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revision 1.6, Sun Mar 21 02:20:55 2004 UTC revision 1.77, Wed Dec 28 04:00:26 2005 UTC
# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package HTML;  package HTML;
19    
20    use Tracer;
21    use FIG;
22  use Carp;  use Carp;
23  use Data::Dumper;  use Data::Dumper;
24  use LWP::UserAgent;  use LWP::UserAgent;
25  use LWP::Simple;  use LWP::Simple;
26    use URI::Escape;  # uri_escape()
27  use URI::URL;  use URI::URL;
28  use HTTP::Request::Common;  use HTTP::Request::Common;
29    use POSIX;
30    
31    
32    my $top_link_cache;
33    
34    
35    sub new
36    {
37        my($class) = @_;
38    
39        my $self = {};
40    
41        return bless $self, $class;
42    }
43    
44    sub top_link
45    {
46    
47        #
48        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
49        # just /p2p).
50        #
51    
52        return $top_link_cache if ($top_link_cache);
53    
54        my @parts = split(/\//, $ENV{SCRIPT_NAME});
55        my $top;
56        if ($parts[-2] eq 'FIG')
57        {
58            $top = '.';
59    #       warn "toplevel @parts\n";
60        }
61        elsif ($parts[-3] eq 'FIG')
62        {
63            $top = '..';
64    #       warn "subdir @parts\n";
65        }
66        else
67        {
68            $top = $FIG_Config::cgi_base;
69    #       warn "other @parts\n";
70        }
71    
72        $top_link_cache = $top;
73        return $top;
74    }
75    
76    sub compute_html_header
77    {
78        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
79        my($additional_insert, $user, %options ) = @_;
80    
81        my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
82        my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
83    
84        my $html_hdr_file = "./Html/$header_name";
85        if (! -f $html_hdr_file)
86        {
87            $html_hdr_file = "$FIG_Config::fig/CGI/Html/$header_name";
88        }
89        my @html_hdr = &FIG::file_read($html_hdr_file);
90    
91        # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
92    
93        #
94        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
95        # just /p2p).
96        #
97    
98        my @parts = split(/\//, $ENV{SCRIPT_NAME});
99        my $top;
100        if ($parts[-2] eq 'FIG')
101        {
102            $top = '.';
103    #       warn "toplevel @parts\n";
104        }
105        elsif ($parts[-3] eq 'FIG')
106        {
107            $top = '..';
108    #       warn "subdir @parts\n";
109        }
110        else
111        {
112            $top = $FIG_Config::cgi_base;
113    #       warn "other @parts\n";
114        }
115    
116        $options{no_fig_search} or push( @html_hdr, "<br><a href=\"$top/index.cgi?user=$user\">FIG search</a>\n" );
117    
118        if (@html_hdr)
119        {
120            my $insert_stuff;
121    
122            if (not $options{no_release_info})
123            {
124                my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
125                my $ver = $ver[0];
126                chomp $ver;
127                if ($ver =~ /^cvs\.(\d+)$/)
128                {
129                    my $d = asctime(localtime($1));
130                    chomp($d);
131                    $ver .=  " ($d)";
132                }
133                my $host = &FIG::get_local_hostname();
134                $insert_stuff = "SEED version <b>$ver</b> on $host";
135            }
136    
137            if ($additional_insert)
138            {
139                $insert_stuff .= "<br>" . $additional_insert;
140            }
141    
142            for $_ (@html_hdr)
143            {
144                s,(href|img\s+src)="/FIG/,$1="$top/,g;
145                    s,(\?user\=)\",$1$user",;
146                if ($_ eq "<!-- HEADER_INSERT -->\n")
147                {
148                    $_ = $insert_stuff;
149                }
150            }
151        }
152    
153        return @html_hdr;
154    }
155    
156  sub show_page {  sub show_page {
157      my($cgi,$html,$no_home) = @_;      #warn "SHOWPAGE: cgi=", Dumper(@_);
158        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
159        my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie) = @_;
160      my $i;      my $i;
161    
162        my $top = top_link();
163    
164        # ARGUMENTS:
165        #     $cgi is the CGI method
166        #     $html is an array with all the html in it. It is just joined by "\n" (and not <br> or <p>
167        #     $no_home eliminates ONLY the bottom FIG search link in a page
168        #     $alt_header is a reference to an array for an alternate header banner that you can replace the standard one with
169        #     $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
170        #               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
171        #               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
172        #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "/FIG/Html/css/styleswitcher.js")
173        #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
174      #      #
175      # Find the HTML header      # Find the HTML header
176      #      #
177    
178      my $html_hdr_file = "./Html/html.hdr";      my $html_tail_file = "./Html/$tail_name";
179      if (! -f $html_hdr_file)      if (! -f $html_tail_file)
180      {      {
181          $html_hdr_file = "$FIG_Config::fig/CGI/Html/html.hdr";          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
182      }      }
183    
184      my $html_tail_file = "./Html/html.tail";      my $user = $cgi->param('user') || "";
185      if (! -f $html_tail_file)      my @html_hdr;
186        if ($alt_header && ref($alt_header) eq "ARRAY")
187        {
188           @html_hdr = @$alt_header;
189        }
190        else
191      {      {
192          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          @html_hdr = compute_html_header(undef,$user);
193      }      }
194    
195        # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.
196        # This modification adds the cookies if necessary
197    
198      print $cgi->header;      # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about
199        # to add cookies back in replace these two header lines with each other
200    
201        #print $cgi->header(-cookie=>$cookie);
202        print $cgi->header();
203    
204      #      #
205      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
# Line 46  Line 217 
217                       meta     => 1,                       meta     => 1,
218                       nextid   => 1,                       nextid   => 1,
219                       style    => 1,                       style    => 1,
220                       title    => 1                       title    => 1,
221                     );                     );
222    
223      #      #
# Line 89  Line 260 
260          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )
261          {          {
262              $body_line = $i;              $body_line = $i;
263              $last;              last;
264          }          }
265    
266          #  Now the general case.          #  Now the general case.
# Line 145  Line 316 
316      #      #
317      #  <BODY> goes after last head line      #  <BODY> goes after last head line
318      #      #
319        #  RAE:
320        #  Added the javascript for the buttons immediately after body.
321        #  Note if no buttons are added we still (at the moment) add the script,
322        #  but it only adds a little text (495 characters) to the html and noone will notice!
323        #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
324    
325      if ( $body_line < 0 )      if ( $body_line < 0 )
326      {      {
# Line 156  Line 332 
332      #  Seed page header (if it exists) goes after <BODY>      #  Seed page header (if it exists) goes after <BODY>
333      #      #
334    
335      if ( -f $html_hdr_file )      if (@html_hdr)
336      {      {
337          splice( @$html, $body_line + 1, 0, `cat $html_hdr_file` );          splice( @$html, $body_line + 1, 0, @html_hdr );
338      }      }
339    
340      #      #
# Line 171  Line 347 
347          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
348      }      }
349    
350        # RAE:
351        # Add css here
352        # Note that at the moment I define these two sheets here. I think this should
353        # be moved out, but I want to try it and see what happens.  css has the format:
354        #
355        # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
356    
357        # convert the default key to the right case. and eliminate dups
358        foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
359    
360        if (!$css || !$css->{'Default'})
361        {
362           $css->{'Default'} = "$top/Html/css/default.css";
363        }
364        if (!$css->{"Sans Serif"})
365        {
366           $css->{'Sans Serif'} = "$top/Html/css/sanserif.css";
367        }
368    
369        my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";
370        $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";
371    
372        foreach my $k (keys %$css)
373        {
374           next if (lc($k) eq "default" || lc($k) eq "sans serif");
375           $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
376        }
377    
378        $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='$top/Html/rss/SEED.rss' type='application/rss+xml'>\n";
379    
380        # RAE: also added support for external javascripts here.
381        # we are cluttering the HTML code with all the javascripts when they could easily be in external files
382        # this solution allows us to source other files
383    
384        # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
385        # it will reduce our overhead.
386    
387        # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
388        push @$javasrc, "$top/Html/css/FIG.js";
389        foreach my $script (@$javasrc) {
390            $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
391        }
392    
393    
394    
395        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.
396    
397      #      #
398      #  <BASE ...> goes before </HEAD>      #  <BASE ...> goes before </HEAD>
399      #      #
# Line 183  Line 406 
406          #  only, or every update?), I provide an alternative derivation          #  only, or every update?), I provide an alternative derivation
407          #  from $cgi_url. -- GJO          #  from $cgi_url. -- GJO
408          #          #
409            # BASE href needs to be absolute. RDO.
410          my $base_url = $FIG_Config::cgi_base;          #
411          if ( ! $base_url )                      # if cgi_base was not defined          #
412          {          $base_url = &FIG::cgi_url;
413              $base_url = $FIG_Config::cgi_url;   # get the full cgi url  #       my $base_url = $FIG_Config::cgi_base;
414              $base_url =~ s~^http://[^/]*~~;     # remove protocol and host  #       if ( ! $base_url )                      # if cgi_base was not defined
415              $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash  #       {
416          }  #           $base_url = $FIG_Config::cgi_url;   # get the full cgi url
417    #           $base_url =~ s~^http://[^/]*~~;     # remove protocol and host
418    #           $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash
419    #       }
420    
421          $base_line = $head_end_line;          $base_line = $head_end_line;
422          splice( @$html, $base_line, 0, "<BASE href=\"$base_url\">\n" );          #
423            # RDO 2005-1006. Remove this so proxying works better.
424            #
425    #        splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );
426      }      }
427    
428      #      #
# Line 228  Line 457 
457      }      }
458    
459      #      #
460        # See if we have a site-specific tail (for disclaimers, etc).
461        #
462    
463        my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
464        my $site_fh;
465        if (open($site_fh, "<$site_tail"))
466        {
467            push(@tail, <$site_fh>);
468            close($site_fh);
469        }
470    
471        #
472      #  Figure out where to insert The SEED tail.  Before </body>,      #  Figure out where to insert The SEED tail.  Before </body>,
473      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
474      #      #
   
475      my @tags = ();      my @tags = ();
476        # Check for a tracing queue.
477        my $traceString = QTrace("HTML");
478        if ($traceString) {
479            push @tags, $traceString;
480        }
481      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
482      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
483      {      {
# Line 255  Line 499 
499          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
500      }      }
501    
502      print @$html;      # RAE the chomp will return any new lines at the ends of elements in the array,
503        # and then we can join  with a "\n". This is because somethings put newlines in,
504        # and others don't. This should make nicer looking html
505        #
506        # chomp(@$html);
507        # print join "\n", @$html;
508        #
509        # Apparently the above still breaks things. This is the correct code:
510    
511        foreach $_ (@$html)
512        {
513            print $_;
514        }
515    
516  }  }
517    
518  sub make_table {  sub make_table {
519      my($col_hdrs,$tab,$title,$instr) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
520      my(@tab);      my(@tab);
521    
522      push( @tab, "\n<table border>\n",      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
523        my $width = defined $options{width} ? "width=\"$options{width}\"" : undef;
524        my $class = defined $options{class} ? "class=\"$options{class}\"" : undef;
525        push( @tab, "\n<table $border $width $class>\n",
526                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
527                  "\t<tr>\n\t\t<th>"                  "\t<tr>\n\t\t"
528                . join( "</th>\n\t\t<th>", @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
529                . "</th>\n\t</tr>\n"                . "\n\t</tr>\n"
530          );          );
531      my($i,$nowrap);      my($i);
   
     for ($i=0; ($i < @$instr) && ($instr->[$i] !~ /nowrap/); $i++) {}  
     $nowrap = ($i == @$instr) ? "" : " nowrap";  
532    
533      my $row;      my $row;
534      foreach $row (@$tab)      foreach $row (@$tab)
535      {      {
536          push( @tab, "\t<tr>\n"          push( @tab, "\t<tr>\n"
537                    . join( "\n", map { &expand($_,$nowrap) } @$row )                    . join( "\n", map { &expand($_) } @$row )
538                    . "\n\t</tr>\n"                    . "\n\t</tr>\n"
539              );              );
540      }      }
# Line 285  Line 542 
542      return join("",@tab);      return join("",@tab);
543  }  }
544    
545    sub abstract_coupling_table {
546        my($cgi,$prot,$coupling) = @_;
547        my %fc;
548    
549        my $col_hdrs = ["coupled to","Score","Type of Coupling", "Type-specific Data"];
550        my $tab = [];
551        my %by_peg;
552        foreach my $x (@$coupling)
553        {
554            my($peg2,$psc,$type,$extra) = @$x;
555            $by_peg{$peg2} += $psc;
556        }
557    
558        foreach my $x (sort { ($by_peg{$b->[0]} <=> $by_peg{$a->[0]})
559                              or ($a->[0] cmp $b->[0])
560                              or ($b->[1] <=> $a->[1])
561                              or ($a->[2] cmp $b->[2]) } @$coupling)
562        {
563            my($peg2,$psc,$type,$extra) = @$x;
564            if (($type !~ /^[ID]FC$/) || (! $fc{$peg2}))
565            {
566                if ($type =~  /^[ID]FC$/)
567                {
568                    $fc{$peg2} = 1;
569                }
570                push(@$tab,[&fid_link($cgi,$peg2,1),$psc,$type,&set_prot_links($cgi,join(", ",@$extra))]);
571            }
572        }
573    
574    
575         my $help = "<a href=\"Html/abstract_coupling.html\" target=\"SEED_or_SPROUT_help\">for help</a>";
576    #    my @html = &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot");
577    #    push(@html,"<hr>\n",$cgi->h3($help),"<br>");
578    #    return @html;
579    
580        return &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot [$help]");
581    }
582    
583  sub expand {  sub expand {
584      my($x,$nowrap) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
585        my( $x, $tag ) = @_;
586    
587        $tag = "td" unless $tag;
588        my $endtag = $tag;
589    
590        # RAE modified this so that you can pass in a reference to an array where
591        # the first element is the data to display and the second element is optional
592        # things like colspan and align. Note that in this case you need to include the td
593        # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
594    
595      if ($x =~ /^\@([^:]+)\:([^:]+)\:(.*)$/)      # per GJO's request modified this line so it can take any tag.
596        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
597    
598        if ( $x =~ /^\@([^:]+)\:(.*)$/ )
599      {      {
600          return "\t\t<td$nowrap $1=\"$2\">$3</td>";          return "\t\t<$tag $1>$2</$endtag>";
601      }      }
602      else      else
603      {      {
604          return "\t\t<td$nowrap>$x</td>";          return "\t\t<$tag>$x</$endtag>";
605        }
606    }
607    
608    
609    =head2 merge_table_rows()
610    
611    Merge table rows together. This will merge a table so that adjacent cells with the same content will only be shown once.
612    
613    Something like this:
614    
615        -----------------------
616        |    1     |    a     |
617        -----------------------
618        |    1     |    b     |
619        -----------------------
620        |    2     |    c     |
621        -----------------------
622        |    3     |    d     |
623        -----------------------
624        |    4     |    d     |
625        -----------------------
626        |    5     |    d     |
627        -----------------------
628    
629    Will become:
630    
631        -----------------------
632        |          |    a     |
633        |    1     |-----------
634        |          |    b     |
635        -----------------------
636        |    2     |    c     |
637        -----------------------
638        |    3     |          |
639        ------------          |
640        |    4     |    5     |
641        ------------          |
642        |    5     |          |
643        -----------------------
644    
645    
646    The method takes two arguments. The reference to the array that is the table ($tab). This is the standard table that is created for HTML.pm to draw, and a reference to a hash of columns that you don't want to merge together. The reference to the hash is optional, and if not included, everything will be merged.
647    
648     $tab=&HTML::merge_table_rows($tab);
649    
650     or
651    
652     $skip=(1=>1, 3=>1, 5=>1);
653     $tab=&HTML::merge_table_rows($tab, $skip);  # will merge all columns except 1, 3 and 5. Note the first column in the table is #0
654    
655    
656    =cut
657    
658    
659    
660    
661    sub merge_table_rows {
662     # RAE:
663     # Experimental piece of code. We often want to have rows or columns were cells are merged. It just looks so much nicer
664     # this block should merge adjacent rows that have the same text in them.
665     # use like this:
666     #      $tab=&HTML::merge_table_rows($tab);
667     # before you do a make_table call
668    
669     my $self=shift if UNIVERSAL::isa($_[0],__PACKAGE__);
670     my ($tab, $skip)=@_;
671    
672     my $newtable;
673     my $lastrow;
674     my $rowspan;
675     my $refs;
676    
677     for (my $y=0; $y <= $#$tab; $y++) {
678     #$y is the row in the table;
679      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
680       # this is the user definable columns not to merge
681       if ($skip->{$x})
682       {
683        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
684        next;
685       }
686    
687       #$x is the column in the table
688       # if the column in the row we are looking at is the same as the column in the previous row, we don't add
689       # this cell to $newtable. Instead we increment the rowspan of the previous row by one
690    
691       # handle cells that are references to arrays
692       if (ref($tab->[$y]->[$x]) eq "ARRAY") {$refs->[$y]->[$x]=$tab->[$y]->[$x]->[1]; $tab->[$y]->[$x]=$tab->[$y]->[$x]->[0]}
693    
694       # now we go back through the table looking where to draw the merge line:
695       my $lasty=$y;
696       while ($lasty >= 0 && $tab->[$y]->[$x] eq $tab->[$lasty]->[$x]) {$lasty--}
697       $lasty++; # this is the last identical cell. If lasty==y it is the current cell, so we just save the data. Otherwise we increment the rowspan
698       if ($lasty == $y) {
699        # we always want to have something in rows that may otherwise be empty but should be there (see below)
700        unless ($tab->[$y]->[$x]) {$tab->[$y]->[$x]=" &nbsp; "}
701        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
702       }
703       else {$rowspan->[$lasty]->[$x]++}
704      }
705     }
706    
707     # now just join everything back together
708     for (my $y=0; $y <= $#$tab; $y++) {
709      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
710       if ($rowspan->[$y]->[$x]) {
711        if ($refs->[$y]->[$x]) {$refs->[$y]->[$x] .= " rowspan=". ($rowspan->[$y]->[$x]+1)}
712        else {$refs->[$y]->[$x] = "td rowspan=". ($rowspan->[$y]->[$x]+1)}
713        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
714       }
715       elsif ($newtable->[$y]->[$x] && $refs->[$y]->[$x]) {
716        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
717       }
718      }
719     }
720    
721    
722     # finally we have to remove any completely empty cells that have been added by the array mechanism
723     # (e.g. if you define $a->[2] then $a->[0] and $a->[1] are now undef).
724     # that is why in the loop above I replace empty cells with nbsp. They are now not undef!
725     # I am sure that Gary can do this in one line, but I am hacking.
726     my @trimmed;
727     foreach my $a (@$newtable) {
728      my @row;
729      foreach my $b (@$a) {
730       push @row, $b if ($b);
731      }
732      push @trimmed, \@row;
733     }
734    
735     return \@trimmed;
736    }
737    
738    
739    
740    
741    sub set_ec_links {
742        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
743        my($cgi,$x) = @_;
744        my($before,$match,$after);
745    
746        if ($x =~ /^(.*)(EC \d+\.\d+\.\d+\.\d+)(.*)/s)
747        {
748            $before = $1;
749            $match = $2;
750            $after = $3;
751            return &set_ec_links($cgi,$before) . &HTML::ec_link($match) . &set_ec_links($cgi,$after);
752      }      }
753        return $x;
754  }  }
755    
756  sub ec_link {  sub ec_link {
757        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
758      my($role) = @_;      my($role) = @_;
759    
760      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)
# Line 312  Line 768 
768  }  }
769    
770  sub role_link {  sub role_link {
771        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
772      my($cgi,$role) = @_;      my($cgi,$role) = @_;
773    
774      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;
# Line 322  Line 779 
779      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
780  }  }
781    
782    #
783    # Local means to eliminate the fig|org.peg from the
784    # text of the link.
785    #
786  sub fid_link {  sub fid_link {
787        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
788      my($cgi,$fid,$local,$just_url) = @_;      my($cgi,$fid,$local,$just_url) = @_;
789      my($n);      my($n);
790    
791        my $top = top_link();
792    
793      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)
794      {      {
795          if ($local)          if ($local)
# Line 343  Line 807 
807          {          {
808              $n = $fid;              $n = $fid;
809          }          }
810          if ($1 ne "peg") { return $n }  
811            my $link;
812            #added to format prophage and path island links to feature.cgi
813            if ($1 ne "peg")
814            {
815               my $user = $cgi->param('user');
816               if (! $user) { $user = "" }
817               my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
818               $link = "$top/feature.cgi?feature=$fid&user=$user$trans$sprout";
819               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
820            }
821            else
822            {
823          my $user = $cgi->param('user');          my $user = $cgi->param('user');
824          if (! $user) { $user = "" }          if (! $user) { $user = "" }
825          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
826          my $link = $cgi->url() . "?prot=$fid&user=$user$trans";              my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
827          $link =~ s/[a-z_A-Z]+\.cgi\?/protein.cgi?/;  ###a
828    
829    ### This used to be
830    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
831    ###
832    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
833    ###
834    ### RAO
835    
836                #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
837                #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
838                $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout";
839                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
840            }
841          if ($just_url)          if ($just_url)
842          {          {
843              return $link;              return $link;
# Line 362  Line 851 
851  }  }
852    
853  sub family_link {  sub family_link {
854        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
855      my($family,$user) = @_;      my($family,$user) = @_;
856    
857      return $family;      return $family;
858  }  }
859    
 use URI::Escape;  
860    
861  sub get_html {  sub get_html {
862        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
863      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
864      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
865    
866      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
867      $ua->timeout( 900 );      $ua->timeout( 900 );
   
868      if ($type =~/post/i)      if ($type =~/post/i)
869      {      {
870          $args = [];          $args = [];
# Line 435  Line 924 
924  }  }
925    
926  sub trim_output {  sub trim_output {
927        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
928      my($out) = @_;      my($out) = @_;
929      my $i;      my $i;
930    
# Line 472  Line 962 
962  }  }
963    
964  sub set_prot_links {  sub set_prot_links {
965        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
966      my($cgi,$x) = @_;      my($cgi,$x) = @_;
967      my($before,$match,$after);      my($before,$match,$after);
968    
969      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
970        {
971            $before = $1;
972            $match = $2;
973            $after = $3;
974            return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);
975        }
976        elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
977      {      {
978          $before = $1;          $before = $1;
979          $match = $2;          $match = $2;
980          $after = $3;          $after = $3;
981          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::refseq_link($cgi,$match) . &set_prot_links($cgi,$after);
982      }      }
983      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)      elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
984      {      {
985          $before = $1;          $before = $1;
986          $match = $2;          $match = $2;
987          $after = $3;          $after = $3;
988          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);
989      }      }
990      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($x =~ /^(.*)(tigr\|[0-9a-zA-Z]+)(.*)/s)
991      {      {
992          $before = $1;          $before = $1;
993          $match = $2;          $match = $2;
994          $after = $3;          $after = $3;
995          return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
996      }      }
997      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
998      {      {
999          $before = $1;          $before = $1;
1000          $match = $2;          $match = $2;
1001          $after = $3;          $after = $3;
1002          return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
1003        }
1004        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
1005        {
1006            $before = $1;
1007            $match = $2;
1008            $after = $3;
1009            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
1010        }
1011        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
1012        {
1013            $before = $1;
1014            $match = $2;
1015            $after = $3;
1016            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
1017        }
1018        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
1019        {
1020            $before = $1;
1021            $match = $2;
1022            $after = $3;
1023            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1024        }
1025        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1026        {
1027            $before = $1;
1028            $match = $2;
1029            $after = $3;
1030            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1031        }
1032        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1033        {
1034            $before = $1;
1035            $match = $2;
1036            $after = $3;
1037            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1038        }
1039        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1040        {
1041            $before = $1;
1042            $match = $2;
1043            $after = $3;
1044            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1045        }
1046        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1047        {
1048            $before = $1;
1049            $match = $2;
1050            $after = $3;
1051            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1052        }
1053        elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1054        {
1055            $before = $1;
1056            $match = $2;
1057            $after = $3;
1058            return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1059        }
1060        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1061        {
1062            #wormbase
1063    
1064            $before = $1;
1065            $match = $2;
1066            $after = $3;
1067            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1068        }
1069        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1070        {
1071            #flybase
1072    
1073            $before = $1;
1074            $match = $2;
1075            $after = $3;
1076            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1077        }
1078        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1079        {
1080            #flybase
1081    
1082            $before = $1;
1083            $match = $2;
1084            $after = $3;
1085            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1086        }
1087        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1088        {
1089            #flybase
1090    
1091            $before = $1;
1092            $match = $2;
1093            $after = $3;
1094            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1095      }      }
1096      return $x;      return $x;
1097  }  }
1098    
1099    sub refseq_link {
1100        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1101        my($cgi,$id) = @_;
1102    
1103        if ($id =~ /^[NXYZA]P_/)
1104        {
1105            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";
1106        }
1107        elsif ($id =~ /^[NXYZA]M_/)
1108        {
1109            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id>$id</a>";
1110        }
1111    }
1112    
1113  sub gi_link {  sub gi_link {
1114        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1115      my($cgi,$gi) = @_;      my($cgi,$gi) = @_;
1116    
1117      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
# Line 516  Line 1121 
1121      return $gi;      return $gi;
1122  }  }
1123    
1124    sub tigr_link {
1125        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1126        my($cgi,$tigr) = @_;
1127    
1128        if ($tigr =~ /^tigr\|([0-9a-zA-Z]+)$/)
1129        {
1130            return "<a href=\"http://pathema.tigr.org/tigr-scripts/CMR/GenePage.cgi?locus=$1\">$tigr</a>";
1131        }
1132        return $tigr;
1133    }
1134    
1135    sub uni_link {
1136        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1137        my($cgi,$uni) = @_;
1138    
1139        if ($uni =~ /^uni\|(\S+)$/)
1140        {
1141            return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1142        }
1143        return $uni;
1144    }
1145    
1146  sub sp_link {  sub sp_link {
1147        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1148      my($cgi,$sp) = @_;      my($cgi,$sp) = @_;
1149    
1150      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
# Line 527  Line 1155 
1155  }  }
1156    
1157  sub pir_link {  sub pir_link {
1158        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1159      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
1160    
1161      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
# Line 536  Line 1165 
1165      return $pir;      return $pir;
1166  }  }
1167    
1168    sub kegg_link {
1169        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1170        my($cgi,$kegg) = @_;
1171    
1172        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1173        {
1174            return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";
1175        }
1176        return $kegg;
1177    }
1178    
1179    sub ensembl_link {
1180        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1181        my($cgi,$ensembl) = @_;
1182    
1183        if ($ensembl =~ /^(\S+):(\S+)$/)
1184        {
1185            my $what=$1;
1186            my $key=$2;
1187            my $idx="all";
1188            if ($what eq "EnsemblGene") { $idx = "Gene" }
1189            if ($what eq "EnsemblTranscript") { $idx = "all" }
1190            if ($what eq "EnsemblProtein") { $idx = "all" }
1191    
1192            #I really want to get right to the transcript and peptide pages, but
1193            #can't see how to do that without knowing the org name too, which
1194            #I don't know at this point. (ensembl org name, not real org name)
1195    
1196            return "<a href=http://www.ensembl.org/Homo_sapiens/textview?species=all&idx=$idx&q=$key>$ensembl</a>";
1197        }
1198        return $ensembl;
1199    }
1200    
1201    sub entrezgene_link {
1202        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1203        my($cgi,$entrezgene) = @_;
1204    
1205        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1206        {
1207            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1>$entrezgene</a>";
1208        }
1209        return $entrezgene;
1210    }
1211    
1212    sub mim_link {
1213        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1214        my($cgi,$mim) = @_;
1215    
1216        if ($mim =~ /^MIM:(\S+)$/)
1217        {
1218            return "<a href=http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1>$mim</a>";
1219        }
1220        return $mim;
1221    }
1222    
1223    sub unigene_link {
1224        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1225        my($cgi,$unigene) = @_;
1226    
1227        if ($unigene =~ /^UniGene:(\S+)$/)
1228        {
1229            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1>$unigene</a>";
1230        }
1231        return $unigene;
1232    }
1233    
1234    sub ipi_link {
1235        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1236        my($cgi,$ipi) = @_;
1237    
1238        if ($ipi =~ /^IPI:(\S+)$/)
1239        {
1240            return "<a href=http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1>$ipi</a>";
1241        }
1242        return $ipi;
1243    }
1244    
1245    sub wp_link {
1246        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1247        my($cgi,$wp) = @_;
1248    
1249        #wormbase
1250    
1251        if ($wp =~ /^WP:(\S+)$/)
1252        {
1253            return "<a href=http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search>$wp</a>";
1254        }
1255        return $wp;
1256    }
1257    
1258    sub fb_link {
1259        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1260        my($cgi,$fb) = @_;
1261    
1262        #flybase
1263    
1264        if ($fb =~ /^FB:(\S+)$/)
1265        {
1266            return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";
1267        }
1268        return $fb;
1269    }
1270    
1271    sub fborf_link {
1272        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1273        my($cgi,$fb) = @_;
1274    
1275        #flybase
1276    
1277        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1278        {
1279            return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";
1280        }
1281        return $fb;
1282    }
1283    
1284    sub sgd_link {
1285        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1286        my($cgi,$sgd) = @_;
1287    
1288        #yeast
1289    
1290        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1291        {
1292            return "<a href=http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1>$sgd</a>";
1293        }
1294        return $sgd;
1295    }
1296    
1297    
1298    
1299    
1300    sub set_map_links {
1301        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1302        my($cgi,$x) = @_;
1303        my($before,$match,$after);
1304    
1305        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
1306    
1307        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
1308        {
1309            $before = $1;
1310            $match = $2;
1311            $after = $3;
1312            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
1313        }
1314        return $x;
1315    }
1316    
1317    
1318    
1319    sub map_link {
1320        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1321        my($cgi,$map,$org) = @_;
1322    
1323        $user = $cgi->param('user');
1324        $user = $user ? $user : "";
1325        $org = $org ? $org : "";
1326    
1327        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1328    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1329        my $link = "<a href=\"$url\">$map</a>";
1330        return $link;
1331    }
1332    
1333    sub java_buttons {
1334        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1335      ## ADDED BY RAE
1336      # Provides code to include check all/first half/second half/none for javascrspt
1337      # this takes two variables - the form name provided in start_form with the
1338      # -name => field and the checkbox name
1339      my ($form, $button)=@_;
1340    
1341      $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1342      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1343      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1344      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1345    
1346      return $java_script;
1347    }
1348    
1349    sub sub_link {
1350        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1351        my($cgi,$sub) = @_;
1352        my($sub_link);
1353    
1354        my $user = $cgi->param('user');
1355        if ($user)
1356        {
1357            my $esc_sub = uri_escape( $sub );
1358            $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";
1359        }
1360        else
1361        {
1362            $sub_link = $sub;
1363        }
1364        return $sub_link;
1365    }
1366    
1367    sub reaction_link {
1368        my($reaction) = @_;
1369    
1370        if ($reaction =~ /^R\d+/)
1371        {
1372            return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";
1373        }
1374        return $reaction;
1375    }
1376    
1377    sub html_for_assignments {
1378        my($fig,$user,$peg_sets) = @_;
1379        my $i;
1380    
1381        my @vals = ();
1382        my $set = 1;
1383        foreach $peg_set (@$peg_sets)
1384        {
1385            for ($i=0; ($i < @$peg_set); $i++)
1386            {
1387                $peg = $peg_set->[$i];
1388                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1389            }
1390            $set++;
1391        }
1392    
1393        $ENV{'REQUEST_METHOD'} = 'GET';
1394        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1395        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1396        $out =~ s/^.*?<form/<form/si;
1397        $out =~ s/^(.*)<table.*/$1/si;
1398        return $out;
1399    }
1400    
1401    =head1 rss_feed
1402    
1403    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1404            SEED.rss                - everything gets written here
1405            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1406            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1407    
1408    
1409    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.
1410    
1411    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.
1412    
1413    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.
1414    
1415    The has can have these keys:
1416    
1417    REQUIRED:
1418    title       : the title. This is usually what is seen by the user in the pull down menu
1419    description : a more complete description that is often seen is rss viewers but not always
1420    link        : link to the item that was added/edited
1421    All other keys are treated as optional RSS arguments and written to the file.
1422    
1423    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1424    
1425    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1426    
1427    
1428    =cut
1429    
1430    sub rss_feed {
1431     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1432     my ($files, $args)=@_;
1433    
1434     # how many entries to store in the file
1435     my $max_entries=50;
1436    
1437     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1438    
1439     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1440     # check for the directory and if not, make it
1441     mkdir $filepath unless (-d $filepath);
1442    
1443     # note that $info is a hash of references to hashes that are written out as headers in the file
1444     my $info=
1445     {
1446      "SEED.rss" =>
1447       {
1448            title           => "The SEED",
1449            description     => "Latest news from the SEED",
1450            link            => "Html/rss/SEED.rss",
1451       },
1452    
1453      "SEEDsubsystems.rss" =>
1454      {
1455            title           => "SEED Subsystems",
1456            description     => "Recently updated SEED subsystems",
1457            link            => "Html/rss/SEEDsubsystems.rss",
1458      },
1459    
1460      "SEEDsubsystems.rss" =>
1461      {
1462            title           => "SEED Genomes",
1463            description     => "Genomes recently added to the SEED",
1464            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1465      },
1466    
1467     };
1468    
1469    
1470     # build the new xml
1471     my $xml = "\t<item>\n";
1472     foreach my $qw ("title", "description", "link") {
1473      unless ($args->{$qw}) {
1474       print STDERR "You need to include a $qw tag in your RSS description\n";
1475       return(0);
1476      }
1477      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1478      # so we are going to pull out the links and uri_escape just the part after the .cgi
1479      if ($qw eq "link")
1480      {
1481       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1482       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1483      }
1484    
1485      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1486      delete $args->{$qw};
1487     }
1488    
1489     foreach my $tag (grep {!/type/i} keys %$args)
1490     {
1491      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1492     }
1493    
1494     $xml .= "\t</item>\n";
1495    
1496    
1497     my @files=("SEED.rss");
1498     if ($args->{"type"}) {push @files, "SEED.$type.rss"}
1499    
1500     foreach my $file ("SEED.rss", @$files)
1501     {
1502      if (-e "$filepath/$file")
1503      {
1504       my @out; # the new content of the file
1505       my $itemcount=0; # how many <item> </item>'s are we keeping
1506       my $initem; # are we in an item?
1507       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1508       while (<IN>)
1509       {
1510        if (/\<item\>/) {
1511         push @out, $xml, unless ($itemcount);
1512         $itemcount++;
1513         $initem=1;
1514        }
1515        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1516        next if ($initem && $itemcount > $max_entries);
1517        push @out, $_;
1518       }
1519       close IN;
1520       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1521       print OUT @out;
1522      }
1523      else
1524      {
1525       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1526       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1527       if ($info->{$file})
1528       {
1529         # we're going to sanity check each of the three options we output, just to be sure
1530         foreach my $qw ("title", "description", "link")
1531         {
1532           if ($info->{$file}->{$qw})
1533           {
1534              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1535           } else {
1536              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1537           }
1538         }
1539       }
1540       else {
1541        print STDERR "Please define title, link, and description information for $file\n";
1542        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1543       }
1544       print OUT "\n", $xml;
1545       print OUT "\n", "</channel>\n</rss>\n"
1546      }
1547     }
1548    }
1549    
1550    
1551    
1552    1;
1553    
 1  

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