cgi-bin/phenotype/index.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 $page->header("Search the Phenotype Database");
  20
  21 #-------------------------------------------------
  22 my @populations = CXGN::DB::PhenoPopulation::get_all_populations;
  23 my $current_pop_id;
  24 my $current_pop_name;
  25
  26 #population selected
  27 if ($pop_id) {
  28   $current_pop_id = $pop_id;
  29   $current_pop_name = CXGN::DB::PhenoPopulation::get_pop_name_from_pop_id($pop_id);
  30 }
  31
  32 #no population selected, first one in DB is used as default
  33 else {
  34   $current_pop_id = $populations[0][0];
  35   $current_pop_name = $populations[0][1];
  36 }
  37
  38 my @genotypes = CXGN::DB::PhenoPopulation::get_all_gen_from_pop_id($current_pop_id);
  39 my @gen_ids;
  40 for my $i (0..$#genotypes) {
  41   push @gen_ids, $genotypes[$i][0];
  42 }
  43 my @prop_info_by_organ = CXGN::DB::PhenoPopulation::get_all_prop_info_by_organ_from_pop_id($current_pop_id);
  44
  45 print <<EOF
  46
  47 <table summary="" width="100%" cellpadding="0" cellspacing="10" border="0">
  48
  49 <tr><td valign="top">
  50 <table summary="" width="100%" cellpadding="0" cellspacing="0" border="0">
  51
  52 <tr><td>
  53 <center>
  54 <h3><u>Welcome to the Phenotype Database</u></h3>
  55 <p>From this page, you can search the phenotype databse for data and images of all plants from all populations.</p>
  56 <p>There are two ways to find specific data and images: searching by genotype and phenotype.</p>
  57 </center>
  58 </td></tr>
  59
  60 <tr><td><img src="/documents/img/dot_clear.gif" width="1" alt="" height="10" /></td></tr>
  61 <tr><td colspan="1" bgcolor="#cccccc"><img src="/documents/img/dot_clear.gif" alt="" width="1" height="1" /></td></tr>
  62 <tr><td><img src="/documents/img/dot_clear.gif" width="1" height="10" alt="" /></td></tr>
  63
  64 <tr><td>
  65 <center><h3><u>Search the Phenotype Database</u></h3></center>
  66
  67 <center>
  68 <table summary="" width="100%" cellpadding="0" cellspacing="0" border="0">
  69
  70 <tr><td>
  71 <!--populations-->
  72 <form action="#" method="get">
  73 <table summary="">
  74 <tr><td valign="top">
  75
  76 EOF
  77 ;
  78
  79 print "<b><u>selected POPULATION:</u> $current_pop_name</b>";
  80
  81 print <<EOF
  82 </td></tr>
  83 <tr><td><p>Below is the list of population(s) currently in the database. Select a population and click the button to search images and data in another population.</p></td></tr>
  84 <tr><td valign="top" align="left">
  85 All Populations:
  86 <select name="pop_id">
  87 EOF
  88 ;
  89
  90 for (0..$#populations) {
  91   print "<option value = \"$populations[$_][0]\">$populations[$_][1]</option>";
  92 }
  93
  94 print <<EOF
  95 </select>
  96 </td>
  97 <td valign="top" align="right">
  98 <input type="submit" value="Change Population" />
  99 </td></tr>
 100 </table>
 101 </form>
 102 </td></tr>
 103
 104 <!--genotypes-->
 105
 106 <tr><td>
 107 <form action="/phenotype/display_plants_from_genotype.pl" method="get">
 108 <table summary="">
 109 <tr><td>
 110 <b><u>Search By GENOTYPES</u></b>
 111 </td></tr>
 112 <tr><td><p>Below is a list of all <b>genotypes</b> in the selected population above -
 113 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:</p></td></tr>
 114 <tr><td valign="top" align="left">
 115
 116 EOF
 117 ;
 118
 119 print "Genotypes in <b>$current_pop_name</b>:";
 120 print "<select name=\"gen_id\">";
 121 for my $i (0..$#genotypes) {
 122   print "<option value = \"$genotypes[$i][0]\"> $genotypes[$i][1]</option>";
 123 }
 124 print "</select>";
 125 print "<input type=\"hidden\" name=\"pop_id\" value=\"$current_pop_id\" />";
 126 print "<input type=\"hidden\" name=\"pop_name\" value=\"$current_pop_name\" />";
 127
 128 print <<EOF
 129 </td>
 130 <td valign="top" align="right">
 131 <input type="submit" value="get Plants by Genotype" />
 132 </td></tr>
 133 </table>
 134 </form>
 135 </td></tr>
 136
 137 <!--properties-->
 138 <tr><td>
 139 <form action="/phenotype/display_plants_from_property.pl" method="get">
 140 <table summary=""><tr><td>
 141 <b><u>Search By PROPERTIES</u></b> (<a href="display_prop_list.pl">Property Descriptions</a>)
 142 </td></tr>
 143 <tr><td>
 144 EOF
 145 ;
 146
 147 print "<p>Below is a list of all <b>properties</b> measured in the selected population above -
 148 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:</p>";
 149
 150 print "</td></tr>";
 151 print "<tr><td width=\"100%\" valign=\"top\" align=\"left\">";
 152
 153 print "Properties in <b>$current_pop_name</b>:";
 154 print "<select name=\"prop_id\">";
 155
 156 for (0..$#prop_info_by_organ) {
 157   my $i = $_;
 158   $prop_info_by_organ[$i] or next;
 159   my $organ_name = $prop_info_by_organ[$i][0][2];
 160   print "<optgroup label=\"$organ_name\">";
 161   for (0..$#{$prop_info_by_organ[$i]}) {
 162     my $j = $_;
 163     my $prop_id = $prop_info_by_organ[$i][$j][0];
 164     my $prop_name = $prop_info_by_organ[$i][$j][1];
 165     print "<option value = \"$prop_id\">$prop_name</option>\n";
 166   }
 167   print "</optgroup>";
 168 }
 169
 170 print "</select>";
 171 print "<input type=\"hidden\" name=\"pop_id\" value=\"$current_pop_id\" />";
 172 print "<input type=\"hidden\" name=\"pop_name\" value=\"$current_pop_name\" />";
 173
 174 print <<EOF
 175
 176 </td>
 177 <td width="100%" valign="top" align="right">
 178 <input type="submit" value="get Plants by Property" />
 179 </td></tr></table>
 180 </form>
 181 </td></tr>
 182
 183 </table>
 184 </center>
 185 </td>
 186 </tr>
 187
 188 </table>
 189 </td></tr>
 190
 191 <tr><td><img src="/documents/img/dot_clear.gif" width="1" height="10" alt="" /></td></tr>
 192 <tr><td bgcolor="#cccccc"><img src="/documents/img/dot_clear.gif" width="1" height="1" alt="" /></td></tr>
 193 <tr><td><img src="/documents/img/dot_clear.gif" width="1" height="10" alt="" /></td></tr>
 194
 195 <!--terminology-->
 196 <tr><td>
 197 <center><h3><u>Terminology</u></h3></center>
 198
 199 <table summary="" width="100%" cellpadding="0" cellspacing="0" border="0">
 200 <tr><td>
 201
 202 <dl>
 203 <dt><b>Population</b></dt>
 204 <dd>all the organisms that constitute a specific group or occur in a specified location.</dd>
 205 <dt><br /><b>Genotype</b></dt>
 206 <dd>a group of organisms sharing a specific genetic constitution.</dd>
 207 <dt><br /><b>Property/Phenotype</b></dt>
 208 <dd>the observable physical or biochemical characteristics of an organism, as determined by both genetic makeup and environmental influences.</dd>
 209 </dl>
 210
 211 </td></tr>
 212 </table>
 213
 214 </td></tr>
 215
 216 </table>
 217 EOF
 218 ;
 219
 220 #--------------------------
 221 $page->footer();