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# 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 strict;
21    use Tracer;
22    use FIG;
23  use Carp;  use Carp;
24  use Data::Dumper;  use Data::Dumper;
25  use LWP::UserAgent;  use LWP::UserAgent;
26  use LWP::Simple;  use LWP::Simple;
27    use URI::Escape;  # uri_escape()
28  use URI::URL;  use URI::URL;
29  use HTTP::Request::Common;  use HTTP::Request::Common;
30    use POSIX;
31    
32    #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
33    my $raelib;
34    
35    
36    my $top_link_cache;
37    
38    
39    sub new
40    {
41        my($class) = @_;
42    
43        my $self = {};
44    
45        return bless $self, $class;
46    }
47    
48    sub top_link
49    {
50    
51        #
52        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
53        # just /p2p).
54        #
55    
56        return $top_link_cache if ($top_link_cache);
57    
58        my @parts = split(/\//, $ENV{SCRIPT_NAME});
59        my $top;
60        if (defined $parts[-2] && $parts[-2] eq 'FIG')
61        {
62            $top = '.';
63    #       warn "toplevel @parts\n";
64        }
65        elsif (defined $parts[-3] && $parts[-3] eq 'FIG')
66        {
67            $top = '..';
68    #       warn "subdir @parts\n";
69        }
70        else
71        {
72            $top = $FIG_Config::cgi_base;
73    #       warn "other @parts\n";
74        }
75    
76        $top_link_cache = $top;
77        return $top;
78    }
79    
80    sub compute_html_header
81    {
82        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
83        my($additional_insert, $user, %options ) = @_;
84    
85        local $/ = "\n";
86    
87        my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
88        my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
89    
90        my $html_hdr_file = "./Html/$header_name";
91        if (! -f $html_hdr_file)
92        {
93            $html_hdr_file = "$FIG_Config::fig/CGI/Html/$header_name";
94        }
95        my @html_hdr = &FIG::file_read($html_hdr_file);
96    
97        # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
98    
99        #
100        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
101        # just /p2p).
102        #
103    
104        my @parts = split(/\//, $ENV{SCRIPT_NAME});
105        my $top;
106        if ($parts[-2] eq 'FIG')
107        {
108            $top = '.';
109    #       warn "toplevel @parts\n";
110        }
111        elsif ($parts[-3] eq 'FIG')
112        {
113            $top = '..';
114    #       warn "subdir @parts\n";
115        }
116        else
117        {
118            $top = $FIG_Config::cgi_base;
119    #       warn "other @parts\n";
120        }
121    
122        $options{no_fig_search} or push( @html_hdr, "<br><a href=\"$top/index.cgi?user=$user\">FIG search</a>\n" );
123    
124        if (@html_hdr)
125        {
126            my $insert_stuff;
127    
128            if (not $options{no_release_info})
129            {
130                my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
131                my $ver = $ver[0];
132                chomp $ver;
133                if ($ver =~ /^cvs\.(\d+)$/)
134                {
135                    my $d = asctime(localtime($1));
136                    chomp($d);
137                    $ver .=  " ($d)";
138                }
139                my $host = &FIG::get_local_hostname();
140                $insert_stuff = "SEED version <b>$ver</b> on $host";
141            }
142    
143            if ($additional_insert)
144            {
145                $insert_stuff .= "<br>" . $additional_insert;
146            }
147    
148            for $_ (@html_hdr)
149            {
150                s,(href|img\s+src)="/FIG/,$1="$top/,g;
151                    s,(\?user\=)\",$1$user",;
152                if ($_ eq "<!-- HEADER_INSERT -->\n")
153                {
154                    $_ = $insert_stuff;
155                }
156            }
157        }
158    
159        return @html_hdr;
160    }
161    
162  sub show_page {  sub show_page {
163      my($cgi,$html,$no_home) = @_;      #warn "SHOWPAGE: cgi=", Dumper(@_);
164        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
165        my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
166      my $i;      my $i;
167    
168        my $top = top_link();
169    
170        # ARGUMENTS:
171        #     $cgi is the CGI method
172        #     $html is an array with all the html in it. It is just joined by "\n" (and not <br> or <p>
173        #     $no_home eliminates ONLY the bottom FIG search link in a page
174        #     $alt_header is a reference to an array for an alternate header banner that you can replace the standard one with
175        #     $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
176        #               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
177        #               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
178        #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")
179        #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
180        #     $options is a reference to a hash of options that you can pass around the pages
181      #      #
182      # Find the HTML header      # Find the HTML header
183      #      #
184    
185      my $html_hdr_file = "./Html/html.hdr";      my $tail_name = $options->{tail_name} ? $options->{tail_name} : "html.tail";
186      if (! -f $html_hdr_file)      my $html_tail_file = "./Html/$tail_name";
187        if (! -f $html_tail_file)
188      {      {
189          $html_hdr_file = "$FIG_Config::fig/CGI/Html/html.hdr";          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
190      }      }
191    
192      my $html_tail_file = "./Html/html.tail";      my $user = $cgi->param('user') || "";
193      if (! -f $html_tail_file)      my @html_hdr;
194        if ($alt_header && ref($alt_header) eq "ARRAY")
195        {
196           @html_hdr = @$alt_header;
197        }
198        else
199      {      {
200          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          @html_hdr = compute_html_header(undef,$user,%$options);
201      }      }
202    
203        # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.
204        # This modification adds the cookies if necessary
205    
206      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
207        # to add cookies back in replace these two header lines with each other
208    
209        #print $cgi->header(-cookie=>$cookie);
210        print $cgi->header();
211    
212      #      #
213      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
# Line 46  Line 225 
225                       meta     => 1,                       meta     => 1,
226                       nextid   => 1,                       nextid   => 1,
227                       style    => 1,                       style    => 1,
228                       title    => 1                       title    => 1,
229                     );                     );
230    
231      #      #
# Line 89  Line 268 
268          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )
269          {          {
270              $body_line = $i;              $body_line = $i;
271              $last;              last;
272          }          }
273    
274          #  Now the general case.          #  Now the general case.
# Line 145  Line 324 
324      #      #
325      #  <BODY> goes after last head line      #  <BODY> goes after last head line
326      #      #
327        #  RAE:
328        #  Added the javascript for the buttons immediately after body.
329        #  Note if no buttons are added we still (at the moment) add the script,
330        #  but it only adds a little text (495 characters) to the html and noone will notice!
331        #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
332    
333      if ( $body_line < 0 )      if ( $body_line < 0 )
334      {      {
# Line 156  Line 340 
340      #  Seed page header (if it exists) goes after <BODY>      #  Seed page header (if it exists) goes after <BODY>
341      #      #
342    
343      if ( -f $html_hdr_file )      if (@html_hdr)
344      {      {
345          splice( @$html, $body_line + 1, 0, `cat $html_hdr_file` );          splice( @$html, $body_line + 1, 0, @html_hdr );
346      }      }
347    
348      #      #
# Line 171  Line 355 
355          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
356      }      }
357    
358        # RAE:
359        # Add css here
360        # Note that at the moment I define these two sheets here. I think this should
361        # be moved out, but I want to try it and see what happens.  css has the format:
362        #
363        # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
364    
365        # convert the default key to the right case. and eliminate dups
366        foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
367    
368        if (!$css || !$css->{'Default'})
369        {
370           $css->{'Default'} = "Html/css/default.css";
371        }
372        if (!$css->{"Sans Serif"})
373        {
374           $css->{'Sans Serif'} = "Html/css/sanserif.css";
375        }
376    
377        my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";
378        $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";
379    
380        foreach my $k (keys %$css)
381        {
382           next if (lc($k) eq "default" || lc($k) eq "sans serif");
383           $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
384        }
385    
386        $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='Html/rss/SEED.rss' type='application/rss+xml'>\n";
387    
388        # RAE: also added support for external javascripts here.
389        # we are cluttering the HTML code with all the javascripts when they could easily be in external files
390        # this solution allows us to source other files
391    
392        # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
393        # it will reduce our overhead.
394    
395        # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
396        push @$javasrc, "Html/css/FIG.js";
397        foreach my $script (@$javasrc) {
398            $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
399        }
400    
401    
402    
403        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.
404    
405      #      #
406      #  <BASE ...> goes before </HEAD>      #  <BASE ...> goes before </HEAD>
407      #      #
# Line 183  Line 414 
414          #  only, or every update?), I provide an alternative derivation          #  only, or every update?), I provide an alternative derivation
415          #  from $cgi_url. -- GJO          #  from $cgi_url. -- GJO
416          #          #
417            # BASE href needs to be absolute. RDO.
418          my $base_url = $FIG_Config::cgi_base;          #
419          if ( ! $base_url )                      # if cgi_base was not defined          #
420          {  #        $base_url = &FIG::cgi_url;
421              $base_url = $FIG_Config::cgi_url;   # get the full cgi url  #       my $base_url = $FIG_Config::cgi_base;
422              $base_url =~ s~^http://[^/]*~~;     # remove protocol and host  #       if ( ! $base_url )                      # if cgi_base was not defined
423              $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash  #       {
424          }  #           $base_url = $FIG_Config::cgi_url;   # get the full cgi url
425    #           $base_url =~ s~^http://[^/]*~~;     # remove protocol and host
426    #           $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash
427    #       }
428    
429          $base_line = $head_end_line;          $base_line = $head_end_line;
430          splice( @$html, $base_line, 0, "<BASE href=\"$base_url\">\n" );          #
431            # RDO 2005-1006. Remove this so proxying works better.
432            #
433    #        splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );
434      }      }
435    
436      #      #
# Line 228  Line 465 
465      }      }
466    
467      #      #
468        # See if we have a site-specific tail (for disclaimers, etc).
469        #
470    
471        my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
472        my $site_fh;
473        if (open($site_fh, "<$site_tail"))
474        {
475            push(@tail, <$site_fh>);
476            close($site_fh);
477        }
478    
479        #
480      #  Figure out where to insert The SEED tail.  Before </body>,      #  Figure out where to insert The SEED tail.  Before </body>,
481      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
482      #      #
   
483      my @tags = ();      my @tags = ();
484        # Check for a tracing queue.
485        my $traceString = QTrace("HTML");
486        if ($traceString) {
487            push @tags, $traceString;
488        }
489      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
490      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
491      {      {
# Line 255  Line 507 
507          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
508      }      }
509    
510      print @$html;      # RAE the chomp will return any new lines at the ends of elements in the array,
511        # and then we can join  with a "\n". This is because somethings put newlines in,
512        # and others don't. This should make nicer looking html
513        #
514        # chomp(@$html);
515        # print join "\n", @$html;
516        #
517        # Apparently the above still breaks things. This is the correct code:
518    
519        foreach $_ (@$html)
520        {
521            print $_;
522        }
523    
524  }  }
525    
526    
527    =head1 make_table
528    
529    The main method to convert an array into a table.
530    
531    The col_hdrs are set to the <th> headers, the $tab is an array of arrays. The first is the rows, and the second is the columns. The title is the title of the table.
532    
533    The options define the settings for the table such as border, width, and class for css formatting. If the option "excelfile" is set to a filename that will be created in FIG_Config::temp, and the link included that allows the user to download the file as an excel file.
534    
535    =cut
536    
537  sub make_table {  sub make_table {
538      my($col_hdrs,$tab,$title,$instr) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
539      my(@tab);      my(@tab);
540    
541      push( @tab, "\n<table border>\n",      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
542        my $width = defined $options{width} ? "width=\"$options{width}\"" : "";
543        my $class = defined $options{class} ? "class=\"$options{class}\"" : "";
544        push( @tab, "\n<table $border $width $class>\n",
545                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
546                  "\t<tr>\n\t\t<th>"                  "\t<tr>\n\t\t"
547                . join( "</th>\n\t\t<th>", @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
548                . "</th>\n\t</tr>\n"                . "\n\t</tr>\n"
549          );          );
550      my($i,$nowrap);      my($i);
   
     for ($i=0; ($i < @$instr) && ($instr->[$i] !~ /nowrap/); $i++) {}  
     $nowrap = ($i == @$instr) ? "" : " nowrap";  
551    
552      my $row;      my $row;
553      foreach $row (@$tab)      foreach $row (@$tab)
554      {      {
555          push( @tab, "\t<tr>\n"          push( @tab, "\t<tr>\n"
556                    . join( "\n", map { &expand($_,$nowrap) } @$row )                    . join( "\n", map { &expand($_) } @$row )
557                    . "\n\t</tr>\n"                    . "\n\t</tr>\n"
558              );              );
559      }      }
560      push(@tab,"</table>\n");      push(@tab,"</table>\n");
561    
562        # excelfile should be appropriate for a filename (no spaces/special characters)
563        if (defined $options{"excelfile"}) {
564            if (! defined($raelib)) {
565                require raelib;
566                $raelib = new raelib;
567            }
568            push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
569    
570      return join("",@tab);      return join("",@tab);
571  }  }
572    
573    sub abstract_coupling_table {
574        my($cgi,$prot,$coupling) = @_;
575        my %fc;
576    
577        my $col_hdrs = ["coupled to","Score","Type of Coupling", "Type-specific Data"];
578        my $tab = [];
579        my %by_peg;
580        foreach my $x (@$coupling)
581        {
582            my($peg2,$psc,$type,$extra) = @$x;
583            if (($type !~ /^[ID]FC$/) || (! $fc{$peg2}))
584            {
585                if ($type =~  /^[ID]FC$/)
586                {
587                    $fc{$peg2} = 1;
588                }
589    
590                $by_peg{$peg2} += $psc;
591            }
592        }
593    
594        foreach my $x (sort { ($by_peg{$b->[0]} <=> $by_peg{$a->[0]})
595                              or ($a->[0] cmp $b->[0])
596                              or ($b->[1] <=> $a->[1])
597                              or ($a->[2] cmp $b->[2]) } @$coupling)
598        {
599            my($peg2,$psc,$type,$extra) = @$x;
600            push(@$tab,[&fid_link($cgi,$peg2,1),$psc,$type,&set_prot_links($cgi,join(", ",@$extra))]);
601        }
602    
603    
604         my $help = "<a href=\"Html/abstract_coupling.html\" target=\"SEED_or_SPROUT_help\">for help</a>";
605    #    my @html = &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot");
606    #    push(@html,"<hr>\n",$cgi->h3($help),"<br>");
607    #    return @html;
608    
609        return &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot [$help]");
610    }
611    
612  sub expand {  sub expand {
613      my($x,$nowrap) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
614        my( $x, $tag ) = @_;
615    
616        $tag = "td" unless $tag;
617        my $endtag = $tag;
618    
619        # RAE modified this so that you can pass in a reference to an array where
620        # the first element is the data to display and the second element is optional
621        # things like colspan and align. Note that in this case you need to include the td
622        # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
623    
624        # per GJO's request modified this line so it can take any tag.
625        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
626    
627      if ($x =~ /^\@([^:]+)\:([^:]+)\:(.*)$/)      if ( $x =~ /^\@([^:]+)\:(.*)$/ )
628      {      {
629          return "\t\t<td$nowrap $1=\"$2\">$3</td>";          return "\t\t<$tag $1>$2</$endtag>";
630      }      }
631      else      else
632      {      {
633          return "\t\t<td$nowrap>$x</td>";          return "\t\t<$tag>$x</$endtag>";
634        }
635    }
636    
637    
638    =head2 merge_table_rows()
639    
640    Merge table rows together. This will merge a table so that adjacent cells with the same content will only be shown once.
641    
642    Something like this:
643    
644        -----------------------
645        |    1     |    a     |
646        -----------------------
647        |    1     |    b     |
648        -----------------------
649        |    2     |    c     |
650        -----------------------
651        |    3     |    d     |
652        -----------------------
653        |    4     |    d     |
654        -----------------------
655        |    5     |    d     |
656        -----------------------
657    
658    Will become:
659    
660        -----------------------
661        |          |    a     |
662        |    1     |-----------
663        |          |    b     |
664        -----------------------
665        |    2     |    c     |
666        -----------------------
667        |    3     |          |
668        ------------          |
669        |    4     |    5     |
670        ------------          |
671        |    5     |          |
672        -----------------------
673    
674    
675    The method takes two arguments. The reference to the array that is the table ($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.
676    
677     $tab=&HTML::merge_table_rows($tab);
678    
679     or
680    
681     $skip=(1=>1, 3=>1, 5=>1);
682     $tab=&HTML::merge_table_rows($tab, $skip);  # will merge all columns except 1, 3 and 5. Note the first column in the table is #0
683    
684    
685    =cut
686    
687    
688    
689    
690    sub merge_table_rows {
691     # RAE:
692     # Experimental piece of code. We often want to have rows or columns were cells are merged. It just looks so much nicer
693     # this block should merge adjacent rows that have the same text in them.
694     # use like this:
695     #      $tab=&HTML::merge_table_rows($tab);
696     # before you do a make_table call
697    
698     my $self=shift if UNIVERSAL::isa($_[0],__PACKAGE__);
699     my ($tab, $skip)=@_;
700    
701     my $newtable;
702     my $lastrow;
703     my $rowspan;
704     my $refs;
705    
706     for (my $y=0; $y <= $#$tab; $y++) {
707     #$y is the row in the table;
708      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
709       # this is the user definable columns not to merge
710       if ($skip->{$x})
711       {
712        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
713        next;
714       }
715    
716       #$x is the column in the table
717       # if the column in the row we are looking at is the same as the column in the previous row, we don't add
718       # this cell to $newtable. Instead we increment the rowspan of the previous row by one
719    
720       # handle cells that are references to arrays
721       if (ref($tab->[$y]->[$x]) eq "ARRAY") {$refs->[$y]->[$x]=$tab->[$y]->[$x]->[1]; $tab->[$y]->[$x]=$tab->[$y]->[$x]->[0]}
722    
723       # now we go back through the table looking where to draw the merge line:
724       my $lasty=$y;
725       while ($lasty >= 0 && $tab->[$y]->[$x] eq $tab->[$lasty]->[$x]) {$lasty--}
726       $lasty++; # this is the last identical cell. If lasty==y it is the current cell, so we just save the data. Otherwise we increment the rowspan
727       if ($lasty == $y) {
728        # we always want to have something in rows that may otherwise be empty but should be there (see below)
729        unless ($tab->[$y]->[$x]) {$tab->[$y]->[$x]=" &nbsp; "}
730        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
731       }
732       else {$rowspan->[$lasty]->[$x]++}
733      }
734     }
735    
736     # now just join everything back together
737     for (my $y=0; $y <= $#$tab; $y++) {
738      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
739       if ($rowspan->[$y]->[$x]) {
740        if ($refs->[$y]->[$x]) {$refs->[$y]->[$x] .= " rowspan=". ($rowspan->[$y]->[$x]+1)}
741        else {$refs->[$y]->[$x] = "td rowspan=". ($rowspan->[$y]->[$x]+1)}
742        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
743       }
744       elsif ($newtable->[$y]->[$x] && $refs->[$y]->[$x]) {
745        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
746       }
747      }
748     }
749    
750    
751     # finally we have to remove any completely empty cells that have been added by the array mechanism
752     # (e.g. if you define $a->[2] then $a->[0] and $a->[1] are now undef).
753     # that is why in the loop above I replace empty cells with nbsp. They are now not undef!
754     # I am sure that Gary can do this in one line, but I am hacking.
755     my @trimmed;
756     foreach my $a (@$newtable) {
757      my @row;
758      foreach my $b (@$a) {
759       push @row, $b if ($b);
760      }
761      push @trimmed, \@row;
762     }
763    
764     return \@trimmed;
765    }
766    
767    
768    
769    
770    sub set_ec_links {
771        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
772        my($cgi,$x) = @_;
773        my($before,$match,$after);
774    
775        if ($x =~ /^(.*)(EC \d+\.\d+\.\d+\.\d+)(.*)/s)
776        {
777            $before = $1;
778            $match = $2;
779            $after = $3;
780            return &set_ec_links($cgi,$before) . &HTML::ec_link($match) . &set_ec_links($cgi,$after);
781      }      }
782        return $x;
783  }  }
784    
785  sub ec_link {  sub ec_link {
786        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
787      my($role) = @_;      my($role) = @_;
788    
789      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)
# Line 312  Line 797 
797  }  }
798    
799  sub role_link {  sub role_link {
800        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
801      my($cgi,$role) = @_;      my($cgi,$role) = @_;
802    
803      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;
# Line 322  Line 808 
808      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
809  }  }
810    
811    =head2 fid_link
812    
813    Get a link to a fid.
814    
815    use: my $html=&HTML::fid_link($cgi, $fid, Local, Just_URL, Full_Path);
816    
817    Local is a boolean means to eliminate the fig|org.peg from the text of the link.
818    
819    Just_URL will only return the URL and not the HTML code. The default is to return the full code.
820    
821    Full_Path is a boolean that will get the full path to the URL not just a relative path. This is required in pages where the base href changes (e.g. if an image is imported like on the metabolic pages).
822    
823    =cut
824    
825    
826  sub fid_link {  sub fid_link {
827      my($cgi,$fid,$local,$just_url) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
828        my($cgi,$fid,$local,$just_url,$fullpath) = @_;
829    
830        my $err=join(" ", $cgi,$fid,$local,$just_url,$fullpath);
831    
832      my($n);      my($n);
833    
834        my $top = top_link();
835        if ($fullpath) {$top=$FIG_Config::cgi_url}
836    
837      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)
838      {      {
839          if ($local)          if ($local)
# Line 343  Line 851 
851          {          {
852              $n = $fid;              $n = $fid;
853          }          }
854          if ($1 ne "peg") { return $n }  
855            my $link;
856            my $new_framework = $cgi->param('new_framework') ? 1 : 0;
857            #added to format prophage and path island links to feature.cgi
858            my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
859            if ($1 ne "peg" && ! $sprout)
860            {
861               my $user = $cgi->param('user');
862               if (! $user) { $user = "" }
863               $link = "$top/feature.cgi?feature=$fid&user=$user$sprout";
864               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
865            }
866            else
867            {
868          my $user = $cgi->param('user');          my $user = $cgi->param('user');
869          if (! $user) { $user = "" }          if (! $user) { $user = "" }
870          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
871          my $link = $cgi->url() . "?prot=$fid&user=$user$trans";              my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
872          $link =~ s/[a-z_A-Z]+\.cgi\?/protein.cgi?/;  ###a
873    
874    ### This used to be
875    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
876    ###
877    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
878    ###
879    ### RAO
880    
881                #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
882                #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
883                $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout\&new_framework=$new_framework";
884                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
885            }
886          if ($just_url)          if ($just_url)
887          {          {
888              return $link;              return $link;
889          }          }
890          else          else
891          {          {
892              return "<a href=$link>$n</a>";              return "<a href='$link'>$n</a>";
893          }          }
894      }      }
895      return $fid;      return $fid;
896  }  }
897    
898  sub family_link {  sub family_link {
899        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
900      my($family,$user) = @_;      my($family,$user) = @_;
901    
902      return $family;      return $family;
903  }  }
904    
 use URI::Escape;  
905    
906  sub get_html {  sub get_html {
907        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
908      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
909      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
910    
911      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
912      $ua->timeout( 900 );      $ua->timeout( 900 );
   
913      if ($type =~/post/i)      if ($type =~/post/i)
914      {      {
915          $args = [];          $args = [];
# Line 387  Line 921 
921          my $response = $ua->request($request);          my $response = $ua->request($request);
922          $out = $response->content;          $out = $response->content;
923      }      }
924      else  
925        if ($type =~/get/i)
926      {      {
927          @args = ();          @args = ();
928          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 399  Line 934 
934          {          {
935              $url .= "?" . join("&",@args);              $url .= "?" . join("&",@args);
936          }          }
937          $request = new HTTP::Request('GET', $url);          my $request = new HTTP::Request('GET', $url);
938          my $response = $ua->request($request);          my $response = $ua->request($request);
939    
940          if ($response->is_success)          if ($response->is_success)
# Line 417  Line 952 
952    
953  #   Now splice in a line of the form <base href=URL> to cause all relative links to work  #   Now splice in a line of the form <base href=URL> to cause all relative links to work
954  #   properly.  Remove the header.  #   properly.  Remove the header.
955        my $i;
956      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}
957      if ($i < @output)      if ($i < @output) {
     {  
   
958          splice(@output,0,$i);          splice(@output,0,$i);
959      }      }
960    
# Line 435  Line 968 
968  }  }
969    
970  sub trim_output {  sub trim_output {
971        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
972      my($out) = @_;      my($out) = @_;
973      my $i;      my ($i, $j);
974    
975      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}
976      splice(@$out,0,$i);      splice(@$out,0,$i);
# Line 465  Line 999 
999      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}
1000      if ($j > 0)      if ($j > 0)
1001      {      {
1002            #
1003            # Hm. We would have tried using the options here:
1004            # my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
1005            # but they're not passed in. So use the default html.tail.
1006            #
1007            my $html_tail_file = "./Html/html.tail";
1008          my @tmp = `cat $html_tail_file`;          my @tmp = `cat $html_tail_file`;
1009          my $n = @tmp;          my $n = @tmp;
1010          splice(@$out,$j-$n,$n+1);          splice(@$out,$j-$n,$n+1);
# Line 472  Line 1012 
1012  }  }
1013    
1014  sub set_prot_links {  sub set_prot_links {
1015        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1016      my($cgi,$x) = @_;      my($cgi,$x) = @_;
1017      my($before,$match,$after);      my($before,$match,$after);
1018    
1019      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
1020      {      {
1021          $before = $1;          $before = $1;
1022          $match = $2;          $match = $2;
1023          $after = $3;          $after = $3;
1024          return &set_prot_links($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,$after);
1025      }      }
1026      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)      elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
1027      {      {
1028          $before = $1;          $before = $1;
1029          $match = $2;          $match = $2;
1030          $after = $3;          $after = $3;
1031          return &set_prot_links($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,$after);
1032      }      }
1033      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
1034      {      {
1035          $before = $1;          $before = $1;
1036          $match = $2;          $match = $2;
1037          $after = $3;          $after = $3;
1038          return &set_prot_links($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,$after);
1039      }      }
1040      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1041      {      {
1042          $before = $1;          $before = $1;
1043          $match = $2;          $match = $2;
1044          $after = $3;          $after = $3;
1045          return &set_prot_links($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);
1046      }      }
1047      return $x;      elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1048        {
1049            $before = $1;
1050            $match = $2;
1051            $after = $3;
1052            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1053  }  }
1054    
1055  sub gi_link {      elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
     my($cgi,$gi) = @_;  
   
     if ($gi =~ /^gi\|(\d+)$/)  
1056      {      {
1057          return "<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept>$gi</a>";          $before = $1;
1058      }          $match = $2;
1059      return $gi;          $after = $3;
1060            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1061  }  }
1062    
1063  sub sp_link {      elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
     my($cgi,$sp) = @_;  
   
     if ($sp =~ /^sp\|(\S+)$/)  
1064      {      {
1065          return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";          $before = $1;
1066      }          $match = $2;
1067            $after = $3;
1068            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1069        }
1070    
1071        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1072        {
1073            $before = $1;
1074            $match = $2;
1075            $after = $3;
1076            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1077        }
1078    
1079        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1080        {
1081            $before = $1;
1082            $match = $2;
1083            $after = $3;
1084            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1085        }
1086    
1087        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1088        {
1089            $before = $1;
1090            $match = $2;
1091            $after = $3;
1092            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1093        }
1094        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1095        {
1096            $before = $1;
1097            $match = $2;
1098            $after = $3;
1099            return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
1100        }
1101        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
1102        {
1103            $before = $1;
1104            $match = $2;
1105            $after = $3;
1106            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
1107        }
1108        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
1109        {
1110            $before = $1;
1111            $match = $2;
1112            $after = $3;
1113            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
1114        }
1115        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
1116        {
1117            $before = $1;
1118            $match = $2;
1119            $after = $3;
1120            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1121        }
1122        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1123        {
1124            $before = $1;
1125            $match = $2;
1126            $after = $3;
1127            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1128        }
1129        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1130        {
1131            $before = $1;
1132            $match = $2;
1133            $after = $3;
1134            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1135        }
1136        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1137        {
1138            $before = $1;
1139            $match = $2;
1140            $after = $3;
1141            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1142        }
1143        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1144        {
1145            $before = $1;
1146            $match = $2;
1147            $after = $3;
1148            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1149        }
1150        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1151        {
1152            $before = $1;
1153            $match = $2;
1154            $after = $3;
1155            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1156        }
1157    # IPI stopped working. turn off for now.
1158    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1159    #    {
1160    #        $before = $1;
1161    #        $match = $2;
1162    #        $after = $3;
1163    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1164    #    }
1165        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1166        {
1167            #wormbase
1168    
1169            $before = $1;
1170            $match = $2;
1171            $after = $3;
1172            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1173        }
1174        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1175        {
1176            #flybase
1177    
1178            $before = $1;
1179            $match = $2;
1180            $after = $3;
1181            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1182        }
1183        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1184        {
1185            #flybase
1186    
1187            $before = $1;
1188            $match = $2;
1189            $after = $3;
1190            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1191        }
1192        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1193        {
1194            #flybase
1195    
1196            $before = $1;
1197            $match = $2;
1198            $after = $3;
1199            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1200        }
1201        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1202        {
1203    
1204          $before = $1;
1205          $match = $2;
1206          $after = $3;
1207    
1208          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1209        }
1210        return $x;
1211    }
1212    
1213    sub trembl_link {
1214        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1215        my($cgi,$id) = @_;
1216    
1217        if ($id =~ /^tr\|(.*)/) {
1218          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1219        } else {
1220          return "invalid call to trembl link";
1221        }
1222    }
1223    
1224    sub refseq_link {
1225        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1226        my($cgi,$id) = @_;
1227    
1228        if ($id =~ /^[NXYZA]P_/)
1229        {
1230            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id' target=_blank>$id</a>";
1231        }
1232        elsif ($id =~ /^[NXYZA]M_/)
1233        {
1234            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1235        }
1236    }
1237    
1238    sub gi_link {
1239        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1240        my($cgi,$gi) = @_;
1241    
1242        if ($gi =~ /^gi\|(\d+)$/)
1243        {
1244            return "<a href='http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept' target=_blank>$gi</a>";
1245        }
1246        return $gi;
1247    }
1248    
1249    sub tigr_link {
1250        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1251        my($cgi,$tigr) = @_;
1252    
1253        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1254        {
1255            my $id=$1.$2;
1256            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1257        }
1258        elsif ($tigr =~ /^tigr\|(\S+)$/)
1259        {
1260            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\" target=_blank>$tigr</a>";
1261        }
1262        return $tigr;
1263    }
1264    
1265    sub eric_link {
1266        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1267        my($cgi,$eric) = @_;
1268    
1269        if ($eric =~ /^eric\|(\S+)/)
1270        {
1271            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1272        }
1273        return $eric;
1274    }
1275    
1276    sub bhb_link {
1277        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1278        my($cgi,$bhb) = @_;
1279    
1280        return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1281    }
1282    
1283    sub apidb_link {
1284        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1285        my($cgi,$api) = @_;
1286    
1287        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1288        {
1289            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1290        }
1291        return $api;
1292    }
1293    
1294    sub patric_link {
1295        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1296        my($cgi,$patric) = @_;
1297    
1298        if ($patric =~ /patric\|(.*)/)
1299        {
1300            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1301        }
1302        return $patric;
1303    }
1304    
1305    sub vbrc_link {
1306        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1307        my($cgi,$vbrc) = @_;
1308    
1309        if ($vbrc =~ /vbrc\|(.*)/)
1310        {
1311            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1312        }
1313        return $vbrc;
1314    }
1315    
1316    sub vectorbase_link {
1317        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1318        my($cgi,$vec) = @_;
1319        return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1320    }
1321    
1322    
1323    sub uni_link {
1324        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1325        my($cgi,$uni) = @_;
1326    
1327        if ($uni =~ /^uni\|(\S+)$/)
1328        {
1329            #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1330            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1331        }
1332        return $uni;
1333    }
1334    
1335    sub sp_link {
1336        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1337        my($cgi,$sp) = @_;
1338    
1339        if ($sp =~ /^sp\|(\S+)$/)
1340        {
1341            return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$sp</a>";
1342        }
1343      return $sp;      return $sp;
1344  }  }
1345    
1346  sub pir_link {  sub pir_link {
1347        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1348      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
1349    
1350      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1351      {      {
1352          return "<a href=http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1>$pir</a>";          return "<a href='http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1' target=_blank>$pir</a>";
1353      }      }
1354      return $pir;      return $pir;
1355  }  }
1356    
1357    sub kegg_link {
1358        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1359        my($cgi,$kegg) = @_;
1360    
1361        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1362        {
1363            return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1364        }
1365        return $kegg;
1366    }
1367    
1368    sub ensembl_link {
1369        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1370        my($cgi,$ensembl) = @_;
1371    
1372        if ($ensembl =~ /^(\S+):(\S+)$/)
1373        {
1374            my $what=$1;
1375            my $key=$2;
1376            my $idx="All";
1377            if ($what eq "EnsemblGene") { $idx = "Gene" }
1378            if ($what eq "EnsemblTranscript") { $idx = "All" }
1379            if ($what eq "EnsemblProtein") { $idx = "All" }
1380    
1381            #I really want to get right to the transcript and peptide pages, but
1382            #can't see how to do that without knowing the org name too, which
1383            #I don't know at this point. (ensembl org name, not real org name)
1384    
1385            return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1386        }
1387        return $ensembl;
1388    }
1389    
1390    sub entrezgene_link {
1391        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1392        my($cgi,$entrezgene) = @_;
1393    
1394        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1395        {
1396            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1' target=_blank>$entrezgene</a>";
1397        }
1398        return $entrezgene;
1399    }
1400    
1401    sub mim_link {
1402        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1403        my($cgi,$mim) = @_;
1404    
1405        if ($mim =~ /^MIM:(\S+)$/)
1406        {
1407            return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1408        }
1409        return $mim;
1410    }
1411    
1412    sub hgnc_link {
1413        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1414        my($cgi,$hgnc) = @_;
1415    
1416        if ($hgnc =~ /^HGNC:(\S+)$/)
1417        {
1418            return "<a href='http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=equals&match=$1&symbol_search=Search&number=50&format=html&sortby=symbol' target=_blank>$hgnc</a>";
1419        }
1420    
1421        return $hgnc;
1422    }
1423    
1424    sub unigene_link {
1425        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1426        my($cgi,$unigene) = @_;
1427    
1428        if ($unigene =~ /^UniGene:(\S+)$/)
1429        {
1430            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1431        }
1432        return $unigene;
1433    }
1434    
1435    sub ipi_link {
1436        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1437        my($cgi,$ipi) = @_;
1438    
1439        if ($ipi =~ /^IPI:(\S+)$/)
1440        {
1441            return "<a href='http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1' target=_blank>$ipi</a>";
1442        }
1443        return $ipi;
1444    }
1445    
1446    sub wp_link {
1447        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1448        my($cgi,$wp) = @_;
1449    
1450        #wormbase
1451    
1452        if ($wp =~ /^WP:(\S+)$/)
1453        {
1454            return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1455        }
1456        return $wp;
1457    }
1458    
1459    sub fb_link {
1460        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1461        my($cgi,$fb) = @_;
1462    
1463        #flybase
1464    
1465        if ($fb =~ /^FB:(\S+)$/)
1466        {
1467            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1468        }
1469        return $fb;
1470    }
1471    
1472    sub fborf_link {
1473        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1474        my($cgi,$fb) = @_;
1475    
1476        #flybase
1477    
1478        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1479        {
1480            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1481        }
1482        return $fb;
1483    }
1484    
1485    sub sgd_link {
1486        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1487        my($cgi,$sgd) = @_;
1488    
1489        #yeast
1490    
1491        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1492        {
1493            return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1494        }
1495        return $sgd;
1496    }
1497    
1498    
1499    
1500    
1501    sub set_map_links {
1502        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1503        my($cgi,$x) = @_;
1504        my($before,$match,$after);
1505    
1506        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
1507    
1508        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
1509        {
1510            $before = $1;
1511            $match = $2;
1512            $after = $3;
1513            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
1514        }
1515        return $x;
1516    }
1517    
1518    
1519    
1520    sub map_link {
1521        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1522        my($cgi,$map,$org) = @_;
1523    
1524        my $user = $cgi->param('user');
1525        $user = $user ? $user : "";
1526        $org = $org ? $org : "";
1527    
1528        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1529    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1530        my $link = "<a href=\"$url\">$map</a>";
1531        return $link;
1532    }
1533    
1534    sub java_buttons {
1535        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1536      ## ADDED BY RAE
1537      # Provides code to include check all/first half/second half/none for javascrspt
1538      # this takes two variables - the form name provided in start_form with the
1539      # -name => field and the checkbox name
1540      my ($form, $button)=@_;
1541    
1542      my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1543      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1544      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1545      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1546    
1547      return $java_script;
1548    }
1549    
1550    sub sub_link {
1551        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1552        my($cgi,$sub) = @_;
1553        my($sub_link);
1554    
1555        my $user = $cgi->param('user');
1556        my $esc_sub = uri_escape( $sub );
1557        $sub =~ s/\_/ /g;
1558        if ($user)
1559        {
1560            $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";
1561        }
1562        else
1563        {
1564            $sub_link = "<a href=\"display_subsys.cgi?ssa_name=$esc_sub&request=show_ssa&sort=by_phylo\">$sub</a>";
1565        }
1566        return $sub_link;
1567    }
1568    
1569    sub reaction_link {
1570        my($reaction) = @_;
1571        if ($reaction =~ /^(\*)?(R\d+)/)
1572        {
1573            return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1574        }
1575        return $reaction;
1576    }
1577    
1578    
1579    sub html_for_assignments {
1580        my($fig,$user,$peg_sets) = @_;
1581        my $i;
1582    
1583        my @vals = ();
1584        my $set = 1;
1585        foreach my $peg_set (@$peg_sets)
1586        {
1587            for ($i=0; ($i < @$peg_set); $i++)
1588            {
1589                my $peg = $peg_set->[$i];
1590                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1591            }
1592            $set++;
1593        }
1594    
1595        $ENV{'REQUEST_METHOD'} = 'GET';
1596        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1597        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1598        $out =~ s/^.*?<form/<form/si;
1599        $out =~ s/^(.*)<table.*/$1/si;
1600        return $out;
1601    }
1602    
1603    =head1 rss_feed
1604    
1605    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1606            SEED.rss                - everything gets written here
1607            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1608            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1609    
1610    
1611    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.
1612    
1613    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.
1614    
1615    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.
1616    
1617    The has can have these keys:
1618    
1619    REQUIRED:
1620    title       : the title. This is usually what is seen by the user in the pull down menu
1621    description : a more complete description that is often seen is rss viewers but not always
1622    link        : link to the item that was added/edited
1623    All other keys are treated as optional RSS arguments and written to the file.
1624    
1625    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1626    
1627    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1628    
1629    
1630    =cut
1631    
1632    sub rss_feed {
1633     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1634     my ($files, $args)=@_;
1635    
1636     # how many entries to store in the file
1637     my $max_entries=50;
1638    
1639     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1640    
1641     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1642     # check for the directory and if not, make it
1643     mkdir $filepath unless (-d $filepath);
1644    
1645     # note that $info is a hash of references to hashes that are written out as headers in the file
1646     my $info=
1647     {
1648      "SEED.rss" =>
1649       {
1650            title           => "The SEED",
1651            description     => "Latest news from the SEED",
1652            link            => "Html/rss/SEED.rss",
1653       },
1654    
1655      "SEEDsubsystems.rss" =>
1656      {
1657            title           => "SEED Subsystems",
1658            description     => "Recently updated SEED subsystems",
1659            link            => "Html/rss/SEEDsubsystems.rss",
1660      },
1661    
1662      "SEEDsubsystems.rss" =>
1663      {
1664            title           => "SEED Genomes",
1665            description     => "Genomes recently added to the SEED",
1666            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1667      },
1668    
1669     };
1670    
1671    
1672     # build the new xml
1673     my $xml = "\t<item>\n";
1674     foreach my $qw ("title", "description", "link") {
1675      unless ($args->{$qw}) {
1676       print STDERR "You need to include a $qw tag in your RSS description\n";
1677       return(0);
1678      }
1679      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1680      # so we are going to pull out the links and uri_escape just the part after the .cgi
1681      if ($qw eq "link")
1682      {
1683       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1684       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1685      }
1686    
1687      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1688      delete $args->{$qw};
1689     }
1690    
1691     foreach my $tag (grep {!/type/i} keys %$args)
1692     {
1693      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1694     }
1695    
1696     $xml .= "\t</item>\n";
1697    
1698    
1699     my @files=("SEED.rss");
1700     if ($args->{"type"}) {
1701        my $type = $args->{type};
1702        push @files, "SEED.$type.rss"
1703    }
1704    
1705     foreach my $file ("SEED.rss", @$files)
1706     {
1707      if (-e "$filepath/$file")
1708      {
1709       my @out; # the new content of the file
1710       my $itemcount=0; # how many <item> </item>'s are we keeping
1711       my $initem; # are we in an item?
1712       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1713       while (<IN>)
1714       {
1715        if (/\<item\>/) {
1716         push @out, $xml, unless ($itemcount);
1717         $itemcount++;
1718         $initem=1;
1719        }
1720        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1721        next if ($initem && $itemcount > $max_entries);
1722        push @out, $_;
1723       }
1724       close IN;
1725       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1726       print OUT @out;
1727      }
1728      else
1729      {
1730       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1731       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1732       if ($info->{$file})
1733       {
1734         # we're going to sanity check each of the three options we output, just to be sure
1735         foreach my $qw ("title", "description", "link")
1736         {
1737           if ($info->{$file}->{$qw})
1738           {
1739              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1740           } else {
1741              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1742           }
1743         }
1744       }
1745       else {
1746        print STDERR "Please define title, link, and description information for $file\n";
1747        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1748       }
1749       print OUT "\n", $xml;
1750       print OUT "\n", "</channel>\n</rss>\n"
1751      }
1752     }
1753    }
1754    
1755    
1756    
1757    1;
1758    
 1  

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