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revision 1.6, Sun Mar 21 02:20:55 2004 UTC revision 1.94, Tue Jun 6 03:14:43 2006 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    use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
32    my $raelib=new raelib;
33    
34    
35    my $top_link_cache;
36    
37    
38    sub new
39    {
40        my($class) = @_;
41    
42        my $self = {};
43    
44        return bless $self, $class;
45    }
46    
47    sub top_link
48    {
49    
50        #
51        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
52        # just /p2p).
53        #
54    
55        return $top_link_cache if ($top_link_cache);
56    
57        my @parts = split(/\//, $ENV{SCRIPT_NAME});
58        my $top;
59        if ($parts[-2] eq 'FIG')
60        {
61            $top = '.';
62    #       warn "toplevel @parts\n";
63        }
64        elsif ($parts[-3] eq 'FIG')
65        {
66            $top = '..';
67    #       warn "subdir @parts\n";
68        }
69        else
70        {
71            $top = $FIG_Config::cgi_base;
72    #       warn "other @parts\n";
73        }
74    
75        $top_link_cache = $top;
76        return $top;
77    }
78    
79    sub compute_html_header
80    {
81        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
82        my($additional_insert, $user, %options ) = @_;
83    
84        local $/ = "\n";
85    
86        my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
87        my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
88    
89        my $html_hdr_file = "./Html/$header_name";
90        if (! -f $html_hdr_file)
91        {
92            $html_hdr_file = "$FIG_Config::fig/CGI/Html/$header_name";
93        }
94        my @html_hdr = &FIG::file_read($html_hdr_file);
95    
96        # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
97    
98        #
99        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
100        # just /p2p).
101        #
102    
103        my @parts = split(/\//, $ENV{SCRIPT_NAME});
104        my $top;
105        if ($parts[-2] eq 'FIG')
106        {
107            $top = '.';
108    #       warn "toplevel @parts\n";
109        }
110        elsif ($parts[-3] eq 'FIG')
111        {
112            $top = '..';
113    #       warn "subdir @parts\n";
114        }
115        else
116        {
117            $top = $FIG_Config::cgi_base;
118    #       warn "other @parts\n";
119        }
120    
121        $options{no_fig_search} or push( @html_hdr, "<br><a href=\"$top/index.cgi?user=$user\">FIG search</a>\n" );
122    
123        if (@html_hdr)
124        {
125            my $insert_stuff;
126    
127            if (not $options{no_release_info})
128            {
129                my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
130                my $ver = $ver[0];
131                chomp $ver;
132                if ($ver =~ /^cvs\.(\d+)$/)
133                {
134                    my $d = asctime(localtime($1));
135                    chomp($d);
136                    $ver .=  " ($d)";
137                }
138                my $host = &FIG::get_local_hostname();
139                $insert_stuff = "SEED version <b>$ver</b> on $host";
140            }
141    
142            if ($additional_insert)
143            {
144                $insert_stuff .= "<br>" . $additional_insert;
145            }
146    
147            for $_ (@html_hdr)
148            {
149                s,(href|img\s+src)="/FIG/,$1="$top/,g;
150                    s,(\?user\=)\",$1$user",;
151                if ($_ eq "<!-- HEADER_INSERT -->\n")
152                {
153                    $_ = $insert_stuff;
154                }
155            }
156        }
157    
158        return @html_hdr;
159    }
160    
161  sub show_page {  sub show_page {
162      my($cgi,$html,$no_home) = @_;      #warn "SHOWPAGE: cgi=", Dumper(@_);
163        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
164        my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
165      my $i;      my $i;
166    
167        my $top = top_link();
168    
169        # ARGUMENTS:
170        #     $cgi is the CGI method
171        #     $html is an array with all the html in it. It is just joined by "\n" (and not <br> or <p>
172        #     $no_home eliminates ONLY the bottom FIG search link in a page
173        #     $alt_header is a reference to an array for an alternate header banner that you can replace the standard one with
174        #     $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
175        #               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
176        #               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
177        #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")
178        #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
179        #     $options is a reference to a hash of options that you can pass around the pages
180      #      #
181      # Find the HTML header      # Find the HTML header
182      #      #
183    
184      my $html_hdr_file = "./Html/html.hdr";      my $html_tail_file = "./Html/$tail_name";
185      if (! -f $html_hdr_file)      if (! -f $html_tail_file)
186      {      {
187          $html_hdr_file = "$FIG_Config::fig/CGI/Html/html.hdr";          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
188      }      }
189    
190      my $html_tail_file = "./Html/html.tail";      my $user = $cgi->param('user') || "";
191      if (! -f $html_tail_file)      my @html_hdr;
192        if ($alt_header && ref($alt_header) eq "ARRAY")
193        {
194           @html_hdr = @$alt_header;
195        }
196        else
197      {      {
198          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          @html_hdr = compute_html_header(undef,$user,%$options);
199      }      }
200    
201        # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.
202        # This modification adds the cookies if necessary
203    
204        # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about
205        # to add cookies back in replace these two header lines with each other
206    
207      print $cgi->header;      #print $cgi->header(-cookie=>$cookie);
208        print $cgi->header();
209    
210      #      #
211      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
# Line 46  Line 223 
223                       meta     => 1,                       meta     => 1,
224                       nextid   => 1,                       nextid   => 1,
225                       style    => 1,                       style    => 1,
226                       title    => 1                       title    => 1,
227                     );                     );
228    
229      #      #
# Line 89  Line 266 
266          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )
267          {          {
268              $body_line = $i;              $body_line = $i;
269              $last;              last;
270          }          }
271    
272          #  Now the general case.          #  Now the general case.
# Line 145  Line 322 
322      #      #
323      #  <BODY> goes after last head line      #  <BODY> goes after last head line
324      #      #
325        #  RAE:
326        #  Added the javascript for the buttons immediately after body.
327        #  Note if no buttons are added we still (at the moment) add the script,
328        #  but it only adds a little text (495 characters) to the html and noone will notice!
329        #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
330    
331      if ( $body_line < 0 )      if ( $body_line < 0 )
332      {      {
# Line 156  Line 338 
338      #  Seed page header (if it exists) goes after <BODY>      #  Seed page header (if it exists) goes after <BODY>
339      #      #
340    
341      if ( -f $html_hdr_file )      if (@html_hdr)
342      {      {
343          splice( @$html, $body_line + 1, 0, `cat $html_hdr_file` );          splice( @$html, $body_line + 1, 0, @html_hdr );
344      }      }
345    
346      #      #
# Line 171  Line 353 
353          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
354      }      }
355    
356        # RAE:
357        # Add css here
358        # Note that at the moment I define these two sheets here. I think this should
359        # be moved out, but I want to try it and see what happens.  css has the format:
360        #
361        # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
362    
363        # convert the default key to the right case. and eliminate dups
364        foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
365    
366        if (!$css || !$css->{'Default'})
367        {
368           $css->{'Default'} = "Html/css/default.css";
369        }
370        if (!$css->{"Sans Serif"})
371        {
372           $css->{'Sans Serif'} = "Html/css/sanserif.css";
373        }
374    
375        my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";
376        $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";
377    
378        foreach my $k (keys %$css)
379        {
380           next if (lc($k) eq "default" || lc($k) eq "sans serif");
381           $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
382        }
383    
384        $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='Html/rss/SEED.rss' type='application/rss+xml'>\n";
385    
386        # RAE: also added support for external javascripts here.
387        # we are cluttering the HTML code with all the javascripts when they could easily be in external files
388        # this solution allows us to source other files
389    
390        # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
391        # it will reduce our overhead.
392    
393        # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
394        push @$javasrc, "Html/css/FIG.js";
395        foreach my $script (@$javasrc) {
396            $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
397        }
398    
399    
400    
401        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.
402    
403      #      #
404      #  <BASE ...> goes before </HEAD>      #  <BASE ...> goes before </HEAD>
405      #      #
# Line 183  Line 412 
412          #  only, or every update?), I provide an alternative derivation          #  only, or every update?), I provide an alternative derivation
413          #  from $cgi_url. -- GJO          #  from $cgi_url. -- GJO
414          #          #
415            # BASE href needs to be absolute. RDO.
416          my $base_url = $FIG_Config::cgi_base;          #
417          if ( ! $base_url )                      # if cgi_base was not defined          #
418          {          $base_url = &FIG::cgi_url;
419              $base_url = $FIG_Config::cgi_url;   # get the full cgi url  #       my $base_url = $FIG_Config::cgi_base;
420              $base_url =~ s~^http://[^/]*~~;     # remove protocol and host  #       if ( ! $base_url )                      # if cgi_base was not defined
421              $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash  #       {
422          }  #           $base_url = $FIG_Config::cgi_url;   # get the full cgi url
423    #           $base_url =~ s~^http://[^/]*~~;     # remove protocol and host
424    #           $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash
425    #       }
426    
427          $base_line = $head_end_line;          $base_line = $head_end_line;
428          splice( @$html, $base_line, 0, "<BASE href=\"$base_url\">\n" );          #
429            # RDO 2005-1006. Remove this so proxying works better.
430            #
431    #        splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );
432      }      }
433    
434      #      #
# Line 228  Line 463 
463      }      }
464    
465      #      #
466        # See if we have a site-specific tail (for disclaimers, etc).
467        #
468    
469        my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
470        my $site_fh;
471        if (open($site_fh, "<$site_tail"))
472        {
473            push(@tail, <$site_fh>);
474            close($site_fh);
475        }
476    
477        #
478      #  Figure out where to insert The SEED tail.  Before </body>,      #  Figure out where to insert The SEED tail.  Before </body>,
479      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
480      #      #
   
481      my @tags = ();      my @tags = ();
482        # Check for a tracing queue.
483        my $traceString = QTrace("HTML");
484        if ($traceString) {
485            push @tags, $traceString;
486        }
487      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
488      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
489      {      {
# Line 255  Line 505 
505          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
506      }      }
507    
508      print @$html;      # RAE the chomp will return any new lines at the ends of elements in the array,
509        # and then we can join  with a "\n". This is because somethings put newlines in,
510        # and others don't. This should make nicer looking html
511        #
512        # chomp(@$html);
513        # print join "\n", @$html;
514        #
515        # Apparently the above still breaks things. This is the correct code:
516    
517        foreach $_ (@$html)
518        {
519            print $_;
520        }
521    
522  }  }
523    
524    
525    =head1 make_table
526    
527    The main method to convert an array into a table.
528    
529    The col_hdrs are set to the <th> headers, the $tab is an array of arrays. The first is the rows, and the second is the columns. The title is the title of the table.
530    
531    The options define the settings for the table such as border, width, and class for css formatting. If the option "excelfile" is set to a filename that will be created in FIG_Config::temp, and the link included that allows the user to download the file as an excel file.
532    
533    =cut
534    
535  sub make_table {  sub make_table {
536      my($col_hdrs,$tab,$title,$instr) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
537      my(@tab);      my(@tab);
538    
539      push( @tab, "\n<table border>\n",      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
540        my $width = defined $options{width} ? "width=\"$options{width}\"" : undef;
541        my $class = defined $options{class} ? "class=\"$options{class}\"" : undef;
542        push( @tab, "\n<table $border $width $class>\n",
543                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
544                  "\t<tr>\n\t\t<th>"                  "\t<tr>\n\t\t"
545                . join( "</th>\n\t\t<th>", @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
546                . "</th>\n\t</tr>\n"                . "\n\t</tr>\n"
547          );          );
548      my($i,$nowrap);      my($i);
   
     for ($i=0; ($i < @$instr) && ($instr->[$i] !~ /nowrap/); $i++) {}  
     $nowrap = ($i == @$instr) ? "" : " nowrap";  
549    
550      my $row;      my $row;
551      foreach $row (@$tab)      foreach $row (@$tab)
552      {      {
553          push( @tab, "\t<tr>\n"          push( @tab, "\t<tr>\n"
554                    . join( "\n", map { &expand($_,$nowrap) } @$row )                    . join( "\n", map { &expand($_) } @$row )
555                    . "\n\t</tr>\n"                    . "\n\t</tr>\n"
556              );              );
557      }      }
558      push(@tab,"</table>\n");      push(@tab,"</table>\n");
559    
560        # excelfile should be appropriate for a filename (no spaces/special characters)
561        if (defined $options{"excelfile"}) {push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
562    
563      return join("",@tab);      return join("",@tab);
564  }  }
565    
566    sub abstract_coupling_table {
567        my($cgi,$prot,$coupling) = @_;
568        my %fc;
569    
570        my $col_hdrs = ["coupled to","Score","Type of Coupling", "Type-specific Data"];
571        my $tab = [];
572        my %by_peg;
573        foreach my $x (@$coupling)
574        {
575            my($peg2,$psc,$type,$extra) = @$x;
576            if (($type !~ /^[ID]FC$/) || (! $fc{$peg2}))
577            {
578                if ($type =~  /^[ID]FC$/)
579                {
580                    $fc{$peg2} = 1;
581                }
582    
583                $by_peg{$peg2} += $psc;
584            }
585        }
586    
587        foreach my $x (sort { ($by_peg{$b->[0]} <=> $by_peg{$a->[0]})
588                              or ($a->[0] cmp $b->[0])
589                              or ($b->[1] <=> $a->[1])
590                              or ($a->[2] cmp $b->[2]) } @$coupling)
591        {
592            my($peg2,$psc,$type,$extra) = @$x;
593            push(@$tab,[&fid_link($cgi,$peg2,1),$psc,$type,&set_prot_links($cgi,join(", ",@$extra))]);
594        }
595    
596    
597         my $help = "<a href=\"Html/abstract_coupling.html\" target=\"SEED_or_SPROUT_help\">for help</a>";
598    #    my @html = &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot");
599    #    push(@html,"<hr>\n",$cgi->h3($help),"<br>");
600    #    return @html;
601    
602        return &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot [$help]");
603    }
604    
605  sub expand {  sub expand {
606      my($x,$nowrap) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
607        my( $x, $tag ) = @_;
608    
609        $tag = "td" unless $tag;
610        my $endtag = $tag;
611    
612      if ($x =~ /^\@([^:]+)\:([^:]+)\:(.*)$/)      # RAE modified this so that you can pass in a reference to an array where
613        # the first element is the data to display and the second element is optional
614        # things like colspan and align. Note that in this case you need to include the td
615        # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
616    
617        # per GJO's request modified this line so it can take any tag.
618        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
619    
620        if ( $x =~ /^\@([^:]+)\:(.*)$/ )
621      {      {
622          return "\t\t<td$nowrap $1=\"$2\">$3</td>";          return "\t\t<$tag $1>$2</$endtag>";
623      }      }
624      else      else
625      {      {
626          return "\t\t<td$nowrap>$x</td>";          return "\t\t<$tag>$x</$endtag>";
627        }
628    }
629    
630    
631    =head2 merge_table_rows()
632    
633    Merge table rows together. This will merge a table so that adjacent cells with the same content will only be shown once.
634    
635    Something like this:
636    
637        -----------------------
638        |    1     |    a     |
639        -----------------------
640        |    1     |    b     |
641        -----------------------
642        |    2     |    c     |
643        -----------------------
644        |    3     |    d     |
645        -----------------------
646        |    4     |    d     |
647        -----------------------
648        |    5     |    d     |
649        -----------------------
650    
651    Will become:
652    
653        -----------------------
654        |          |    a     |
655        |    1     |-----------
656        |          |    b     |
657        -----------------------
658        |    2     |    c     |
659        -----------------------
660        |    3     |          |
661        ------------          |
662        |    4     |    5     |
663        ------------          |
664        |    5     |          |
665        -----------------------
666    
667    
668    The method takes two arguments. The reference to the array that is the table ($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.
669    
670     $tab=&HTML::merge_table_rows($tab);
671    
672     or
673    
674     $skip=(1=>1, 3=>1, 5=>1);
675     $tab=&HTML::merge_table_rows($tab, $skip);  # will merge all columns except 1, 3 and 5. Note the first column in the table is #0
676    
677    
678    =cut
679    
680    
681    
682    
683    sub merge_table_rows {
684     # RAE:
685     # Experimental piece of code. We often want to have rows or columns were cells are merged. It just looks so much nicer
686     # this block should merge adjacent rows that have the same text in them.
687     # use like this:
688     #      $tab=&HTML::merge_table_rows($tab);
689     # before you do a make_table call
690    
691     my $self=shift if UNIVERSAL::isa($_[0],__PACKAGE__);
692     my ($tab, $skip)=@_;
693    
694     my $newtable;
695     my $lastrow;
696     my $rowspan;
697     my $refs;
698    
699     for (my $y=0; $y <= $#$tab; $y++) {
700     #$y is the row in the table;
701      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
702       # this is the user definable columns not to merge
703       if ($skip->{$x})
704       {
705        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
706        next;
707       }
708    
709       #$x is the column in the table
710       # if the column in the row we are looking at is the same as the column in the previous row, we don't add
711       # this cell to $newtable. Instead we increment the rowspan of the previous row by one
712    
713       # handle cells that are references to arrays
714       if (ref($tab->[$y]->[$x]) eq "ARRAY") {$refs->[$y]->[$x]=$tab->[$y]->[$x]->[1]; $tab->[$y]->[$x]=$tab->[$y]->[$x]->[0]}
715    
716       # now we go back through the table looking where to draw the merge line:
717       my $lasty=$y;
718       while ($lasty >= 0 && $tab->[$y]->[$x] eq $tab->[$lasty]->[$x]) {$lasty--}
719       $lasty++; # this is the last identical cell. If lasty==y it is the current cell, so we just save the data. Otherwise we increment the rowspan
720       if ($lasty == $y) {
721        # we always want to have something in rows that may otherwise be empty but should be there (see below)
722        unless ($tab->[$y]->[$x]) {$tab->[$y]->[$x]=" &nbsp; "}
723        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
724       }
725       else {$rowspan->[$lasty]->[$x]++}
726      }
727     }
728    
729     # now just join everything back together
730     for (my $y=0; $y <= $#$tab; $y++) {
731      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
732       if ($rowspan->[$y]->[$x]) {
733        if ($refs->[$y]->[$x]) {$refs->[$y]->[$x] .= " rowspan=". ($rowspan->[$y]->[$x]+1)}
734        else {$refs->[$y]->[$x] = "td rowspan=". ($rowspan->[$y]->[$x]+1)}
735        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
736       }
737       elsif ($newtable->[$y]->[$x] && $refs->[$y]->[$x]) {
738        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
739       }
740      }
741     }
742    
743    
744     # finally we have to remove any completely empty cells that have been added by the array mechanism
745     # (e.g. if you define $a->[2] then $a->[0] and $a->[1] are now undef).
746     # that is why in the loop above I replace empty cells with nbsp. They are now not undef!
747     # I am sure that Gary can do this in one line, but I am hacking.
748     my @trimmed;
749     foreach my $a (@$newtable) {
750      my @row;
751      foreach my $b (@$a) {
752       push @row, $b if ($b);
753      }
754      push @trimmed, \@row;
755     }
756    
757     return \@trimmed;
758    }
759    
760    
761    
762    
763    sub set_ec_links {
764        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
765        my($cgi,$x) = @_;
766        my($before,$match,$after);
767    
768        if ($x =~ /^(.*)(EC \d+\.\d+\.\d+\.\d+)(.*)/s)
769        {
770            $before = $1;
771            $match = $2;
772            $after = $3;
773            return &set_ec_links($cgi,$before) . &HTML::ec_link($match) . &set_ec_links($cgi,$after);
774      }      }
775        return $x;
776  }  }
777    
778  sub ec_link {  sub ec_link {
779        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
780      my($role) = @_;      my($role) = @_;
781    
782      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)
# Line 312  Line 790 
790  }  }
791    
792  sub role_link {  sub role_link {
793        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
794      my($cgi,$role) = @_;      my($cgi,$role) = @_;
795    
796      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;
# Line 322  Line 801 
801      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
802  }  }
803    
804    #
805    # Local means to eliminate the fig|org.peg from the
806    # text of the link.
807    #
808  sub fid_link {  sub fid_link {
809        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
810      my($cgi,$fid,$local,$just_url) = @_;      my($cgi,$fid,$local,$just_url) = @_;
811      my($n);      my($n);
812    
813        my $top = top_link();
814    
815      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)
816      {      {
817          if ($local)          if ($local)
# Line 343  Line 829 
829          {          {
830              $n = $fid;              $n = $fid;
831          }          }
832          if ($1 ne "peg") { return $n }  
833            my $link;
834            #added to format prophage and path island links to feature.cgi
835            if ($1 ne "peg")
836            {
837               my $user = $cgi->param('user');
838               if (! $user) { $user = "" }
839               my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
840               $link = "$top/feature.cgi?feature=$fid&user=$user$trans$sprout";
841               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
842            }
843            else
844            {
845          my $user = $cgi->param('user');          my $user = $cgi->param('user');
846          if (! $user) { $user = "" }          if (! $user) { $user = "" }
847          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
848          my $link = $cgi->url() . "?prot=$fid&user=$user$trans";              my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
849          $link =~ s/[a-z_A-Z]+\.cgi\?/protein.cgi?/;  ###a
850    
851    ### This used to be
852    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
853    ###
854    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
855    ###
856    ### RAO
857    
858                #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
859                #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
860                $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout";
861                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
862            }
863          if ($just_url)          if ($just_url)
864          {          {
865              return $link;              return $link;
866          }          }
867          else          else
868          {          {
869              return "<a href=$link>$n</a>";              return "<a href='$link'>$n</a>";
870          }          }
871      }      }
872      return $fid;      return $fid;
873  }  }
874    
875  sub family_link {  sub family_link {
876        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
877      my($family,$user) = @_;      my($family,$user) = @_;
878    
879      return $family;      return $family;
880  }  }
881    
 use URI::Escape;  
882    
883  sub get_html {  sub get_html {
884        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
885      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
886      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
887    
888      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
889      $ua->timeout( 900 );      $ua->timeout( 900 );
   
890      if ($type =~/post/i)      if ($type =~/post/i)
891      {      {
892          $args = [];          $args = [];
# Line 387  Line 898 
898          my $response = $ua->request($request);          my $response = $ua->request($request);
899          $out = $response->content;          $out = $response->content;
900      }      }
901      else  
902        if ($type =~/get/i)
903      {      {
904          @args = ();          @args = ();
905          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 435  Line 947 
947  }  }
948    
949  sub trim_output {  sub trim_output {
950        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
951      my($out) = @_;      my($out) = @_;
952      my $i;      my $i;
953    
# Line 472  Line 985 
985  }  }
986    
987  sub set_prot_links {  sub set_prot_links {
988        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
989      my($cgi,$x) = @_;      my($cgi,$x) = @_;
990      my($before,$match,$after);      my($before,$match,$after);
991    
992      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
993      {      {
994          $before = $1;          $before = $1;
995          $match = $2;          $match = $2;
996          $after = $3;          $after = $3;
997          return &set_prot_links($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,$after);
998      }      }
999      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)      elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
1000      {      {
1001          $before = $1;          $before = $1;
1002          $match = $2;          $match = $2;
1003          $after = $3;          $after = $3;
1004          return &set_prot_links($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,$after);
1005      }      }
1006      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
1007      {      {
1008          $before = $1;          $before = $1;
1009          $match = $2;          $match = $2;
1010          $after = $3;          $after = $3;
1011          return &set_prot_links($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,$after);
1012      }      }
1013      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1014      {      {
1015          $before = $1;          $before = $1;
1016          $match = $2;          $match = $2;
1017          $after = $3;          $after = $3;
1018          return &set_prot_links($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);
1019      }      }
1020      return $x;      elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1021        {
1022            $before = $1;
1023            $match = $2;
1024            $after = $3;
1025            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1026  }  }
1027    
1028  sub gi_link {      elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
     my($cgi,$gi) = @_;  
   
     if ($gi =~ /^gi\|(\d+)$/)  
1029      {      {
1030          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;
1031      }          $match = $2;
1032      return $gi;          $after = $3;
1033            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1034  }  }
1035    
1036  sub sp_link {      elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
     my($cgi,$sp) = @_;  
   
     if ($sp =~ /^sp\|(\S+)$/)  
1037      {      {
1038          return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";          $before = $1;
1039      }          $match = $2;
1040      return $sp;          $after = $3;
1041            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1042  }  }
1043    
1044  sub pir_link {      elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1045      my($cgi,$pir) = @_;      {
1046            $before = $1;
1047            $match = $2;
1048            $after = $3;
1049            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1050        }
1051    
1052      if ($pir =~ /^pirnr\|(NF\d+)$/)      elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1053      {      {
1054          return "<a href=http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1>$pir</a>";          $before = $1;
1055            $match = $2;
1056            $after = $3;
1057            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1058        }
1059    
1060        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1061        {
1062            $before = $1;
1063            $match = $2;
1064            $after = $3;
1065            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1066        }
1067        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1068        {
1069            $before = $1;
1070            $match = $2;
1071            $after = $3;
1072            return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
1073        }
1074        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
1075        {
1076            $before = $1;
1077            $match = $2;
1078            $after = $3;
1079            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
1080        }
1081        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
1082        {
1083            $before = $1;
1084            $match = $2;
1085            $after = $3;
1086            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
1087        }
1088        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
1089        {
1090            $before = $1;
1091            $match = $2;
1092            $after = $3;
1093            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1094        }
1095        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1096        {
1097            $before = $1;
1098            $match = $2;
1099            $after = $3;
1100            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1101        }
1102        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1103        {
1104            $before = $1;
1105            $match = $2;
1106            $after = $3;
1107            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1108        }
1109        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1110        {
1111            $before = $1;
1112            $match = $2;
1113            $after = $3;
1114            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1115        }
1116        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1117        {
1118            $before = $1;
1119            $match = $2;
1120            $after = $3;
1121            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1122        }
1123        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1124        {
1125            $before = $1;
1126            $match = $2;
1127            $after = $3;
1128            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1129        }
1130    # IPI stopped working. turn off for now.
1131    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1132    #    {
1133    #        $before = $1;
1134    #        $match = $2;
1135    #        $after = $3;
1136    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1137    #    }
1138        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1139        {
1140            #wormbase
1141    
1142            $before = $1;
1143            $match = $2;
1144            $after = $3;
1145            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1146        }
1147        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1148        {
1149            #flybase
1150    
1151            $before = $1;
1152            $match = $2;
1153            $after = $3;
1154            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1155        }
1156        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1157        {
1158            #flybase
1159    
1160            $before = $1;
1161            $match = $2;
1162            $after = $3;
1163            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1164        }
1165        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1166        {
1167            #flybase
1168    
1169            $before = $1;
1170            $match = $2;
1171            $after = $3;
1172            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1173        }
1174        return $x;
1175    }
1176    
1177    sub refseq_link {
1178        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1179        my($cgi,$id) = @_;
1180    
1181        if ($id =~ /^[NXYZA]P_/)
1182        {
1183            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";
1184        }
1185        elsif ($id =~ /^[NXYZA]M_/)
1186        {
1187            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id>$id</a>";
1188        }
1189    }
1190    
1191    sub gi_link {
1192        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1193        my($cgi,$gi) = @_;
1194    
1195        if ($gi =~ /^gi\|(\d+)$/)
1196        {
1197            return "<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept>$gi</a>";
1198        }
1199        return $gi;
1200    }
1201    
1202    sub tigr_link {
1203        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1204        my($cgi,$tigr) = @_;
1205    
1206        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1207        {
1208            my $id=$1.$2;
1209            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\">$tigr</a> (Pathema)";
1210        }
1211        elsif ($tigr =~ /^tigr\|(\S+)$/)
1212        {
1213            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\">$tigr</a>";
1214        }
1215        return $tigr;
1216    }
1217    
1218    sub eric_link {
1219        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1220        my($cgi,$eric) = @_;
1221    
1222        if ($eric =~ /^eric\|(\S+)/)
1223        {
1224            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\">$eric</a>";
1225        }
1226        return $eric;
1227    }
1228    
1229    sub bhb_link {
1230        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1231        my($cgi,$bhb) = @_;
1232    
1233        return "<a href=\"http://www.biohealthbase.org\">$bhb</a>";
1234    }
1235    
1236    sub apidb_link {
1237        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1238        my($cgi,$api) = @_;
1239    
1240        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1241        {
1242            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\">$api</a>";
1243        }
1244        return $api;
1245    }
1246    
1247    sub patric_link {
1248        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1249        my($cgi,$patric) = @_;
1250    
1251        if ($patric =~ /patric\|(.*)/)
1252        {
1253            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\">$patric</a>";
1254        }
1255        return $patric;
1256    }
1257    
1258    sub vbrc_link {
1259        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1260        my($cgi,$vbrc) = @_;
1261    
1262        if ($vbrc =~ /vbrc\|(.*)/)
1263        {
1264            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\">$vbrc</a>";
1265        }
1266        return $vbrc;
1267    }
1268    
1269    sub vectorbase_link {
1270        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1271        my($cgi,$vec) = @_;
1272        return "<a href=\"http://www.vectorbase.org\">$vec</a>";
1273    }
1274    
1275    
1276    sub uni_link {
1277        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1278        my($cgi,$uni) = @_;
1279    
1280        if ($uni =~ /^uni\|(\S+)$/)
1281        {
1282            #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1283            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1'>$uni</a>";
1284        }
1285        return $uni;
1286    }
1287    
1288    sub sp_link {
1289        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1290        my($cgi,$sp) = @_;
1291    
1292        if ($sp =~ /^sp\|(\S+)$/)
1293        {
1294            return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";
1295        }
1296        return $sp;
1297    }
1298    
1299    sub pir_link {
1300        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1301        my($cgi,$pir) = @_;
1302    
1303        if ($pir =~ /^pirnr\|(NF\d+)$/)
1304        {
1305            return "<a href=http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1>$pir</a>";
1306      }      }
1307      return $pir;      return $pir;
1308  }  }
1309    
1310    sub kegg_link {
1311        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1312        my($cgi,$kegg) = @_;
1313    
1314        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1315        {
1316            return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";
1317        }
1318        return $kegg;
1319    }
1320    
1321    sub ensembl_link {
1322        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1323        my($cgi,$ensembl) = @_;
1324    
1325        if ($ensembl =~ /^(\S+):(\S+)$/)
1326        {
1327            my $what=$1;
1328            my $key=$2;
1329            my $idx="All";
1330            if ($what eq "EnsemblGene") { $idx = "Gene" }
1331            if ($what eq "EnsemblTranscript") { $idx = "All" }
1332            if ($what eq "EnsemblProtein") { $idx = "All" }
1333    
1334            #I really want to get right to the transcript and peptide pages, but
1335            #can't see how to do that without knowing the org name too, which
1336            #I don't know at this point. (ensembl org name, not real org name)
1337    
1338            return "<a href=http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key>$ensembl</a>";
1339        }
1340        return $ensembl;
1341    }
1342    
1343    sub entrezgene_link {
1344        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1345        my($cgi,$entrezgene) = @_;
1346    
1347        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1348        {
1349            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1>$entrezgene</a>";
1350        }
1351        return $entrezgene;
1352    }
1353    
1354    sub mim_link {
1355        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1356        my($cgi,$mim) = @_;
1357    
1358        if ($mim =~ /^MIM:(\S+)$/)
1359        {
1360            return "<a href=http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1>$mim</a>";
1361        }
1362        return $mim;
1363    }
1364    
1365    sub hgnc_link {
1366        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1367        my($cgi,$hgnc) = @_;
1368    
1369        if ($hgnc =~ /^HGNC:(\S+)$/)
1370        {
1371            return "<a href=http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=equals&match=$1&symbol_search=Search&number=50&format=html&sortby=symbol>$hgnc</a>";
1372        }
1373        return $mim;
1374    }
1375    
1376    sub unigene_link {
1377        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1378        my($cgi,$unigene) = @_;
1379    
1380        if ($unigene =~ /^UniGene:(\S+)$/)
1381        {
1382            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1>$unigene</a>";
1383        }
1384        return $unigene;
1385    }
1386    
1387    sub ipi_link {
1388        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1389        my($cgi,$ipi) = @_;
1390    
1391        if ($ipi =~ /^IPI:(\S+)$/)
1392        {
1393            return "<a href=http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1>$ipi</a>";
1394        }
1395        return $ipi;
1396    }
1397    
1398    sub wp_link {
1399        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1400        my($cgi,$wp) = @_;
1401    
1402        #wormbase
1403    
1404        if ($wp =~ /^WP:(\S+)$/)
1405        {
1406            return "<a href=http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search>$wp</a>";
1407        }
1408        return $wp;
1409    }
1410    
1411    sub fb_link {
1412        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1413        my($cgi,$fb) = @_;
1414    
1415        #flybase
1416    
1417        if ($fb =~ /^FB:(\S+)$/)
1418        {
1419            return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";
1420        }
1421        return $fb;
1422    }
1423    
1424    sub fborf_link {
1425        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1426        my($cgi,$fb) = @_;
1427    
1428        #flybase
1429    
1430        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1431        {
1432            return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";
1433        }
1434        return $fb;
1435    }
1436    
1437    sub sgd_link {
1438        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1439        my($cgi,$sgd) = @_;
1440    
1441        #yeast
1442    
1443        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1444        {
1445            return "<a href=http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1>$sgd</a>";
1446        }
1447        return $sgd;
1448    }
1449    
1450    
1451    
1452    
1453    sub set_map_links {
1454        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1455        my($cgi,$x) = @_;
1456        my($before,$match,$after);
1457    
1458        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
1459    
1460        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
1461        {
1462            $before = $1;
1463            $match = $2;
1464            $after = $3;
1465            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
1466        }
1467        return $x;
1468    }
1469    
1470    
1471    
1472    sub map_link {
1473        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1474        my($cgi,$map,$org) = @_;
1475    
1476        $user = $cgi->param('user');
1477        $user = $user ? $user : "";
1478        $org = $org ? $org : "";
1479    
1480        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1481    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1482        my $link = "<a href=\"$url\">$map</a>";
1483        return $link;
1484    }
1485    
1486    sub java_buttons {
1487        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1488      ## ADDED BY RAE
1489      # Provides code to include check all/first half/second half/none for javascrspt
1490      # this takes two variables - the form name provided in start_form with the
1491      # -name => field and the checkbox name
1492      my ($form, $button)=@_;
1493    
1494      $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1495      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1496      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1497      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1498    
1499      return $java_script;
1500    }
1501    
1502    sub sub_link {
1503        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1504        my($cgi,$sub) = @_;
1505        my($sub_link);
1506    
1507        my $user = $cgi->param('user');
1508        my $esc_sub = uri_escape( $sub );
1509        $sub =~ s/\_/ /g;
1510        if ($user)
1511        {
1512            $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";
1513        }
1514        else
1515        {
1516            $sub_link = "<a href=\"display_subsys.cgi?ssa_name=$esc_sub&request=show_ssa&sort=by_phylo\">$sub</a>";
1517        }
1518        return $sub_link;
1519    }
1520    
1521    sub reaction_link {
1522        my($reaction) = @_;
1523    
1524        if ($reaction =~ /^R\d+/)
1525        {
1526            return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";
1527        }
1528        return $reaction;
1529    }
1530    
1531    sub html_for_assignments {
1532        my($fig,$user,$peg_sets) = @_;
1533        my $i;
1534    
1535        my @vals = ();
1536        my $set = 1;
1537        foreach $peg_set (@$peg_sets)
1538        {
1539            for ($i=0; ($i < @$peg_set); $i++)
1540            {
1541                $peg = $peg_set->[$i];
1542                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1543            }
1544            $set++;
1545        }
1546    
1547        $ENV{'REQUEST_METHOD'} = 'GET';
1548        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1549        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1550        $out =~ s/^.*?<form/<form/si;
1551        $out =~ s/^(.*)<table.*/$1/si;
1552        return $out;
1553    }
1554    
1555    =head1 rss_feed
1556    
1557    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1558            SEED.rss                - everything gets written here
1559            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1560            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1561    
1562    
1563    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.
1564    
1565    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.
1566    
1567    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.
1568    
1569    The has can have these keys:
1570    
1571    REQUIRED:
1572    title       : the title. This is usually what is seen by the user in the pull down menu
1573    description : a more complete description that is often seen is rss viewers but not always
1574    link        : link to the item that was added/edited
1575    All other keys are treated as optional RSS arguments and written to the file.
1576    
1577    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1578    
1579    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1580    
1581    
1582    =cut
1583    
1584    sub rss_feed {
1585     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1586     my ($files, $args)=@_;
1587    
1588     # how many entries to store in the file
1589     my $max_entries=50;
1590    
1591     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1592    
1593     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1594     # check for the directory and if not, make it
1595     mkdir $filepath unless (-d $filepath);
1596    
1597     # note that $info is a hash of references to hashes that are written out as headers in the file
1598     my $info=
1599     {
1600      "SEED.rss" =>
1601       {
1602            title           => "The SEED",
1603            description     => "Latest news from the SEED",
1604            link            => "Html/rss/SEED.rss",
1605       },
1606    
1607      "SEEDsubsystems.rss" =>
1608      {
1609            title           => "SEED Subsystems",
1610            description     => "Recently updated SEED subsystems",
1611            link            => "Html/rss/SEEDsubsystems.rss",
1612      },
1613    
1614      "SEEDsubsystems.rss" =>
1615      {
1616            title           => "SEED Genomes",
1617            description     => "Genomes recently added to the SEED",
1618            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1619      },
1620    
1621     };
1622    
1623    
1624     # build the new xml
1625     my $xml = "\t<item>\n";
1626     foreach my $qw ("title", "description", "link") {
1627      unless ($args->{$qw}) {
1628       print STDERR "You need to include a $qw tag in your RSS description\n";
1629       return(0);
1630      }
1631      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1632      # so we are going to pull out the links and uri_escape just the part after the .cgi
1633      if ($qw eq "link")
1634      {
1635       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1636       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1637      }
1638    
1639      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1640      delete $args->{$qw};
1641     }
1642    
1643     foreach my $tag (grep {!/type/i} keys %$args)
1644     {
1645      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1646     }
1647    
1648     $xml .= "\t</item>\n";
1649    
1650    
1651     my @files=("SEED.rss");
1652     if ($args->{"type"}) {push @files, "SEED.$type.rss"}
1653    
1654     foreach my $file ("SEED.rss", @$files)
1655     {
1656      if (-e "$filepath/$file")
1657      {
1658       my @out; # the new content of the file
1659       my $itemcount=0; # how many <item> </item>'s are we keeping
1660       my $initem; # are we in an item?
1661       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1662       while (<IN>)
1663       {
1664        if (/\<item\>/) {
1665         push @out, $xml, unless ($itemcount);
1666         $itemcount++;
1667         $initem=1;
1668        }
1669        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1670        next if ($initem && $itemcount > $max_entries);
1671        push @out, $_;
1672       }
1673       close IN;
1674       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1675       print OUT @out;
1676      }
1677      else
1678      {
1679       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1680       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1681       if ($info->{$file})
1682       {
1683         # we're going to sanity check each of the three options we output, just to be sure
1684         foreach my $qw ("title", "description", "link")
1685         {
1686           if ($info->{$file}->{$qw})
1687           {
1688              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1689           } else {
1690              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1691           }
1692         }
1693       }
1694       else {
1695        print STDERR "Please define title, link, and description information for $file\n";
1696        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1697       }
1698       print OUT "\n", $xml;
1699       print OUT "\n", "</channel>\n</rss>\n"
1700      }
1701     }
1702    }
1703    
1704    
1705    
1706    1;
1707    
 1  

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