXYZA]P_/)
1273        {
1274            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id' target=_blank>$id</a>";
1275        }
1276        elsif ($id =~ /^[NXYZA]M_/)
1277        {
1278            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1279        }
1280    }
1281    
1282    sub gi_link {
1283        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1284        my($cgi,$gi) = @_;
1285    
1286        if ($gi =~ /^gi\|(\d+)$/)
1287        {
1288            return "<a href='http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept' target=_blank>$gi</a>";
1289        }
1290        return $gi;
1291    }
1292    
1293    sub tigr_link {
1294        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1295        my($cgi,$tigr) = @_;
1296    
1297        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1298        {
1299            my $id=$1.$2;
1300            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1301        }
1302        elsif ($tigr =~ /^tigr\|(\S+)$/)
1303        {
1304            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\" target=_blank>$tigr</a>";
1305        }
1306        return $tigr;
1307    }
1308    
1309    sub eric_link {
1310        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1311        my($cgi,$eric) = @_;
1312    
1313        if ($eric =~ /^eric\|(\S+)/)
1314        {
1315            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1316        }
1317        return $eric;
1318    }
1319    
1320    sub bhb_link {
1321        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1322        my($cgi,$bhb) = @_;
1323    
1324        return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1325    }
1326    
1327    sub apidb_link {
1328        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1329        my($cgi,$api) = @_;
1330    
1331        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1332        {
1333            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1334        }
1335        return $api;
1336    }
1337    
1338    sub patric_link {
1339        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1340        my($cgi,$patric) = @_;
1341    
1342        if ($patric =~ /patric\|(.*)/)
1343        {
1344            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1345        }
1346        return $patric;
1347    }
1348    
1349    sub vbrc_link {
1350        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1351        my($cgi,$vbrc) = @_;
1352    
1353        if ($vbrc =~ /vbrc\|(.*)/)
1354        {
1355            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1356        }
1357        return $vbrc;
1358    }
1359    
1360    sub vectorbase_link {
1361        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1362        my($cgi,$vec) = @_;
1363        return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1364    }
1365    
1366    
1367    sub uni_link {
1368        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1369        my($cgi,$uni) = @_;
1370    
1371        if ($uni =~ /^uni\|(\S+)$/)
1372        {
1373            #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1374            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1375        }
1376        return $uni;
1377    }
1378    
1379    sub sp_link {
1380        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1381        my($cgi,$sp) = @_;
1382    
1383        if ($sp =~ /^sp\|(\S+)$/)
1384        {
1385            return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$sp</a>";
1386      }      }
1387      return $sp;      return $sp;
1388  }  }
1389    
1390  sub pir_link {  sub pir_link {
1391        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1392      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
1393    
1394      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1395      {      {
1396          return "<a href=http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1>$pir</a>";          return "<a href='http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1' target=_blank>$pir</a>";
1397      }      }
1398      return $pir;      return $pir;
1399  }  }
1400    
1401    sub kegg_link {
1402        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1403        my($cgi,$kegg) = @_;
1404    
1405        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1406        {
1407            return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1408        }
1409        return $kegg;
1410    }
1411    
1412    sub img_link {
1413        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1414        my($cgi,$img) = @_;
1415    
1416        if ($img =~ /^img\|(\S+)$/)
1417        {
1418            return "<a href='http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$1' target=_blank>$img</a>";
1419        }
1420        return $img;
1421    }
1422    
1423    sub ensembl_link {
1424        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1425        my($cgi,$ensembl) = @_;
1426    
1427        if ($ensembl =~ /^(\S+):(\S+)$/)
1428        {
1429            my $what=$1;
1430            my $key=$2;
1431            my $idx="All";
1432            if ($what eq "EnsemblGene") { $idx = "Gene" }
1433            if ($what eq "EnsemblTranscript") { $idx = "All" }
1434            if ($what eq "EnsemblProtein") { $idx = "All" }
1435    
1436            #I really want to get right to the transcript and peptide pages, but
1437            #can't see how to do that without knowing the org name too, which
1438            #I don't know at this point. (ensembl org name, not real org name)
1439    
1440            return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1441        }
1442        return $ensembl;
1443    }
1444    
1445    sub entrezgene_link {
1446        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1447        my($cgi,$entrezgene) = @_;
1448    
1449        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1450        {
1451            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1' target=_blank>$entrezgene</a>";
1452        }
1453        return $entrezgene;
1454    }
1455    
1456    sub mim_link {
1457        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1458        my($cgi,$mim) = @_;
1459    
1460        if ($mim =~ /^MIM:(\S+)$/)
1461        {
1462            return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1463        }
1464        return $mim;
1465    }
1466    
1467    sub hgnc_link {
1468        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1469        my($cgi,$hgnc) = @_;
1470    
1471        if ($hgnc =~ /^HGNC:(\S+)$/)
1472        {
1473            return "<a href='http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=equals&match=$1&symbol_search=Search&number=50&format=html&sortby=symbol' target=_blank>$hgnc</a>";
1474        }
1475    
1476        return $hgnc;
1477    }
1478    
1479    sub unigene_link {
1480        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1481        my($cgi,$unigene) = @_;
1482    
1483        if ($unigene =~ /^UniGene:(\S+)$/)
1484        {
1485            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1486        }
1487        return $unigene;
1488    }
1489    
1490    sub ipi_link {
1491        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1492        my($cgi,$ipi) = @_;
1493    
1494        if ($ipi =~ /^IPI:(\S+)$/)
1495        {
1496            return "<a href='http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1' target=_blank>$ipi</a>";
1497        }
1498        return $ipi;
1499    }
1500    
1501    sub wp_link {
1502        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1503        my($cgi,$wp) = @_;
1504    
1505        #wormbase
1506    
1507        if ($wp =~ /^WP:(\S+)$/)
1508        {
1509            return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1510        }
1511        return $wp;
1512    }
1513    
1514    sub fb_link {
1515        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1516        my($cgi,$fb) = @_;
1517    
1518        #flybase
1519    
1520        if ($fb =~ /^FB:(\S+)$/)
1521        {
1522            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1523        }
1524        return $fb;
1525    }
1526    
1527    sub fborf_link {
1528        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1529        my($cgi,$fb) = @_;
1530    
1531        #flybase
1532    
1533        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1534        {
1535            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1536        }
1537        return $fb;
1538    }
1539    
1540    sub sgd_link {
1541        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1542        my($cgi,$sgd) = @_;
1543    
1544        #yeast
1545    
1546        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1547        {
1548            return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1549        }
1550        return $sgd;
1551    }
1552    
1553    
1554    
1555    
1556    sub set_map_links {
1557        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1558        my($cgi,$x) = @_;
1559        my($before,$match,$after);
1560    
1561        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
1562    
1563        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
1564        {
1565            $before = $1;
1566            $match = $2;
1567            $after = $3;
1568            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
1569        }
1570        return $x;
1571    }
1572    
1573    
1574    
1575    sub map_link {
1576        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1577        my($cgi,$map,$org) = @_;
1578    
1579        my $user = $cgi->param('user');
1580        $user = $user ? $user : "";
1581        $org = $org ? $org : "";
1582    
1583        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1584    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1585        my $link = "<a href=\"$url\">$map</a>";
1586        return $link;
1587    }
1588    
1589    sub java_buttons {
1590        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1591      ## ADDED BY RAE
1592      # Provides code to include check all/first half/second half/none for javascrspt
1593      # this takes two variables - the form name provided in start_form with the
1594      # -name => field and the checkbox name
1595      my ($form, $button)=@_;
1596    
1597      my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1598      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1599      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1600      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1601    
1602      return $java_script;
1603    }
1604    
1605    =head3 sub_link
1606    
1607    C<< my $htmlText = HTML::sub_link($cgi, $sub, gid); >>
1608    
1609    Create a subsystem link. The link will be to the display page if there is no
1610    user or we are in SPROUT mode; otherwise it will be to the edit page.
1611    
1612    =over 4
1613    
1614    =item cgi
1615    
1616    CGI query object for the current web session. The parameters of special interest
1617    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1618    the subsystem's edit page will be shown rather than its display page.
1619    
1620    =item sub
1621    
1622    Name of the desired subsystem. It will be cleaned of underscores before the
1623    hyperlink is applied.
1624    
1625    =item gid
1626    
1627    Genome ID to be specified as the focus.
1628    
1629    =back
1630    
1631    =cut
1632    
1633    sub sub_link {
1634        # Allow call as an instance in addition to the authorized method.
1635        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1636        # Get the parameters.
1637        my ($cgi, $sub, $gid) = @_;
1638        # Declare the return variable.
1639        my $retVal;
1640        # Clean the subsystem name for display purposes. This is a very
1641        # different thing from URL-escaping.
1642        my $cleaned = CGI::escapeHTML($sub);
1643        $cleaned =~ s/_/ /g;
1644        # URL-escape the subsystem name for use in the link.
1645        my $linkable = uri_escape($sub);
1646        # Determine the mode. Note we use the little OR trick to insure that
1647        # we have the correct value for plugging into the output link.
1648        my $user = $cgi->param('user') || "";
1649        my $sproutMode = $cgi->param('SPROUT') || 0;
1650        if ($user && ! $sproutMode) {
1651            # A SEED user is calling, so we go to the edit page.
1652            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1653        } else {
1654            # A visitor or SPROUT user is calling, so we go to the display page.
1655            $retVal = "<a href=\"display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;focus=$gid;SPROUT=$sproutMode\">$cleaned</a>";
1656        }
1657        # Return the result.
1658        return $retVal;
1659    }
1660    
1661    sub reaction_map_link {
1662        my($mapID, @reaction_list) = @_;
1663        if($mapID =~ /\d+/)
1664        {
1665            my $reactions = join "+", @reaction_list;
1666            if ($reactions ne "")
1667            {
1668                $reactions = "+".$reactions;
1669            }
1670    
1671            return "<a href=http://www.genome.jp/dbget-bin/show_pathway?rn$mapID$reactions>$mapID</a>";
1672        }
1673        else
1674        {
1675            return $mapID;
1676        }
1677    }
1678    
1679    sub compound_link {
1680        my($compound) = @_;
1681        if($compound =~ /^C\d+/)
1682        {
1683            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.jp/dbget-bin/www_bget?compound+$compound','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes')\">$compound</a>";
1684        }
1685        else
1686        {
1687            return $compound;
1688        }
1689    }
1690    
1691    
1692    sub reaction_link {
1693        my($reaction) = @_;
1694        if ($reaction =~ /^(\*)?(R\d+)/)
1695        {
1696            # return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1697            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes')\">$reaction</a>";
1698        }
1699        return $reaction;
1700    }
1701    
1702    
1703    sub html_for_assignments {
1704        my($fig,$user,$peg_sets) = @_;
1705        my $i;
1706    
1707        my @vals = ();
1708        my $set = 1;
1709        foreach my $peg_set (@$peg_sets)
1710        {
1711            for ($i=0; ($i < @$peg_set); $i++)
1712            {
1713                my $peg = $peg_set->[$i];
1714                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1715            }
1716            $set++;
1717        }
1718    
1719        $ENV{'REQUEST_METHOD'} = 'GET';
1720        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1721        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1722        $out =~ s/^.*?<form/<form/si;
1723        $out =~ s/^(.*)<table.*/$1/si;
1724        return $out;
1725    }
1726    
1727    =head1 rss_feed
1728    
1729    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1730            SEED.rss                - everything gets written here
1731            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1732            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1733    
1734    
1735    RSS feeds must contain a title, description, and link. The title is what is seen e.g. from the firefox or safari pull down menu. The description is seen from within an rss aggregator, and may be displayed on web pages and so on.
1736    
1737    The method takes a reference to an array containing the file names for the RSS feeds to add your item to, and a hash of items for the xml. Only title, description, and link are required tags in the XML.
1738    
1739    The file names are the full name of the file, eg SEEDsubsystems.rss, SEEDgenomes.rss. Be aware that this is a file name, though, so don't uses special characters. The path will be added.
1740    
1741    The has can have these keys:
1742    
1743    REQUIRED:
1744    title       : the title. This is usually what is seen by the user in the pull down menu
1745    description : a more complete description that is often seen is rss viewers but not always
1746    link        : link to the item that was added/edited
1747    All other keys are treated as optional RSS arguments and written to the file.
1748    
1749    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1750    
1751    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1752    
1753    
1754    =cut
1755    
1756    sub rss_feed {
1757     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1758     my ($files, $args)=@_;
1759    
1760     # how many entries to store in the file
1761     my $max_entries=50;
1762    
1763     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1764    
1765     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1766     # check for the directory and if not, make it
1767     mkdir $filepath unless (-d $filepath);
1768    
1769     # note that $info is a hash of references to hashes that are written out as headers in the file
1770     my $info=
1771     {
1772      "SEED.rss" =>
1773       {
1774            title           => "The SEED",
1775            description     => "Latest news from the SEED",
1776            link            => "Html/rss/SEED.rss",
1777       },
1778    
1779      "SEEDsubsystems.rss" =>
1780      {
1781            title           => "SEED Subsystems",
1782            description     => "Recently updated SEED subsystems",
1783            link            => "Html/rss/SEEDsubsystems.rss",
1784      },
1785    
1786      "SEEDsubsystems.rss" =>
1787      {
1788            title           => "SEED Genomes",
1789            description     => "Genomes recently added to the SEED",
1790            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1791      },
1792    
1793     };
1794    
1795    
1796     # build the new xml
1797     my $xml = "\t<item>\n";
1798     foreach my $qw ("title", "description", "link") {
1799      unless ($args->{$qw}) {
1800       print STDERR "You need to include a $qw tag in your RSS description\n";
1801       return(0);
1802      }
1803      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1804      # so we are going to pull out the links and uri_escape just the part after the .cgi
1805      if ($qw eq "link")
1806      {
1807       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1808       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1809      }
1810    
1811      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1812      delete $args->{$qw};
1813     }
1814    
1815     foreach my $tag (grep {!/type/i} keys %$args)
1816     {
1817      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1818     }
1819    
1820     $xml .= "\t</item>\n";
1821    
1822    
1823     my @files=("SEED.rss");
1824     if ($args->{"type"}) {
1825        my $type = $args->{type};
1826        push @files, "SEED.$type.rss"
1827    }
1828    
1829     foreach my $file ("SEED.rss", @$files)
1830     {
1831      if (-e "$filepath/$file")
1832      {
1833       my @out; # the new content of the file
1834       my $itemcount=0; # how many <item> </item>'s are we keeping
1835       my $initem; # are we in an item?
1836       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1837       while (<IN>)
1838       {
1839        if (/\<item\>/) {
1840         push @out, $xml, unless ($itemcount);
1841         $itemcount++;
1842         $initem=1;
1843        }
1844        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1845        next if ($initem && $itemcount > $max_entries);
1846        push @out, $_;
1847       }
1848       close IN;
1849       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1850       print OUT @out;
1851      }
1852      else
1853      {
1854       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1855       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1856       if ($info->{$file})
1857       {
1858         # we're going to sanity check each of the three options we output, just to be sure
1859         foreach my $qw ("title", "description", "link")
1860         {
1861           if ($info->{$file}->{$qw})
1862           {
1863              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1864           } else {
1865              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1866           }
1867         }
1868       }
1869       else {
1870        print STDERR "Please define title, link, and description information for $file\n";
1871        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1872       }
1873       print OUT "\n", $xml;
1874       print OUT "\n", "</channel>\n</rss>\n"
1875      }
1876     }
1877    }
1878    
1879    
1880    
1881    1;
1882    
 1  

Legend:
Removed from v.1.6  
changed lines
  Added in v.1.115

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3