cgi-bin/maps/physical/clone_il_view.pl

   1 use strict;
   2 use warnings;
   3
   4 use CXGN::Page;
   5 use CXGN::DB::Connection;
   6 use CXGN::Page::FormattingHelpers qw( info_section_html
   7                                       modesel
   8                                       columnar_table_html
   9                                       simple_selectbox_html
  10                                       info_table_html
  11                                     );
  12 use CXGN::Tools::List qw/distinct str_in/;
  13
  14 my $page = CXGN::Page->new('Clone IL Mapping Assignments','Robert Buels');
  15 $page->jsan_use(qw/MochiKit.Base MochiKit.Async MochiKit.Iter MochiKit.DOM MochiKit.Style/);
  16
  17 $page->header(('Clone IL Mapping Assignments') x 2);
  18
  19 my ($curr_proj) = $page->get_encoded_arguments('p');
  20 $curr_proj ||= 1;
  21
  22 # map project IDs to country names
  23 my @projmap = qw/dummy USA Korea China UK India Netherlands France Japan Spain USA USA Italy/;
  24
  25 # map project IDs to modesel button indexes
  26 my @indexmap = (     0,  0,    1,    2, 3,    4,          5,     6,    7,    8,  0,  0,    9);
  27
  28 print modesel([ map { [ "?p=$_" => $projmap[$_] ] } 1..9,12 ],
  29               $indexmap[$curr_proj],
  30              );
  31
  32 #look up all the il assignments for this project
  33 my $dbh = CXGN::DB::Connection->new;
  34 my $clone_name_sql = CXGN::Genomic::Clone->
  35   clone_name_sql('l.shortname',
  36                  'c.platenum',
  37                  'c.wellrow',
  38                  'c.wellcol',
  39                 );
  40 my $bacs = $dbh->selectall_arrayref(<<EOQ,undef,$curr_proj);
  41 select  cl.clone_id,
  42         $clone_name_sql,
  43         cl.sp_project_id,
  44         ill.individual_id,
  45         i.name
  46 from sgn_people.sp_project_il_mapping_clone_log cl
  47 join genomic.clone c using(clone_id)
  48 join genomic.library l using(library_id)
  49 left join sgn_people.sp_clone_il_mapping_segment_log ill on cl.clone_id=ill.clone_id and ill.is_current = true
  50 left join phenome.individual i using(individual_id)
  51 where cl.sp_project_id = ?
  52   and cl.is_current = true
  53 order by $clone_name_sql
  54 EOQ
  55
  56 #if logged in, add edit controls
  57 my $person = do {
  58   if(my $person_id = CXGN::Login->new($dbh)->has_session) {
  59     CXGN::People::Person->new($dbh, $person_id);
  60   }
  61 };
  62
  63 my $can_edit = $person                                                #< person is logged in
  64   && str_in($person->get_user_type,qw/sequencer curator/)             #< and is the right user type
  65   && str_in($curr_proj,$person->get_projects_associated_with_person); #< and has edit rights on this project
  66
  67 my @data = map {
  68   my ($clone_id,$clone_name,$project_id,$il_id,$il_name) = @$_;
  69   [
  70    #link to clone info page
  71    qq|<a href="/maps/physical/clone_info.pl?id=$clone_id">$clone_name</a>|,
  72
  73    #the project name
  74    qq|<span id="proj_name_$clone_id">$projmap[$project_id]</span><span id="proj_id_$clone_id" style="display: none">$project_id</span>|,
  75
  76    #the IL line
  77    qq|<span id="il_name_$clone_id">|.($il_name || '-').qq|</span><span style="display: none" id="il_id_$clone_id">|.($il_id||'').'</span>',
  78
  79    $can_edit ? edit_controls_html($clone_id,$il_id) : (),
  80   ]
  81 } @$bacs;
  82
  83 my @headings = ('BAC', 'Project', 'IL Bin', $can_edit ? 'Edit' : ());
  84
  85 print columnar_table_html( headings     => \@headings,
  86                            data         => \@data,
  87                            __border     => 1,
  88                            __align      => 'lccr',
  89                            __tableattrs => 'align="center" width="60%" summary="" cellspacing="0"',
  90                          );
  91
  92 print editform_html($dbh,$person,$curr_proj);
  93
  94 #now here are the JS functions to do the updating
  95 print <<EOJS;
  96 <script language="JavaScript" type="text/javascript">
  97
  98   var TR = MochiKit.DOM.TR;
  99   var TD = MochiKit.DOM.TD;
 100   var A = MochiKit.DOM.A;
 101   var map = MochiKit.Base.map;
 102   var partial = MochiKit.Base.partial;
 103   var TABLE = MochiKit.DOM.TABLE;
 104   var THEAD = MochiKit.DOM.THEAD;
 105
 106   var set_row_content = function(row,req) {
 107     var data = MochiKit.Async.evalJSONRequest(req);
 108
 109     row.proj_name.innerHTML = data.il_proj.disp;
 110     row.proj_id.innerHTML   = data.il_proj.val;
 111     row.il_name.innerHTML   = data.il_bin.disp;
 112     row.il_id.innerHTML     = data.il_bin.val;
 113
 114     check_editor_enable();
 115   };
 116
 117   var set_row_error = function(row) {
 118     row.proj_name.innerHTML = 'error';
 119     row.il_name.innerHTML = 'error';
 120   }
 121
 122   //get the three span elements in the relevant table row
 123   var get_row_elements = function(clone_id) {
 124     var row = { proj_name:  document.getElementById('proj_name_'+clone_id),
 125                 proj_id:    document.getElementById('proj_id_'+clone_id),
 126                 il_name:    document.getElementById('il_name_'+clone_id),
 127                 il_id:      document.getElementById('il_id_'+clone_id),
 128                 editbutton: document.getElementById('editbutton_'+clone_id),
 129                 posdiv:     document.getElementById('posdiv_'+clone_id)
 130               };
 131     row.disabled = (row.proj_id.innerHTML == 'disabled') || (row.il_id.innerHTML == 'disabled');
 132     return row;
 133   };
 134
 135   var edform = document.clone_il_editor_form;
 136   var edtable = document.getElementById('clone_il_editor_table');
 137
 138   //set the editor either enabled or disabled,
 139   //depending on which clone it's currently
 140   //editing
 141   var check_editor_enable = function() {
 142
 143     var clone_id = edform.clone_id.value;
 144
 145     if(!clone_id) return;
 146
 147     var row = get_row_elements(clone_id);
 148
 149     if(row.disabled) {
 150       edform.il.disabled = true;
 151       edform.proj.disabled = true;
 152     } else {
 153       edform.il.disabled = false;
 154       edform.proj.disabled = false;
 155     }
 156   };
 157
 158   //do a POST XHR to alter the clone in the database,
 159   //also update its display fields
 160   var alter_clone = function(clone_id,type,newvalue) {
 161     var row = get_row_elements(clone_id);
 162
 163     var postcontent = type == 'proj' ? { clone_id: clone_id, action: 'set_il_proj', val:     newvalue }
 164                                      : { clone_id: clone_id, action: 'set_il_bin',  val: newvalue };
 165
 166     var xhr_opt =
 167       {  headers:     [["Content-type","application/x-www-form-urlencoded"]],
 168          method:      'POST',
 169          sendContent: MochiKit.Base.queryString(postcontent)
 170       };
 171
 172     row.proj_name.innerHTML =
 173       row.il_name.innerHTML =
 174         '<div style="background: red; color: white; font-weight:bold; border: 2px outset gray;">wait</span>';
 175     row.proj_id.innerHTML = row.il_id.innerHTML = 'disabled';
 176
 177     check_editor_enable();
 178
 179     var res = MochiKit.Async.doXHR('clone_async.pl',xhr_opt);
 180     res.addCallbacks(partial(set_row_content,row),
 181                      partial(set_row_error,row)
 182                     );
 183   };
 184
 185   var last_active_edit_button;
 186
 187   //pop up the edit form at the given button
 188   var edit_row = function(clone_id) {
 189     var row = get_row_elements(clone_id);
 190
 191     row.editbutton.blur();
 192     edform.clone_id.value = clone_id;
 193
 194     edform.il.value = row.il_id.innerHTML || 'none';
 195     edform.proj.value = row.proj_id.innerHTML;
 196
 197     edtable.style.display = 'block';
 198
 199     MochiKit.DOM.removeElement(edform);
 200     MochiKit.DOM.appendChildNodes(row.posdiv,edform);
 201     var divdims = MochiKit.Style.getElementDimensions(row.posdiv);
 202     MochiKit.Style.setElementPosition(edtable,{x: divdims.w-4, y: 0});
 203
 204     check_editor_enable();
 205
 206     if(last_active_edit_button) {
 207       MochiKit.Style.setStyle(last_active_edit_button,{background: 'none', fontWeight: 'normal', color: 'black'});
 208     }
 209     last_active_edit_button = row.editbutton;
 210     MochiKit.Style.setStyle(row.editbutton,{background: '#666', fontWeight: 'bold', color: 'white' });
 211   };
 212
 213 </script>
 214 EOJS
 215
 216 $page->footer;
 217
 218 ############ SUBROUTINES ##############
 219
 220 sub il_bin_list {
 221   return @{our $il_list ||= shift->selectall_arrayref(<<EOQ)}
 222 select genotype_region_id, name
 223 from phenome.genotype_region gr
 224 join sgn.linkage_group lg using(lg_id)
 225 join sgn.map_version mv using(map_version_id)
 226 join sgn.map m using(map_id)
 227 where type = 'bin' and m.short_name like '%1992%' and m.short_name like '%EXPEN%';
 228 EOQ
 229 }
 230
 231 sub edit_controls_html {
 232   my ($clone_id,$il_id) = @_;
 233   $il_id ||= 'null';
 234   return qq|<div style="position: relative; padding: 0" id="posdiv_$clone_id"><button id="editbutton_$clone_id" value="edit" style="background: none; border: 1px solid black;" onclick="edit_row($clone_id)">edit</button></div>|;
 235 }
 236
 237 sub editform_html {
 238   my ($dbh,$person,$curr_proj) = @_;
 239
 240   return '' unless $person;
 241
 242   my @person_projects = $person->get_projects_associated_with_person;
 243
 244   #@projmap is a array of [project_id,country name]
 245   my $c;
 246   my @projmap = map {
 247     [++$c,$_]
 248   } qw/USA Korea China UK India Netherlands France Japan Spain USA USA Italy/;
 249   @projmap[9,10] = ($projmap[0]) x 2;
 250
 251   my @ils = il_bin_list($dbh);
 252
 253   #the values of all these form fields will be set by javascript each
 254   #time this form is popped up at a given location
 255   return join '',
 256     (
 257      '<form name="clone_il_editor_form">',
 258      qq|<input name="clone_id" value="" type="hidden"/>|,
 259      '<table id="clone_il_editor_table" style="display: none; position: absolute; background: #bbbbff; border: 1px solid black; z-index: 3"><tr><td><b>Project</b></td><td>',
 260      simple_selectbox_html(name     => "proj",
 261                            choices  => [['','none'],
 262                                         distinct map {$projmap[$_-1]} @person_projects
 263                                        ],
 264                            params   => { onchange => "alter_clone(this.form.clone_id.value,'proj',this.value)" },
 265                            selected => $curr_proj,
 266                           ),
 267      '</td></tr><tr><td><b>IL</b></td><td>',
 268      simple_selectbox_html(name    => "il",
 269                            choices => [['','none'],
 270                                        @ils,
 271                                       ],
 272                            params  => { onchange => "alter_clone(this.form.clone_id.value,'il',this.value)" },
 273                           ),
 274      '</td></tr></table></form>',
 275     );
 276 }