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revision 1.12, Thu Jul 17 15:44:26 2014 UTC revision 1.13, Thu Jul 17 19:09:58 2014 UTC
# Line 17  Line 17 
17  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
18  #  #
19    
20    eval {
21        require FIG_Config;
22    };
23    
24  use URI::Escape;  # uri_escape  use URI::Escape;  # uri_escape
25  use gjoseqlib;  use gjoseqlib;
26  use HTML;  use HTML;
# Line 50  Line 54 
54  my $function = $cgi->param('function');  my $function = $cgi->param('function');
55  my $reaction = $cgi->param('reaction');  my $reaction = $cgi->param('reaction');
56  my $dataD    = $cgi->param('dataD');  my $dataD    = $cgi->param('dataD');
57    
58    #
59    # If we are operating in RAST, the csD sits within the
60    # RAST job directory and the dataD setting is the
61    # RAST job number.
62    #
63    
64  my $csD      = "/homes/overbeek/Ross/MakeCS.Kbase/Data/CS";  my $csD      = "/homes/overbeek/Ross/MakeCS.Kbase/Data/CS";
65    
66    if ($FIG_Config::rast_jobs && -d $FIG_Config::rast_jobs)
67    {
68        $csD = "$FIG_Config::rast_jobs/$dataD/CloseStrains";
69    }
70    
71  my $dataDF   = "$csD/$dataD";  my $dataDF   = "$csD/$dataD";
72    
73  my $parms = {};  my $parms = {};
# Line 207  Line 224 
224          my @genera = grep { $_ !~ /^\./ } readdir(GENERA);          my @genera = grep { $_ !~ /^\./ } readdir(GENERA);
225          closedir(GENERA);          closedir(GENERA);
226          print "<h1>What Changed?</h1>\n";          print "<h1>What Changed?</h1>\n";
227  #       print "<h2><a target=_blank href=\"http://bioseed.mcs.anl.gov/~overbeek/what_changed.html\">Getting Started: a short Tutorial</a></h2>\n";  #       print "<h2><a target='_blank' href=\"http://bioseed.mcs.anl.gov/~overbeek/what_changed.html\">Getting Started: a short Tutorial</a></h2>\n";
228          print "<h2>Genera Available</h2>\n";          print "<h2>Genera Available</h2>\n";
229          foreach my $g (sort @genera)          foreach my $g (sort @genera)
230          {          {
231              print "<h3><a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/wc.cgi?request=show_options_for_otu&dataD=$g>$g</a>\n";              print "<h3><a target='_blank' href='wc.cgi?request=show_options_for_otu&dataD=$g'>$g</a>\n";
232          }          }
233      }      }
234      else      else
# Line 226  Line 243 
243      if ((-s "$dataDF/virulence.functions") && ($dataDF =~ /([^\/]+)$/))      if ((-s "$dataDF/virulence.functions") && ($dataDF =~ /([^\/]+)$/))
244      {      {
245          my $dataDQ = uri_escape($1);          my $dataDQ = uri_escape($1);
246          return "<a target=_blank href=http://bioseed.mcs.anl.gov/ross/FIG/wc.cgi?request=show_virulence_functions&dataD=$dataDQ>Some Posssible Functions Associated with Virulence</a>";          return "<a target='_blank' href='wc.cgi?request=show_virulence_functions&dataD=$dataDQ'>Some Posssible Functions Associated with Virulence</a>";
247      }      }
248      return '';      return '';
249  }  }

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