cgi-bin/phenome/qtl_form.pl

   1 =head1 DESCRIPTION
   2 creates all the web forms for the qtl data submission
   3 and sends the data to qtl_load.pl for processing
   4 and loading it to the database.
   5
   6 =head1 AUTHOR
   7 Isaak Y Tecle (iyt2@cornell.edu)
   8
   9 =cut
  10
  11
  12
  13 use strict;
  14 my $qtl_form_detail_page = CXGN::Phenome::QtlFormDetailPage->new();
  15
  16 package CXGN::Phenome::QtlFormDetailPage;
  17
  18
  19
  20 use File::Spec;
  21 use CXGN::VHost;
  22 use CXGN::Page;
  23 use CXGN::Scrap;
  24 use CXGN::Scrap::AjaxPage;
  25 use CXGN::Page::FormattingHelpers qw /info_section_html
  26                                       page_title_html
  27                                       columnar_table_html
  28                                       html_optional_show
  29                                       info_table_html
  30                                       tooltipped_text
  31                                       html_alternate_show
  32                                       /;
  33 use CXGN::DB::Connection;
  34 use CXGN::Phenome::Qtl;
  35 use CXGN::Phenome::Qtl::Tools;
  36 use CXGN::Phenome::Population;
  37 use CXGN::Login;
  38
  39
  40 sub new {
  41     my $class = shift;
  42     my $self = bless {}, $class;
  43     $self->display();
  44
  45     return $self;
  46 }
  47
  48
  49 sub display {
  50     my $self = shift;
  51     my $dbh = CXGN::DB::Connection->new();
  52     my $login = CXGN::Login->new($dbh);
  53
  54     my $sp_person_id = $login->verify_session();
  55
  56
  57     my %args = {};
  58     my $page = CXGN::Page->new("SGN", "isaak");
  59     $page->jsan_use("CXGN.Phenome.Tools");
  60     $page->jsan_use("CXGN.Phenome.Qtl");
  61     $page->jsan_use("MochiKit.DOM");
  62     $page->jsan_use("MochiKit.Async");
  63     $page->jsan_use("Prototype");
  64     $page->jsan_use("jquery");
  65
  66     %args = $page->get_all_encoded_arguments();
  67     my $type = $args{type};
  68
  69     my $pop_id = $args{pop_id};
  70     if ($sp_person_id) {
  71         my $intro = $self->intro();
  72         my ($org_submit, $pop_submit) = $self->org_pop_form();
  73         my $traits_submit = $self->traits_form($pop_id);
  74         my $pheno_submit = $self->pheno_form($pop_id);
  75         my $geno_submit = $self->geno_form($pop_id);
  76         my $stat_submit = $self->stat_form($pop_id);
  77         my $conf_submit = $self->conf_form($pop_id);
  78
  79
  80         if(!$type) {
  81             $page->header("QTL Data Submission Page");
  82             print page_title_html("Step 0:  Introduction");
  83             print $intro;
  84
  85         }
  86
  87         elsif($type eq 'pop_form') {
  88             $page->header("QTL Data Submission Page");
  89             print page_title_html("Step 1:  Submit Population Details");
  90             print $org_submit;
  91             print $pop_submit;
  92         }
  93
  94
  95         elsif ($type eq 'trait_form') {
  96              $page->header("QTL Data Submission Page");
  97              print page_title_html("Step 2: Submit the List of Traits");
  98              print $traits_submit;
  99
 100         }
 101
 102
 103         elsif ($type eq 'pheno_form') {
 104             $page->header("QTL Data Submission Page");
 105              print page_title_html("Step 3: Submit the Phenotype Data");
 106              print $pheno_submit;
 107
 108         }
 109
 110         elsif ($type eq 'geno_form') {
 111             $page->header("QTL Data Submission Page");
 112              print page_title_html("Step 4: Submit the Genotype Data");
 113              print $geno_submit;
 114
 115         }
 116
 117
 118         elsif ($type eq 'stat_form') {
 119             $page->header("QTL Data Submission Page");
 120
 121             print page_title_html("Step 5: Set the Statistical Parameters
 122                                     for the QTL Analysis"
 123                                   );
 124              print $stat_submit;
 125
 126         }
 127
 128         elsif ($type eq 'confirm') {
 129             $page->header("Confirmation page");
 130             print page_title_html("Step 6: Confirmation");
 131             print $conf_submit;
 132
 133         }
 134
 135         $page->footer();
 136
 137 }
 138
 139     else {
 140         print "To access the QTL data submission form and analysis, please login first.
 141            <br/>If you don't have an account with SGN, you can create
 142            one using this <a href= /solpeople/new-account.pl>form</a>.";
 143
 144         $page->footer();
 145
 146         exit();
 147
 148     }
 149
 150 }
 151
 152
 153 sub org_pop_form {
 154     my $self = shift;
 155
 156     my $taxon_subtitle = qq| <a href="javascript:Qtl.toggleAssociateTaxon()">[Select Organism]</a> |;
 157     my $required = qq | <font color="red"><sup>*</sup></font>|;
 158     my $organism_form = $self->associate_organism();
 159
 160     my $guide = $self->guideline();
 161
 162     my $org_sec = CXGN::Page::FormattingHelpers::info_section_html(
 163                                                                    title     =>"Select Organism",
 164                                                                    subtitle  =>$taxon_subtitle . " | " . $guide ,
 165                                                                    contents  => $organism_form,
 166                                                                    id        =>"organism_search",
 167                                                                   );
 168     my $pop_sec = CXGN::Page::FormattingHelpers::info_section_html(
 169                                                                   title    =>'Population Details',
 170                                                                   contents =>"$required <i>must be filled.</i> ",
 171                                                                   );
 172
 173     my $qtltools = CXGN::Phenome::Qtl::Tools->new();
 174     my %cross_types =  $qtltools->cross_types();
 175
 176
 177     my $cross_options;
 178     foreach my $key (keys %cross_types) {
 179         $cross_options .= qq |<option value="$key">$cross_types{$key} |;
 180     }
 181
 182
 183     my $parent_m = tooltipped_text('Male parent', 'format eg. Solanum lycopersicum cv moneymaker');
 184
 185     my $parent_f = tooltipped_text('Female parent', 'format eg. Solanum lycopersicum cv micro tom');
 186
 187     my $pop_form = qq^
 188     <form action="qtl_load.pl" method="POST" enctype="MULTIPART/FORM-DATA">
 189      $pop_sec
 190      <table>
 191      <tr>
 192          <td>Cross type$required</td>
 193          <td> <select name="pop_type">
 194                   $cross_options
 195              </select>
 196          </td>
 197      </tr>
 198      <tr>
 199         <td>Population name$required</td>
 200         <td><input type="text" name="pop_name" size=42></td>
 201      </tr>
 202      <tr>
 203          <td>Population description$required</td>
 204          <td><textarea name="pop_desc" rows = 5 cols=44></textarea></td>
 205      </tr>
 206      <tr>
 207         <td>$parent_f$required</td>
 208         <td><input type="text" name="pop_female_parent" size=24></td>
 209         <td>$parent_m$required</td>
 210         <td><input type="text" name="pop_male_parent" size=24></td>
 211      </tr>
 212      <tr>
 213         <td>Recurrent parent</td>
 214         <td><input type="text" name="pop_recurrent_parent" size=24></td>
 215         <td>Donor parent</td>
 216         <td><input type="text" name="pop_donor_parent" size=24></td>
 217      </tr>
 218      <tr>
 219       <td>Do you want to make the data public?</td>
 220       <td><input type="radio" name="pop_is_public" value="true" checked />Yes</td>
 221       <td><input type="radio" name="pop_is_public" value="false" />No</td>
 222      </tr>
 223      <tr>
 224        <td>&nbsp;</td><td>&nbsp;</td>
 225        <td><input type="hidden" name="type" value="pop_form"></td>
 226        <td><input type="submit" value="Submit"></td>
 227      </tr>
 228      </table>
 229      </form>
 230
 231 ^;
 232
 233 return $org_sec, $pop_form;
 234
 235 }
 236 #########################
 237
 238
 239
 240
 241 sub traits_form {
 242     my $self = shift;
 243     my $pop_id = shift;
 244
 245     my $guide = $self->guideline();
 246     my $trait = tooltipped_text('Traits list', 'in tab delimited format');
 247
 248     my $traits_sec = CXGN::Page::FormattingHelpers::info_section_html(
 249                                                                   title    => 'Traits list',
 250                                                                   subtitle => $guide,
 251                                                                   contents => " ",
 252                                                                   );
 253
 254     my $traits_form = qq^
 255     <form action="qtl_load.pl" method="POST" enctype="MULTIPART/FORM-DATA">
 256      $traits_sec
 257      <table cellspacing=20>
 258      <tr>
 259        <td>$trait:</td>
 260        <td><input type="file" name="trait_file" size=40>
 261        <td> <input type="hidden" name="type" value="trait_form"></td>
 262        <td> <input type="hidden" name="pop_id" value = $pop_id></td>
 263        <td><input type="submit" value="Submit"> </td>
 264      </tr>
 265      </table>
 266      </form>
 267 ^;
 268
 269 return $traits_form;
 270
 271 }
 272
 273 sub pheno_form {
 274     my $self = shift;
 275     my $pop_id = shift;
 276     my $guide= $self->guideline();
 277
 278     my $phenotype = tooltipped_text('Phenotype dataset', 'in tab delimited format');
 279
 280     my $pheno_sec = CXGN::Page::FormattingHelpers::info_section_html(
 281                                                                   title    => 'Phenotype dataset',
 282                                                                   subtitle => "$guide",
 283                                                                   contents => " ",
 284                                                                   );
 285
 286     my $pheno_form = qq^
 287     <form action="qtl_load.pl" method="POST" enctype="MULTIPART/FORM-DATA">
 288      $pheno_sec
 289      <table cellspacing=20>
 290      <tr>
 291        <td>$phenotype:</td>
 292        <td><input type="file" name="pheno_file" size=40>
 293        <td> <input type="hidden" name="type" value="pheno_form"></td>
 294        <td> <input type="hidden" name="pop_id" value = $pop_id></td>
 295        <td><input type="submit" value="Submit"> </td>
 296      </tr>
 297     </table>
 298 </form>
 299 ^;
 300
 301 return $pheno_form;
 302
 303 }
 304
 305
 306 sub geno_form {
 307     my $self = shift;
 308     my $pop_id = shift;
 309     my $guide= $self->guideline();
 310
 311     my $genotype = tooltipped_text('Genotype dataset', 'in tab delimited format');
 312     my $geno_sec = CXGN::Page::FormattingHelpers::info_section_html(
 313                                                                   title    => 'Genotype dataset',
 314                                                                   subtitle => $guide,
 315                                                                   contents => " ",
 316                                                                   );
 317     my $geno_form = qq^
 318     <form action="qtl_load.pl" method="POST" enctype="MULTIPART/FORM-DATA">
 319      $geno_sec
 320      <table cellspacing=20>
 321      <tr>
 322         <td>$genotype:</td>
 323         <td><input type="file" name="geno_file" size=40>
 324         <td> <input type="hidden" name="type" value="geno_form"></td>
 325         <td> <input type="hidden" name="pop_id" value=$pop_id></td>
 326         <td><input type="submit" value="Submit"> </td>
 327      </tr>
 328      </table>
 329      </form>
 330 ^;
 331
 332 return $geno_form;
 333
 334 }
 335
 336
 337 sub stat_form {
 338     my $self = shift;
 339     my $pop_id = shift;
 340     my $guide = $self->guideline();
 341     my $no_draws = tooltipped_text('No. of imputations', 'required only if the
 342                                     Simulate method is selected for the
 343                                     calculation of QTL genotype probability method and Multiple Imputation');
 344     my $permu_level = tooltipped_text('Significance level of permutation test',
 345                                       'required only if permutation analysis
 346                                       (LOD threshold) is run');
 347     my $genome_scan = tooltipped_text('Genome scan size (cM):', 'not required for Marker Regression'
 348                                       );
 349     my $qtl_prob = tooltipped_text('QTL genotype probablity method:', 'not required for Marker Regression'
 350                                       );
 351
 352     my $stat_sec =CXGN::Page::FormattingHelpers::info_section_html(
 353                                                                   title   => 'Statistical Parameters',
 354                                                                   subtitle => $guide,
 355                                                                   contents => " ",
 356                                                                   );
 357
 358
 359     my $stat_form = qq^
 360     <form action="qtl_load.pl" method="POST" enctype="MULTIPART/FORM-DATA">
 361
 362         $stat_sec
 363
 364     <table cellspacing=20>
 365         <tr><td>QTL model: </td>
 366             <td> <select name="stat_qtl_model">
 367                          <option>
 368                          <option>Single-QTL Scan
 369                          <option style="color: #FF0000;text-decoration: line-through">Two-QTL Scan--currently not available
 370                          </select>
 371            </td>
 372            <td>QTL mapping method:</td>
 373            <td><select name="stat_qtl_method">
 374                     <option>
 375                     <option>Marker Regression
 376                     <option>Maximum Likelihood
 377                     <option>Haley-Knott Regression
 378                     <option>Multiple Imputation
 379                 </select>
 380            </td>
 381       </tr>
 382       <tr><td>$qtl_prob</td>
 383           <td><select name="stat_prob_method">
 384                       <option>
 385                       <option>Calculate
 386                       <option>Simulate
 387               </select>
 388          </td>
 389          <td>QTL genotype probability significance level:</td>
 390          <td><select name="stat_prob_level">
 391                     <option>
 392                     <option>0.001
 393                     <option>0.05
 394                     <option>0.1
 395            </select>
 396          </td>
 397          </tr>
 398          <tr>
 399          <td>$genome_scan</td>
 400          <td><select name="stat_step_size">
 401                      <option>
 402                      <option>zero
 403                      <option>1
 404                      <option>2.5
 405                      <option>5
 406                      <option>10
 407               </select>
 408          </td>
 409          <td>$no_draws</td>
 410          <td><select name="stat_no_draws">
 411                     <option>
 412                     <option>5
 413                     <option>10
 414                     <option>15
 415                     <option>20
 416             </select>
 417         </td>
 418     </tr>
 419     <tr>
 420        <td>No. of permutations:</td>
 421        <td><select name="stat_permu_test">
 422                     <option>
 423                     <option>None
 424                     <option>100
 425                     <option>1000
 426            </select>
 427        </td>
 428        <td>$permu_level:</td>
 429        <td> <select name="stat_permu_level">
 430                     <option>
 431                     <option>0.05
 432                     <option>0.001
 433                     <option>0.1
 434            </select>
 435        </td>
 436     </tr>
 437     <tr>
 438       <td> <input type="hidden" name="type" value="stat_form"></td>
 439       <td> <input type="hidden" name="pop_id" value = $pop_id ></td>
 440     </tr>
 441     <tr>
 442       <td></td>
 443       <td><input type="submit" value="Submit"> </td>
 444       <td></td>
 445       <td> <input type="reset"  value="Reset"></td>
 446     </tr>
 447    </table>
 448    </form>
 449 ^;
 450
 451
 452 return $stat_form;
 453
 454 }
 455
 456
 457 sub associate_organism {
 458     my $self = shift;
 459
 460     my $associate = qq^
 461      <div id= 'associateTaxonForm' style="display: none">
 462      <div id= "organism_search">
 463     Common name:
 464     <input type="text"
 465            style="width: 50%"
 466            id="organism_name"
 467            onkeyup="Qtl.getTaxons(this.value)">
 468     <input type="button"
 469            id="associate_taxon_button"
 470            value="associate organism"
 471            disabled="true"
 472            onclick="Qtl.associateTaxon();this.disabled=false;">
 473     <select id="taxon_select"
 474             style="width: 100%"
 475             onchange="Tools.enableButton('associate_taxon_button');"
 476             size=10>
 477        </select>
 478   </div>
 479
 480 </div>
 481 ^;
 482
 483     return $associate;
 484
 485
 486 }
 487
 488 sub conf_form {
 489     my $self = shift;
 490     my $pop_id = shift;
 491     my $guide = $self->guideline();
 492     my $dbh = CXGN::DB::Connection->new();
 493
 494     my $conf_sec =CXGN::Page::FormattingHelpers::info_section_html(
 495                                                                   title   => ' ',
 496                                                                   subtitle => "$guide",
 497                                                                   contents => ' ',
 498                                                                );
 499
 500     my ($pop_link, $pop_name);
 501
 502     if ($pop_id)  {
 503         my $pop = CXGN::Phenome::Population->new($dbh, $pop_id);
 504         $pop_name = $pop->get_name();
 505         $pop_link = qq | <a href="/phenome/population.pl?population_id=$pop_id"><b>$pop_name</b></a> |;
 506     }
 507
 508     my $conf_form = qq^
 509     <form action=" " method="POST" enctype="MULTIPART/FORM-DATA">
 510     $conf_sec
 511     <table cellspacing=20>
 512     <tr>
 513       <td><b><p>You have successfully  uploaded your QTL data.</p>
 514            <p>On the next page you will see the population data summary.
 515           The qtl analysis is performed on-the-fly and you need to click the
 516           graph icon  corresponding to the trait of your interest to proceed
 517           with the QTL mapping analysis. The QTL analysis takes a few minutes,
 518           so please be patient. </p>
 519           <p>To continue to the QTL analysis page, follow the link below:</p>
 520           $pop_link</b>
 521       </td>
 522      </tr>
 523    </table>
 524   </form>
 525
 526 ^;
 527
 528 return $conf_form;
 529
 530 }
 531
 532
 533 sub intro {
 534     my $self = shift;
 535     my $guide = $self->guideline();
 536     my $intro_sec =CXGN::Page::FormattingHelpers::info_section_html(
 537                                                                  title => 'Introduction',
 538                                                                   subtitle   => $guide,
 539                                                                   contents => ' ',
 540                                                                );
 541
 542
 543     my $intro = qq^
 544        <form action="qtl_load.pl" method="POST" enctype="MULTIPART/FORM-DATA">
 545         $intro_sec
 546       <table cellspacing=20>
 547         <tr><td>
 548
 549         <p>The uploading of QTL data needs to be done in one session.
 550            Therefore, have ready your data files before starting the
 551            process.
 552         </p>
 553
 554         <p>The data you need are:</p>
 555
 556         <ul>
 557            <li>Some basic information about the population
 558            <li>Traits file (tab delimited): List of traits,
 559                 definition, units of measurement.
 560            <li>Phenotype data file (tab delimited):
 561            <li>Genotype data file (tab delimited):
 562            <li>Statistical parameters.
 563         </ul>
 564
 565         <p>The QTL data  uploading software is at Beta stage. If you have any problems
 566            uploading your data or remarks, please send us your feedback.
 567         </p>
 568      </td>
 569     </tr>
 570     <tr>
 571       <td> <input type="hidden"  name = "type" value="begin"> </td>
 572       <td> <input type="submit" value="Begin Uploading"> </td>
 573     </tr>
 574    </table>
 575   </form>
 576 ^;
 577
 578 return $intro;
 579
 580 }
 581
 582
 583 sub guideline {
 584     my $self = shift;
 585     return my $guideline = qq |<a  href="http://docs.google.com/View?id=dgvczrcd_1c479cgfb">Guidelines</a> |;
 586 }