cgi-bin/solpeople/top-level.pl

   1 #DEPRECATED
   2 #####################
   3 #This page now points to the url /solpeople/profile/<sp_person_id> in the controller SGN::Controller::People
   4 #####################
   5
   6 use strict;
   7
   8 use CXGN::DB::Connection;
   9 use CXGN::Page;
  10 use CXGN::Login;
  11 use CXGN::People;
  12 use CXGN::People::Person;
  13 use CXGN::BlastWatch;
  14 use CXGN::Phenome::Locus;
  15 use CXGN::Cview::MapFactory;
  16 use CXGN::Page::FormattingHelpers qw/info_section_html page_title_html
  17   info_table_html simple_selectbox_html
  18   html_optional_show columnar_table_html/;
  19
  20 our $c;
  21 use CatalystX::GlobalContext qw($c);
  22
  23
  24 my $page = CXGN::Page->new( "solpeople main menu", "john" );
  25 my $dbh = CXGN::DB::Connection->new();
  26 my $site_name = $c->config->{project_name};
  27
  28 my $sp_person_id = CXGN::Login->new($dbh)->verify_session();
  29
  30 my $sp = CXGN::People::Person->new( $dbh, $sp_person_id );
  31 unless ($sp_person_id) {
  32     $page->error_page( "Login ID not found.",
  33         "", "", "Login ID not found: $sp_person_id" );
  34 }
  35 unless ( $sp->get_username() ) {
  36     $page->error_page( "Username not found.",
  37         "", "", "Username not found for sp_person_id '$sp_person_id'" );
  38 }
  39 my $username = $sp->get_first_name() . " " . $sp->get_last_name();
  40
  41 #my $research_update=$sp->get_research_update();
  42 #my $contact_update=$sp->get_contact_update();
  43
  44 $page->add_style( text => <<EOS);
  45 div#queryTable
  46 {
  47 margin: 0px 0px 0px 0px;
  48 display: none;
  49 }
  50 EOS
  51 $page->header();
  52
  53 print <<END_HTML;
  54
  55 <script type = "text/javascript">
  56 <!--
  57     function toggleLayer(whichLayer) {
  58         if (document.getElementById) {
  59             var style2 = document.getElementById(whichLayer).style;
  60             style2.display = style2.display? "":"block";
  61         }
  62         else if (document.all) {
  63             var style2 = document.all[whichLayer].style;
  64             style2.display = style2.display? "":"block";
  65         }
  66         else if (document.layers) {
  67             var style2 = document.layers[whichLayer].style;
  68             style2.display = style2.display? "":"block";
  69         }
  70     }
  71     function showSequence(sequence) {
  72         document.getElementById("Heading").innerHTML="<strong>Full sequence: </strong>";
  73         document.getElementById("fullSequence").innerHTML=sequence;
  74     }
  75     function hideSequence() {
  76         document.getElementById("Heading").innerHTML="";
  77         document.getElementById("fullSequence").innerHTML="";
  78     }
  79 //-->
  80 </script>
  81 END_HTML
  82
  83 print page_title_html("My $site_name");
  84 print qq|<div align="center">Welcome <b>$username</b></div>\n|;
  85 print
  86 qq|<div align="right" style="margin-bottom: 0.5em">Not $username? <a href="login.pl?logout=yes">[log out]</a></div>\n|;
  87 print info_section_html( title => 'General Tools', contents => <<EOHTML);
  88     <a href="personal-info.pl?action=edit&sp_person_id=$sp_person_id">View or update personal (contact and research) information</a><br />
  89     <a href="change-account.pl?action=edit&sp_person_id=$sp_person_id">Update account information</a><br />
  90     <a href="/forum/topics.pl">Post to SGN forum</a><br />
  91 EOHTML
  92
  93 # my $queries =
  94 #     qq|<div id="queryTable">|
  95 #   . CXGN::BlastWatch::get_queries( $dbh, $sp_person_id )
  96 #   . '</div>';
  97 # print info_section_html( title => 'BLAST Watch', contents => <<EOHTML);
  98 #     <div style="margin-bottom: 1em">BLAST Watch is an SGN service that lets users submit recurring BLAST queries to SGN.  Our software repeats your BLAST search every week and notifies you by email if the BLAST results change.</div>
  99 #     <a href="/tools/blast/watch/index.pl">Submit a query to SGN BLAST Watch</a><br />
 100 #     <a href="javascript:toggleLayer('queryTable');" title="View your BLAST Watch queries">View your BLAST Watch queries</a>
 101 #     $queries
 102 # EOHTML
 103
 104 #return 1 if the first term is eq to one of the other terms given
 105 sub in(@) {
 106     my $t = shift;
 107     ( grep { $t eq $_ } @_ ) ? 1 : 0;
 108 }
 109
 110 #now assemble the sequencing tools stuff
 111 if ( in( $sp->get_user_type, qw/curator sequencer/ ) ) {
 112
 113     #make a form for uploading TPF and AGP files
 114     my $tpf_agp_upload = do {
 115         if ( $sp->get_user_type eq 'curator' ) {
 116             tpf_agp_upload_forms(<<EOHTML);
 117       <!-- the string 'TYPE' will be replaced in each instance by tpf_agp_upload_forms() -->
 118 <label for="chrnuminputTYPE">For Chromosome #: </label><input id="chrnuminputTYPE" name="chr" type="text" size="2" maxlength="2" />
 119 EOHTML
 120         }
 121         elsif ( $sp->get_user_type eq 'sequencer'
 122             and my @projects =
 123             grep { $_ >= 1 && $_ <= 12 }
 124             $sp->get_projects_associated_with_person )
 125         {
 126             my $chrinput =
 127               @projects > 1
 128               ? simple_selectbox_html(
 129                 name    => 'chr',
 130                 choices => \@projects,
 131                 label   => 'For Chromosome #:',
 132               )
 133               : qq|For Chromosome #: <b>$projects[0]</b> <input type="hidden" value="$projects[0]" name="chr" />|;
 134             tpf_agp_upload_forms($chrinput);
 135         }
 136     };
 137
 138     print info_section_html( title => 'Sequencer Tools', contents => <<EOHTML);
 139 <a href="attribute_bacs.pl">Attribute a BAC to your chromosome sequencing project</a><br />
 140 <a href="/maps/physical/clone_il_view.pl">View/update BAC IL mapping information (list view)</a><br />
 141 <div style="vertical-align: middle; font-weight: bold"><a href="/maps/physical/clone_reg.pl">View/update all BAC registry info (list view) <img style="border: none" src="/documents/img/new.gif" /></a></div>
 142 <a href="/sequencing/tpf.pl">View TPF Files</a><br />
 143 <a href="/sequencing/agp.pl">View AGP Files</a><br />
 144 $tpf_agp_upload
 145 EOHTML
 146 }
 147
 148 # if( in( $sp->get_user_type(), qw/submitter curator/ ) )
 149 # {
 150 #   print info_section_html(title => 'EST Submission Pages', contents => <<EOHTML);
 151 # <a href="/data-submit/top-level.pl">Data submission start page</a>
 152 # EOHTML
 153 # }
 154
 155 if ( in( $sp->get_user_type(), qw/submitter curator/ ) ) {
 156     print info_section_html( title => 'QTL data submission',
 157         contents => <<EOHTML);
 158 <a href="/phenome/qtl_form.pl">Upload and analyse your QTL data</a>
 159 EOHTML
 160 }
 161
 162 my @pops = CXGN::Phenome::Population->my_populations($sp_person_id);
 163
 164 if (@pops) {
 165     my $pop_list = my_populations(@pops);
 166     print info_section_html( title => 'Populations', contents => $pop_list );
 167 }
 168
 169 #### solGS submitted jobs list ##########
 170 my $solgs_jobs = SGN::Controller::solGS::AnalysisQueue->solgs_analysis_status_log($c);
 171
 172 my $solgs_jobs_table;
 173
 174 if(@$solgs_jobs) {
 175     $solgs_jobs_table =  columnar_table_html(
 176         headings   => [ 'Analysis name', 'Submitted on', 'Status', 'Result page'],
 177         data       => $solgs_jobs,
 178         __alt_freq => 2,
 179         __align    => 'llll',
 180         );
 181 } else {
 182     $solgs_jobs_table = 'You have no submitted jobs.'
 183 }
 184
 185 print info_section_html(
 186     title    => 'solGS submitted analysis jobs',
 187     contents => $solgs_jobs_table
 188     );
 189
 190 #######
 191
 192
 193 if ( $sp->get_user_type() eq 'curator' ) {
 194     print info_section_html( title => 'Curator Tools', contents => <<EOHTML);
 195 <a href="/solpeople/admin/crash_test.pl">Test website error handling</a><br />
 196 <a href="/solpeople/admin/stats.pl">View user stats</a><br />
 197 <a href="/solpeople/admin/quick_create_account.pl">Create new user account</a><br />
 198 <a href="/solpeople/admin/create_organization.pl">Create new organization</a>
 199 EOHTML
 200 }
 201
 202 if ( $sp->get_user_type() =~ /curator/i ) {
 203     my $publications =
 204 qq| <a href= "/search/pub_search.pl">Search the SGN publication database </a><br />|;
 205     $publications .=
 206 qq| <a href= "/search/pub_search.pl?w9b3_assigned_to=$sp_person_id">See your assigned publications</a><br />|;
 207     $publications .=
 208 qq| <a href= "/search/pub_search.pl?w9b3_status=pending">See publications pending curation</a><br />|;
 209     $publications .=
 210 qq| <a href= "/chado/fetch_pubmed.pl">Load new publications from PubMed</a><br />|;
 211
 212     print info_section_html(
 213         title    => 'Literature mining',
 214         contents => $publications
 215     );
 216 }
 217
 218 if ( $sp->get_user_type() =~ /submitter|curator|sequencer/i ) {
 219
 220     my @loci =
 221       CXGN::Phenome::Locus::get_locus_ids_by_editor( $dbh, $sp_person_id );
 222     my $top  = 50;
 223     my $more = 0;
 224     my $max  = @loci;
 225     if ( @loci > 24 ) {
 226         $more = @loci - 24;
 227         $max  = 24;
 228     }
 229
 230     my $locus_editor_info = qq { None.<br /> };
 231     if ( @loci > 0 ) {
 232         $locus_editor_info = "";
 233     }
 234
 235     for ( my $i = 0 ; $i < ($max) ; $i++ ) {
 236         my $locus    = CXGN::Phenome::Locus->new( $dbh, $loci[$i] );
 237         my $symbol   = $locus->get_locus_symbol();
 238         my $locus_id = $locus->get_locus_id();
 239
 240         $locus_editor_info .=
 241 qq { <a href="/phenome/locus_display.pl?locus_id=$locus_id&amp;action=view">$symbol</a> };
 242     }
 243     if ($more) {
 244         $locus_editor_info .=
 245 qq|<br><b>and <a href="/search/locus/>$more more</a></b><br />|;
 246     }
 247
 248     print info_section_html(
 249         title    => 'Loci with Editor Privileges',
 250         contents => $locus_editor_info
 251     );
 252
 253     my @annotated_loci =
 254       CXGN::Phenome::Locus::get_locus_ids_by_annotator( $dbh, $sp_person_id );
 255
 256     my $more = 0;
 257     my $max  = @annotated_loci;
 258     if ( @annotated_loci > 24 ) {
 259         $more = @annotated_loci - 24;
 260         $max  = 24;
 261     }
 262
 263     my ( $locus_annotations, $more_annotations );
 264
 265     for ( my $i = 0 ; $i < $top ; $i++ ) {
 266         my $locus    = CXGN::Phenome::Locus->new( $dbh, $annotated_loci[$i] );
 267         my $symbol   = $locus->get_locus_symbol();
 268         my $locus_id = $locus->get_locus_id();
 269
 270         if ( $i < $max ) {
 271             $locus_annotations .=
 272 qq | <a href="/locus/$locus_id/view">$symbol</a> |;
 273         }
 274         else {
 275             $more_annotations .=
 276 qq { <a href="/locus/$locus_id/view">$symbol</a> };
 277         }
 278     }
 279
 280     if ($more) {
 281         $locus_annotations .= " and $more more, not shown.<br />";
 282
 283         $locus_annotations .=
 284           html_optional_show( 'locus_annotations', 'Show more',
 285             qq|<div class="minorbox">$more_annotations</div> |,
 286           );
 287     }
 288
 289     $locus_annotations .=
 290 qq| <a href="../phenome/recent_annotated_loci.pl">[View annotated loci by date]</a> |;
 291     print info_section_html(
 292         title    => 'Annotated Loci',
 293         contents => $locus_annotations
 294     );
 295
 296     my $map_factory = CXGN::Cview::MapFactory->new($dbh);
 297     my @user_maps   = $map_factory->get_user_maps();
 298     my $html        = "";
 299
 300     if ( @user_maps > 0 ) {
 301         $html .=
 302 "<table alt=\"\" ><tr><td><i>Name</i></td><td></td><td></td><td><i>status</i></td></tr>";
 303         foreach my $um (@user_maps) {
 304             my $public = " (not public) ";
 305             if ( $um->get_map()->get_is_public() ) { $public = "(public)"; }
 306             $html .=
 307                 "<tr><td><b>"
 308               . $um->get_short_name()
 309               . "</b></td><td> <a href=\"/cview/umap.pl?action=view&amp;user_map_id="
 310               . $um->get_id()
 311               . "\" >[view]</a></td><td><a href=\"/cview/umap.pl?action=edit&amp;user_map_id="
 312               . $um->get_id()
 313               . "\">[configure]</a></td><td>$public</td></tr>";
 314
 315         }
 316         $html .= "</table>";
 317     }
 318
 319     # BROKEN!
 320     #    print info_section_html(title => 'User Maps', contents=> <<EOHTML);
 321     #    <a href="/cview/upload_usermap.pl">Upload new user map</a><br />
 322     #   <br />
 323     #   $html
 324     #EOHTML
 325
 326 }
 327
 328 my $user_type = $sp->get_user_type();
 329 my $user_info = {
 330     user => qq{ Your current user status is <b>$user_type</b>. Please contact <a href="mailto:sgn-feedback\@sgn.cornell.edu">SGN</a> to upgrade to a <b>submitter</b> account with more privileges. Submitters can upload user maps, EST data, and become locus editors. },
 331
 332     submitter => qq{ Your current user status is <b>$user_type</b>. You have the maximum user privileges on SGN. Please contact <a href="mailto:sgn-feedback\@sgn.cornell.edu">SGN</a> if you would like to change your user status.},
 333
 334     curator => qq{ Your current user status is <b>$user_type</b>. },
 335
 336     sequencer => qq{ Your current user status is <b>$user_type</b>. You have maximum user privileges on SGN. },
 337
 338     genefamily_editor => qq{ Your current user status is <b>$user_type</b>. },
 339 };
 340
 341 print info_section_html( title => 'User Status',
 342     contents => $user_info->{$user_type} );
 343
 344 $page->footer();
 345
 346 #returns a string containing a TPF and an AGP upload form,
 347 #with the single argument interpolated in
 348 sub tpf_agp_upload_forms {
 349     my $chrinput = shift;
 350     my ( $chrinput_agp, $chrinput_tpf ) = ( $chrinput, $chrinput );
 351     $chrinput_agp =~ s/TYPE/_agp/g;
 352     $chrinput_tpf =~ s/TYPE/_tpf/g;
 353     return <<EOHTML;
 354 <div style="margin-top: 1em">
 355   <b>Upload Accessioned Golden Path (AGP) File</b><br />
 356   <form action="/sequencing/agp.pl" method="post" enctype="multipart/form-data">
 357     $chrinput_agp
 358     <input type="hidden" name="filetype" value="agp" />
 359     <label for="agpinput">File: </label>
 360     <input id="agpinput" type="file" name="agp_file" value="Upload AGP file" /><input type="submit" value="Submit" />
 361   </form>
 362 </div>
 363 <div style="margin-top: 1em">
 364   <b>Upload Tiling Path Format (TPF) File</b><br />
 365   <form action="/sequencing/tpf.pl" method="post" enctype="multipart/form-data">
 366     $chrinput_tpf
 367     <input type="hidden" name="filetype" value="tpf" />
 368     <label for="tpfinput">File: </label>
 369     <input id="tpfinput" type="file" name="tpf_file" value="Upload TPF file" /><input type="submit" value="Submit" />
 370   </form>
 371 </div>
 372 EOHTML
 373 }
 374
 375 sub my_populations {
 376     my @pops = @_;
 377     my $pops_list;
 378
 379     foreach my $pop (@pops) {
 380         my $pop_name  = $pop->get_name();
 381         my $pop_id    = $pop->get_population_id();
 382         my $is_public = $pop->get_privacy_status();
 383         if ($is_public)    { $is_public = 'is publicly available'; }
 384         if ( !$is_public ) { $is_public = 'is not publicly available yet'; }
 385         $pops_list .=
 386 qq |<a href="/qtl/population/$pop_id">$pop_name</a> <i>($is_public)</i><br/>|;
 387     }
 388
 389     return $pops_list;
 390 }