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revision 1.41, Thu Apr 28 20:56:37 2005 UTC revision 1.111, Mon Jan 22 19:57:19 2007 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 strict;
21    use Tracer;
22  use FIG;  use FIG;
23  use Carp;  use Carp;
24  use Data::Dumper;  use Data::Dumper;
# Line 9  Line 28 
28  use URI::URL;  use URI::URL;
29  use HTTP::Request::Common;  use HTTP::Request::Common;
30  use POSIX;  use POSIX;
31    use CGI;
32    
33    #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
34    my $raelib;
35    
36    
37    my $top_link_cache;
38    
39    
40  sub new  sub new
41  {  {
# Line 19  Line 46 
46      return bless $self, $class;      return bless $self, $class;
47  }  }
48    
49    sub top_link
50    {
51    
52        #
53        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
54        # just /p2p).
55        #
56    
57        return $top_link_cache if ($top_link_cache);
58    
59        my @parts = split(/\//, $ENV{SCRIPT_NAME});
60        my $top;
61        if (defined $parts[-2] && $parts[-2] eq 'FIG')
62        {
63            $top = '.';
64    #       warn "toplevel @parts\n";
65        }
66        elsif (defined $parts[-3] && $parts[-3] eq 'FIG')
67        {
68            $top = '..';
69    #       warn "subdir @parts\n";
70        }
71        else
72        {
73            $top = $FIG_Config::cgi_base;
74    #       warn "other @parts\n";
75        }
76    
77        $top_link_cache = $top;
78        return $top;
79    }
80    
81  sub compute_html_header  sub compute_html_header
82  {  {
83      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
84      my($additional_insert,$user) = @_;      my($additional_insert, $user, %options ) = @_;
85      my $html_hdr_file = "./Html/html.hdr";  
86        local $/ = "\n";
87    
88        my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
89        my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
90    
91        my $html_hdr_file = "./Html/$header_name";
92      if (! -f $html_hdr_file)      if (! -f $html_hdr_file)
93      {      {
94          $html_hdr_file = "$FIG_Config::fig/CGI/Html/html.hdr";          $html_hdr_file = "$FIG_Config::fig/CGI/Html/$header_name";
95      }      }
96      my @html_hdr = &FIG::file_read($html_hdr_file);      my @html_hdr = &FIG::file_read($html_hdr_file);
97      push( @html_hdr, "<br><a href=\"index.cgi?user=$user\">FIG search</a>\n" );  
98        # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
99    
100        #
101        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
102        # just /p2p).
103        #
104    
105        my @parts = split(/\//, $ENV{SCRIPT_NAME});
106        my $top;
107        if ($parts[-2] eq 'FIG')
108        {
109            $top = '.';
110    #       warn "toplevel @parts\n";
111        }
112        elsif ($parts[-3] eq 'FIG')
113        {
114            $top = '..';
115    #       warn "subdir @parts\n";
116        }
117        else
118        {
119            $top = $FIG_Config::cgi_base;
120    #       warn "other @parts\n";
121        }
122    
123        $options{no_fig_search} or push( @html_hdr, "<br><a href=\"$top/index.cgi?user=$user\">FIG search</a>\n" );
124    
125      if (@html_hdr)      if (@html_hdr)
126      {      {
127          my $insert_stuff;          my $insert_stuff;
128    
129            if (not $options{no_release_info})
130            {
131          my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);          my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
132          my $ver = $ver[0];          my $ver = $ver[0];
133          chomp $ver;          chomp $ver;
# Line 45  Line 139 
139          }          }
140          my $host = &FIG::get_local_hostname();          my $host = &FIG::get_local_hostname();
141          $insert_stuff = "SEED version <b>$ver</b> on $host";          $insert_stuff = "SEED version <b>$ver</b> on $host";
142            }
143    
144          if ($additional_insert)          if ($additional_insert)
145          {          {
146              $insert_stuff .= "<br>" . $additional_insert;              $insert_stuff .= "<br>" . $additional_insert;
# Line 52  Line 148 
148    
149          for $_ (@html_hdr)          for $_ (@html_hdr)
150          {          {
151              s,(href|img\s+src)="/FIG/,\1="$FIG_Config::cgi_base,g;              s,(href|img\s+src)="/FIG/,$1="$top/,g;
152                    s,(\?user\=)\",$1$user",;
153              if ($_ eq "<!-- HEADER_INSERT -->\n")              if ($_ eq "<!-- HEADER_INSERT -->\n")
154              {              {
155                  $_ = $insert_stuff;                  $_ = $insert_stuff;
# Line 66  Line 163 
163  sub show_page {  sub show_page {
164      #warn "SHOWPAGE: cgi=", Dumper(@_);      #warn "SHOWPAGE: cgi=", Dumper(@_);
165      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
166      my($cgi,$html,$no_home, $alt_header, $css, $javasrc) = @_;      my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
167      my $i;      my $i;
168        Trace("Setting top link.") if T(3);
169        my $top = top_link();
170    
171      # ARGUMENTS:      # ARGUMENTS:
172      #     $cgi is the CGI method      #     $cgi is the CGI method
# Line 78  Line 176 
176      #     $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      #     $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
177      #               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      #               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
178      #               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      #               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
179      #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "/FIG/Html/css/styleswitcher.js")      #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")
180        #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
181        #     $options is a reference to a hash of options that you can pass around the pages
182      #      #
183      # Find the HTML header      # Find the HTML header
184      #      #
185        Trace("Reading tail.") if T(3);
186      my $html_tail_file = "./Html/html.tail";      my $tail_name = $options->{tail_name} ? $options->{tail_name} : "html.tail";
187        my $html_tail_file = "./Html/$tail_name";
188      if (! -f $html_tail_file)      if (! -f $html_tail_file)
189      {      {
190          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
191      }      }
192        Trace("Extracting user name and header data.") if T(3);
193      my $user = $cgi->param('user') || "";      my $user = $cgi->param('user') || "";
194      my @html_hdr;      my @html_hdr;
195      if ($alt_header && ref($alt_header) eq "ARRAY")      if ($alt_header && ref($alt_header) eq "ARRAY")
# Line 97  Line 198 
198      }      }
199      else      else
200      {      {
201          @html_hdr = compute_html_header(undef,$user);          @html_hdr = compute_html_header(undef,$user,%$options);
202      }      }
203    
204        # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.
205        # This modification adds the cookies if necessary
206    
207      print $cgi->header;      # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about
208        # to add cookies back in replace these two header lines with each other
209        #my $hdr_thing = $cgi->header(-cookie=>$cookie);
210        my $hdr_thing = $cgi->header();
211        Trace("Printing HTML header: $hdr_thing.") if T(3);
212        print $hdr_thing;
213        Trace("Header printed.") if T(3);
214      #      #
215      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
216      #  what parts of the HTML document skeleton are there, and fill in      #  what parts of the HTML document skeleton are there, and fill in
# Line 119  Line 227 
227                       meta     => 1,                       meta     => 1,
228                       nextid   => 1,                       nextid   => 1,
229                       style    => 1,                       style    => 1,
230                       title    => 1                       title    => 1,
231                     );                     );
232    
233      #      #
# Line 147  Line 255 
255      my $body_line = -1;      my $body_line = -1;
256      my $last_head_line = -1;  #  If no head tags are found, text goes at top.      my $last_head_line = -1;  #  If no head tags are found, text goes at top.
257      my $done = 0;      my $done = 0;
258        Trace("Processing special cases.") if T(3);
259      for ( $i = 0; $i < @$html; $i++ )      for ( $i = 0; $i < @$html; $i++ )
260      {      {
261          #  Some special cases:          #  Some special cases:
# Line 162  Line 270 
270          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )
271          {          {
272              $body_line = $i;              $body_line = $i;
273              $last;              last;
274          }          }
275    
276          #  Now the general case.          #  Now the general case.
# Line 193  Line 301 
301    
302      if ( 1 )      if ( 1 )
303      {      {
304            Trace("Sanity checks in progress.") if T(3);
305          if ( $html_line >= 0 )          if ( $html_line >= 0 )
306          {          {
307              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )
308              {              {
309                  print STDERR "<HTML> tag follows <HEAD> tag\n";                  Trace("<HTML> tag follows <HEAD> tag.") if T(1);
310              }              }
311              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )
312              {              {
313                  print STDERR "<HTML> tag follows </HEAD> tag\n";                  Trace("<HTML> tag follows </HEAD> tag.") if T(1);
314              }              }
315          }          }
316          if ( $head_line >= 0 )          if ( $head_line >= 0 )
317          {          {
318              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )
319              {              {
320                  print STDERR "<HEAD> tag follows </HEAD> tag\n";                  Trace("<HEAD> tag follows </HEAD> tag.") if T(1);
321              }              }
322          }          }
323      }      }
324        Trace("Sanity checks complete.") if T(3);
325      #      #
326      #  Okay.  Let's put in the html header file, and missing tags:      #  Okay.  Let's put in the html header file, and missing tags:
327      #      #
# Line 222  Line 331 
331      #  Added the javascript for the buttons immediately after body.      #  Added the javascript for the buttons immediately after body.
332      #  Note if no buttons are added we still (at the moment) add the script,      #  Note if no buttons are added we still (at the moment) add the script,
333      #  but it only adds a little text (495 characters) to the html and noone will notice!      #  but it only adds a little text (495 characters) to the html and noone will notice!
334        #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
335      if ( $body_line < 0 )      if ( $body_line < 0 )
336      {      {
         my $js=&javascript;  
337          $body_line = $last_head_line + 1;          $body_line = $last_head_line + 1;
338          splice( @$html, $body_line, 0, "<BODY>\n$js\n" );          Trace("Splicing body line at $body_line.") if T(3);
339            splice( @$html, $body_line, 0, "<BODY>\n" );
340      }      }
341    
342      #      #
# Line 236  Line 345 
345    
346      if (@html_hdr)      if (@html_hdr)
347      {      {
348            Trace("Splicing SEED page header after $body_line.") if T(3);
349          splice( @$html, $body_line + 1, 0, @html_hdr );          splice( @$html, $body_line + 1, 0, @html_hdr );
350      }      }
351    
# Line 246  Line 356 
356      if ( $head_end_line < 0 )      if ( $head_end_line < 0 )
357      {      {
358          $head_end_line = $body_line;          $head_end_line = $body_line;
359            Trace("Splicing header terminater at $body_line.") if T(3);
360          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
361      }      }
362    
# Line 255  Line 366 
366      # be moved out, but I want to try it and see what happens.  css has the format:      # be moved out, but I want to try it and see what happens.  css has the format:
367      #      #
368      # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>      # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
369        Trace("Formatting CSS.") if T(3);
370      # convert the default key to the right case. and eliminate dups      # convert the default key to the right case. and eliminate dups
371      foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}      foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
372    
373      if (!$css || !$css->{'Default'})      if (!$css || !$css->{'Default'})
374      {      {
375         $css->{'Default'}="/FIG/Html/css/default.css";         $css->{'Default'} = "Html/css/default.css";
376      }      }
377      if (!$css->{"Sans Serif"})      if (!$css->{"Sans Serif"})
378      {      {
379         $css->{'Sans Serif'}="/FIG/Html/css/sanserif.css";         $css->{'Sans Serif'} = "Html/css/sanserif.css";
380      }      }
381    
382      my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";      my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";
383      $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";      $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";
384    
# Line 276  Line 388 
388         $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";         $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
389      }      }
390    
391        $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='Html/rss/SEED.rss' type='application/rss+xml'>\n";
392    
393      # RAE: also added support for external javascripts here.      # RAE: also added support for external javascripts here.
394      # we are cluttering the HTML code with all the javascripts when they could easily be in external files      # we are cluttering the HTML code with all the javascripts when they could easily be in external files
395      # this solution allows us to source other files      # this solution allows us to source other files
396    
397        # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
398        # it will reduce our overhead.
399        Trace("Formatting javascript.") if T(3);
400      # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts      # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
401      if ($javasrc && ref($javasrc) eq "ARRAY") {      push @$javasrc, "Html/css/FIG.js";
402       foreach my $script (@$javasrc) {       foreach my $script (@$javasrc) {
403        $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";        $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
404       }       }
     }  
   
   
405    
406        Trace("Re-splicing the header terminator at $head_end_line.") if T(3);
407      splice( @$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.      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.
408    
409      #      #
# Line 307  Line 421 
421          # BASE href needs to be absolute. RDO.          # BASE href needs to be absolute. RDO.
422          #          #
423          #          #
424          $base_url = &FIG::cgi_url;  #        $base_url = &FIG::cgi_url;
425  #       my $base_url = $FIG_Config::cgi_base;  #       my $base_url = $FIG_Config::cgi_base;
426  #       if ( ! $base_url )                      # if cgi_base was not defined  #       if ( ! $base_url )                      # if cgi_base was not defined
427  #       {  #       {
# Line 317  Line 431 
431  #       }  #       }
432    
433          $base_line = $head_end_line;          $base_line = $head_end_line;
434          splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );          #
435            # RDO 2005-1006. Remove this so proxying works better.
436            #
437    #        splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );
438      }      }
439    
440      #      #
# Line 327  Line 444 
444      if ( $html_line < 0 )      if ( $html_line < 0 )
445      {      {
446          $html_line = 0;          $html_line = 0;
447            Trace("Splicing the HTML tag at $html_line.") if T(3);
448          splice( @$html, $html_line, 0, "<HTML>\n" );          splice( @$html, $html_line, 0, "<HTML>\n" );
449      }      }
450    
# Line 337  Line 455 
455      if ( $head_line < 0 )      if ( $head_line < 0 )
456      {      {
457          $head_line = $html_line + 1;          $head_line = $html_line + 1;
458            Trace("Splicing the HEAD tag at $head_line.") if T(3);
459          splice( @$html, $head_line, 0, "<HEAD>\n" );          splice( @$html, $head_line, 0, "<HEAD>\n" );
460      }      }
461    
462      #      #
463      #  Place FIG search link at bottom of page      #  Place FIG search link at bottom of page
464      #      #
465        Trace("Placing FIG search link.") if T(3);
466      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();
467      if (! $no_home)      if (! $no_home)
468      {      {
# Line 354  Line 473 
473      #      #
474      # See if we have a site-specific tail (for disclaimers, etc).      # See if we have a site-specific tail (for disclaimers, etc).
475      #      #
476        Trace("Placing site tail.") if T(3);
477      my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";      my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
478      my $site_fh;      my $site_fh;
479      if (open($site_fh, "<$site_tail"))      if (open($site_fh, "<$site_tail"))
# Line 367  Line 486 
486      #  Figure out where to insert The SEED tail.  Before </body>,      #  Figure out where to insert The SEED tail.  Before </body>,
487      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
488      #      #
   
489      my @tags = ();      my @tags = ();
490        Trace("Processing closing tags.") if T(3);
491      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
492      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
493      {      {
# Line 384  Line 502 
502    
503      if ( @tail )      if ( @tail )
504      {      {
505            Trace("Splicing tail.") if T(3);
506          splice( @$html, $i, 0, @tail, @tags );          splice( @$html, $i, 0, @tail, @tags );
507      }      }
508      elsif ( @tags )      elsif ( @tags )
509      {      {
510            Trace("Splicing tags.") if T(3);
511          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
512      }      }
513    
514        Trace("Printing the HTML array.") if T(3);
515      # RAE the chomp will return any new lines at the ends of elements in the array,      # RAE the chomp will return any new lines at the ends of elements in the array,
516      # and then we can join  with a "\n". This is because somethings put newlines in,      # and then we can join  with a "\n". This is because somethings put newlines in,
517      # and others don't. This should make nicer looking html      # and others don't. This should make nicer looking html
# Line 399  Line 520 
520      # print join "\n", @$html;      # print join "\n", @$html;
521      #      #
522      # Apparently the above still breaks things. This is the correct code:      # Apparently the above still breaks things. This is the correct code:
523        foreach $_ (@$html)
524        {
525            my $line = $_;
526            if (T(4)) {
527                my $escapedLine = CGI::escapeHTML($line);
528                Trace("Printing:\n$escapedLine") if T(4);
529            }
530            print $line;
531        }
532    
     print @$html;  
533  }  }
534    
535    
536    =head1 make_table
537    
538    The main method to convert an array into a table.
539    
540    The col_hdrs are set to the <th> headers, the $tab is an array of arrays. The first is the rows, and the second is the columns. The title is the title of the table.
541    
542    The options define the settings for the table such as border, width, and class for css formatting. If the option "excelfile" is set to a filename that will be created in FIG_Config::temp, and the link included that allows the user to download the file as an excel file.
543    
544    =cut
545    
546  sub make_table {  sub make_table {
547      my($col_hdrs,$tab,$title, %options ) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
548      my(@tab);      my(@tab);
549    
550      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
551      push( @tab, "\n<table $border>\n",      my $width = defined $options{width} ? "width=\"$options{width}\"" : "";
552        my $class = defined $options{class} ? "class=\"$options{class}\"" : "";
553        push( @tab, "\n<table $border $width $class>\n",
554                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
555                  "\t<tr>\n\t\t"                  "\t<tr>\n\t\t"
556                . join( "\n", map { &expand($_, "th") } @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
# Line 425  Line 567 
567              );              );
568      }      }
569      push(@tab,"</table>\n");      push(@tab,"</table>\n");
570    
571        # excelfile should be appropriate for a filename (no spaces/special characters)
572        if (defined $options{"excelfile"}) {
573            if (! defined($raelib)) {
574                require raelib;
575                $raelib = new raelib;
576            }
577            push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
578    
579      return join("",@tab);      return join("",@tab);
580  }  }
581    
582    sub abstract_coupling_table {
583        my($cgi,$prot,$coupling) = @_;
584        my %fc;
585    
586        my $col_hdrs = ["coupled to","Score","Type of Coupling", "Type-specific Data"];
587        my $tab = [];
588        my %by_peg;
589        foreach my $x (@$coupling)
590        {
591            my($peg2,$psc,$type,$extra) = @$x;
592            if (($type !~ /^[ID]FC$/) || (! $fc{$peg2}))
593            {
594                if ($type =~  /^[ID]FC$/)
595                {
596                    $fc{$peg2} = 1;
597                }
598    
599                $by_peg{$peg2} += $psc;
600            }
601        }
602    
603        foreach my $x (sort { ($by_peg{$b->[0]} <=> $by_peg{$a->[0]})
604                              or ($a->[0] cmp $b->[0])
605                              or ($b->[1] <=> $a->[1])
606                              or ($a->[2] cmp $b->[2]) } @$coupling)
607        {
608            my($peg2,$psc,$type,$extra) = @$x;
609            push(@$tab,[&fid_link($cgi,$peg2,1),$psc,$type,&set_prot_links($cgi,join(", ",@$extra))]);
610        }
611    
612    
613         my $help = "<a href=\"Html/abstract_coupling.html\" target=\"SEED_or_SPROUT_help\">for help</a>";
614    #    my @html = &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot");
615    #    push(@html,"<hr>\n",$cgi->h3($help),"<br>");
616    #    return @html;
617    
618        return &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot [$help]");
619    }
620    
621  sub expand {  sub expand {
622      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
623      my( $x, $tag ) = @_;      my( $x, $tag ) = @_;
# Line 440  Line 630 
630      # things like colspan and align. Note that in this case you need to include the td      # things like colspan and align. Note that in this case you need to include the td
631      # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]      # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
632    
633      if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; if ($tag =~ /td/) { $endtag = "td" } }      # per GJO's request modified this line so it can take any tag.
634        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
635    
636      if ( $x =~ /^\@([^:]+)\:(.*)$/ )      if ( $x =~ /^\@([^:]+)\:(.*)$/ )
637      {      {
# Line 452  Line 643 
643      }      }
644  }  }
645    
646    
647    =head2 merge_table_rows()
648    
649    Merge table rows together. This will merge a table so that adjacent cells with the same content will only be shown once.
650    
651    Something like this:
652    
653        -----------------------
654        |    1     |    a     |
655        -----------------------
656        |    1     |    b     |
657        -----------------------
658        |    2     |    c     |
659        -----------------------
660        |    3     |    d     |
661        -----------------------
662        |    4     |    d     |
663        -----------------------
664        |    5     |    d     |
665        -----------------------
666    
667    Will become:
668    
669        -----------------------
670        |          |    a     |
671        |    1     |-----------
672        |          |    b     |
673        -----------------------
674        |    2     |    c     |
675        -----------------------
676        |    3     |          |
677        ------------          |
678        |    4     |    5     |
679        ------------          |
680        |    5     |          |
681        -----------------------
682    
683    
684    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.
685    
686     $tab=&HTML::merge_table_rows($tab);
687    
688     or
689    
690     $skip=(1=>1, 3=>1, 5=>1);
691     $tab=&HTML::merge_table_rows($tab, $skip);  # will merge all columns except 1, 3 and 5. Note the first column in the table is #0
692    
693    
694    =cut
695    
696    
697    
698    
699    sub merge_table_rows {
700     # RAE:
701     # Experimental piece of code. We often want to have rows or columns were cells are merged. It just looks so much nicer
702     # this block should merge adjacent rows that have the same text in them.
703     # use like this:
704     #      $tab=&HTML::merge_table_rows($tab);
705     # before you do a make_table call
706    
707     my $self=shift if UNIVERSAL::isa($_[0],__PACKAGE__);
708     my ($tab, $skip)=@_;
709    
710     my $newtable;
711     my $lastrow;
712     my $rowspan;
713     my $refs;
714    
715     for (my $y=0; $y <= $#$tab; $y++) {
716     #$y is the row in the table;
717      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
718       # this is the user definable columns not to merge
719       if ($skip->{$x})
720       {
721        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
722        next;
723       }
724    
725       #$x is the column in the table
726       # if the column in the row we are looking at is the same as the column in the previous row, we don't add
727       # this cell to $newtable. Instead we increment the rowspan of the previous row by one
728    
729       # handle cells that are references to arrays
730       if (ref($tab->[$y]->[$x]) eq "ARRAY") {$refs->[$y]->[$x]=$tab->[$y]->[$x]->[1]; $tab->[$y]->[$x]=$tab->[$y]->[$x]->[0]}
731    
732       # now we go back through the table looking where to draw the merge line:
733       my $lasty=$y;
734       while ($lasty >= 0 && $tab->[$y]->[$x] eq $tab->[$lasty]->[$x]) {$lasty--}
735       $lasty++; # this is the last identical cell. If lasty==y it is the current cell, so we just save the data. Otherwise we increment the rowspan
736       if ($lasty == $y) {
737        # we always want to have something in rows that may otherwise be empty but should be there (see below)
738        unless ($tab->[$y]->[$x]) {$tab->[$y]->[$x]=" &nbsp; "}
739        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
740       }
741       else {$rowspan->[$lasty]->[$x]++}
742      }
743     }
744    
745     # now just join everything back together
746     for (my $y=0; $y <= $#$tab; $y++) {
747      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
748       if ($rowspan->[$y]->[$x]) {
749        if ($refs->[$y]->[$x]) {$refs->[$y]->[$x] .= " rowspan=". ($rowspan->[$y]->[$x]+1)}
750        else {$refs->[$y]->[$x] = "td rowspan=". ($rowspan->[$y]->[$x]+1)}
751        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
752       }
753       elsif ($newtable->[$y]->[$x] && $refs->[$y]->[$x]) {
754        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
755       }
756      }
757     }
758    
759    
760     # finally we have to remove any completely empty cells that have been added by the array mechanism
761     # (e.g. if you define $a->[2] then $a->[0] and $a->[1] are now undef).
762     # that is why in the loop above I replace empty cells with nbsp. They are now not undef!
763     # I am sure that Gary can do this in one line, but I am hacking.
764     my @trimmed;
765     foreach my $a (@$newtable) {
766      my @row;
767      foreach my $b (@$a) {
768       push @row, $b if ($b);
769      }
770      push @trimmed, \@row;
771     }
772    
773     return \@trimmed;
774    }
775    
776    
777    
778    
779  sub set_ec_links {  sub set_ec_links {
780      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
781      my($cgi,$x) = @_;      my($cgi,$x) = @_;
# Line 493  Line 817 
817      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
818  }  }
819    
820  #  =head2 fid_link
821  # Local means to eliminate the fig|org.peg from the  
822  # text of the link.  Get a link to a fid.
823  #  
824    use: my $html=&HTML::fid_link($cgi, $fid, Local, Just_URL, Full_Path);
825    
826    Local is a boolean means to eliminate the fig|org.peg from the text of the link.
827    
828    Just_URL will only return the URL and not the HTML code. The default is to return the full code.
829    
830    Full_Path is a boolean that will get the full path to the URL not just a relative path. This is required in pages where the base href changes (e.g. if an image is imported like on the metabolic pages).
831    
832    =cut
833    
834    
835  sub fid_link {  sub fid_link {
836      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
837      my($cgi,$fid,$local,$just_url) = @_;      my($cgi,$fid,$local,$just_url,$fullpath) = @_;
838        Trace("Creating link for feature $fid.") if T(4);
839        my $err=join(" ", $cgi,$fid,$local,$just_url,$fullpath);
840    
841      my($n);      my($n);
842    
843        my $top = top_link();
844        if ($fullpath) {$top=$FIG_Config::cgi_url}
845    
846      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)
847      {      {
848          if ($local)          if ($local)
# Line 519  Line 860 
860          {          {
861              $n = $fid;              $n = $fid;
862          }          }
863          if ($1 ne "peg") { return $n }  
864            my $link;
865            my $new_framework = $cgi->param('new_framework') ? 1 : 0;
866            #added to format prophage and path island links to feature.cgi
867            my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
868            my $virt = "&48hr_job=" . $cgi->param("48hr_job");
869            Trace("Sprout mode is \"$sprout\".") if T(4);
870            if ($1 ne "peg" && ! $sprout)
871            {
872               Trace("Creating feature link for $fid.") if T(4);
873               my $user = $cgi->param('user');
874               if (! $user) { $user = "" }
875               $link = "$top/feature.cgi?feature=$fid&user=$user$sprout$virt";
876               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
877            }
878            else
879            {
880                Trace("Creating protein link for $fid.") if T(4);
881          my $user = $cgi->param('user');          my $user = $cgi->param('user');
882          if (! $user) { $user = "" }          if (! $user) { $user = "" }
883          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
884          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
885          my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";  ###a
         $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;  
         #  
         # Elimin the p2p part if we're in that subdir. Ugh.  
         #  
         $link =~ s,p2p/protein.cgi,protein.cgi,;  
886    
887    ### This used to be
888    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
889    ###
890    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
891    ###
892    ### RAO
893    
894                #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
895                #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
896                $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout$virt\&new_framework=$new_framework";
897                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
898            }
899          if ($just_url)          if ($just_url)
900          {          {
901              return $link;              return $link;
902          }          }
903          else          else
904          {          {
905              return "<a href=$link>$n</a>";              return "<a href='$link'>$n</a>";
906          }          }
907      }      }
908      return $fid;      return $fid;
# Line 550  Line 915 
915      return $family;      return $family;
916  }  }
917    
918    =head2 evidence_codes_explain
919    
920    Given an evidence code, returns a string that explains this eveidence code.
921    
922    =cut
923    
924    sub evidence_codes_explain {
925     my($ec)=@_;
926     return unless ($ec);
927    
928     $ec=uc($ec);
929     return "IDA: Inferred from Direct Assay" if ($ec =~ /IDA/);
930     return "IGI: Inferred from Genetic Interaction" if ($ec =~ /IGI/);
931     return "TAS: Traceable Author Statement" if ($ec =~ /TAS/);
932     return "ISU: in subsystem unique" if ($ec =~ /ISU/);
933     return "$ec: in subsystem duplicates" if ($ec =~ /IDU/);
934     return "$ec: in cluster with" if ($ec =~ /ICW/);
935     return "FF: in FIGfam" if ($ec =~ /FF/);
936     return "CWN: clustered with nonhypothetical" if ($ec =~ /CWN/);
937     return "CWH: clustered, but only with hypotheticals" if ($ec =~ /CWH/);
938     return "DLIT: literature references to this gene exist" if ($ec =~ /DLIT/);
939     return "ILIT: no references to this gene exist, but they do to other genes with the same functional role" if ($ec =~ /ILIT/);
940     return "$ec: unknown!";
941    }
942    
943  sub get_html {  sub get_html {
944      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
# Line 569  Line 958 
958          my $response = $ua->request($request);          my $response = $ua->request($request);
959          $out = $response->content;          $out = $response->content;
960      }      }
961      else  
962        if ($type =~/get/i)
963      {      {
964          @args = ();          @args = ();
965          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 581  Line 971 
971          {          {
972              $url .= "?" . join("&",@args);              $url .= "?" . join("&",@args);
973          }          }
974          $request = new HTTP::Request('GET', $url);          my $request = new HTTP::Request('GET', $url);
975          my $response = $ua->request($request);          my $response = $ua->request($request);
976    
977          if ($response->is_success)          if ($response->is_success)
# Line 599  Line 989 
989    
990  #   Now splice in a line of the form <base href=URL> to cause all relative links to work  #   Now splice in a line of the form <base href=URL> to cause all relative links to work
991  #   properly.  Remove the header.  #   properly.  Remove the header.
992        my $i;
993      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}
994      if ($i < @output)      if ($i < @output) {
     {  
   
995          splice(@output,0,$i);          splice(@output,0,$i);
996      }      }
997    
# Line 619  Line 1007 
1007  sub trim_output {  sub trim_output {
1008      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1009      my($out) = @_;      my($out) = @_;
1010      my $i;      my ($i, $j);
1011    
1012      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}
1013      splice(@$out,0,$i);      splice(@$out,0,$i);
# Line 648  Line 1036 
1036      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}
1037      if ($j > 0)      if ($j > 0)
1038      {      {
1039            #
1040            # Hm. We would have tried using the options here:
1041            # my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
1042            # but they're not passed in. So use the default html.tail.
1043            #
1044            my $html_tail_file = "./Html/html.tail";
1045          my @tmp = `cat $html_tail_file`;          my @tmp = `cat $html_tail_file`;
1046          my $n = @tmp;          my $n = @tmp;
1047          splice(@$out,$j-$n,$n+1);          splice(@$out,$j-$n,$n+1);
# Line 666  Line 1060 
1060          $after = $3;          $after = $3;
1061          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);
1062      }      }
1063      elsif ($x =~ /^(.*)\b([NXYZA]P_[0-9\.]+)\b(.*)/s)      elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
1064      {      {
1065          $before = $1;          $before = $1;
1066          $match = $2;          $match = $2;
# Line 680  Line 1074 
1074          $after = $3;          $after = $3;
1075          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);
1076      }      }
1077        elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1078        {
1079            $before = $1;
1080            $match = $2;
1081            $after = $3;
1082            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1083        }
1084        elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1085        {
1086            $before = $1;
1087            $match = $2;
1088            $after = $3;
1089            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1090        }
1091    
1092        elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
1093        {
1094            $before = $1;
1095            $match = $2;
1096            $after = $3;
1097            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1098        }
1099    
1100        elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1101        {
1102            $before = $1;
1103            $match = $2;
1104            $after = $3;
1105            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1106        }
1107    
1108        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1109        {
1110            $before = $1;
1111            $match = $2;
1112            $after = $3;
1113            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1114        }
1115    
1116        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1117        {
1118            $before = $1;
1119            $match = $2;
1120            $after = $3;
1121            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1122        }
1123    
1124        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1125        {
1126            $before = $1;
1127            $match = $2;
1128            $after = $3;
1129            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1130        }
1131      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1132      {      {
1133          $before = $1;          $before = $1;
# Line 708  Line 1156 
1156          $after = $3;          $after = $3;
1157          return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1158      }      }
1159        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1160        {
1161            $before = $1;
1162            $match = $2;
1163            $after = $3;
1164            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1165        }
1166        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1167        {
1168            $before = $1;
1169            $match = $2;
1170            $after = $3;
1171            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1172        }
1173        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1174        {
1175            $before = $1;
1176            $match = $2;
1177            $after = $3;
1178            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1179        }
1180        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1181        {
1182            $before = $1;
1183            $match = $2;
1184            $after = $3;
1185            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1186        }
1187        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1188        {
1189            $before = $1;
1190            $match = $2;
1191            $after = $3;
1192            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1193        }
1194    # IPI stopped working. turn off for now.
1195    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1196    #    {
1197    #        $before = $1;
1198    #        $match = $2;
1199    #        $after = $3;
1200    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1201    #    }
1202        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1203        {
1204            #wormbase
1205    
1206            $before = $1;
1207            $match = $2;
1208            $after = $3;
1209            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1210        }
1211        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1212        {
1213            #flybase
1214    
1215            $before = $1;
1216            $match = $2;
1217            $after = $3;
1218            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1219        }
1220        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1221        {
1222            #flybase
1223    
1224            $before = $1;
1225            $match = $2;
1226            $after = $3;
1227            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1228        }
1229        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1230        {
1231            #flybase
1232    
1233            $before = $1;
1234            $match = $2;
1235            $after = $3;
1236            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1237        }
1238        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1239        {
1240    
1241          $before = $1;
1242          $match = $2;
1243          $after = $3;
1244    
1245          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1246        }
1247      return $x;      return $x;
1248  }  }
1249    
1250    sub trembl_link {
1251        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1252        my($cgi,$id) = @_;
1253    
1254        if ($id =~ /^tr\|(.*)/) {
1255          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1256        } else {
1257          return "invalid call to trembl link";
1258        }
1259    }
1260    
1261  sub refseq_link {  sub refseq_link {
1262      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1263      my($cgi,$id) = @_;      my($cgi,$id) = @_;
1264    
1265      if ($id =~ /^[NXYZA]P_/)      if ($id =~ /^[NXYZA]P_/)
1266      {      {
1267          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";          return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id' target=_blank>$id</a>";
1268        }
1269        elsif ($id =~ /^[NXYZA]M_/)
1270        {
1271            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1272      }      }
1273  }  }
1274    
# Line 727  Line 1278 
1278    
1279      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
1280      {      {
1281          return "<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept>$gi</a>";          return "<a href='http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept' target=_blank>$gi</a>";
1282      }      }
1283      return $gi;      return $gi;
1284  }  }
1285    
1286    sub tigr_link {
1287        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1288        my($cgi,$tigr) = @_;
1289    
1290        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1291        {
1292            my $id=$1.$2;
1293            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1294        }
1295        elsif ($tigr =~ /^tigr\|(\S+)$/)
1296        {
1297            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\" target=_blank>$tigr</a>";
1298        }
1299        return $tigr;
1300    }
1301    
1302    sub eric_link {
1303        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1304        my($cgi,$eric) = @_;
1305    
1306        if ($eric =~ /^eric\|(\S+)/)
1307        {
1308            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1309        }
1310        return $eric;
1311    }
1312    
1313    sub bhb_link {
1314        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1315        my($cgi,$bhb) = @_;
1316    
1317        return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1318    }
1319    
1320    sub apidb_link {
1321        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1322        my($cgi,$api) = @_;
1323    
1324        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1325        {
1326            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1327        }
1328        return $api;
1329    }
1330    
1331    sub patric_link {
1332        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1333        my($cgi,$patric) = @_;
1334    
1335        if ($patric =~ /patric\|(.*)/)
1336        {
1337            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1338        }
1339        return $patric;
1340    }
1341    
1342    sub vbrc_link {
1343        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1344        my($cgi,$vbrc) = @_;
1345    
1346        if ($vbrc =~ /vbrc\|(.*)/)
1347        {
1348            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1349        }
1350        return $vbrc;
1351    }
1352    
1353    sub vectorbase_link {
1354        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1355        my($cgi,$vec) = @_;
1356        return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1357    }
1358    
1359    
1360  sub uni_link {  sub uni_link {
1361      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1362      my($cgi,$uni) = @_;      my($cgi,$uni) = @_;
1363    
1364      if ($uni =~ /^uni\|(\S+)$/)      if ($uni =~ /^uni\|(\S+)$/)
1365      {      {
1366          return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";          #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1367            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1368      }      }
1369      return $uni;      return $uni;
1370  }  }
# Line 749  Line 1375 
1375    
1376      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1377      {      {
1378          return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";          return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$sp</a>";
1379      }      }
1380      return $sp;      return $sp;
1381  }  }
# Line 760  Line 1386 
1386    
1387      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1388      {      {
1389          return "<a href=http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1>$pir</a>";          return "<a href='http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1' target=_blank>$pir</a>";
1390      }      }
1391      return $pir;      return $pir;
1392  }  }
# Line 771  Line 1397 
1397    
1398      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1399      {      {
1400          return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";          return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1401      }      }
1402      return $kegg;      return $kegg;
1403  }  }
1404    
1405    sub ensembl_link {
1406        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1407        my($cgi,$ensembl) = @_;
1408    
1409        if ($ensembl =~ /^(\S+):(\S+)$/)
1410        {
1411            my $what=$1;
1412            my $key=$2;
1413            my $idx="All";
1414            if ($what eq "EnsemblGene") { $idx = "Gene" }
1415            if ($what eq "EnsemblTranscript") { $idx = "All" }
1416            if ($what eq "EnsemblProtein") { $idx = "All" }
1417    
1418            #I really want to get right to the transcript and peptide pages, but
1419            #can't see how to do that without knowing the org name too, which
1420            #I don't know at this point. (ensembl org name, not real org name)
1421    
1422            return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1423        }
1424        return $ensembl;
1425    }
1426    
1427    sub entrezgene_link {
1428        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1429        my($cgi,$entrezgene) = @_;
1430    
1431        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1432        {
1433            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1' target=_blank>$entrezgene</a>";
1434        }
1435        return $entrezgene;
1436    }
1437    
1438    sub mim_link {
1439        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1440        my($cgi,$mim) = @_;
1441    
1442        if ($mim =~ /^MIM:(\S+)$/)
1443        {
1444            return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1445        }
1446        return $mim;
1447    }
1448    
1449    sub hgnc_link {
1450        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1451        my($cgi,$hgnc) = @_;
1452    
1453        if ($hgnc =~ /^HGNC:(\S+)$/)
1454        {
1455            return "<a href='http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=equals&match=$1&symbol_search=Search&number=50&format=html&sortby=symbol' target=_blank>$hgnc</a>";
1456        }
1457    
1458        return $hgnc;
1459    }
1460    
1461    sub unigene_link {
1462        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1463        my($cgi,$unigene) = @_;
1464    
1465        if ($unigene =~ /^UniGene:(\S+)$/)
1466        {
1467            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1468        }
1469        return $unigene;
1470    }
1471    
1472    sub ipi_link {
1473        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1474        my($cgi,$ipi) = @_;
1475    
1476        if ($ipi =~ /^IPI:(\S+)$/)
1477        {
1478            return "<a href='http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1' target=_blank>$ipi</a>";
1479        }
1480        return $ipi;
1481    }
1482    
1483    sub wp_link {
1484        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1485        my($cgi,$wp) = @_;
1486    
1487        #wormbase
1488    
1489        if ($wp =~ /^WP:(\S+)$/)
1490        {
1491            return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1492        }
1493        return $wp;
1494    }
1495    
1496    sub fb_link {
1497        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1498        my($cgi,$fb) = @_;
1499    
1500        #flybase
1501    
1502        if ($fb =~ /^FB:(\S+)$/)
1503        {
1504            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1505        }
1506        return $fb;
1507    }
1508    
1509    sub fborf_link {
1510        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1511        my($cgi,$fb) = @_;
1512    
1513        #flybase
1514    
1515        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1516        {
1517            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1518        }
1519        return $fb;
1520    }
1521    
1522    sub sgd_link {
1523        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1524        my($cgi,$sgd) = @_;
1525    
1526        #yeast
1527    
1528        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1529        {
1530            return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1531        }
1532        return $sgd;
1533    }
1534    
1535    
1536    
1537    
1538  sub set_map_links {  sub set_map_links {
1539      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1540      my($cgi,$x) = @_;      my($cgi,$x) = @_;
# Line 793  Line 1552 
1552      return $x;      return $x;
1553  }  }
1554    
1555    
1556    
1557  sub map_link {  sub map_link {
1558      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1559      my($cgi,$map,$org) = @_;      my($cgi,$map,$org) = @_;
1560    
1561      $user = $cgi->param('user');      my $user = $cgi->param('user');
1562      $user = $user ? $user : "";      $user = $user ? $user : "";
1563      $org = $org ? $org : "";      $org = $org ? $org : "";
1564      my $url = "$FIG_Config::cgi_url/show_kegg_map.cgi?user=$user&map=$map&org=$org";  
1565        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1566    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1567      my $link = "<a href=\"$url\">$map</a>";      my $link = "<a href=\"$url\">$map</a>";
1568      return $link;      return $link;
1569  }  }
1570    
1571  sub javascript {  sub java_buttons {
1572      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1573          #### MODIFIED BY RAE TO ADD JAVA SUPPORT FOR CHECK ALL/UNCHECK ALL    ## ADDED BY RAE
1574          # This routine takes three arguments, $html, $form, and $button    # Provides code to include check all/first half/second half/none for javascrspt
1575          # $html is the ref to the array with the html in it    # this takes two variables - the form name provided in start_form with the
1576          # $form is the name of the form. This must be added whenever start_form is called    # -name => field and the checkbox name
1577          # by including a -name entry. This is only used for the javascript    my ($form, $button)=@_;
         # $button is the name of the button that should be checked/unchecked.  
         #  
         # At the moment this add's four buttons:  
         # Check all, check's all  
         # Check first half will check the first 50% of the entries  
         # Check second half will check the second 50% of the entries  
         # Uncheck all will remove the checks.  
1578    
1579          # Note that the other change is I added a -name=>'fig_checked' to the start_form    my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1580          # field. The name is needed for the java script.    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1581          #    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1582      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1583    
1584            $java_script=<<EOF;    return $java_script;
   <SCRIPT LANGUAGE="JavaScript">  
   <!-- Begin  
   function checkAll(field)  
   {  
    for (i = 0; i < field.length; i++)  
    field[i].checked = true ;  
1585    }    }
1586    
1587    function checkFirst(field)  =head3 sub_link
1588    {  
1589     for (i = 0; i < field.length/2; i++)  C<< my $htmlText = HTML::sub_link($cgi, $sub); >>
1590     field[i].checked = true;  
1591    Create a subsystem link. The link will be to the display page if there is no
1592    user or we are in SPROUT mode; otherwise it will be to the edit page.
1593    
1594    =over 4
1595    
1596    =item cgi
1597    
1598    CGI query object for the current web session. The parameters of special interest
1599    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1600    the subsystem's edit page will be shown rather than its display page.
1601    
1602    =item sub
1603    
1604    Name of the desired subsystem. It will be cleaned of underscores before the
1605    hyperlink is applied.
1606    
1607    =back
1608    
1609    =cut
1610    
1611    sub sub_link {
1612        # Allow call as an instance in addition to the authorized method.
1613        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1614        # Get the parameters.
1615        my ($cgi, $sub) = @_;
1616        # Declare the return variable.
1617        my $retVal;
1618        # Clean the subsystem name for display purposes. This is a very
1619        # different thing from URL-escaping.
1620        my $cleaned = CGI::escapeHTML($sub);
1621        $cleaned =~ s/_/ /g;
1622        # URL-escape the subsystem name for use in the link.
1623        my $linkable = uri_escape($sub);
1624        # Determine the mode. Note we use the little OR trick to insure that
1625        # we have the correct value for plugging into the output link.
1626        my $user = $cgi->param('user') || "";
1627        my $sproutMode = $cgi->param('SPROUT') || 0;
1628        if ($user && ! $sproutMode) {
1629            # A SEED user is calling, so we go to the edit page.
1630            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1631        } else {
1632            # A visitor or SPROUT user is calling, so we go to the display page.
1633            $retVal = "<a href=\"display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;SPROUT=$sproutMode\">$cleaned</a>";
1634        }
1635        # Return the result.
1636        return $retVal;
1637    }    }
1638    
1639    function checkSecond(field)  
1640    sub reaction_link {
1641        my($reaction) = @_;
1642        if ($reaction =~ /^(\*)?(R\d+)/)
1643    {    {
1644     for (i=Math.round(field.length/2); i < field.length; i++)          return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1645     field[i].checked = true ;      }
1646        return $reaction;
1647    }    }
1648    
1649    function uncheckAll(field)  
1650    sub html_for_assignments {
1651        my($fig,$user,$peg_sets) = @_;
1652        my $i;
1653    
1654        my @vals = ();
1655        my $set = 1;
1656        foreach my $peg_set (@$peg_sets)
1657        {
1658            for ($i=0; ($i < @$peg_set); $i++)
1659    {    {
1660     for (i = 0; i < field.length; i++)              my $peg = $peg_set->[$i];
1661     field[i].checked = false ;              push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1662    }    }
1663    //  End -->          $set++;
   </script>  
 EOF  
         return $java_script;  
1664  }  }
1665    
1666  sub java_buttons {      $ENV{'REQUEST_METHOD'} = 'GET';
1667        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1668        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1669        $out =~ s/^.*?<form/<form/si;
1670        $out =~ s/^(.*)<table.*/$1/si;
1671        return $out;
1672    }
1673    
1674    =head1 rss_feed
1675    
1676    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1677            SEED.rss                - everything gets written here
1678            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1679            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1680    
1681    
1682    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.
1683    
1684    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.
1685    
1686    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.
1687    
1688    The has can have these keys:
1689    
1690    REQUIRED:
1691    title       : the title. This is usually what is seen by the user in the pull down menu
1692    description : a more complete description that is often seen is rss viewers but not always
1693    link        : link to the item that was added/edited
1694    All other keys are treated as optional RSS arguments and written to the file.
1695    
1696    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1697    
1698    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1699    
1700    
1701    =cut
1702    
1703    sub rss_feed {
1704      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1705    ## ADDED BY RAE   my ($files, $args)=@_;
   # Provides code to include check all/first half/second half/none for javascrspt  
   # this takes two variables - the form name provided in start_form with the  
   # -name => field and the checkbox name  
   my ($form, $button)=@_;  
1706    
1707    $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";   # how many entries to store in the file
1708    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";   my $max_entries=50;
   $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";  
   $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";  
1709    
1710    return $java_script;   foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1711    
1712     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1713     # check for the directory and if not, make it
1714     mkdir $filepath unless (-d $filepath);
1715    
1716     # note that $info is a hash of references to hashes that are written out as headers in the file
1717     my $info=
1718     {
1719      "SEED.rss" =>
1720       {
1721            title           => "The SEED",
1722            description     => "Latest news from the SEED",
1723            link            => "Html/rss/SEED.rss",
1724       },
1725    
1726      "SEEDsubsystems.rss" =>
1727      {
1728            title           => "SEED Subsystems",
1729            description     => "Recently updated SEED subsystems",
1730            link            => "Html/rss/SEEDsubsystems.rss",
1731      },
1732    
1733      "SEEDsubsystems.rss" =>
1734      {
1735            title           => "SEED Genomes",
1736            description     => "Genomes recently added to the SEED",
1737            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1738      },
1739    
1740     };
1741    
1742    
1743     # build the new xml
1744     my $xml = "\t<item>\n";
1745     foreach my $qw ("title", "description", "link") {
1746      unless ($args->{$qw}) {
1747       print STDERR "You need to include a $qw tag in your RSS description\n";
1748       return(0);
1749      }
1750      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1751      # so we are going to pull out the links and uri_escape just the part after the .cgi
1752      if ($qw eq "link")
1753      {
1754       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1755       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1756  }  }
1757    
1758  sub sub_link {    $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1759      shift if UNIVERSAL::isa($_[0],__PACKAGE__);    delete $args->{$qw};
1760      my($cgi,$sub) = @_;   }
     my($sub_link);  
1761    
1762      my $user = $cgi->param('user');   foreach my $tag (grep {!/type/i} keys %$args)
     if ($user)  
1763      {      {
1764          my $esc_sub = uri_escape( $sub );    $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1765          $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";   }
1766    
1767     $xml .= "\t</item>\n";
1768    
1769    
1770     my @files=("SEED.rss");
1771     if ($args->{"type"}) {
1772        my $type = $args->{type};
1773        push @files, "SEED.$type.rss"
1774    }
1775    
1776     foreach my $file ("SEED.rss", @$files)
1777     {
1778      if (-e "$filepath/$file")
1779      {
1780       my @out; # the new content of the file
1781       my $itemcount=0; # how many <item> </item>'s are we keeping
1782       my $initem; # are we in an item?
1783       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1784       while (<IN>)
1785       {
1786        if (/\<item\>/) {
1787         push @out, $xml, unless ($itemcount);
1788         $itemcount++;
1789         $initem=1;
1790        }
1791        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1792        next if ($initem && $itemcount > $max_entries);
1793        push @out, $_;
1794       }
1795       close IN;
1796       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1797       print OUT @out;
1798      }      }
1799      else      else
1800      {      {
1801          $sub_link = $sub;     open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1802       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1803       if ($info->{$file})
1804       {
1805         # we're going to sanity check each of the three options we output, just to be sure
1806         foreach my $qw ("title", "description", "link")
1807         {
1808           if ($info->{$file}->{$qw})
1809           {
1810              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1811           } else {
1812              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1813           }
1814      }      }
     return $sub_link;  
1815  }  }
1816       else {
1817        print STDERR "Please define title, link, and description information for $file\n";
1818        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1819       }
1820       print OUT "\n", $xml;
1821       print OUT "\n", "</channel>\n</rss>\n"
1822      }
1823     }
1824    }
1825    
1826    
1827    
1828    1;
1829    
 1  

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