cgi-bin/maps/physical/clone_reg.pl

   1 use strict;
   2 use warnings;
   3
   4 use Memoize;
   5
   6 use JSON;
   7
   8 use Tie::UrlEncoder;
   9 our %urlencode;
  10
  11 use CXGN::Page;
  12 use CXGN::Page::FormattingHelpers qw( info_section_html
  13                                       modesel
  14                                       columnar_table_html
  15                                       simple_selectbox_html
  16                                       info_table_html
  17                                       tooltipped_text
  18                                       truncate_string
  19                                     );
  20 use CXGN::Tools::List qw/distinct str_in evens/;
  21
  22 use CXGN::People::BACStatusLog;
  23 use CXGN::Genomic::Search::Clone;
  24 use CXGN::Search::CannedForms;
  25
  26 ##########   DATA FIELD DEFINITIONS #######
  27 my @data_fields_defs =
  28   (
  29    seq_proj     => { column_name => 'Seq Chrom',
  30                      tooltip => 'The chromosome project (if any) that is sequencing the BAC',
  31                    },
  32    seq_status   => { tooltip => "The BAC's status in sequencing",
  33                    },
  34 #    gb_status    => { column_name => 'GB Status',
  35 #                    tooltip => "User-reported HTGS level of this BAC's sequence in GenBank, if any",
  36 #                  },
  37    il_proj      => { column_name => 'IL Proj',
  38                      tooltip => "The sequencing project assigned to map this BAC to the Zamir IL bins",
  39                      value => 'il_proj_id',
  40                      display => 'il_proj_name',
  41                    },
  42    il_chr       => { column_name => 'IL Chr',
  43                      tooltip => "Chromosome this BAC matches (from IL mapping)",
  44                      value => 'il_chr',
  45                    },
  46    il_bin       => { column_name => 'IL Bin',
  47                      tooltip => "IL bin this BAC matches",
  48                      value => 'il_bin_id',
  49                      display => 'il_bin_name',
  50                    },
  51    il_notes     => { column_name => 'IL Notes',
  52                      tooltip => "Any special notes about this BAC's IL mapping results",
  53                      value => 'il_notes',
  54                    },
  55    ver_int_read => { column_name => 'Ver IR',
  56                      tooltip => "Check this box if this BAC has been verified with an additional internal read",
  57                    },
  58    ver_bac_end  => { column_name => 'Ver BE',
  59                      tooltip => "Check this box if this BAC has been verified with an additional BAC end read",
  60                    },
  61   );
  62 ##########  /DATA FIELD DEFINITIONS #######
  63 ## data field def post-processing
  64 #fills in defaults in the above data structure, so we don't have to
  65 #write out every damn little thing
  66 { my @it = @data_fields_defs;
  67   while(my ($k,$v) = splice @it,0,2) {
  68     $v->{column_name} ||= do {my @w = split /_/,$k; join ' ',map {ucfirst $_} @w};
  69     $v->{value} ||= $k;
  70     $v->{display} ||= $v->{value};
  71   }
  72 }
  73 my %data_fields_defs = @data_fields_defs; #< make a hash of the same
  74                                           #name for convenient access
  75
  76
  77 ################################
  78 ########## PAGE CODE START
  79 ################################
  80
  81 #TODO:
  82 # - do activated search term highlighting in search forms
  83
  84 #build some alternate HTML from the search results, adding edit
  85 #controls if the user is logged in
  86
  87 my $dbh = CXGN::Genomic::Clone->db_Main;
  88
  89 my $page = CXGN::Page->new('BAC Registry Editor','Robert Buels');
  90 $page->jsan_use(qw/MochiKit.Base MochiKit.Async MochiKit.Iter MochiKit.DOM MochiKit.Style MochiKit.Logging/);
  91 $page->add_style( text => <<EOS );
  92 td.columnar_table {
  93   vertical-align: middle;
  94 }
  95 EOS
  96
  97 my ($person,$projects_json,@person_projects) = get_person($dbh);
  98
  99 $page->header(('BAC Registry Viewer/Editor') x 2);
 100
 101
 102 #if logged in, add edit controls
 103 sub get_person {
 104     my $dbh = shift;
 105   if(my $person_id = CXGN::Login->new($dbh)->has_session) {
 106     my $p = CXGN::People::Person->new($dbh, $person_id);
 107
 108     return unless str_in($p->get_user_type,qw/sequencer curator/);
 109
 110     my @projects = #do {warn 'THIS IS BOGUS'; @{all_projects()}};
 111       $p->get_projects_associated_with_person;
 112     my $pjs = objToJson(\@projects);
 113
 114     return ($p,$pjs,@projects);
 115   }
 116   return;
 117 };
 118
 119
 120
 121 #do a clone search for the BACs to edit here, using the Clone search
 122 my $search = CXGN::Genomic::Search::Clone->new;
 123 my $query = $search->new_query;
 124 my %params = $page->get_all_encoded_arguments;
 125 $query->from_request(\%params);
 126 my $result = $search->do_search($query);
 127
 128 ####### now start the actual work
 129
 130 my @table_rows;
 131 while(my $clone = $result->next_result) {
 132
 133   my $clone_data = $clone->reg_info_hashref;
 134
 135   my $clone_id = $clone->clone_id;
 136
 137   my $make_spans = sub {
 138     my ($name,$data) = @_;
 139     #make ID'd spans from a clone ID and some key-value pairs
 140     #if there is more than one pair, the first one will be invisible
 141     my $val = $data->{val} || '';
 142     my $disp = $data->{disp} || $val;
 143     $disp = '-' if $disp eq '';
 144     return {
 145             class => "clone_reg_edit edit_$name",
 146             content => qq|<div style="position: relative"><span id="${name}_val_$clone_id" class="invisible">$val</span><span id="${name}_disp_$clone_id">$disp</span></div>|,
 147            };
 148   };
 149
 150   # fix up the il_notes field with truncation and a mouseover if it is
 151   # too long
 152   if( length(my $iln = $clone_data->{il_notes}->{disp}) > 15 ) {
 153       $clone_data->{il_notes}->{disp} =
 154           tooltipped_text(scalar(truncate_string($iln,8)),$iln)
 155   }
 156
 157   push @table_rows,
 158     [
 159      qq|<span class="invisible">$clone_id</span><a href="/maps/physical/clone_info.pl?id=$clone_id">|.($clone->clone_name_with_chromosome || $clone->clone_name).'</a>',
 160      map { $make_spans->($_ => $clone_data->{$_}) } evens @data_fields_defs
 161     ];
 162 }
 163
 164 my $pagination = $search->pagination_buttons_html($query,$result);
 165 my $page_size = $search->page_size_control_html($query);
 166 my $stats = $result->time_html;
 167 my $count = $result->total_results;
 168 my $stat_string = qq|<b>BACs $stats</b>&nbsp;&nbsp;&nbsp;$page_size&nbsp;per&nbsp;page|;
 169
 170 if($person) {
 171   print <<EOH;
 172 <div id="instructions">
 173   <dl><dt>Instructions</dt>
 174       <dd>
 175       To edit BAC registry information, select BACs to edit using
 176       the controls at the bottom of the page, then page through and edit
 177       the BACs by clicking the table cells below.
 178       </dd>
 179   </dl>
 180 </div>
 181 EOH
 182 } else {
 183   print <<EOH;
 184 <div style="text-align: center; margin-bottom: 1em">
 185   You must be <a href="/solpeople/login.pl">logged in</a> to edit BAC registry information.
 186 </div>
 187 EOH
 188 }
 189 print info_section_html( title => 'Edit Clones',
 190                          contents =>
 191                          qq|<div style="text-align: center">$stat_string $pagination</div>|
 192                          .columnar_table_html( headings =>
 193                                                [
 194                                                 'Clone',
 195                                                 map {
 196                                                   qq|<span class="invisible">$_</span> |
 197                                                     .tooltipped_text($data_fields_defs{$_}{column_name},$data_fields_defs{$_}{tooltip})
 198                                                   } evens @data_fields_defs
 199                                                ],
 200
 201                                                data => \@table_rows,
 202                                                __tableattrs => 'summary="" id="editingtable" cellspacing="0" align="center" style="margin-top: 1.2em; margin-bottom: 1.2em"',
 203                                                __border => 1,
 204                                              )
 205                          .qq|<div style="text-align: center; margin-bottom: 1em">$pagination</div>\n|
 206                        );
 207
 208
 209 #searches through an array like [query obj,text],[query_obj,text]
 210 #and returns an array like [[qstr,text],[qstr,text]], selected_index
 211 #where the selected_index is the index in the array of the query
 212 #that matches the current page query $query, or undef if none match
 213 #this function is just for use in assembling the args to modesel() below
 214 my $find_selected = sub {
 215   my $selected;
 216   my $index = 0;
 217   my @qs = map {
 218     my ($q,$t) = @$_;
 219     $q->page($query->page);
 220     $q->page_size($query->page_size);
 221
 222     if ($q->same_bindvals_as($query)) {
 223       $selected = $index;
 224     } else {
 225       $q->page(0);
 226     }
 227
 228     $index++;
 229
 230     [ '?'.$q->to_query_string, $t ]
 231   } @_;
 232
 233   return \@qs, $selected;
 234 };
 235
 236 my @seq_searches =
 237     (
 238      do {
 239      my $q = $search->new_query;
 240      $q->seq_project_name(q(ilike '%Tomato%'|| ? '%'),'unmapped');
 241      [$q,'unmapped']
 242    },
 243    map {
 244      my $chr = $_;
 245      my $q = $search->new_query;
 246      $q->seq_project_name(q(ilike '%Tomato%Chromosome ' || ? || ' %'),$chr);
 247     [$q,$chr]
 248   } 1..12
 249 );
 250
 251 my @il_searches = map {
 252   my ($pid,$country) = @$_;
 253   my $q = $search->new_query;
 254   $q->il_project_id('=?',$pid);
 255   [$q,$country]
 256 } @{ CXGN::People::Project->distinct_country_projects($dbh) };
 257
 258 my @search_sets =
 259   ( 'BACs to be Sequenced on Chromosome:' =>
 260     modesel( $find_selected->(@seq_searches) ),
 261     'BACs to be IL Mapped by Project:' =>
 262     modesel( $find_selected->(@il_searches) ),
 263   );
 264
 265 print info_section_html( title => 'Sequencing Stats Overview',
 266                          contents => '<div id="stats_img_div" style="text-align: center">javascript required</div>'
 267                        );
 268
 269 print info_section_html( title => 'Select BACs',
 270                          contents =>
 271                          info_section_html(title => 'Predefined Sets',
 272                                            is_subsection => 1,
 273                                            contents =>
 274                                            info_table_html( __border => 0,
 275                                                             @search_sets,
 276                                                           )
 277                                           )
 278                          .info_section_html(title => 'Custom Set',
 279                                             is_subsection => 1,
 280                                             contents => '<form method="GET">'.$query->to_html.'</form>',
 281                                            )
 282                        );
 283 #make the javascript for loading the overview image
 284 print <<EOJS;
 285 <script language="JavaScript" type="text/javascript">
 286   var update_status_image = function() {
 287     var img_div = document.getElementById('stats_img_div');
 288     img_div.innerHTML = '<img src="/documents/img/throbber.gif" /><br />updating...';
 289     var xhr = MochiKit.Async.doSimpleXMLHttpRequest('clone_async.pl',{ action: 'project_stats_img_html' });
 290     xhr.addCallbacks(function(req) { img_div.innerHTML = req.responseText },
 291                      function(req) { img_div.getElementById('stats_img_div').innerHTML = 'error fetching image' }
 292                     );
 293   };
 294   update_status_image(); //< update the status image on load
 295 </script>
 296 EOJS
 297
 298 #now print all the hidden edit forms
 299 if($person) {
 300
 301   print editforms_html($dbh,$person);
 302
 303   print <<EOS;
 304 <style>
 305 td.clone_reg_edit {
 306   height: 2.5em;
 307   cursor: pointer;
 308 }
 309 </style>
 310 EOS
 311
 312   #UI strategy:
 313   # - mouseover highlight row, column, and intersection.  highlight shows row locks
 314   # - click and table cell turns into an edit control if the row is not locked
 315   # - onchange, locks the table row and POSTs the change to clone_async.pl
 316   # - on return of the POST, unlocks the row
 317
 318   #now here is all the JS to do the UI
 319
 320   #put the data field definitions in the javascript too
 321   my $data_fields_defs_json = objToJson(\%data_fields_defs);
 322
 323   print <<EOJS;
 324 <script language="JavaScript" type="text/javascript">
 325
 326   //import some useful stuff
 327   var map     = MochiKit.Base.map;
 328   var partial = MochiKit.Base.partial;
 329   var foreach = MochiKit.Iter.forEach;
 330   var keys    = MochiKit.Base.keys;
 331   var values  = MochiKit.Base.values;
 332   var log     = MochiKit.Logging.log;
 333
 334   //this is the color for mouseover-highlighted cells
 335   var hilite_color = '#c5c5ee';
 336   var hilite_color_overlap = '#b9b9e0';
 337   var locked_color = '#f7878f';
 338
 339   //this is the table where our editing is done
 340   var edit_table = document.getElementById('editingtable');
 341
 342   //functions for locking and unlocking rows
 343   var locks = {};
 344   var lock_clone = function(row) {
 345     locks[row.clone_id] = 1;
 346     foreach( row.tr.cells,
 347              function(td) {  td.style.backgroundColor = locked_color }
 348            );
 349
 350     //create a little 'loading' throbber on the end of the row
 351     var throbber = MochiKit.DOM.IMG({ src: '/documents/img/throbber.gif',
 352                                       style: 'display: block; z-index: 3; position: absolute;'
 353                                     });
 354     var end_div = row.ver_bac_end.div;
 355     var end_div_dims = MochiKit.Style.getElementDimensions(end_div);
 356     MochiKit.Style.setElementPosition(throbber,{x: end_div_dims.w+10, y: 0});
 357     MochiKit.DOM.appendChildNodes(end_div,throbber);
 358   };
 359   var unlock_clone = function(row) {
 360     locks[row.clone_id] = 0;
 361     foreach( row.tr.cells,
 362              function(td) { td.style.backgroundColor = '' }
 363            );
 364     //get rid of the throbber
 365     var end_div = row.ver_bac_end.div;
 366     foreach(  MochiKit.DOM.getElementsByTagAndClassName('img',null,end_div),
 367              MochiKit.DOM.removeElement );
 368   };
 369   var is_locked = function(a) {
 370     var clone_id = typeof(a) == 'object' ? get_cell_clone(a) : a;
 371     return locks[clone_id] ? true : false;
 372   }
 373
 374   //determines if a cell is not editable, due to its
 375   //either being locked by an ongoing XHR, or because this
 376   //user doesn't have permission to edit it
 377   //also, the permissions are also checked server-side,
 378   //so if you're reading this, don't get any funny ideas ;-)
 379   var is_not_editable = function(cell,clone_id,fieldname) {
 380     clone_id = clone_id || get_cell_clone(cell);
 381     fieldname = fieldname || get_cell_field(cell);
 382
 383     //if the cell isn't locked, check some other permission conditions
 384     var row = get_clone_elements(clone_id);
 385
 386     var seq_proj_in_projects_list = MochiKit.Base.findValue(person_projects,row.seq_proj.val.innerHTML.valueOf()) != -1;
 387     var il_proj_in_projects_list  = MochiKit.Base.findValue(person_projects,row.il_proj.val.innerHTML.valueOf()) != -1;
 388
 389     switch(fieldname) {
 390       case 'seq_proj':
 391         //proj must be null, or in the person's projects list
 392         if(row.seq_proj.val.innerHTML != '' && !seq_proj_in_projects_list)
 393           return 'this BAC is already being sequenced by another sequencing project, they must release their claim on this BAC before you can claim it';
 394       break;
 395       case 'seq_status':
 396       case 'gb_status':
 397         //seq_proj must be in the person's projects list
 398         if(!seq_proj_in_projects_list)
 399           return 'this BAC must be assigned to your sequencing project for you to edit its seq or GB status';
 400       break;
 401       case 'il_proj':
 402         //il_proj must be null, or in the person's projects list
 403         if(row.il_proj.val.innerHTML != '' && !il_proj_in_projects_list)
 404           return 'this BAC is already being IL bin mapped by another sequencing project, they must release their claim on this BAC before you can claim it';
 405       break;
 406       case 'il_bin':
 407       case 'il_notes':
 408       case 'il_chr':
 409         if(!il_proj_in_projects_list)
 410           return 'this BAC must be assigned to your sequencing project before you can report IL mapping results for it';
 411       break;
 412     };
 413
 414     return;
 415   };
 416
 417   var field_defs      = $data_fields_defs_json;
 418   var person_projects = $projects_json;
 419
 420   //get the span elements that hold and display data for the relevant clone,
 421   //and their enclosing td's
 422   var get_clone_elements = function(clone_id) {
 423     var elements = { 'clone_id': clone_id };
 424     foreach( keys(field_defs),
 425              function( field ) {
 426                elements[field] = { val:  document.getElementById(field+'_val_'+clone_id),
 427                                    disp: document.getElementById(field+'_disp_'+clone_id)
 428                                  };
 429                if(elements[field].disp) {
 430                  elements[field].div = elements[field].disp.parentNode;
 431                  elements[field].td = elements[field].div.parentNode;
 432                  elements.tr = elements[field].td.parentNode;
 433                } else {
 434                  //grab the elements that the form is holding
 435                  var my_ed = get_editor(field);
 436                  if(my_ed.is_at_spot(clone_id)) {
 437                      elements[field] = my_ed.curr_spot;
 438                  }
 439                }
 440              }
 441            );
 442     return elements;
 443   };
 444
 445
 446   //*** Editor class, used to work with the editors for each data item
 447   function Editor(n) {
 448     this.name = n;
 449     this.myform = document[n+'_edit'];
 450   }
 451   //get the element for the appropriate edit form
 452   Editor.prototype.form = function() {
 453     return this.myform;
 454   }
 455   //hide this editor form
 456   Editor.prototype.hide = function(cell) {
 457     if(this.curr_spot) {
 458       var edform = this.form();
 459       MochiKit.DOM.removeElement( edform );
 460       document.getElementById('editor_corral').appendChild( edform );
 461
 462       //restore the data cells and the onclick handler in the cell we just vacated
 463       this.curr_spot.td.appendChild(this.curr_spot.div);
 464
 465       //reinstall the table cell's onclick handler
 466       this.curr_spot.td.onclick = td_onclick_edit
 467       //release it
 468       this.curr_spot = null;
 469     }
 470   };
 471   //is this editor open in this spot?
 472   Editor.prototype.is_at_spot = function(clone_id) {
 473     return this.curr_spot && get_cell_clone(this.curr_spot.td) == clone_id;
 474   };
 475   //open the editor at a specific clone
 476   Editor.prototype.open = function(clone_id) {
 477     //hide any other open editors, including this one
 478     hide_all_editors();
 479
 480     var row = get_clone_elements(clone_id);
 481     this.curr_spot = row[this.name]; //< the two spans that hold this clone's data
 482
 483     //hide the data in the new cell
 484     MochiKit.DOM.removeElement(this.curr_spot.div);
 485
 486     var edform = this.form();
 487
 488     //set the form's value
 489     edform.clone_id.value = clone_id;
 490     if(edform.val_input.type == 'checkbox') {
 491       edform.val_input.checked = this.curr_spot.val.innerHTML == '1' ? true : false;
 492     } else {
 493       edform.val_input.value = this.curr_spot.val.innerHTML;
 494     }
 495
 496     //swap the edit form into the td next to the display span
 497     MochiKit.DOM.removeElement(edform);
 498     this.curr_spot.td.appendChild(edform);
 499
 500     //set a checkbox's value again
 501     if(edform.val_input.type == 'checkbox') {
 502       edform.val_input.checked = this.curr_spot.val.innerHTML == '1' ? true : false;
 503     }
 504
 505     //disable this table cell's onclick handler
 506     this.curr_spot.td.onclick = null;
 507   };
 508
 509   var editors = {};
 510   //get the clone_id for any cell in the editing table
 511   var get_cell_clone = function(td) {
 512     if(td.cellclone) return td.cellclone;
 513     return td.cellclone = td.parentNode.cells[0].childNodes[0].innerHTML;
 514   }
 515   var get_cell_field = function(td) {
 516     return edit_table.rows[0].cells[td.cellIndex].childNodes[0].innerHTML;
 517   }
 518
 519   //the onclick handler for an inactive table cell
 520   var td_onclick_edit = function() {
 521     //get the data field name from the invisible span in the head of this column
 522     var name     = get_cell_field(this);
 523     var clone_id = get_cell_clone(this);
 524
 525     if(is_locked(clone_id)) {
 526       return;
 527     }
 528     var not_editable_str = is_not_editable(this,clone_id,name);
 529     if(not_editable_str) {
 530       alert('cell not editable: '+not_editable_str);
 531       return;
 532     }
 533
 534     get_editor(name).open(clone_id);
 535   }
 536   var hide_all_editors = function() {
 537     foreach( values(editors),
 538              function(ed) {
 539                ed.hide()
 540              }
 541            );
 542   };
 543   var get_editor = function(name) {
 544     if(! editors[name]) {
 545       editors[name] = new Editor(name);
 546     }
 547     return editors[name];
 548   };
 549
 550   //this function turns row and column highlighting on and off,
 551   //when given the cell that's under the mouse and whether the highlighting
 552   //should be turned on or off
 553   var table_highlight = function(onoff) {
 554     var cell_coords = [this.parentNode.rowIndex,this.cellIndex];
 555     var hilite  = function(td,c) {
 556       c = c || hilite_color;
 557       if(is_locked(td))
 558         return;
 559       td.style.backgroundColor = onoff ? c : '';
 560     };
 561
 562     if( is_not_editable(this) ) {
 563       hilite(this,locked_color);
 564     } else {
 565       foreach( edit_table.rows[cell_coords[0]].cells, hilite );
 566       //foreach( edit_table.rows, function(tr) { hilite(tr.cells[cell_coords[1]]) } );
 567       hilite(this,hilite_color_overlap);
 568     }
 569   };
 570   var table_highlight_on  = partial(table_highlight,1);
 571   var table_highlight_off = partial(table_highlight,0);
 572
 573   //find all the editing TD elements and install their event handlers
 574   foreach( MochiKit.DOM.getElementsByTagAndClassName('td','clone_reg_edit',edit_table),
 575            function(cell) {
 576              cell.onclick     = td_onclick_edit;
 577              cell.onmouseover = table_highlight_on;
 578              cell.onmouseout  = table_highlight_off;
 579            }
 580          );
 581
 582   //set the width of all the TH heading elements to be wide enough to
 583   //accomodate the editing forms in all the cells below
 584   var set_col_widths = function() {
 585     foreach( edit_table.rows[0].cells,
 586              function(th) {
 587                var name = th.childNodes[0].innerHTML;
 588                if(! name) return;
 589                var ed = get_editor(name);
 590                var edform = ed.form();
 591                var min_col_width = edform.offsetWidth + 3;
 592 //               log('for '+name+', th width is ' + th.offsetWidth + ' and min is '+min_col_width);
 593                th.style.width = min_col_width+'px';
 594              }
 595            );
 596   };
 597   set_col_widths();
 598
 599
 600   //do a POST XHR to alter the clone in the database,
 601   //also update its display fields
 602   var alter_clone = function(edname,clone_id,postcontent) {
 603     //hide this editor
 604     get_editor(edname).hide();
 605
 606     var row = get_clone_elements(clone_id);
 607     lock_clone(row);
 608
 609     postcontent.clone_id = clone_id;
 610
 611     var xhr_opt =
 612       {  headers:     [["Content-type","application/x-www-form-urlencoded"]],
 613          method:      'POST',
 614          sendContent: MochiKit.Base.queryString(postcontent)
 615       };
 616
 617     var success_callback = partial(set_row_content,row);
 618     var err_callback = partial(set_row_error,row);
 619
 620     //if the action involves the seq status, schedule the overview image to get updated
 621     //when this comes back
 622     if(    postcontent.action == 'set_seq_proj'
 623         || postcontent.action == 'set_gb_status'
 624         || postcontent.action == 'set_seq_status'
 625       ) {
 626       var old_success = success_callback;
 627       success_callback = function(req) {
 628         old_success(req);
 629         update_status_image();
 630       };
 631     }
 632
 633     var res = MochiKit.Async.doXHR('clone_async.pl',xhr_opt);
 634     res.addCallbacks(success_callback, err_callback);
 635   };
 636
 637
 638   var set_row_content = function(row,req) {
 639     var data;
 640 //    log('set_row_content callback');
 641     try {
 642       data = MochiKit.Async.evalJSONRequest(req);
 643 //      log('setting fields...');
 644       foreach( keys(data),
 645                function(field) {
 646 //                 log('setting '+field+' contents');
 647                  if( row[field] ) {
 648                    row[field].val.innerHTML  = data[field].val;
 649                    row[field].disp.innerHTML = data[field].disp;
 650                  }
 651                }
 652              );
 653 //      log('unlocking clone '+row.clone_id);
 654       unlock_clone(row);
 655     } catch(e) {
 656       log(e);
 657       set_row_error(row);
 658     }
 659   };
 660
 661   var set_row_error = function(row) {
 662 //    log('error callback on clone_id '+row.clone_id);
 663     foreach( values(row),
 664              function(spans) {
 665                if(typeof(spans) != 'object' || ! spans.disp)
 666                  return;
 667
 668                spans.disp.innerHTML = 'error';
 669              }
 670            )
 671 //    log('unlocking clone '+row.clone_id);
 672
 673     unlock_clone(row);
 674   };
 675
 676 </script>
 677 EOJS
 678 }
 679
 680 $page->footer;
 681
 682 ############ SUBROUTINES ##############
 683
 684 sub il_bin_list {
 685   return @{our $il_list ||= shift->selectall_arrayref(<<EOQ)}
 686 select genotype_region_id, name
 687 from phenome.genotype_region gr
 688 join sgn.linkage_group lg using(lg_id)
 689 join sgn.map_version mv using(map_version_id)
 690 join sgn.map m using(map_id)
 691 where type = 'bin' and m.short_name like '%1992%' and m.short_name like '%EXPEN%';
 692 EOQ
 693 }
 694
 695 sub editforms_html {
 696   my ($dbh,$person) = @_;
 697
 698   return '' unless $person;
 699
 700   my @person_projects = #do {warn 'THIS IS BOGUS'; @{all_projects()}};
 701     $person->get_projects_associated_with_person;
 702
 703   #lookup the name for each of the projects and parse out the chromosome numbers
 704   @person_projects =
 705     map {
 706       my $proj_id = $_;
 707       my ($chr_name) = $dbh->selectrow_array('select name from sgn_people.sp_project where sp_project_id = ? order by name',undef,$proj_id);
 708       $chr_name =~ s/\D//g; #remove all non-digits
 709       #and if nothing's left then it must be the unmapped one
 710       $chr_name ||= 'unmapped';
 711       [$proj_id, $chr_name]
 712     } @person_projects;
 713
 714   my @ils = il_bin_list($dbh);
 715
 716   #the values of all these form fields will be set by javascript each
 717   #time this form is popped up at a given location
 718   my $clone_id_hidden =  '<input name="clone_id" value="" type="hidden" />';
 719   my $sel_edit = sub {
 720     my ($name,@choices) = @_;
 721
 722     ( qq|<form name="${name}_edit" onsubmit="return false" style="display: inline">|,
 723       (
 724        $clone_id_hidden,
 725        simple_selectbox_html(name     => "val_input",
 726                              choices  => \@choices,
 727                              params   => { onchange => "alter_clone('$name',this.form.clone_id.value,{ action: 'set_$name', val: this.value})" },
 728                             ),
 729       ),
 730       '</form>',
 731     )
 732   };
 733   my $cb_edit = sub {
 734     my ($name,$checked) = @_;
 735     $checked = $checked ? 'checked="checked"' : '';
 736     ( qq|<form name="${name}_edit" onsubmit="return false" style="display: inline">|,
 737       (
 738        $clone_id_hidden,
 739        qq|<input id="cb_$name" type="checkbox" name="val_input" onclick="alter_clone('$name',this.form.clone_id.value,{ action: 'set_$name', val: this.checked ? 1 : 0})"$checked/>|,
 740       ),
 741       '</form>',
 742     )
 743   };
 744   my $t_edit = sub {
 745     no warnings 'uninitialized';
 746     my ($name,$size,$text) = @_;
 747     ( qq|<form name="${name}_edit" onsubmit="alter_clone('$name',this.clone_id.value,{action: 'set_$name', val: this.val_input.value}); return false" style="display: inline">|,
 748       (
 749        $clone_id_hidden,
 750        qq|<input id="text_$name" type="text" value="$urlencode{$text}" size="$size" maxlength="200" name="val_input" />|,
 751       ),
 752       '</form>',
 753     )
 754   };
 755   return join '', map {my $s = $_; chomp $s; "$s\n"}
 756     (
 757       '<div id="editor_corral" style="position: absolute; left: -800px;">',
 758       (
 759        $sel_edit->('seq_proj',['','none'],@person_projects),
 760        $sel_edit->('seq_status','none','not_sequenced','in_progress','complete'),
 761        $sel_edit->('gb_status','none',map {"htgs$_"} 1..3),
 762        $sel_edit->('il_proj',['','none'],grep {my $id = $_->[0]; str_in($id,map $_->[0],@person_projects)} @{CXGN::People::Project->distinct_country_projects($dbh)}),
 763        $sel_edit->('il_chr',['','none'],1..12),
 764        $sel_edit->('il_bin',['','none'],@ils),
 765        $t_edit  ->('il_notes',15),
 766        $cb_edit ->('ver_int_read'),
 767        $cb_edit ->('ver_bac_end'),
 768       ),
 769      '</div>',
 770     );
 771 }
 772
 773 sub metadata {
 774   our $metadata ||= CXGN::Metadata->new(); # metadata object
 775 }
 776
 777 sub bac_status_log {
 778     my $dbh = shift;
 779   our $bac_status_log ||= CXGN::People::BACStatusLog->new($dbh); # bac ... status ... object
 780 }
 781