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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 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 = [];          $args = [];
# Line 435  Line 946 
946  }  }
947    
948  sub trim_output {  sub trim_output {
949        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
950      my($out) = @_;      my($out) = @_;
951      my $i;      my $i;
952    
# Line 472  Line 984 
984  }  }
985    
986  sub set_prot_links {  sub set_prot_links {
987        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
988      my($cgi,$x) = @_;      my($cgi,$x) = @_;
989      my($before,$match,$after);      my($before,$match,$after);
990    
991      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
992      {      {
993          $before = $1;          $before = $1;
994          $match = $2;          $match = $2;
995          $after = $3;          $after = $3;
996          return &set_prot_links($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,$after);
997      }      }
998      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)      elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
999      {      {
1000          $before = $1;          $before = $1;
1001          $match = $2;          $match = $2;
1002          $after = $3;          $after = $3;
1003          return &set_prot_links($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,$after);
1004      }      }
1005      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
1006      {      {
1007          $before = $1;          $before = $1;
1008          $match = $2;          $match = $2;
1009          $after = $3;          $after = $3;
1010          return &set_prot_links($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,$after);
1011      }      }
1012      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1013      {      {
1014          $before = $1;          $before = $1;
1015          $match = $2;          $match = $2;
1016          $after = $3;          $after = $3;
1017          return &set_prot_links($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);
1018      }      }
1019      return $x;      elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1020        {
1021            $before = $1;
1022            $match = $2;
1023            $after = $3;
1024            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1025  }  }
1026    
1027  sub gi_link {      elsif ($x =~ /^(.*)\bbhb\|.*?\b(.*)/s)
     my($cgi,$gi) = @_;  
   
     if ($gi =~ /^gi\|(\d+)$/)  
1028      {      {
1029          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;
1030      }          $match = $2;
1031      return $gi;          $after = $3;
1032            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1033  }  }
1034    
1035  sub sp_link {      elsif ($x =~ /^(.*)\bapidb\|.*?\..*\b(.*)/s)
     my($cgi,$sp) = @_;  
   
     if ($sp =~ /^sp\|(\S+)$/)  
1036      {      {
1037          return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";          $before = $1;
1038      }          $match = $2;
1039      return $sp;          $after = $3;
1040            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1041  }  }
1042    
1043  sub pir_link {      elsif ($x =~ /^(.*)\bpatric\|.*?\b(.*)/s)
     my($cgi,$pir) = @_;  
   
     if ($pir =~ /^pirnr\|(NF\d+)$/)  
1044      {      {
1045          return "<a href=http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1>$pir</a>";          $before = $1;
1046            $match = $2;
1047            $after = $3;
1048            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1049      }      }
1050      return $pir;  
1051        elsif ($x =~ /^(.*)\bvbrc\|.*?\b(.*)/s)
1052        {
1053            $before = $1;
1054            $match = $2;
1055            $after = $3;
1056            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1057  }  }
1058    
1059        elsif ($x =~ /^(.*)\bvectorbase\|.*?\b(.*)/s)
1060        {
1061            $before = $1;
1062            $match = $2;
1063            $after = $3;
1064            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1065        }
1066        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1067        {
1068            $before = $1;
1069            $match = $2;
1070            $after = $3;
1071            return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
1072        }
1073        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
1074        {
1075            $before = $1;
1076            $match = $2;
1077            $after = $3;
1078            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
1079        }
1080        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
1081        {
1082            $before = $1;
1083            $match = $2;
1084            $after = $3;
1085            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
1086        }
1087        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
1088        {
1089            $before = $1;
1090            $match = $2;
1091            $after = $3;
1092            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1093        }
1094        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1095        {
1096            $before = $1;
1097            $match = $2;
1098            $after = $3;
1099            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1100        }
1101        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1102        {
1103            $before = $1;
1104            $match = $2;
1105            $after = $3;
1106            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1107        }
1108        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1109        {
1110            $before = $1;
1111            $match = $2;
1112            $after = $3;
1113            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1114        }
1115        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1116        {
1117            $before = $1;
1118            $match = $2;
1119            $after = $3;
1120            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1121        }
1122        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1123        {
1124            $before = $1;
1125            $match = $2;
1126            $after = $3;
1127            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1128        }
1129    # IPI stopped working. turn off for now.
1130    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1131    #    {
1132    #        $before = $1;
1133    #        $match = $2;
1134    #        $after = $3;
1135    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1136    #    }
1137        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1138        {
1139            #wormbase
1140    
1141            $before = $1;
1142            $match = $2;
1143            $after = $3;
1144            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1145        }
1146        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1147        {
1148            #flybase
1149    
1150            $before = $1;
1151            $match = $2;
1152            $after = $3;
1153            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1154        }
1155        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1156        {
1157            #flybase
1158    
1159            $before = $1;
1160            $match = $2;
1161            $after = $3;
1162            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1163        }
1164        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1165        {
1166            #flybase
1167    
1168            $before = $1;
1169            $match = $2;
1170            $after = $3;
1171            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1172        }
1173        return $x;
1174    }
1175    
1176    sub refseq_link {
1177        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1178        my($cgi,$id) = @_;
1179    
1180        if ($id =~ /^[NXYZA]P_/)
1181        {
1182            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";
1183        }
1184        elsif ($id =~ /^[NXYZA]M_/)
1185        {
1186            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id>$id</a>";
1187        }
1188    }
1189    
1190    sub gi_link {
1191        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1192        my($cgi,$gi) = @_;
1193    
1194        if ($gi =~ /^gi\|(\d+)$/)
1195        {
1196            return "<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept>$gi</a>";
1197        }
1198        return $gi;
1199    }
1200    
1201    sub tigr_link {
1202        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1203        my($cgi,$tigr) = @_;
1204    
1205        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1206        {
1207            my $id=$1.$2;
1208            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\">$tigr</a> (Pathema)";
1209        }
1210        elsif ($tigr =~ /^tigr\|(\S+)$/)
1211        {
1212            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\">$tigr</a>";
1213        }
1214        return $tigr;
1215    }
1216    
1217    sub eric_link {
1218        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1219        my($cgi,$eric) = @_;
1220    
1221        if ($eric =~ /^eric\|(\S+)/)
1222        {
1223            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\">$eric</a>";
1224        }
1225        return $eric;
1226    }
1227    
1228    sub bhb_link {
1229        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1230        my($cgi,$bhb) = @_;
1231    
1232        return "<a href=\"http://www.biohealthbase.org\">$bhb</a>";
1233    }
1234    
1235    sub apidb_link {
1236        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1237        my($cgi,$api) = @_;
1238    
1239        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1240        {
1241            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\">$api</a>";
1242        }
1243        return $api;
1244    }
1245    
1246    sub patric_link {
1247        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1248        my($cgi,$patric) = @_;
1249    
1250        if ($patric =~ /patric\|(.*)/)
1251        {
1252            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\">$patric</a>";
1253        }
1254        return $patric;
1255    }
1256    
1257    sub vbrc_link {
1258        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1259        my($cgi,$vbrc) = @_;
1260    
1261        if ($vbrc =~ /vbrc\|(.*)/)
1262        {
1263            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\">$vbrc</a>";
1264        }
1265        return $vbrc;
1266    }
1267    
1268    sub vectorbase_link {
1269        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1270        my($cgi,$vec) = @_;
1271        return "<a href=\"http://www.vectorbase.org\">$vec</a>";
1272    }
1273    
1274    
1275    sub uni_link {
1276        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1277        my($cgi,$uni) = @_;
1278    
1279        if ($uni =~ /^uni\|(\S+)$/)
1280        {
1281            return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1282        }
1283        return $uni;
1284    }
1285    
1286    sub sp_link {
1287        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1288        my($cgi,$sp) = @_;
1289    
1290        if ($sp =~ /^sp\|(\S+)$/)
1291        {
1292            return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";
1293        }
1294        return $sp;
1295    }
1296    
1297    sub pir_link {
1298        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1299        my($cgi,$pir) = @_;
1300    
1301        if ($pir =~ /^pirnr\|(NF\d+)$/)
1302        {
1303            return "<a href=http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1>$pir</a>";
1304        }
1305        return $pir;
1306    }
1307    
1308    sub kegg_link {
1309        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1310        my($cgi,$kegg) = @_;
1311    
1312        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1313        {
1314            return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";
1315        }
1316        return $kegg;
1317    }
1318    
1319    sub ensembl_link {
1320        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1321        my($cgi,$ensembl) = @_;
1322    
1323        if ($ensembl =~ /^(\S+):(\S+)$/)
1324        {
1325            my $what=$1;
1326            my $key=$2;
1327            my $idx="All";
1328            if ($what eq "EnsemblGene") { $idx = "Gene" }
1329            if ($what eq "EnsemblTranscript") { $idx = "All" }
1330            if ($what eq "EnsemblProtein") { $idx = "All" }
1331    
1332            #I really want to get right to the transcript and peptide pages, but
1333            #can't see how to do that without knowing the org name too, which
1334            #I don't know at this point. (ensembl org name, not real org name)
1335    
1336            return "<a href=http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key>$ensembl</a>";
1337        }
1338        return $ensembl;
1339    }
1340    
1341    sub entrezgene_link {
1342        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1343        my($cgi,$entrezgene) = @_;
1344    
1345        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1346        {
1347            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1>$entrezgene</a>";
1348        }
1349        return $entrezgene;
1350    }
1351    
1352    sub mim_link {
1353        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1354        my($cgi,$mim) = @_;
1355    
1356        if ($mim =~ /^MIM:(\S+)$/)
1357        {
1358            return "<a href=http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1>$mim</a>";
1359        }
1360        return $mim;
1361    }
1362    
1363    sub hgnc_link {
1364        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1365        my($cgi,$hgnc) = @_;
1366    
1367        if ($hgnc =~ /^HGNC:(\S+)$/)
1368        {
1369            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>";
1370        }
1371        return $mim;
1372    }
1373    
1374    sub unigene_link {
1375        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1376        my($cgi,$unigene) = @_;
1377    
1378        if ($unigene =~ /^UniGene:(\S+)$/)
1379        {
1380            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1>$unigene</a>";
1381        }
1382        return $unigene;
1383    }
1384    
1385    sub ipi_link {
1386        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1387        my($cgi,$ipi) = @_;
1388    
1389        if ($ipi =~ /^IPI:(\S+)$/)
1390        {
1391            return "<a href=http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1>$ipi</a>";
1392        }
1393        return $ipi;
1394    }
1395    
1396    sub wp_link {
1397        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1398        my($cgi,$wp) = @_;
1399    
1400        #wormbase
1401    
1402        if ($wp =~ /^WP:(\S+)$/)
1403        {
1404            return "<a href=http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search>$wp</a>";
1405        }
1406        return $wp;
1407    }
1408    
1409    sub fb_link {
1410        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1411        my($cgi,$fb) = @_;
1412    
1413        #flybase
1414    
1415        if ($fb =~ /^FB:(\S+)$/)
1416        {
1417            return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";
1418        }
1419        return $fb;
1420    }
1421    
1422    sub fborf_link {
1423        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1424        my($cgi,$fb) = @_;
1425    
1426        #flybase
1427    
1428        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1429        {
1430            return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";
1431        }
1432        return $fb;
1433    }
1434    
1435    sub sgd_link {
1436        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1437        my($cgi,$sgd) = @_;
1438    
1439        #yeast
1440    
1441        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1442        {
1443            return "<a href=http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1>$sgd</a>";
1444        }
1445        return $sgd;
1446    }
1447    
1448    
1449    
1450    
1451    sub set_map_links {
1452        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1453        my($cgi,$x) = @_;
1454        my($before,$match,$after);
1455    
1456        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
1457    
1458        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
1459        {
1460            $before = $1;
1461            $match = $2;
1462            $after = $3;
1463            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
1464        }
1465        return $x;
1466    }
1467    
1468    
1469    
1470    sub map_link {
1471        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1472        my($cgi,$map,$org) = @_;
1473    
1474        $user = $cgi->param('user');
1475        $user = $user ? $user : "";
1476        $org = $org ? $org : "";
1477    
1478        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1479    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1480        my $link = "<a href=\"$url\">$map</a>";
1481        return $link;
1482    }
1483    
1484    sub java_buttons {
1485        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1486      ## ADDED BY RAE
1487      # Provides code to include check all/first half/second half/none for javascrspt
1488      # this takes two variables - the form name provided in start_form with the
1489      # -name => field and the checkbox name
1490      my ($form, $button)=@_;
1491    
1492      $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1493      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1494      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1495      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1496    
1497      return $java_script;
1498    }
1499    
1500    sub sub_link {
1501        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1502        my($cgi,$sub) = @_;
1503        my($sub_link);
1504    
1505        my $user = $cgi->param('user');
1506        my $esc_sub = uri_escape( $sub );
1507        $sub =~ s/\_/ /g;
1508        if ($user)
1509        {
1510            $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";
1511        }
1512        else
1513        {
1514            $sub_link = "<a href=\"display_subsys.cgi?ssa_name=$esc_sub&request=show_ssa&sort=by_phylo\">$sub</a>";
1515        }
1516        return $sub_link;
1517    }
1518    
1519    sub reaction_link {
1520        my($reaction) = @_;
1521    
1522        if ($reaction =~ /^R\d+/)
1523        {
1524            return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";
1525        }
1526        return $reaction;
1527    }
1528    
1529    sub html_for_assignments {
1530        my($fig,$user,$peg_sets) = @_;
1531        my $i;
1532    
1533        my @vals = ();
1534        my $set = 1;
1535        foreach $peg_set (@$peg_sets)
1536        {
1537            for ($i=0; ($i < @$peg_set); $i++)
1538            {
1539                $peg = $peg_set->[$i];
1540                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1541            }
1542            $set++;
1543        }
1544    
1545        $ENV{'REQUEST_METHOD'} = 'GET';
1546        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1547        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1548        $out =~ s/^.*?<form/<form/si;
1549        $out =~ s/^(.*)<table.*/$1/si;
1550        return $out;
1551    }
1552    
1553    =head1 rss_feed
1554    
1555    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1556            SEED.rss                - everything gets written here
1557            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1558            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1559    
1560    
1561    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.
1562    
1563    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.
1564    
1565    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.
1566    
1567    The has can have these keys:
1568    
1569    REQUIRED:
1570    title       : the title. This is usually what is seen by the user in the pull down menu
1571    description : a more complete description that is often seen is rss viewers but not always
1572    link        : link to the item that was added/edited
1573    All other keys are treated as optional RSS arguments and written to the file.
1574    
1575    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1576    
1577    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1578    
1579    
1580    =cut
1581    
1582    sub rss_feed {
1583     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1584     my ($files, $args)=@_;
1585    
1586     # how many entries to store in the file
1587     my $max_entries=50;
1588    
1589     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1590    
1591     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1592     # check for the directory and if not, make it
1593     mkdir $filepath unless (-d $filepath);
1594    
1595     # note that $info is a hash of references to hashes that are written out as headers in the file
1596     my $info=
1597     {
1598      "SEED.rss" =>
1599       {
1600            title           => "The SEED",
1601            description     => "Latest news from the SEED",
1602            link            => "Html/rss/SEED.rss",
1603       },
1604    
1605      "SEEDsubsystems.rss" =>
1606      {
1607            title           => "SEED Subsystems",
1608            description     => "Recently updated SEED subsystems",
1609            link            => "Html/rss/SEEDsubsystems.rss",
1610      },
1611    
1612      "SEEDsubsystems.rss" =>
1613      {
1614            title           => "SEED Genomes",
1615            description     => "Genomes recently added to the SEED",
1616            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1617      },
1618    
1619     };
1620    
1621    
1622     # build the new xml
1623     my $xml = "\t<item>\n";
1624     foreach my $qw ("title", "description", "link") {
1625      unless ($args->{$qw}) {
1626       print STDERR "You need to include a $qw tag in your RSS description\n";
1627       return(0);
1628      }
1629      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1630      # so we are going to pull out the links and uri_escape just the part after the .cgi
1631      if ($qw eq "link")
1632      {
1633       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1634       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1635      }
1636    
1637      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1638      delete $args->{$qw};
1639     }
1640    
1641     foreach my $tag (grep {!/type/i} keys %$args)
1642     {
1643      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1644     }
1645    
1646     $xml .= "\t</item>\n";
1647    
1648    
1649     my @files=("SEED.rss");
1650     if ($args->{"type"}) {push @files, "SEED.$type.rss"}
1651    
1652     foreach my $file ("SEED.rss", @$files)
1653     {
1654      if (-e "$filepath/$file")
1655      {
1656       my @out; # the new content of the file
1657       my $itemcount=0; # how many <item> </item>'s are we keeping
1658       my $initem; # are we in an item?
1659       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1660       while (<IN>)
1661       {
1662        if (/\<item\>/) {
1663         push @out, $xml, unless ($itemcount);
1664         $itemcount++;
1665         $initem=1;
1666        }
1667        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1668        next if ($initem && $itemcount > $max_entries);
1669        push @out, $_;
1670       }
1671       close IN;
1672       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1673       print OUT @out;
1674      }
1675      else
1676      {
1677       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1678       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1679       if ($info->{$file})
1680       {
1681         # we're going to sanity check each of the three options we output, just to be sure
1682         foreach my $qw ("title", "description", "link")
1683         {
1684           if ($info->{$file}->{$qw})
1685           {
1686              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1687           } else {
1688              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1689           }
1690         }
1691       }
1692       else {
1693        print STDERR "Please define title, link, and description information for $file\n";
1694        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1695       }
1696       print OUT "\n", $xml;
1697       print OUT "\n", "</channel>\n</rss>\n"
1698      }
1699     }
1700    }
1701    
1702    
1703    
1704    1;
1705    
 1  

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