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revision 1.6, Sun Mar 21 02:20:55 2004 UTC revision 1.58, Fri Sep 16 15:09:32 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          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";         @html_hdr = @$alt_header;
108        }
109        else
110        {
111            @html_hdr = compute_html_header(undef,$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 343  Line 616 
616          {          {
617              $n = $fid;              $n = $fid;
618          }          }
619          if ($1 ne "peg") { return $n }  
620            #added to format prophage and path island links to feature.cgi
621            if ($1 ne "peg")
622            {
623               my $user = $cgi->param('user');
624               if (! $user) { $user = "" }
625               my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
626               my $link = &FIG::cgi_url . "/feature.cgi?feature=$fid&user=$user$trans$sprout";
627               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
628               return "<a href=$link>$n</a>";
629            }
630    
631            if ($1 eq "peg")
632            {
633          my $user = $cgi->param('user');          my $user = $cgi->param('user');
634          if (! $user) { $user = "" }          if (! $user) { $user = "" }
635          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
636          my $link = $cgi->url() . "?prot=$fid&user=$user$trans";              my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
637          $link =~ s/[a-z_A-Z]+\.cgi\?/protein.cgi?/;  ###a
638    
639    ### This used to be
640    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
641    ###
642    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
643    ###
644    ### RAO
645    
646                if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
647                my $link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
648                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
649                #
650                # Elimin the p2p part if we're in that subdir. Ugh.
651                #
652                $link =~ s,p2p/protein.cgi,protein.cgi,;
653    
654                }
655          if ($just_url)          if ($just_url)
656          {          {
657              return $link;              return $link;
# Line 362  Line 665 
665  }  }
666    
667  sub family_link {  sub family_link {
668        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
669      my($family,$user) = @_;      my($family,$user) = @_;
670    
671      return $family;      return $family;
672  }  }
673    
 use URI::Escape;  
674    
675  sub get_html {  sub get_html {
676        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
677      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
678      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
679    
680      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
681      $ua->timeout( 900 );      $ua->timeout( 900 );
   
682      if ($type =~/post/i)      if ($type =~/post/i)
683      {      {
684          $args = [];          $args = [];
# Line 435  Line 738 
738  }  }
739    
740  sub trim_output {  sub trim_output {
741        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
742      my($out) = @_;      my($out) = @_;
743      my $i;      my $i;
744    
# Line 472  Line 776 
776  }  }
777    
778  sub set_prot_links {  sub set_prot_links {
779        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
780      my($cgi,$x) = @_;      my($cgi,$x) = @_;
781      my($before,$match,$after);      my($before,$match,$after);
782    
783      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
784        {
785            $before = $1;
786            $match = $2;
787            $after = $3;
788            return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);
789        }
790        elsif ($x =~ /^(.*)\b([NXYZA]P_[0-9\.]+)\b(.*)/s)
791        {
792            $before = $1;
793            $match = $2;
794            $after = $3;
795            return &set_prot_links($cgi,$before) . &HTML::refseq_link($cgi,$match) . &set_prot_links($cgi,$after);
796        }
797        elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
798        {
799            $before = $1;
800            $match = $2;
801            $after = $3;
802            return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);
803        }
804        elsif ($x =~ /^(.*)(tigr\|[0-9a-zA-Z]+)(.*)/s)
805        {
806            $before = $1;
807            $match = $2;
808            $after = $3;
809            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
810        }
811        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
812      {      {
813          $before = $1;          $before = $1;
814          $match = $2;          $match = $2;
815          $after = $3;          $after = $3;
816          return &set_prot_links($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,$after);
817      }      }
818      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
819      {      {
820          $before = $1;          $before = $1;
821          $match = $2;          $match = $2;
822          $after = $3;          $after = $3;
823          return &set_prot_links($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,$after);
824      }      }
825      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
826      {      {
827          $before = $1;          $before = $1;
828          $match = $2;          $match = $2;
829          $after = $3;          $after = $3;
830          return &set_prot_links($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,$after);
831      }      }
832      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
833      {      {
834          $before = $1;          $before = $1;
835          $match = $2;          $match = $2;
836          $after = $3;          $after = $3;
837          return &set_prot_links($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);
838      }      }
839      return $x;      return $x;
840  }  }
841    
842    sub refseq_link {
843        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
844        my($cgi,$id) = @_;
845    
846        if ($id =~ /^[NXYZA]P_/)
847        {
848            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";
849        }
850    }
851    
852  sub gi_link {  sub gi_link {
853        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
854      my($cgi,$gi) = @_;      my($cgi,$gi) = @_;
855    
856      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
# Line 516  Line 860 
860      return $gi;      return $gi;
861  }  }
862    
863    sub tigr_link {
864        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
865        my($cgi,$tigr) = @_;
866    
867        if ($tigr =~ /^tigr\|([0-9a-zA-Z]+)$/)
868        {
869            return "<a href=\"http://pathema.tigr.org/tigr-scripts/CMR/GenePage.cgi?locus=$1\">$tigr</a>";
870        }
871        return $tigr;
872    }
873    
874    sub uni_link {
875        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
876        my($cgi,$uni) = @_;
877    
878        if ($uni =~ /^uni\|(\S+)$/)
879        {
880            return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
881        }
882        return $uni;
883    }
884    
885  sub sp_link {  sub sp_link {
886        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
887      my($cgi,$sp) = @_;      my($cgi,$sp) = @_;
888    
889      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
# Line 527  Line 894 
894  }  }
895    
896  sub pir_link {  sub pir_link {
897        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
898      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
899    
900      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
# Line 536  Line 904 
904      return $pir;      return $pir;
905  }  }
906    
907    sub kegg_link {
908        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
909        my($cgi,$kegg) = @_;
910    
911        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
912        {
913            return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";
914        }
915        return $kegg;
916    }
917    
918    sub set_map_links {
919        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
920        my($cgi,$x) = @_;
921        my($before,$match,$after);
922    
923        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
924    
925        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
926        {
927            $before = $1;
928            $match = $2;
929            $after = $3;
930            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
931        }
932        return $x;
933    }
934    
935    sub map_link {
936        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
937        my($cgi,$map,$org) = @_;
938    
939        $user = $cgi->param('user');
940        $user = $user ? $user : "";
941        $org = $org ? $org : "";
942    
943        my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
944        my $link = "<a href=\"$url\">$map</a>";
945        return $link;
946    }
947    
948    sub java_buttons {
949        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
950      ## ADDED BY RAE
951      # Provides code to include check all/first half/second half/none for javascrspt
952      # this takes two variables - the form name provided in start_form with the
953      # -name => field and the checkbox name
954      my ($form, $button)=@_;
955    
956      $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
957      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
958      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
959      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
960    
961      return $java_script;
962    }
963    
964    sub sub_link {
965        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
966        my($cgi,$sub) = @_;
967        my($sub_link);
968    
969        my $user = $cgi->param('user');
970        if ($user)
971        {
972            my $esc_sub = uri_escape( $sub );
973            $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";
974        }
975        else
976        {
977            $sub_link = $sub;
978        }
979        return $sub_link;
980    }
981    
982    sub reaction_link {
983        my($reaction) = @_;
984    
985        if ($reaction =~ /^R\d+/)
986        {
987            return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";
988        }
989        return $reaction;
990    }
991    
992    sub html_for_assignments {
993        my($fig,$user,$peg_sets) = @_;
994        my $i;
995    
996        my @vals = ();
997        my $set = 1;
998        foreach $peg_set (@$peg_sets)
999        {
1000            for ($i=0; ($i < @$peg_set); $i++)
1001            {
1002                $peg = $peg_set->[$i];
1003                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1004            }
1005            $set++;
1006        }
1007    
1008        $ENV{'REQUEST_METHOD'} = 'GET';
1009        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1010        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1011        $out =~ s/^.*?<form/<form/si;
1012        $out =~ s/^(.*)<table.*/$1/si;
1013        return $out;
1014    }
1015    
1016    =head1 rss_feed
1017    
1018    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1019            SEED.rss                - everything gets written here
1020            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1021            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1022    
1023    
1024    RSS feeds must contain a title, description, and link. The title is what is seen e.g. from the firefox or safari pull down menu. The description is seen from within an rss aggregator, and may be displayed on web pages and so on.
1025    
1026    The method takes a reference to an array containing the file names for the RSS feeds to add your item to, and a hash of items for the xml. Only title, description, and link are required tags in the XML.
1027    
1028    The file names are the full name of the file, eg SEEDsubsystems.rss, SEEDgenomes.rss. Be aware that this is a file name, though, so don't uses special characters. The path will be added.
1029    
1030    The has can have these keys:
1031    
1032    REQUIRED:
1033    title       : the title. This is usually what is seen by the user in the pull down menu
1034    description : a more complete description that is often seen is rss viewers but not always
1035    link        : link to the item that was added/edited
1036    All other keys are treated as optional RSS arguments and written to the file. At most, 10 recent entries are stored in the rss file.
1037    
1038    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1039    
1040    
1041    =cut
1042    
1043    sub rss_feed {
1044     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1045     my ($files, $args)=@_;
1046     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1047    
1048     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1049     # check for the directory and if not, make it
1050     mkdir $filepath unless (-d $filepath);
1051    
1052     # note that $info is a hash of references to hashes that are written out as headers in the file
1053     my $info=
1054     {
1055      "SEED.rss" =>
1056       {
1057            title           => "The SEED",
1058            description     => "Latest news from the SEED",
1059            link            => &FIG::cgi_url()."/Html/rss/SEED.rss",
1060       },
1061    
1062      "SEEDsubsystems.rss" =>
1063      {
1064            title           => "SEED Subsystems",
1065            description     => "Recently updated SEED subsystems",
1066            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1067      },
1068    
1069      "SEEDsubsystems.rss" =>
1070      {
1071            title           => "SEED Genomes",
1072            description     => "Genomes recently added to the SEED",
1073            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1074      },
1075    
1076     };
1077    
1078    
1079     # build the new xml
1080     my $xml = "\t<item>\n";
1081     foreach my $qw ("title", "description", "link") {
1082      unless ($args->{$qw}) {
1083       print STDERR "You need to include a $qw tag in your RSS description\n";
1084       return(0);
1085      }
1086      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1087      # so we are going to pull out the links and uri_escape just the part after the .cgi
1088      if ($qw eq "link")
1089      {
1090       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1091       print STDERR "Got ->>$1<<- and ->>$2<<-\n";
1092       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1093      }
1094    
1095      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1096      delete $args->{$qw};
1097     }
1098    
1099     foreach my $tag (grep {!/type/i} keys %$args)
1100     {
1101      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1102     }
1103    
1104     $xml .= "\t</item>\n";
1105    
1106    
1107     my @files=("SEED.rss");
1108     if ($args->{"type"}) {push @files, "SEED.$type.rss"}
1109    
1110     foreach my $file ("SEED.rss", @$files)
1111     {
1112      if (-e "$filepath/$file")
1113      {
1114       my @out; # the new content of the file
1115       my $itemcount=0; # how many <item> </item>'s are we keeping
1116       my $initem; # are we in an item?
1117       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1118       while (<IN>)
1119       {
1120        if (/\<item\>/) {
1121         push @out, $xml, unless ($itemcount);
1122         $itemcount++;
1123         $initem=1;
1124        }
1125        if (/\<\/item\>/) {$initem=0; next if ($itemcount > 9)}
1126        next if ($initem && $itemcount > 9);
1127        push @out, $_;
1128       }
1129       close IN;
1130       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1131       print OUT @out;
1132      }
1133      else
1134      {
1135       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1136       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1137       if ($info->{$file})
1138       {
1139         # we're going to sanity check each of the three options we output, just to be sure
1140         foreach my $qw ("title", "description", "link")
1141         {
1142           if ($info->{$file}->{$qw})
1143           {
1144              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1145           } else {
1146              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1147           }
1148         }
1149       }
1150       else {
1151        print STDERR "Please define title, link, and description information for $file\n";
1152        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1153       }
1154       print OUT "\n", $xml;
1155       print OUT "\n", "</channel>\n</rss>\n"
1156      }
1157     }
1158    }
1159    
1160    1;
1161    
 1  

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