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revision 1.41, Thu Apr 28 20:56:37 2005 UTC revision 1.112, Thu Mar 1 12:49:13 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 =~ /^(.*)(img\|\d+)(.*)/s)
1078        {
1079            $before = $1;
1080            $match = $2;
1081            $after = $3;
1082            return &set_prot_links($cgi,$before) . &HTML::img_link($cgi,$match) . &set_prot_links($cgi,$after);
1083        }
1084        elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1085        {
1086            $before = $1;
1087            $match = $2;
1088            $after = $3;
1089            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1090        }
1091        elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1092        {
1093            $before = $1;
1094            $match = $2;
1095            $after = $3;
1096            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1097        }
1098    
1099        elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
1100        {
1101            $before = $1;
1102            $match = $2;
1103            $after = $3;
1104            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1105        }
1106    
1107        elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1108        {
1109            $before = $1;
1110            $match = $2;
1111            $after = $3;
1112            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1113        }
1114    
1115        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1116        {
1117            $before = $1;
1118            $match = $2;
1119            $after = $3;
1120            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1121        }
1122    
1123        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1124        {
1125            $before = $1;
1126            $match = $2;
1127            $after = $3;
1128            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1129        }
1130    
1131        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1132        {
1133            $before = $1;
1134            $match = $2;
1135            $after = $3;
1136            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1137        }
1138      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1139      {      {
1140          $before = $1;          $before = $1;
# Line 708  Line 1163 
1163          $after = $3;          $after = $3;
1164          return &set_prot_links($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,$after);
1165      }      }
1166        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1167        {
1168            $before = $1;
1169            $match = $2;
1170            $after = $3;
1171            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1172        }
1173        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1174        {
1175            $before = $1;
1176            $match = $2;
1177            $after = $3;
1178            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1179        }
1180        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1181        {
1182            $before = $1;
1183            $match = $2;
1184            $after = $3;
1185            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1186        }
1187        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1188        {
1189            $before = $1;
1190            $match = $2;
1191            $after = $3;
1192            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1193        }
1194        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1195        {
1196            $before = $1;
1197            $match = $2;
1198            $after = $3;
1199            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1200        }
1201    # IPI stopped working. turn off for now.
1202    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1203    #    {
1204    #        $before = $1;
1205    #        $match = $2;
1206    #        $after = $3;
1207    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1208    #    }
1209        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1210        {
1211            #wormbase
1212    
1213            $before = $1;
1214            $match = $2;
1215            $after = $3;
1216            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1217        }
1218        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1219        {
1220            #flybase
1221    
1222            $before = $1;
1223            $match = $2;
1224            $after = $3;
1225            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1226        }
1227        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1228        {
1229            #flybase
1230    
1231            $before = $1;
1232            $match = $2;
1233            $after = $3;
1234            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1235        }
1236        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1237        {
1238            #flybase
1239    
1240            $before = $1;
1241            $match = $2;
1242            $after = $3;
1243            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1244        }
1245        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1246        {
1247    
1248          $before = $1;
1249          $match = $2;
1250          $after = $3;
1251    
1252          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1253        }
1254      return $x;      return $x;
1255  }  }
1256    
1257    sub trembl_link {
1258        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1259        my($cgi,$id) = @_;
1260    
1261        if ($id =~ /^tr\|(.*)/) {
1262          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1263        } else {
1264          return "invalid call to trembl link";
1265        }
1266    }
1267    
1268  sub refseq_link {  sub refseq_link {
1269      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1270      my($cgi,$id) = @_;      my($cgi,$id) = @_;
1271    
1272      if ($id =~ /^[NXYZA]P_/)      if ($id =~ /^[NXYZA]P_/)
1273      {      {
1274          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>";
1275        }
1276        elsif ($id =~ /^[NXYZA]M_/)
1277        {
1278            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1279      }      }
1280  }  }
1281    
# Line 727  Line 1285 
1285    
1286      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
1287      {      {
1288          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>";
1289      }      }
1290      return $gi;      return $gi;
1291  }  }
1292    
1293    sub tigr_link {
1294        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1295        my($cgi,$tigr) = @_;
1296    
1297        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1298        {
1299            my $id=$1.$2;
1300            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1301        }
1302        elsif ($tigr =~ /^tigr\|(\S+)$/)
1303        {
1304            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\" target=_blank>$tigr</a>";
1305        }
1306        return $tigr;
1307    }
1308    
1309    sub eric_link {
1310        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1311        my($cgi,$eric) = @_;
1312    
1313        if ($eric =~ /^eric\|(\S+)/)
1314        {
1315            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1316        }
1317        return $eric;
1318    }
1319    
1320    sub bhb_link {
1321        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1322        my($cgi,$bhb) = @_;
1323    
1324        return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1325    }
1326    
1327    sub apidb_link {
1328        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1329        my($cgi,$api) = @_;
1330    
1331        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1332        {
1333            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1334        }
1335        return $api;
1336    }
1337    
1338    sub patric_link {
1339        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1340        my($cgi,$patric) = @_;
1341    
1342        if ($patric =~ /patric\|(.*)/)
1343        {
1344            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1345        }
1346        return $patric;
1347    }
1348    
1349    sub vbrc_link {
1350        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1351        my($cgi,$vbrc) = @_;
1352    
1353        if ($vbrc =~ /vbrc\|(.*)/)
1354        {
1355            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1356        }
1357        return $vbrc;
1358    }
1359    
1360    sub vectorbase_link {
1361        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1362        my($cgi,$vec) = @_;
1363        return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1364    }
1365    
1366    
1367  sub uni_link {  sub uni_link {
1368      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1369      my($cgi,$uni) = @_;      my($cgi,$uni) = @_;
1370    
1371      if ($uni =~ /^uni\|(\S+)$/)      if ($uni =~ /^uni\|(\S+)$/)
1372      {      {
1373          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>";
1374            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1375      }      }
1376      return $uni;      return $uni;
1377  }  }
# Line 749  Line 1382 
1382    
1383      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1384      {      {
1385          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>";
1386      }      }
1387      return $sp;      return $sp;
1388  }  }
# Line 760  Line 1393 
1393    
1394      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1395      {      {
1396          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>";
1397      }      }
1398      return $pir;      return $pir;
1399  }  }
# Line 771  Line 1404 
1404    
1405      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1406      {      {
1407          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>";
1408      }      }
1409      return $kegg;      return $kegg;
1410  }  }
1411    
1412    sub img_link {
1413        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1414        my($cgi,$img) = @_;
1415    
1416        if ($img =~ /^img\|(\S+)$/)
1417        {
1418            return "<a href='http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$1' target=_blank>$img</a>";
1419        }
1420        return $img;
1421    }
1422    
1423    sub ensembl_link {
1424        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1425        my($cgi,$ensembl) = @_;
1426    
1427        if ($ensembl =~ /^(\S+):(\S+)$/)
1428        {
1429            my $what=$1;
1430            my $key=$2;
1431            my $idx="All";
1432            if ($what eq "EnsemblGene") { $idx = "Gene" }
1433            if ($what eq "EnsemblTranscript") { $idx = "All" }
1434            if ($what eq "EnsemblProtein") { $idx = "All" }
1435    
1436            #I really want to get right to the transcript and peptide pages, but
1437            #can't see how to do that without knowing the org name too, which
1438            #I don't know at this point. (ensembl org name, not real org name)
1439    
1440            return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1441        }
1442        return $ensembl;
1443    }
1444    
1445    sub entrezgene_link {
1446        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1447        my($cgi,$entrezgene) = @_;
1448    
1449        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1450        {
1451            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>";
1452        }
1453        return $entrezgene;
1454    }
1455    
1456    sub mim_link {
1457        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1458        my($cgi,$mim) = @_;
1459    
1460        if ($mim =~ /^MIM:(\S+)$/)
1461        {
1462            return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1463        }
1464        return $mim;
1465    }
1466    
1467    sub hgnc_link {
1468        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1469        my($cgi,$hgnc) = @_;
1470    
1471        if ($hgnc =~ /^HGNC:(\S+)$/)
1472        {
1473            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>";
1474        }
1475    
1476        return $hgnc;
1477    }
1478    
1479    sub unigene_link {
1480        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1481        my($cgi,$unigene) = @_;
1482    
1483        if ($unigene =~ /^UniGene:(\S+)$/)
1484        {
1485            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1486        }
1487        return $unigene;
1488    }
1489    
1490    sub ipi_link {
1491        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1492        my($cgi,$ipi) = @_;
1493    
1494        if ($ipi =~ /^IPI:(\S+)$/)
1495        {
1496            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>";
1497        }
1498        return $ipi;
1499    }
1500    
1501    sub wp_link {
1502        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1503        my($cgi,$wp) = @_;
1504    
1505        #wormbase
1506    
1507        if ($wp =~ /^WP:(\S+)$/)
1508        {
1509            return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1510        }
1511        return $wp;
1512    }
1513    
1514    sub fb_link {
1515        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1516        my($cgi,$fb) = @_;
1517    
1518        #flybase
1519    
1520        if ($fb =~ /^FB:(\S+)$/)
1521        {
1522            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1523        }
1524        return $fb;
1525    }
1526    
1527    sub fborf_link {
1528        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1529        my($cgi,$fb) = @_;
1530    
1531        #flybase
1532    
1533        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1534        {
1535            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1536        }
1537        return $fb;
1538    }
1539    
1540    sub sgd_link {
1541        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1542        my($cgi,$sgd) = @_;
1543    
1544        #yeast
1545    
1546        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1547        {
1548            return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1549        }
1550        return $sgd;
1551    }
1552    
1553    
1554    
1555    
1556  sub set_map_links {  sub set_map_links {
1557      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1558      my($cgi,$x) = @_;      my($cgi,$x) = @_;
# Line 793  Line 1570 
1570      return $x;      return $x;
1571  }  }
1572    
1573    
1574    
1575  sub map_link {  sub map_link {
1576      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1577      my($cgi,$map,$org) = @_;      my($cgi,$map,$org) = @_;
1578    
1579      $user = $cgi->param('user');      my $user = $cgi->param('user');
1580      $user = $user ? $user : "";      $user = $user ? $user : "";
1581      $org = $org ? $org : "";      $org = $org ? $org : "";
1582      my $url = "$FIG_Config::cgi_url/show_kegg_map.cgi?user=$user&map=$map&org=$org";  
1583        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1584    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1585      my $link = "<a href=\"$url\">$map</a>";      my $link = "<a href=\"$url\">$map</a>";
1586      return $link;      return $link;
1587  }  }
1588    
1589  sub javascript {  sub java_buttons {
1590      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1591          #### MODIFIED BY RAE TO ADD JAVA SUPPORT FOR CHECK ALL/UNCHECK ALL    ## ADDED BY RAE
1592          # This routine takes three arguments, $html, $form, and $button    # Provides code to include check all/first half/second half/none for javascrspt
1593          # $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
1594          # $form is the name of the form. This must be added whenever start_form is called    # -name => field and the checkbox name
1595          # by including a -name entry. This is only used for the javascript    my ($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.  
1596    
1597          # 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";
1598          # 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";
1599          #    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1600      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1601    
1602            $java_script=<<EOF;    return $java_script;
   <SCRIPT LANGUAGE="JavaScript">  
   <!-- Begin  
   function checkAll(field)  
   {  
    for (i = 0; i < field.length; i++)  
    field[i].checked = true ;  
1603    }    }
1604    
1605    function checkFirst(field)  =head3 sub_link
1606    {  
1607     for (i = 0; i < field.length/2; i++)  C<< my $htmlText = HTML::sub_link($cgi, $sub); >>
1608     field[i].checked = true;  
1609    Create a subsystem link. The link will be to the display page if there is no
1610    user or we are in SPROUT mode; otherwise it will be to the edit page.
1611    
1612    =over 4
1613    
1614    =item cgi
1615    
1616    CGI query object for the current web session. The parameters of special interest
1617    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1618    the subsystem's edit page will be shown rather than its display page.
1619    
1620    =item sub
1621    
1622    Name of the desired subsystem. It will be cleaned of underscores before the
1623    hyperlink is applied.
1624    
1625    =back
1626    
1627    =cut
1628    
1629    sub sub_link {
1630        # Allow call as an instance in addition to the authorized method.
1631        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1632        # Get the parameters.
1633        my ($cgi, $sub) = @_;
1634        # Declare the return variable.
1635        my $retVal;
1636        # Clean the subsystem name for display purposes. This is a very
1637        # different thing from URL-escaping.
1638        my $cleaned = CGI::escapeHTML($sub);
1639        $cleaned =~ s/_/ /g;
1640        # URL-escape the subsystem name for use in the link.
1641        my $linkable = uri_escape($sub);
1642        # Determine the mode. Note we use the little OR trick to insure that
1643        # we have the correct value for plugging into the output link.
1644        my $user = $cgi->param('user') || "";
1645        my $sproutMode = $cgi->param('SPROUT') || 0;
1646        if ($user && ! $sproutMode) {
1647            # A SEED user is calling, so we go to the edit page.
1648            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1649        } else {
1650            # A visitor or SPROUT user is calling, so we go to the display page.
1651            $retVal = "<a href=\"display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;SPROUT=$sproutMode\">$cleaned</a>";
1652    }    }
1653        # Return the result.
1654        return $retVal;
1655    }
1656    
1657    
1658    function checkSecond(field)  sub reaction_link {
1659        my($reaction) = @_;
1660        if ($reaction =~ /^(\*)?(R\d+)/)
1661    {    {
1662     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>";
    field[i].checked = true ;  
1663    }    }
1664        return $reaction;
1665    }
1666    
1667    
1668    sub html_for_assignments {
1669        my($fig,$user,$peg_sets) = @_;
1670        my $i;
1671    
1672    function uncheckAll(field)      my @vals = ();
1673        my $set = 1;
1674        foreach my $peg_set (@$peg_sets)
1675    {    {
1676     for (i = 0; i < field.length; i++)          for ($i=0; ($i < @$peg_set); $i++)
1677     field[i].checked = false ;          {
1678                my $peg = $peg_set->[$i];
1679                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1680    }    }
1681    //  End -->          $set++;
   </script>  
 EOF  
         return $java_script;  
1682  }  }
1683    
1684  sub java_buttons {      $ENV{'REQUEST_METHOD'} = 'GET';
1685        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1686        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1687        $out =~ s/^.*?<form/<form/si;
1688        $out =~ s/^(.*)<table.*/$1/si;
1689        return $out;
1690    }
1691    
1692    =head1 rss_feed
1693    
1694    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1695            SEED.rss                - everything gets written here
1696            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1697            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1698    
1699    
1700    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.
1701    
1702    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.
1703    
1704    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.
1705    
1706    The has can have these keys:
1707    
1708    REQUIRED:
1709    title       : the title. This is usually what is seen by the user in the pull down menu
1710    description : a more complete description that is often seen is rss viewers but not always
1711    link        : link to the item that was added/edited
1712    All other keys are treated as optional RSS arguments and written to the file.
1713    
1714    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1715    
1716    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1717    
1718    
1719    =cut
1720    
1721    sub rss_feed {
1722      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1723    ## ADDED BY RAE   my ($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)=@_;  
1724    
1725    $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";   # how many entries to store in the file
1726    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$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";  
1727    
1728    return $java_script;   foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1729    
1730     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1731     # check for the directory and if not, make it
1732     mkdir $filepath unless (-d $filepath);
1733    
1734     # note that $info is a hash of references to hashes that are written out as headers in the file
1735     my $info=
1736     {
1737      "SEED.rss" =>
1738       {
1739            title           => "The SEED",
1740            description     => "Latest news from the SEED",
1741            link            => "Html/rss/SEED.rss",
1742       },
1743    
1744      "SEEDsubsystems.rss" =>
1745      {
1746            title           => "SEED Subsystems",
1747            description     => "Recently updated SEED subsystems",
1748            link            => "Html/rss/SEEDsubsystems.rss",
1749      },
1750    
1751      "SEEDsubsystems.rss" =>
1752      {
1753            title           => "SEED Genomes",
1754            description     => "Genomes recently added to the SEED",
1755            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1756      },
1757    
1758     };
1759    
1760    
1761     # build the new xml
1762     my $xml = "\t<item>\n";
1763     foreach my $qw ("title", "description", "link") {
1764      unless ($args->{$qw}) {
1765       print STDERR "You need to include a $qw tag in your RSS description\n";
1766       return(0);
1767      }
1768      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1769      # so we are going to pull out the links and uri_escape just the part after the .cgi
1770      if ($qw eq "link")
1771      {
1772       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1773       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1774  }  }
1775    
1776  sub sub_link {    $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1777      shift if UNIVERSAL::isa($_[0],__PACKAGE__);    delete $args->{$qw};
1778      my($cgi,$sub) = @_;   }
     my($sub_link);  
1779    
1780      my $user = $cgi->param('user');   foreach my $tag (grep {!/type/i} keys %$args)
     if ($user)  
1781      {      {
1782          my $esc_sub = uri_escape( $sub );    $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1783          $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";   }
1784    
1785     $xml .= "\t</item>\n";
1786    
1787    
1788     my @files=("SEED.rss");
1789     if ($args->{"type"}) {
1790        my $type = $args->{type};
1791        push @files, "SEED.$type.rss"
1792    }
1793    
1794     foreach my $file ("SEED.rss", @$files)
1795     {
1796      if (-e "$filepath/$file")
1797      {
1798       my @out; # the new content of the file
1799       my $itemcount=0; # how many <item> </item>'s are we keeping
1800       my $initem; # are we in an item?
1801       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1802       while (<IN>)
1803       {
1804        if (/\<item\>/) {
1805         push @out, $xml, unless ($itemcount);
1806         $itemcount++;
1807         $initem=1;
1808        }
1809        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1810        next if ($initem && $itemcount > $max_entries);
1811        push @out, $_;
1812       }
1813       close IN;
1814       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1815       print OUT @out;
1816      }      }
1817      else      else
1818      {      {
1819          $sub_link = $sub;     open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1820       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1821       if ($info->{$file})
1822       {
1823         # we're going to sanity check each of the three options we output, just to be sure
1824         foreach my $qw ("title", "description", "link")
1825         {
1826           if ($info->{$file}->{$qw})
1827           {
1828              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1829           } else {
1830              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1831           }
1832      }      }
     return $sub_link;  
1833  }  }
1834       else {
1835        print STDERR "Please define title, link, and description information for $file\n";
1836        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1837       }
1838       print OUT "\n", $xml;
1839       print OUT "\n", "</channel>\n</rss>\n"
1840      }
1841     }
1842    }
1843    
1844    
1845    
1846    1;
1847    
 1  

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