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revision 1.6, Sun Mar 21 02:20:55 2004 UTC revision 1.56, Mon Sep 12 14:53:13 2005 UTC
# Line 1  Line 1 
1  package HTML;  package HTML;
2    
3    use Tracer;
4    use FIG;
5  use Carp;  use Carp;
6  use Data::Dumper;  use Data::Dumper;
7  use LWP::UserAgent;  use LWP::UserAgent;
8  use LWP::Simple;  use LWP::Simple;
9    use URI::Escape;  # uri_escape()
10  use URI::URL;  use URI::URL;
11  use HTTP::Request::Common;  use HTTP::Request::Common;
12    use POSIX;
13    
14    sub new
15    {
16        my($class) = @_;
17    
18        my $self = {};
19    
20        return bless $self, $class;
21    }
22    
23    sub compute_html_header
24    {
25        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
26        my($additional_insert, $user, %options ) = @_;
27    
28        my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
29        my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
30    
31        my $html_hdr_file = "./Html/$header_name";
32        if (! -f $html_hdr_file)
33        {
34            $html_hdr_file = "$FIG_Config::fig/CGI/Html/$header_name";
35        }
36        my @html_hdr = &FIG::file_read($html_hdr_file);
37    
38        $options{no_fig_search} or push( @html_hdr, "<br><a href=\"index.cgi?user=$user\">FIG search</a>\n" );
39    
40        if (@html_hdr)
41        {
42            my $insert_stuff;
43    
44            if (not $options{no_release_info})
45            {
46                my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
47                my $ver = $ver[0];
48                chomp $ver;
49                if ($ver =~ /^cvs\.(\d+)$/)
50                {
51                    my $d = asctime(localtime($1));
52                    chomp($d);
53                    $ver .=  " ($d)";
54                }
55                my $host = &FIG::get_local_hostname();
56                $insert_stuff = "SEED version <b>$ver</b> on $host";
57            }
58    
59            if ($additional_insert)
60            {
61                $insert_stuff .= "<br>" . $additional_insert;
62            }
63    
64            for $_ (@html_hdr)
65            {
66                s,(href|img\s+src)="/FIG/,\1="$FIG_Config::cgi_base,g;
67                s,(\?user\=)\",$1$user",;
68                if ($_ eq "<!-- HEADER_INSERT -->\n")
69                {
70                    $_ = $insert_stuff;
71                }
72            }
73        }
74    
75        return @html_hdr;
76    }
77    
78  sub show_page {  sub show_page {
79      my($cgi,$html,$no_home) = @_;      #warn "SHOWPAGE: cgi=", Dumper(@_);
80        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
81        my($cgi,$html,$no_home, $alt_header, $css, $javasrc) = @_;
82      my $i;      my $i;
83    
84        # ARGUMENTS:
85        #     $cgi is the CGI method
86        #     $html is an array with all the html in it. It is just joined by "\n" (and not <br> or <p>
87        #     $no_home eliminates ONLY the bottom FIG search link in a page
88        #     $alt_header is a reference to an array for an alternate header banner that you can replace the standard one with
89        #     $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
90        #               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
91        #               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
92        #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "/FIG/Html/css/styleswitcher.js")
93      #      #
94      # Find the HTML header      # Find the HTML header
95      #      #
96    
97      my $html_hdr_file = "./Html/html.hdr";      my $html_tail_file = "./Html/$tail_name";
98      if (! -f $html_hdr_file)      if (! -f $html_tail_file)
99      {      {
100          $html_hdr_file = "$FIG_Config::fig/CGI/Html/html.hdr";          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
101      }      }
102    
103      my $html_tail_file = "./Html/html.tail";      my $user = $cgi->param('user') || "";
104      if (! -f $html_tail_file)      my @html_hdr;
105        if ($alt_header && ref($alt_header) eq "ARRAY")
106        {
107           @html_hdr = @$alt_header;
108        }
109        else
110      {      {
111          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          @html_hdr = compute_html_header(undef,$user);
112      }      }
113    
114    
# Line 145  Line 229 
229      #      #
230      #  <BODY> goes after last head line      #  <BODY> goes after last head line
231      #      #
232        #  RAE:
233        #  Added the javascript for the buttons immediately after body.
234        #  Note if no buttons are added we still (at the moment) add the script,
235        #  but it only adds a little text (495 characters) to the html and noone will notice!
236        #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
237    
238      if ( $body_line < 0 )      if ( $body_line < 0 )
239      {      {
# Line 156  Line 245 
245      #  Seed page header (if it exists) goes after <BODY>      #  Seed page header (if it exists) goes after <BODY>
246      #      #
247    
248      if ( -f $html_hdr_file )      if (@html_hdr)
249      {      {
250          splice( @$html, $body_line + 1, 0, `cat $html_hdr_file` );          splice( @$html, $body_line + 1, 0, @html_hdr );
251      }      }
252    
253      #      #
# Line 171  Line 260 
260          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
261      }      }
262    
263        # RAE:
264        # Add css here
265        # Note that at the moment I define these two sheets here. I think this should
266        # be moved out, but I want to try it and see what happens.  css has the format:
267        #
268        # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
269    
270        # convert the default key to the right case. and eliminate dups
271        foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
272    
273        if (!$css || !$css->{'Default'})
274        {
275           $css->{'Default'} = &FIG::cgi_url() . "/Html/css/default.css";
276        }
277        if (!$css->{"Sans Serif"})
278        {
279           $css->{'Sans Serif'} = &FIG::cgi_url() . "/Html/css/sanserif.css";
280        }
281    
282        my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";
283        $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";
284    
285        foreach my $k (keys %$css)
286        {
287           next if (lc($k) eq "default" || lc($k) eq "sans serif");
288           $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
289        }
290    
291        $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='".&FIG::cgi_url()."/Html/rss/SEED.rss' type='application/rss+xml'>\n";
292    
293        # RAE: also added support for external javascripts here.
294        # we are cluttering the HTML code with all the javascripts when they could easily be in external files
295        # this solution allows us to source other files
296    
297        # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
298        # it will reduce our overhead.
299    
300        # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
301        push @$javasrc, &FIG::cgi_url() . "/Html/css/FIG.js";
302        foreach my $script (@$javasrc) {
303            $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
304        }
305    
306    
307    
308        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.
309    
310      #      #
311      #  <BASE ...> goes before </HEAD>      #  <BASE ...> goes before </HEAD>
312      #      #
# Line 183  Line 319 
319          #  only, or every update?), I provide an alternative derivation          #  only, or every update?), I provide an alternative derivation
320          #  from $cgi_url. -- GJO          #  from $cgi_url. -- GJO
321          #          #
322            # BASE href needs to be absolute. RDO.
323          my $base_url = $FIG_Config::cgi_base;          #
324          if ( ! $base_url )                      # if cgi_base was not defined          #
325          {          $base_url = &FIG::cgi_url;
326              $base_url = $FIG_Config::cgi_url;   # get the full cgi url  #       my $base_url = $FIG_Config::cgi_base;
327              $base_url =~ s~^http://[^/]*~~;     # remove protocol and host  #       if ( ! $base_url )                      # if cgi_base was not defined
328              $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash  #       {
329          }  #           $base_url = $FIG_Config::cgi_url;   # get the full cgi url
330    #           $base_url =~ s~^http://[^/]*~~;     # remove protocol and host
331    #           $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash
332    #       }
333    
334          $base_line = $head_end_line;          $base_line = $head_end_line;
335          splice( @$html, $base_line, 0, "<BASE href=\"$base_url\">\n" );          splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );
336      }      }
337    
338      #      #
# Line 228  Line 367 
367      }      }
368    
369      #      #
370        # See if we have a site-specific tail (for disclaimers, etc).
371        #
372    
373        my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
374        my $site_fh;
375        if (open($site_fh, "<$site_tail"))
376        {
377            push(@tail, <$site_fh>);
378            close($site_fh);
379        }
380    
381        #
382      #  Figure out where to insert The SEED tail.  Before </body>,      #  Figure out where to insert The SEED tail.  Before </body>,
383      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
384      #      #
   
385      my @tags = ();      my @tags = ();
386        # Check for a tracing queue.
387        my $traceString = QTrace("HTML");
388        if ($traceString) {
389            push @tags, $traceString;
390        }
391      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
392      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
393      {      {
# Line 255  Line 409 
409          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
410      }      }
411    
412      print @$html;      # RAE the chomp will return any new lines at the ends of elements in the array,
413        # and then we can join  with a "\n". This is because somethings put newlines in,
414        # and others don't. This should make nicer looking html
415        #
416        # chomp(@$html);
417        # print join "\n", @$html;
418        #
419        # Apparently the above still breaks things. This is the correct code:
420    
421        foreach $_ (@$html)
422        {
423            print $_;
424        }
425    
426  }  }
427    
428  sub make_table {  sub make_table {
429      my($col_hdrs,$tab,$title,$instr) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
430      my(@tab);      my(@tab);
431    
432      push( @tab, "\n<table border>\n",      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
433        push( @tab, "\n<table $border>\n",
434                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
435                  "\t<tr>\n\t\t<th>"                  "\t<tr>\n\t\t"
436                . join( "</th>\n\t\t<th>", @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
437                . "</th>\n\t</tr>\n"                . "\n\t</tr>\n"
438          );          );
439      my($i,$nowrap);      my($i);
   
     for ($i=0; ($i < @$instr) && ($instr->[$i] !~ /nowrap/); $i++) {}  
     $nowrap = ($i == @$instr) ? "" : " nowrap";  
440    
441      my $row;      my $row;
442      foreach $row (@$tab)      foreach $row (@$tab)
443      {      {
444          push( @tab, "\t<tr>\n"          push( @tab, "\t<tr>\n"
445                    . join( "\n", map { &expand($_,$nowrap) } @$row )                    . join( "\n", map { &expand($_) } @$row )
446                    . "\n\t</tr>\n"                    . "\n\t</tr>\n"
447              );              );
448      }      }
# Line 286  Line 451 
451  }  }
452    
453  sub expand {  sub expand {
454      my($x,$nowrap) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
455        my( $x, $tag ) = @_;
456    
457        $tag = "td" unless $tag;
458        my $endtag = $tag;
459    
460      if ($x =~ /^\@([^:]+)\:([^:]+)\:(.*)$/)      # RAE modified this so that you can pass in a reference to an array where
461        # the first element is the data to display and the second element is optional
462        # things like colspan and align. Note that in this case you need to include the td
463        # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
464    
465        # per GJO's request modified this line so it can take any tag.
466        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
467    
468        if ( $x =~ /^\@([^:]+)\:(.*)$/ )
469      {      {
470          return "\t\t<td$nowrap $1=\"$2\">$3</td>";          return "\t\t<$tag $1>$2</$endtag>";
471      }      }
472      else      else
473      {      {
474          return "\t\t<td$nowrap>$x</td>";          return "\t\t<$tag>$x</$endtag>";
475        }
476    }
477    
478    
479    sub merge_table_rows {
480     # RAE:
481     # Experimental piece of code. We often want to have rows or columns were cells are merged. It just looks so much nicer
482     # this block should merge adjacent rows that have the same text in them.
483     # use like this:
484     #      $tab=&HTML::merge_table_rows($tab);
485     # before you do a make_table call
486    
487     my $self=shift if UNIVERSAL::isa($_[0],__PACKAGE__);
488     my ($tab)=@_;
489    
490     my $newtable;
491     my $lastrow;
492     my $rowspan;
493     my $refs;
494    
495     for (my $y=0; $y <= $#$tab; $y++) {
496     #$y is the row in the table;
497      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
498       #$x is the column in the table
499       # if the column in the row we are looking at is the same as the column in the previous row, we don't add
500       # this cell to $newtable. Instead we increment the rowspan of the previous row by one
501    
502       # handle cells that are references to arrays
503       if (ref($tab->[$y]->[$x]) eq "ARRAY") {$refs->[$y]->[$x]=$tab->[$y]->[$x]->[1]; $tab->[$y]->[$x]=$tab->[$y]->[$x]->[0]}
504    
505       # now we go back through the table looking where to draw the merge line:
506       my $lasty=$y;
507       while ($lasty >= 0 && $tab->[$y]->[$x] eq $tab->[$lasty]->[$x]) {$lasty--}
508       $lasty++; # this is the last identical cell. If lasty==y it is the current cell, so we just save the data. Otherwise we increment the rowspan
509       if ($lasty == $y) {
510        # we always want to have something in rows that may otherwise be empty but should be there (see below)
511        unless ($tab->[$y]->[$x]) {$tab->[$y]->[$x]=" &nbsp; "}
512        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
513       }
514       else {$rowspan->[$lasty]->[$x]++}
515      }
516     }
517    
518     # now just join everything back together
519     for (my $y=0; $y <= $#$tab; $y++) {
520      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
521       if ($rowspan->[$y]->[$x]) {
522        if ($refs->[$y]->[$x]) {$refs->[$y]->[$x] .= " rowspan=". ($rowspan->[$y]->[$x]+1)}
523        else {$refs->[$y]->[$x] = "td rowspan=". ($rowspan->[$y]->[$x]+1)}
524        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
525       }
526       elsif ($newtable->[$y]->[$x] && $refs->[$y]->[$x]) {
527        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
528       }
529      }
530     }
531    
532    
533     # finally we have to remove any completely empty cells that have been added by the array mechanism
534     # (e.g. if you define $a->[2] then $a->[0] and $a->[1] are now undef).
535     # that is why in the loop above I replace empty cells with nbsp. They are now not undef!
536     # I am sure that Gary can do this in one line, but I am hacking.
537     my @trimmed;
538     foreach my $a (@$newtable) {
539      my @row;
540      foreach my $b (@$a) {
541       push @row, $b if ($b);
542      }
543      push @trimmed, \@row;
544     }
545    
546     return \@trimmed;
547    }
548    
549    
550    
551    
552    sub set_ec_links {
553        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
554        my($cgi,$x) = @_;
555        my($before,$match,$after);
556    
557        if ($x =~ /^(.*)(EC \d+\.\d+\.\d+\.\d+)(.*)/s)
558        {
559            $before = $1;
560            $match = $2;
561            $after = $3;
562            return &set_ec_links($cgi,$before) . &HTML::ec_link($match) . &set_ec_links($cgi,$after);
563      }      }
564        return $x;
565  }  }
566    
567  sub ec_link {  sub ec_link {
568        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
569      my($role) = @_;      my($role) = @_;
570    
571      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)
# Line 312  Line 579 
579  }  }
580    
581  sub role_link {  sub role_link {
582        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
583      my($cgi,$role) = @_;      my($cgi,$role) = @_;
584    
585      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;
# Line 322  Line 590 
590      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
591  }  }
592    
593    #
594    # Local means to eliminate the fig|org.peg from the
595    # text of the link.
596    #
597  sub fid_link {  sub fid_link {
598        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
599      my($cgi,$fid,$local,$just_url) = @_;      my($cgi,$fid,$local,$just_url) = @_;
600      my($n);      my($n);
601    
# Line 347  Line 620 
620          my $user = $cgi->param('user');          my $user = $cgi->param('user');
621          if (! $user) { $user = "" }          if (! $user) { $user = "" }
622          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
623          my $link = $cgi->url() . "?prot=$fid&user=$user$trans";          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
624          $link =~ s/[a-z_A-Z]+\.cgi\?/protein.cgi?/;  ###a
625    
626    ### This used to be
627    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
628    ###
629    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
630    ###
631    ### RAO
632    
633            if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
634            my $link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
635            $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
636            #
637            # Elimin the p2p part if we're in that subdir. Ugh.
638            #
639            $link =~ s,p2p/protein.cgi,protein.cgi,;
640    
641          if ($just_url)          if ($just_url)
642          {          {
643              return $link;              return $link;
# Line 362  Line 651 
651  }  }
652    
653  sub family_link {  sub family_link {
654        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
655      my($family,$user) = @_;      my($family,$user) = @_;
656    
657      return $family;      return $family;
658  }  }
659    
 use URI::Escape;  
660    
661  sub get_html {  sub get_html {
662        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
663      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
664      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
665    
666      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
667      $ua->timeout( 900 );      $ua->timeout( 900 );
   
668      if ($type =~/post/i)      if ($type =~/post/i)
669      {      {
670          $args = [];          $args = [];
# Line 435  Line 724 
724  }  }
725    
726  sub trim_output {  sub trim_output {
727        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
728      my($out) = @_;      my($out) = @_;
729      my $i;      my $i;
730    
# Line 472  Line 762 
762  }  }
763    
764  sub set_prot_links {  sub set_prot_links {
765        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
766      my($cgi,$x) = @_;      my($cgi,$x) = @_;
767      my($before,$match,$after);      my($before,$match,$after);
768    
769      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
770      {      {
771          $before = $1;          $before = $1;
772          $match = $2;          $match = $2;
773          $after = $3;          $after = $3;
774          return &set_prot_links($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,$after);
775      }      }
776      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)      elsif ($x =~ /^(.*)\b([NXYZA]P_[0-9\.]+)\b(.*)/s)
777      {      {
778          $before = $1;          $before = $1;
779          $match = $2;          $match = $2;
780          $after = $3;          $after = $3;
781          return &set_prot_links($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,$after);
782      }      }
783      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
784      {      {
785          $before = $1;          $before = $1;
786          $match = $2;          $match = $2;
787          $after = $3;          $after = $3;
788          return &set_prot_links($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,$after);
789      }      }
790      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~ /^(.*)(tigr\|[0-9a-zA-Z]+)(.*)/s)
791      {      {
792          $before = $1;          $before = $1;
793          $match = $2;          $match = $2;
794          $after = $3;          $after = $3;
795          return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
796        }
797        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
798        {
799            $before = $1;
800            $match = $2;
801            $after = $3;
802            return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
803        }
804        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
805        {
806            $before = $1;
807            $match = $2;
808            $after = $3;
809            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
810        }
811        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
812        {
813            $before = $1;
814            $match = $2;
815            $after = $3;
816            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
817        }
818        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
819        {
820            $before = $1;
821            $match = $2;
822            $after = $3;
823            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
824      }      }
825      return $x;      return $x;
826  }  }
827    
828    sub refseq_link {
829        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
830        my($cgi,$id) = @_;
831    
832        if ($id =~ /^[NXYZA]P_/)
833        {
834            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";
835        }
836    }
837    
838  sub gi_link {  sub gi_link {
839        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
840      my($cgi,$gi) = @_;      my($cgi,$gi) = @_;
841    
842      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
# Line 516  Line 846 
846      return $gi;      return $gi;
847  }  }
848    
849    sub tigr_link {
850        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
851        my($cgi,$tigr) = @_;
852    
853        if ($tigr =~ /^tigr\|([0-9a-zA-Z]+)$/)
854        {
855            return "<a href=\"http://pathema.tigr.org/tigr-scripts/CMR/GenePage.cgi?locus=$1\">$tigr</a>";
856        }
857        return $tigr;
858    }
859    
860    sub uni_link {
861        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
862        my($cgi,$uni) = @_;
863    
864        if ($uni =~ /^uni\|(\S+)$/)
865        {
866            return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
867        }
868        return $uni;
869    }
870    
871  sub sp_link {  sub sp_link {
872        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
873      my($cgi,$sp) = @_;      my($cgi,$sp) = @_;
874    
875      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
# Line 527  Line 880 
880  }  }
881    
882  sub pir_link {  sub pir_link {
883        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
884      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
885    
886      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
# Line 536  Line 890 
890      return $pir;      return $pir;
891  }  }
892    
893    sub kegg_link {
894        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
895        my($cgi,$kegg) = @_;
896    
897        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
898        {
899            return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";
900        }
901        return $kegg;
902    }
903    
904    sub set_map_links {
905        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
906        my($cgi,$x) = @_;
907        my($before,$match,$after);
908    
909        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
910    
911        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
912        {
913            $before = $1;
914            $match = $2;
915            $after = $3;
916            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
917        }
918        return $x;
919    }
920    
921    sub map_link {
922        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
923        my($cgi,$map,$org) = @_;
924    
925        $user = $cgi->param('user');
926        $user = $user ? $user : "";
927        $org = $org ? $org : "";
928    
929        my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
930        my $link = "<a href=\"$url\">$map</a>";
931        return $link;
932    }
933    
934    sub java_buttons {
935        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
936      ## ADDED BY RAE
937      # Provides code to include check all/first half/second half/none for javascrspt
938      # this takes two variables - the form name provided in start_form with the
939      # -name => field and the checkbox name
940      my ($form, $button)=@_;
941    
942      $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
943      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
944      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
945      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
946    
947      return $java_script;
948    }
949    
950    sub sub_link {
951        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
952        my($cgi,$sub) = @_;
953        my($sub_link);
954    
955        my $user = $cgi->param('user');
956        if ($user)
957        {
958            my $esc_sub = uri_escape( $sub );
959            $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";
960        }
961        else
962        {
963            $sub_link = $sub;
964        }
965        return $sub_link;
966    }
967    
968    sub reaction_link {
969        my($reaction) = @_;
970    
971        if ($reaction =~ /^R\d+/)
972        {
973            return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";
974        }
975        return $reaction;
976    }
977    
978    sub html_for_assignments {
979        my($fig,$user,$peg_sets) = @_;
980        my $i;
981    
982        my @vals = ();
983        my $set = 1;
984        foreach $peg_set (@$peg_sets)
985        {
986            for ($i=0; ($i < @$peg_set); $i++)
987            {
988                $peg = $peg_set->[$i];
989                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
990            }
991            $set++;
992        }
993    
994        $ENV{'REQUEST_METHOD'} = 'GET';
995        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
996        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
997        $out =~ s/^.*?<form/<form/si;
998        $out =~ s/^(.*)<table.*/$1/si;
999        return $out;
1000    }
1001    
1002    =head1 rss_feed
1003    
1004    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1005            SEED.rss                - everything gets written here
1006            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1007            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1008    
1009    
1010    RSS feeds must contain a title, description, and link. The title is what is seen e.g. from the firefox or safari pull down menu. The description is seen from within an rss aggregator, and may be displayed on web pages and so on.
1011    
1012    The method takes a reference to an array containing the file names for the RSS feeds to add your item to, and a hash of items for the xml. Only title, description, and link are required tags in the XML.
1013    
1014    The file names are the full name of the file, eg SEEDsubsystems.rss, SEEDgenomes.rss. Be aware that this is a file name, though, so don't uses special characters. The path will be added.
1015    
1016    The has can have these keys:
1017    
1018    REQUIRED:
1019    title       : the title. This is usually what is seen by the user in the pull down menu
1020    description : a more complete description that is often seen is rss viewers but not always
1021    link        : link to the item that was added/edited
1022    All other keys are treated as optional RSS arguments and written to the file. At most, 10 recent entries are stored in the rss file.
1023    
1024    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1025    
1026    
1027    =cut
1028    
1029    sub rss_feed {
1030     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1031     my ($files, $args)=@_;
1032     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1033    
1034     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1035     # check for the directory and if not, make it
1036     mkdir $filepath unless (-d $filepath);
1037    
1038     # note that $info is a hash of references to hashes that are written out as headers in the file
1039     my $info=
1040     {
1041      "SEED.rss" =>
1042       {
1043            title           => "The SEED",
1044            description     => "Latest news from the SEED",
1045            link            => &FIG::cgi_url()."/Html/rss/SEED.rss",
1046       },
1047    
1048      "SEEDsubsystems.rss" =>
1049      {
1050            title           => "SEED Subsystems",
1051            description     => "Recently updated SEED subsystems",
1052            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1053      },
1054    
1055      "SEEDsubsystems.rss" =>
1056      {
1057            title           => "SEED Genomes",
1058            description     => "Genomes recently added to the SEED",
1059            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1060      },
1061    
1062     };
1063    
1064    
1065     # build the new xml
1066     my $xml = "\t<item>\n";
1067     foreach my $qw ("title", "description", "link") {
1068      unless ($args->{$qw}) {
1069       print STDERR "You need to include a $qw tag in your RSS description\n";
1070       return(0);
1071      }
1072      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1073      # so we are going to pull out the links and uri_escape just the part after the .cgi
1074      if ($qw eq "link")
1075      {
1076       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1077       print STDERR "Got ->>$1<<- and ->>$2<<-\n";
1078       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1079      }
1080    
1081      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1082      delete $args->{$qw};
1083     }
1084    
1085     foreach my $tag (grep {!/type/i} keys %$args)
1086     {
1087      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1088     }
1089    
1090     $xml .= "\t</item>\n";
1091    
1092    
1093     my @files=("SEED.rss");
1094     if ($args->{"type"}) {push @files, "SEED.$type.rss"}
1095    
1096     foreach my $file ("SEED.rss", @$files)
1097     {
1098      if (-e "$filepath/$file")
1099      {
1100       my @out; # the new content of the file
1101       my $itemcount=0; # how many <item> </item>'s are we keeping
1102       my $initem; # are we in an item?
1103       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1104       while (<IN>)
1105       {
1106        if (/\<item\>/) {
1107         push @out, $xml, unless ($itemcount);
1108         $itemcount++;
1109         $initem=1;
1110        }
1111        if (/\<\/item\>/) {$initem=0; next if ($itemcount > 9)}
1112        next if ($initem && $itemcount > 9);
1113        push @out, $_;
1114       }
1115       close IN;
1116       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1117       print OUT @out;
1118      }
1119      else
1120      {
1121       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1122       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1123       if ($info->{$file})
1124       {
1125         # we're going to sanity check each of the three options we output, just to be sure
1126         foreach my $qw ("title", "description", "link")
1127         {
1128           if ($info->{$file}->{$qw})
1129           {
1130              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1131           } else {
1132              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1133           }
1134         }
1135       }
1136       else {
1137        print STDERR "Please define title, link, and description information for $file\n";
1138        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1139       }
1140       print OUT "\n", $xml;
1141       print OUT "\n", "</channel>\n</rss>\n"
1142      }
1143     }
1144    }
1145    
1146    1;
1147    
 1  

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