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revision 1.6, Sun Mar 21 02:20:55 2004 UTC revision 1.55, Fri Aug 19 15:47:54 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, $tag ) = @_;
456    
457      if ($x =~ /^\@([^:]+)\:([^:]+)\:(.*)$/)      $tag = "td" unless $tag;
458        my $endtag = $tag;
459    
460        # RAE modified this so that you can pass in a reference to an array where
461        # the first element is the data to display and the second element is optional
462        # things like colspan and align. Note that in this case you need to include the td
463        # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
464    
465        # per GJO's request modified this line so it can take any tag.
466        if ( ref($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?/;          my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
625            $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
626            #
627            # Elimin the p2p part if we're in that subdir. Ugh.
628            #
629            $link =~ s,p2p/protein.cgi,protein.cgi,;
630    
631          if ($just_url)          if ($just_url)
632          {          {
633              return $link;              return $link;
# Line 362  Line 641 
641  }  }
642    
643  sub family_link {  sub family_link {
644        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
645      my($family,$user) = @_;      my($family,$user) = @_;
646    
647      return $family;      return $family;
648  }  }
649    
 use URI::Escape;  
650    
651  sub get_html {  sub get_html {
652        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
653      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
654      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
655    
656      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
657      $ua->timeout( 900 );      $ua->timeout( 900 );
   
658      if ($type =~/post/i)      if ($type =~/post/i)
659      {      {
660          $args = [];          $args = [];
# Line 435  Line 714 
714  }  }
715    
716  sub trim_output {  sub trim_output {
717        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
718      my($out) = @_;      my($out) = @_;
719      my $i;      my $i;
720    
# Line 472  Line 752 
752  }  }
753    
754  sub set_prot_links {  sub set_prot_links {
755        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
756      my($cgi,$x) = @_;      my($cgi,$x) = @_;
757      my($before,$match,$after);      my($before,$match,$after);
758    
759      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
760        {
761            $before = $1;
762            $match = $2;
763            $after = $3;
764            return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);
765        }
766        elsif ($x =~ /^(.*)\b([NXYZA]P_[0-9\.]+)\b(.*)/s)
767        {
768            $before = $1;
769            $match = $2;
770            $after = $3;
771            return &set_prot_links($cgi,$before) . &HTML::refseq_link($cgi,$match) . &set_prot_links($cgi,$after);
772        }
773        elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
774        {
775            $before = $1;
776            $match = $2;
777            $after = $3;
778            return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);
779        }
780        elsif ($x =~ /^(.*)(tigr\|[0-9a-zA-Z]+)(.*)/s)
781        {
782            $before = $1;
783            $match = $2;
784            $after = $3;
785            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
786        }
787        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
788      {      {
789          $before = $1;          $before = $1;
790          $match = $2;          $match = $2;
791          $after = $3;          $after = $3;
792          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
793      }      }
794      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
795      {      {
796          $before = $1;          $before = $1;
797          $match = $2;          $match = $2;
798          $after = $3;          $after = $3;
799          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
800      }      }
801      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
802      {      {
803          $before = $1;          $before = $1;
804          $match = $2;          $match = $2;
805          $after = $3;          $after = $3;
806          return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
807      }      }
808      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
809      {      {
810          $before = $1;          $before = $1;
811          $match = $2;          $match = $2;
812          $after = $3;          $after = $3;
813          return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
814      }      }
815      return $x;      return $x;
816  }  }
817    
818    sub refseq_link {
819        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
820        my($cgi,$id) = @_;
821    
822        if ($id =~ /^[NXYZA]P_/)
823        {
824            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";
825        }
826    }
827    
828  sub gi_link {  sub gi_link {
829        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
830      my($cgi,$gi) = @_;      my($cgi,$gi) = @_;
831    
832      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
# Line 516  Line 836 
836      return $gi;      return $gi;
837  }  }
838    
839    sub tigr_link {
840        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
841        my($cgi,$tigr) = @_;
842    
843        if ($tigr =~ /^tigr\|([0-9a-zA-Z]+)$/)
844        {
845            return "<a href=\"http://pathema.tigr.org/tigr-scripts/CMR/GenePage.cgi?locus=$1\">$tigr</a>";
846        }
847        return $tigr;
848    }
849    
850    sub uni_link {
851        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
852        my($cgi,$uni) = @_;
853    
854        if ($uni =~ /^uni\|(\S+)$/)
855        {
856            return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
857        }
858        return $uni;
859    }
860    
861  sub sp_link {  sub sp_link {
862        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
863      my($cgi,$sp) = @_;      my($cgi,$sp) = @_;
864    
865      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
# Line 527  Line 870 
870  }  }
871    
872  sub pir_link {  sub pir_link {
873        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
874      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
875    
876      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
# Line 536  Line 880 
880      return $pir;      return $pir;
881  }  }
882    
883    sub kegg_link {
884        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
885        my($cgi,$kegg) = @_;
886    
887        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
888        {
889            return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";
890        }
891        return $kegg;
892    }
893    
894    sub set_map_links {
895        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
896        my($cgi,$x) = @_;
897        my($before,$match,$after);
898    
899        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
900    
901        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
902        {
903            $before = $1;
904            $match = $2;
905            $after = $3;
906            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
907        }
908        return $x;
909    }
910    
911    sub map_link {
912        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
913        my($cgi,$map,$org) = @_;
914    
915        $user = $cgi->param('user');
916        $user = $user ? $user : "";
917        $org = $org ? $org : "";
918    
919        my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
920        my $link = "<a href=\"$url\">$map</a>";
921        return $link;
922    }
923    
924    sub java_buttons {
925        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
926      ## ADDED BY RAE
927      # Provides code to include check all/first half/second half/none for javascrspt
928      # this takes two variables - the form name provided in start_form with the
929      # -name => field and the checkbox name
930      my ($form, $button)=@_;
931    
932      $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
933      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
934      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
935      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
936    
937      return $java_script;
938    }
939    
940    sub sub_link {
941        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
942        my($cgi,$sub) = @_;
943        my($sub_link);
944    
945        my $user = $cgi->param('user');
946        if ($user)
947        {
948            my $esc_sub = uri_escape( $sub );
949            $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";
950        }
951        else
952        {
953            $sub_link = $sub;
954        }
955        return $sub_link;
956    }
957    
958    sub reaction_link {
959        my($reaction) = @_;
960    
961        if ($reaction =~ /^R\d+/)
962        {
963            return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";
964        }
965        return $reaction;
966    }
967    
968    sub html_for_assignments {
969        my($fig,$user,$peg_sets) = @_;
970        my $i;
971    
972        my @vals = ();
973        my $set = 1;
974        foreach $peg_set (@$peg_sets)
975        {
976            for ($i=0; ($i < @$peg_set); $i++)
977            {
978                $peg = $peg_set->[$i];
979                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
980            }
981            $set++;
982        }
983    
984        $ENV{'REQUEST_METHOD'} = 'GET';
985        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
986        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
987        $out =~ s/^.*?<form/<form/si;
988        $out =~ s/^(.*)<table.*/$1/si;
989        return $out;
990    }
991    
992    =head1 rss_feed
993    
994    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
995            SEED.rss                - everything gets written here
996            SEEDgenomes.rss                 - whenever a genome is added to the SEED
997            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
998    
999    
1000    RSS feeds must contain a title, description, and link. The title is what is seen e.g. from the firefox or safari pull down menu. The description is seen from within an rss aggregator, and may be displayed on web pages and so on.
1001    
1002    The method takes a reference to an array containing the file names for the RSS feeds to add your item to, and a hash of items for the xml. Only title, description, and link are required tags in the XML.
1003    
1004    The file names are the full name of the file, eg SEEDsubsystems.rss, SEEDgenomes.rss. Be aware that this is a file name, though, so don't uses special characters. The path will be added.
1005    
1006    The has can have these keys:
1007    
1008    REQUIRED:
1009    title       : the title. This is usually what is seen by the user in the pull down menu
1010    description : a more complete description that is often seen is rss viewers but not always
1011    link        : link to the item that was added/edited
1012    All other keys are treated as optional RSS arguments and written to the file. At most, 10 recent entries are stored in the rss file.
1013    
1014    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1015    
1016    
1017    =cut
1018    
1019    sub rss_feed {
1020     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1021     my ($files, $args)=@_;
1022     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1023    
1024     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1025     # check for the directory and if not, make it
1026     mkdir $filepath unless (-d $filepath);
1027    
1028     # note that $info is a hash of references to hashes that are written out as headers in the file
1029     my $info=
1030     {
1031      "SEED.rss" =>
1032       {
1033            title           => "The SEED",
1034            description     => "Latest news from the SEED",
1035            link            => &FIG::cgi_url()."/Html/rss/SEED.rss",
1036       },
1037    
1038      "SEEDsubsystems.rss" =>
1039      {
1040            title           => "SEED Subsystems",
1041            description     => "Recently updated SEED subsystems",
1042            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1043      },
1044    
1045      "SEEDsubsystems.rss" =>
1046      {
1047            title           => "SEED Genomes",
1048            description     => "Genomes recently added to the SEED",
1049            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1050      },
1051    
1052     };
1053    
1054    
1055     # build the new xml
1056     my $xml = "\t<item>\n";
1057     foreach my $qw ("title", "description", "link") {
1058      unless ($args->{$qw}) {
1059       print STDERR "You need to include a $qw tag in your RSS description\n";
1060       return(0);
1061      }
1062      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1063      # so we are going to pull out the links and uri_escape just the part after the .cgi
1064      if ($qw eq "link")
1065      {
1066       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1067       print STDERR "Got ->>$1<<- and ->>$2<<-\n";
1068       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1069      }
1070    
1071      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1072      delete $args->{$qw};
1073     }
1074    
1075     foreach my $tag (grep {!/type/i} keys %$args)
1076     {
1077      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1078     }
1079    
1080     $xml .= "\t</item>\n";
1081    
1082    
1083     my @files=("SEED.rss");
1084     if ($args->{"type"}) {push @files, "SEED.$type.rss"}
1085    
1086     foreach my $file ("SEED.rss", @$files)
1087     {
1088      if (-e "$filepath/$file")
1089      {
1090       my @out; # the new content of the file
1091       my $itemcount=0; # how many <item> </item>'s are we keeping
1092       my $initem; # are we in an item?
1093       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1094       while (<IN>)
1095       {
1096        if (/\<item\>/) {
1097         push @out, $xml, unless ($itemcount);
1098         $itemcount++;
1099         $initem=1;
1100        }
1101        if (/\<\/item\>/) {$initem=0; next if ($itemcount > 9)}
1102        next if ($initem && $itemcount > 9);
1103        push @out, $_;
1104       }
1105       close IN;
1106       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1107       print OUT @out;
1108      }
1109      else
1110      {
1111       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1112       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1113       if ($info->{$file})
1114       {
1115         # we're going to sanity check each of the three options we output, just to be sure
1116         foreach my $qw ("title", "description", "link")
1117         {
1118           if ($info->{$file}->{$qw})
1119           {
1120              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1121           } else {
1122              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1123           }
1124         }
1125       }
1126       else {
1127        print STDERR "Please define title, link, and description information for $file\n";
1128        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1129       }
1130       print OUT "\n", $xml;
1131       print OUT "\n", "</channel>\n</rss>\n"
1132      }
1133     }
1134    }
1135    
1136    1;
1137    
 1  

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