cgi-bin/solpeople/cosii_submission.pl

   1 use Modern::Perl;
   2 use CXGN::Page;
   3 use CXGN::DB::Connection;
   4 use CXGN::Marker::Tools;
   5 use CXGN::Accession;
   6 use CXGN::Accession::Tools;
   7 use CXGN::Login;
   8 use CXGN::Tools::Text;
   9
  10 my $dbh=CXGN::DB::Connection->new();
  11
  12 my $login=CXGN::Login->new($dbh);
  13 $login->verify_session();
  14
  15 my $page=CXGN::Page->new('cosii_submission.pl','john');
  16
  17 $page->header('Submit COSII primer experiment');
  18 my($action,$marker_name,$accession_id,$primer_type,$temp,$mg,$bands)=$page->get_encoded_arguments('action','marker_name','accession_id','primer_type','temp','mg','bands');
  19 my $marker_id;
  20 my $accession_name;
  21
  22 if($action eq 'verify' or $action eq 'insert') {
  23     my @marker_ids=CXGN::Marker::Tools::marker_name_to_ids($dbh,$marker_name);
  24
  25     unless(@marker_ids) {
  26         $page->message_page("Marker '$marker_name' not found.");
  27     }
  28
  29     #i don't want to write any error handling here, because all cosii marker names (currently) refer to one marker each
  30     if(@marker_ids>1) {
  31         $page->message_page("Multiple markers found with name '$marker_name'. Please contact us to resolve this issue.");
  32     }
  33
  34     ($marker_id)=@marker_ids;
  35
  36     #test accession
  37     my $accession=CXGN::Accession->new($dbh,$accession_id);
  38     unless($accession) {
  39         $page->message_page("Accession ID '$accession_id' not found in database");
  40     }
  41     $accession_name=$accession->verbose_name();
  42
  43     #test primer type
  44     unless($primer_type eq 'iUPA' or $primer_type eq 'eUPA') {
  45         $page->message_page("Primer type '$primer_type' is unknown");
  46     }
  47
  48     #test temp
  49     unless($temp=~/^\d+$/) {
  50         $page->message_page("Temperature '$temp' is unrecognized, please submit a whole number only");
  51     }
  52     if($temp>500) {
  53         $page->message_page("Temperature '$temp' is invalid");
  54     }
  55
  56     #test mg
  57     unless(CXGN::Tools::Text::is_number($mg)) {
  58         $page->message_page("Mg concentration is unrecognized, please submit a number or a number including one decimal point only");
  59     }
  60
  61     #test bands
  62     unless($bands eq 'M' or $bands eq 'm' or $bands=~/^\d+$/ or $bands=~/^\d+\+\d+$/) {
  63         $page->message_page("Band sizes are unrecognized, please see examples and be sure not to include any spaces in your input");
  64     }
  65     if($bands eq 'm') {
  66         $bands='M';
  67     }
  68 }
  69
  70
  71
  72
  73
  74 if($action eq 'verify')
  75 {
  76     print CXGN::Page::FormattingHelpers::page_title_html('Verify data');
  77     print"<b>Marker name:</b> $marker_name (SGN-M$marker_id)<br />";
  78     print"<b>Accession:</b> $accession_name (SGN accession ID:</b> $accession_id)<br />";
  79     print"<b>Primer type:</b> $primer_type<br />";
  80     print"<b>Temperature:</b> $temp<br />";
  81     print"<b>Mg concentration:</b> $mg<br />";
  82     print"<b>Bands:</b> $bands<br /><br />";
  83     print <<END_HTML;
  84 <form method="post" action="">
  85 <input type="hidden" name="marker_id" value="$marker_id" />
  86 <input type="hidden" name="marker_name" value="$marker_name" />
  87 <input type="hidden" name="accession_id" value="$accession_id" />
  88 <input type="hidden" name="primer_type" value="$primer_type" />
  89 <input type="hidden" name="temp" value="$temp" />
  90 <input type="hidden" name="mg" value="$mg" />
  91 <input type="hidden" name="bands" value="$bands" />
  92 <input type="hidden" name="action" value="insert" />
  93 <input type="submit" value="Add new data" />
  94 END_HTML
  95     exit(0);
  96 }
  97
  98
  99
 100
 101
 102 if($action eq 'insert')
 103 {
 104     print CXGN::Page::FormattingHelpers::page_title_html('Pretended to add this data');
 105     print"<a href=\"/search/markers/markerinfo.pl?marker_id=$marker_id\">[View marker with new data]</a><br /><br />";
 106     print"<b>Marker name:</b> $marker_name (SGN-M$marker_id)<br />";
 107     print"<b>Accession:</b> $accession_name (SGN accession ID:</b> $accession_id)<br />";
 108     print"<b>Primer type:</b> $primer_type<br />";
 109     print"<b>Temperature:</b> $temp<br />";
 110     print"<b>Mg concentration:</b> $mg<br />";
 111     print"<b>Bands:</b> $bands<br />";
 112     print"<hr />"
 113 }
 114
 115
 116
 117
 118
 119 my $marker_name_filled_in='C2_At';
 120 if($marker_name)
 121 {
 122     $marker_name_filled_in=$marker_name;
 123 }
 124 my $temp_filled_in='55';
 125 if($temp)
 126 {
 127     $temp_filled_in=$temp;
 128 }
 129 my $mg_filled_in='1.5';
 130 if($mg)
 131 {
 132     $mg_filled_in=$mg;
 133 }
 134 my $bands_filled_in='';
 135 if($bands)
 136 {
 137     $bands_filled_in=$bands;
 138 }
 139 my @accessions=CXGN::Accession::Tools::all_accessions($dbh);
 140 my $accessions_selector='<select name="accession_id">';
 141 for my $accession_hash(sort {$a->{verbose_name} cmp $b->{verbose_name}} @accessions)
 142 {
 143     my $each_accession_id=$accession_hash->{accession_id};
 144     my $each_accession_name=$accession_hash->{verbose_name};
 145     #warn"$each_accession_id\n";
 146     my $selected='';
 147     if($each_accession_id==$accession_id)
 148     {
 149         $selected=' selected="selected" ';
 150     }
 151     $accessions_selector.="<option value=\"$each_accession_id\" $selected>$each_accession_name</option>";
 152 }
 153 $accessions_selector.='</select>';
 154 my $iupa_selected='checked="checked"';
 155 my $eupa_selected='';
 156 if($primer_type and $primer_type eq 'eUPA')
 157 {
 158     $iupa_selected='';
 159     $eupa_selected='checked="checked"';
 160 }
 161 print <<END_HTML;
 162 <center>
 163 <form method="post" action="">
 164 <table cellspacing="10" cellpadding="10" border="0">
 165
 166 <tr>
 167 <td>
 168 Marker name<br />
 169 <input type="text" name="marker_name" value="$marker_name_filled_in" /><br />
 170 </td>
 171 <td>
 172 Primer type<br />
 173 <input type="radio" name="primer_type" value="iUPA" $iupa_selected />iUPA<br />
 174 <input type="radio" name="primer_type" value="eUPA" $eupa_selected />eUPA
 175 </td>
 176 </tr>
 177
 178 <tr>
 179 <td colspan="2">
 180 Accession<br />
 181 $accessions_selector
 182 <br />To add an accession to this list, <a href="/contact/form">contact SGN</a>.
 183 </td>
 184 </tr>
 185
 186 <tr>
 187 <td>
 188 Temperature (C)<br />
 189 <input type="text" name="temp" value="$temp_filled_in" /><br />
 190 </td>
 191 <td>
 192 Mg concentration<br />
 193 <input type="text" name="mg" value="$mg_filled_in" /><br /><br />
 194 </td>
 195 </tr>
 196
 197 <tr>
 198 <td>
 199 Band sizes<br />
 200 <input type="text" name="bands" value="$bands_filled_in" />
 201 </td>
 202 <td>
 203 Band size examples:<br />
 204 1 band: <b>300</b><br />
 205 2 bands separated by a '+' sign: <b>300+500</b><br />
 206 'M' for more than 2: <b>M</b>
 207 </td>
 208 </tr>
 209
 210 <tr>
 211 <td colspan="2">
 212 <input type="hidden" name="action" value="verify" />
 213 <input type="submit" value="Verify" />
 214 </td>
 215 </tr>
 216
 217 </table>
 218 </form>
 219 </center>
 220 END_HTML
 221 $page->footer();