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revision 1.6, Sun Mar 21 02:20:55 2004 UTC revision 1.60, Fri Sep 16 20:00:12 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 = $tag;
459    
460        # RAE modified this so that you can pass in a reference to an array where
461        # the first element is the data to display and the second element is optional
462        # things like colspan and align. Note that in this case you need to include the td
463        # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
464    
465        # per GJO's request modified this line so it can take any tag.
466        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
467    
468      if ($x =~ /^\@([^:]+)\:([^:]+)\:(.*)$/)      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            my $link;
621            #added to format prophage and path island links to feature.cgi
622            if ($1 ne "peg")
623            {
624               my $user = $cgi->param('user');
625               if (! $user) { $user = "" }
626               my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
627               $link = &FIG::cgi_url . "/feature.cgi?feature=$fid&user=$user$trans$sprout";
628               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
629            }
630            else
631            {
632          my $user = $cgi->param('user');          my $user = $cgi->param('user');
633          if (! $user) { $user = "" }          if (! $user) { $user = "" }
634          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
635          my $link = $cgi->url() . "?prot=$fid&user=$user$trans";              my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
636          $link =~ s/[a-z_A-Z]+\.cgi\?/protein.cgi?/;  ###a
637    
638    ### This used to be
639    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
640    ###
641    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
642    ###
643    ### RAO
644    
645                if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
646                $link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
647                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
648                #
649                # Elimin the p2p part if we're in that subdir. Ugh.
650                #
651                $link =~ s,p2p/protein.cgi,protein.cgi,;
652            }
653          if ($just_url)          if ($just_url)
654          {          {
655              return $link;              return $link;
# Line 362  Line 663 
663  }  }
664    
665  sub family_link {  sub family_link {
666        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
667      my($family,$user) = @_;      my($family,$user) = @_;
668    
669      return $family;      return $family;
670  }  }
671    
 use URI::Escape;  
672    
673  sub get_html {  sub get_html {
674        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
675      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
676      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
677    
678      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
679      $ua->timeout( 900 );      $ua->timeout( 900 );
   
680      if ($type =~/post/i)      if ($type =~/post/i)
681      {      {
682          $args = [];          $args = [];
# Line 435  Line 736 
736  }  }
737    
738  sub trim_output {  sub trim_output {
739        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
740      my($out) = @_;      my($out) = @_;
741      my $i;      my $i;
742    
# Line 472  Line 774 
774  }  }
775    
776  sub set_prot_links {  sub set_prot_links {
777        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
778      my($cgi,$x) = @_;      my($cgi,$x) = @_;
779      my($before,$match,$after);      my($before,$match,$after);
780    
781      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
782      {      {
783          $before = $1;          $before = $1;
784          $match = $2;          $match = $2;
785          $after = $3;          $after = $3;
786          return &set_prot_links($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,$after);
787      }      }
788      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)      elsif ($x =~ /^(.*)\b([NXYZA]P_[0-9\.]+)\b(.*)/s)
789      {      {
790          $before = $1;          $before = $1;
791          $match = $2;          $match = $2;
792          $after = $3;          $after = $3;
793          return &set_prot_links($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,$after);
794      }      }
795      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
796      {      {
797          $before = $1;          $before = $1;
798          $match = $2;          $match = $2;
799          $after = $3;          $after = $3;
800          return &set_prot_links($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,$after);
801      }      }
802      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~ /^(.*)(tigr\|[0-9a-zA-Z]+)(.*)/s)
803      {      {
804          $before = $1;          $before = $1;
805          $match = $2;          $match = $2;
806          $after = $3;          $after = $3;
807          return &set_prot_links($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,$after);
808        }
809        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
810        {
811            $before = $1;
812            $match = $2;
813            $after = $3;
814            return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
815        }
816        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
817        {
818            $before = $1;
819            $match = $2;
820            $after = $3;
821            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
822        }
823        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
824        {
825            $before = $1;
826            $match = $2;
827            $after = $3;
828            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
829        }
830        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
831        {
832            $before = $1;
833            $match = $2;
834            $after = $3;
835            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
836      }      }
837      return $x;      return $x;
838  }  }
839    
840    sub refseq_link {
841        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
842        my($cgi,$id) = @_;
843    
844        if ($id =~ /^[NXYZA]P_/)
845        {
846            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";
847        }
848    }
849    
850  sub gi_link {  sub gi_link {
851        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
852      my($cgi,$gi) = @_;      my($cgi,$gi) = @_;
853    
854      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
# Line 516  Line 858 
858      return $gi;      return $gi;
859  }  }
860    
861    sub tigr_link {
862        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
863        my($cgi,$tigr) = @_;
864    
865        if ($tigr =~ /^tigr\|([0-9a-zA-Z]+)$/)
866        {
867            return "<a href=\"http://pathema.tigr.org/tigr-scripts/CMR/GenePage.cgi?locus=$1\">$tigr</a>";
868        }
869        return $tigr;
870    }
871    
872    sub uni_link {
873        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
874        my($cgi,$uni) = @_;
875    
876        if ($uni =~ /^uni\|(\S+)$/)
877        {
878            return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
879        }
880        return $uni;
881    }
882    
883  sub sp_link {  sub sp_link {
884        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
885      my($cgi,$sp) = @_;      my($cgi,$sp) = @_;
886    
887      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
# Line 527  Line 892 
892  }  }
893    
894  sub pir_link {  sub pir_link {
895        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
896      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
897    
898      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
# Line 536  Line 902 
902      return $pir;      return $pir;
903  }  }
904    
905    sub kegg_link {
906        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
907        my($cgi,$kegg) = @_;
908    
909        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
910        {
911            return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";
912        }
913        return $kegg;
914    }
915    
916    sub set_map_links {
917        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
918        my($cgi,$x) = @_;
919        my($before,$match,$after);
920    
921        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
922    
923        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
924        {
925            $before = $1;
926            $match = $2;
927            $after = $3;
928            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
929        }
930        return $x;
931    }
932    
933    sub map_link {
934        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
935        my($cgi,$map,$org) = @_;
936    
937        $user = $cgi->param('user');
938        $user = $user ? $user : "";
939        $org = $org ? $org : "";
940    
941        my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
942        my $link = "<a href=\"$url\">$map</a>";
943        return $link;
944    }
945    
946    sub java_buttons {
947        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
948      ## ADDED BY RAE
949      # Provides code to include check all/first half/second half/none for javascrspt
950      # this takes two variables - the form name provided in start_form with the
951      # -name => field and the checkbox name
952      my ($form, $button)=@_;
953    
954      $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
955      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
956      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
957      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
958    
959      return $java_script;
960    }
961    
962    sub sub_link {
963        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
964        my($cgi,$sub) = @_;
965        my($sub_link);
966    
967        my $user = $cgi->param('user');
968        if ($user)
969        {
970            my $esc_sub = uri_escape( $sub );
971            $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";
972        }
973        else
974        {
975            $sub_link = $sub;
976        }
977        return $sub_link;
978    }
979    
980    sub reaction_link {
981        my($reaction) = @_;
982    
983        if ($reaction =~ /^R\d+/)
984        {
985            return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";
986        }
987        return $reaction;
988    }
989    
990    sub html_for_assignments {
991        my($fig,$user,$peg_sets) = @_;
992        my $i;
993    
994        my @vals = ();
995        my $set = 1;
996        foreach $peg_set (@$peg_sets)
997        {
998            for ($i=0; ($i < @$peg_set); $i++)
999            {
1000                $peg = $peg_set->[$i];
1001                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1002            }
1003            $set++;
1004        }
1005    
1006        $ENV{'REQUEST_METHOD'} = 'GET';
1007        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1008        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1009        $out =~ s/^.*?<form/<form/si;
1010        $out =~ s/^(.*)<table.*/$1/si;
1011        return $out;
1012    }
1013    
1014    =head1 rss_feed
1015    
1016    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1017            SEED.rss                - everything gets written here
1018            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1019            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1020    
1021    
1022    RSS feeds must contain a title, description, and link. The title is what is seen e.g. from the firefox or safari pull down menu. The description is seen from within an rss aggregator, and may be displayed on web pages and so on.
1023    
1024    The method takes a reference to an array containing the file names for the RSS feeds to add your item to, and a hash of items for the xml. Only title, description, and link are required tags in the XML.
1025    
1026    The file names are the full name of the file, eg SEEDsubsystems.rss, SEEDgenomes.rss. Be aware that this is a file name, though, so don't uses special characters. The path will be added.
1027    
1028    The has can have these keys:
1029    
1030    REQUIRED:
1031    title       : the title. This is usually what is seen by the user in the pull down menu
1032    description : a more complete description that is often seen is rss viewers but not always
1033    link        : link to the item that was added/edited
1034    All other keys are treated as optional RSS arguments and written to the file. At most, 10 recent entries are stored in the rss file.
1035    
1036    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1037    
1038    
1039    =cut
1040    
1041    sub rss_feed {
1042     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1043     my ($files, $args)=@_;
1044     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1045    
1046     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1047     # check for the directory and if not, make it
1048     mkdir $filepath unless (-d $filepath);
1049    
1050     # note that $info is a hash of references to hashes that are written out as headers in the file
1051     my $info=
1052     {
1053      "SEED.rss" =>
1054       {
1055            title           => "The SEED",
1056            description     => "Latest news from the SEED",
1057            link            => &FIG::cgi_url()."/Html/rss/SEED.rss",
1058       },
1059    
1060      "SEEDsubsystems.rss" =>
1061      {
1062            title           => "SEED Subsystems",
1063            description     => "Recently updated SEED subsystems",
1064            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1065      },
1066    
1067      "SEEDsubsystems.rss" =>
1068      {
1069            title           => "SEED Genomes",
1070            description     => "Genomes recently added to the SEED",
1071            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1072      },
1073    
1074     };
1075    
1076    
1077     # build the new xml
1078     my $xml = "\t<item>\n";
1079     foreach my $qw ("title", "description", "link") {
1080      unless ($args->{$qw}) {
1081       print STDERR "You need to include a $qw tag in your RSS description\n";
1082       return(0);
1083      }
1084      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1085      # so we are going to pull out the links and uri_escape just the part after the .cgi
1086      if ($qw eq "link")
1087      {
1088       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1089       print STDERR "Got ->>$1<<- and ->>$2<<-\n";
1090       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1091      }
1092    
1093      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1094      delete $args->{$qw};
1095     }
1096    
1097     foreach my $tag (grep {!/type/i} keys %$args)
1098     {
1099      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1100     }
1101    
1102     $xml .= "\t</item>\n";
1103    
1104    
1105     my @files=("SEED.rss");
1106     if ($args->{"type"}) {push @files, "SEED.$type.rss"}
1107    
1108     foreach my $file ("SEED.rss", @$files)
1109     {
1110      if (-e "$filepath/$file")
1111      {
1112       my @out; # the new content of the file
1113       my $itemcount=0; # how many <item> </item>'s are we keeping
1114       my $initem; # are we in an item?
1115       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1116       while (<IN>)
1117       {
1118        if (/\<item\>/) {
1119         push @out, $xml, unless ($itemcount);
1120         $itemcount++;
1121         $initem=1;
1122        }
1123        if (/\<\/item\>/) {$initem=0; next if ($itemcount > 9)}
1124        next if ($initem && $itemcount > 9);
1125        push @out, $_;
1126       }
1127       close IN;
1128       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1129       print OUT @out;
1130      }
1131      else
1132      {
1133       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1134       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1135       if ($info->{$file})
1136       {
1137         # we're going to sanity check each of the three options we output, just to be sure
1138         foreach my $qw ("title", "description", "link")
1139         {
1140           if ($info->{$file}->{$qw})
1141           {
1142              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1143           } else {
1144              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1145           }
1146         }
1147       }
1148       else {
1149        print STDERR "Please define title, link, and description information for $file\n";
1150        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1151       }
1152       print OUT "\n", $xml;
1153       print OUT "\n", "</channel>\n</rss>\n"
1154      }
1155     }
1156    }
1157    
1158    1;
1159    
 1  

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