cgi-bin/phenotype/population.pl

   1 #!/usr/bin/perl -w
   2
   3 #Main Page for Phenotypic Database
   4
   5 use strict;
   6 use CXGN::Page;
   7 use CXGN::DB::PhenoPopulation;
   8 use CGI;
   9
  10 #get parameters from form on previous page
  11 use CatalystX::GlobalContext qw( $c );
  12 my %params = %{$c->req->params};
  13 my $pop_id = $params{pop_id};
  14
  15 my $page = CXGN::Page->new('phenotype', 'Adri');
  16
  17 print "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 transitional//EN\" \"http://www.w3.org/tr/xhtml1/DTD/xhtml1-transitional.dtd\">";
  18
  19 #-------------------------------------------------
  20 my @populations = CXGN::DB::PhenoPopulation::get_all_populations;
  21 my $current_pop_id;
  22 my $current_pop_name;
  23
  24 #population selected
  25 if ($pop_id) {
  26   $current_pop_id = $pop_id;
  27   $current_pop_name = CXGN::DB::PhenoPopulation::get_pop_name_from_pop_id($pop_id);
  28 }
  29
  30 #no population selected, first one in DB is used as default
  31 else {
  32   $current_pop_id = $populations[0][0];
  33   $current_pop_name = $populations[0][1];
  34 }
  35
  36 my @genotypes = CXGN::DB::PhenoPopulation::get_all_gen_from_pop_id($current_pop_id);
  37 my @gen_ids;
  38 for my $i (0..$#genotypes) {
  39   push @gen_ids, $genotypes[$i][0];
  40 }
  41 my @prop_info_by_organ = CXGN::DB::PhenoPopulation::get_all_prop_info_by_organ_from_pop_id($current_pop_id);
  42
  43 $page->header($current_pop_name." Population");
  44
  45 print <<EOF
  46
  47 <table summary="" width="100%" cellpadding="0" cellspacing="10" border="0">
  48
  49 <tr><td valign="top">
  50 <center><h2><b><u>$current_pop_name Population</u></b></h2></center>
  51 </td></tr>
  52 EOF
  53 ;
  54
  55 #select box for populations
  56 if ($#populations > 0) {
  57   print "<tr><td valign=\"top\">";
  58   print "<table summary=\"\"><tr><td colspan=\"2\">";
  59   print "<form action=\"/phenotype/main_phenotype.pl\" method=\"get\">";
  60   print "<br />";
  61   print "<b><u>Change Population</u></b>\n<br />";
  62   print "Below is the list of population(s) currently in the database.  Select a population and click the button to search images and data in another population.";
  63   print "</td></tr>";
  64   print "<tr><td valign=\"top\" align=\"left\">";
  65   print "All Populations:  ";
  66   print "<select name=\"pop_id\">\n";
  67   for my $i (0..$#populations) {
  68     print "<option value=\"$populations[$i][0]\"> $populations[$i][1]</option>";
  69   }
  70   print "</select>";
  71   print "</td>";
  72   print "<td valign=\"top\" align=\"right\">";
  73   print "<input type=\"submit\" value=\"Change Population\" />";
  74   print "<br />";
  75   print "</form>";
  76   print "</td></tr></table>";
  77   print "</td></tr>";
  78
  79   #line
  80   print "<tr><td><img src=\"/documents/img/dot_clear.gif\" width=\"1\" height=\"10\" alt=\"\" /></td></tr>";
  81   print "<tr><td colspan=\"1\" bgcolor=\"#cccccc\"><img src=\"/documents/img/dot_clear.gif\" width=\"1\" height=\"1\" alt=\"\" /></td></tr>";
  82   print "<tr><td><img src=\"/documents/img/dot_clear.gif\" width=\"1\" height=\"10\" alt=\"\" /></td></tr>";
  83 }
  84
  85 print <<EOF
  86 <tr><td valign="top">
  87
  88 <table summary="" width="100%" cellpadding="0" cellspacing="0" border="0">
  89
  90 <!--genotypes-->
  91 <tr><td colspan="2">
  92 <form action="/phenotype/display_plants_from_genotype.pl" method="get">
  93 <table summary="" width="100%" cellpadding="0" cellspacing="0" border="0">
  94 <tr><td>
  95 <b><u>Search By GENOTYPES</u></b>
  96 </td></tr>
  97 <tr><td>
  98 Below is a list of all <b>genotypes</b> in the selected population above - selecting a genotype will take you to a page of plants with the selected genotype.  This new page will have links to all images and data of these plants:
  99 </td></tr>
 100 <tr><td valign="top" align="left">
 101 Genotypes in <b>$current_pop_name</b>:
 102 <select name="gen_id">
 103
 104 EOF
 105 ;
 106
 107 for my $i (0..$#genotypes) {
 108   print "<option value = \"$genotypes[$i][0]\"> $genotypes[$i][1]</option>";
 109 }
 110
 111 print <<EOF
 112 </select>
 113 <input type="hidden" name="pop_id" value="$current_pop_id" />
 114 <input type="hidden" name="pop_name" value="$current_pop_name" />
 115 </td>
 116 <td valign="top" align="right">
 117 <input type="submit" value="get Plants by Genotype" />
 118 </td></tr>
 119 </table>
 120 </form>
 121 </td></tr>
 122 EOF
 123     ;
 124
 125 my $current_pop_name_2 = $current_pop_name;
 126 $current_pop_name_2 =~ s/\s/%20/g;
 127
 128 print<<EOF
 129
 130 <!--properties-->
 131 <tr><td colspan="2">
 132 <form action="/phenotype/display_plants_from_property.pl" method="get">
 133 <table summary="">
 134 <tr><td>
 135 <b><u>Search By PROPERTIES</u></b> (<a href="display_prop_list.pl?pop_id=$current_pop_id&amp;pop_name=$current_pop_name_2">Property Descriptions</a>)
 136 </td></tr>
 137
 138 EOF
 139 ;
 140
 141 print "<tr><td>Below is a list of all <b>properties</b> measured in the selected population above - selecting a property will take you to a page of plants with the selected property measured.  This new page will have links to each plant's sample data and images:</td></tr>";
 142
 143 print "<tr><td width=\"100%\" valign=\"top\" align=\"left\">";
 144 print "Properties in <b>$current_pop_name</b>:";
 145 print "<select name=\"prop_id\">";
 146
 147 for my $i (0..$#prop_info_by_organ) {
 148   $prop_info_by_organ[$i] or next;
 149
 150   my $organ_name = $prop_info_by_organ[$i][0][2];
 151   print "<optgroup label=\"$organ_name\">";
 152   for my $j (0..$#{$prop_info_by_organ[$i]}) {
 153     my $prop_id = $prop_info_by_organ[$i][$j][0];
 154     my $prop_name = $prop_info_by_organ[$i][$j][1];
 155     print "<option value=\"$prop_id\"> $prop_name</option>";
 156   }
 157   print "</optgroup>";
 158 }
 159
 160 print <<EOF
 161 </select>
 162 <input type="hidden" name="pop_id" value="$current_pop_id" />
 163 <input type="hidden" name="pop_name" value="$current_pop_name" />
 164 </td>
 165 <td width="100%" valign="top" align="right">
 166 <input type="submit" value="get Plants by Property" />
 167 </td></tr>
 168 </table>
 169 </form>
 170 </td></tr>
 171
 172 <tr><td><img src="/documents/img/dot_clear.gif" width="1" height="10" alt="" /></td></tr>
 173 <tr><td colspan="1" bgcolor="#cccccc"><img src="/documents/img/dot_clear.gif" width="1" height="1" alt="" /></td></tr>
 174 <tr><td><img src="/documents/img/dot_clear.gif" width="1" height="10" alt="" /></td></tr>
 175
 176 <tr><td>
 177 <center><h3><u>Terminology</u></h3></center>
 178 </td></tr>
 179 <tr><td>
 180   <dl>
 181   <dt><b>Population</b></dt>
 182   <dd>all the organisms that constitute a specific group or occur in a specified location</dd>
 183   <dt><br /><b>Genotype</b></dt>
 184   <dd>a group of organisms sharing a specific genetic constitution</dd>
 185   <dt><br /><b>Property/Phenotype</b></dt>
 186   <dd>the observable physical or biochemical characteristics of an organism, as determined by both genetic makeup and environmental influences</dd>
 187   </dl>
 188
 189 </td></tr>
 190 </table>
 191 </td></tr>
 192 </table>
 193
 194 EOF
 195 ;
 196
 197 $page->footer();