cgi-bin/solpeople/top-level.pl

   1 use strict;
   2
   3 use CXGN::DB::Connection;
   4 use CXGN::Page;
   5 use CXGN::Login;
   6 use CXGN::People;
   7 use CXGN::People::Person;
   8 use CXGN::BlastWatch;
   9 use CXGN::Phenome::Locus;
  10 use CXGN::Cview::MapFactory;
  11 use CXGN::Page::FormattingHelpers qw/info_section_html page_title_html
  12   info_table_html simple_selectbox_html
  13   html_optional_show/;
  14
  15 our $c;
  16 use CatalystX::GlobalContext qw($c);
  17
  18
  19 my $page = CXGN::Page->new( "solpeople main menu", "john" );
  20 my $dbh = CXGN::DB::Connection->new();
  21 my $site_name = $c->config->{project_name};
  22
  23 my $sp_person_id = CXGN::Login->new($dbh)->verify_session();
  24
  25 my $sp = CXGN::People::Person->new( $dbh, $sp_person_id );
  26 unless ($sp_person_id) {
  27     $page->error_page( "Login ID not found.",
  28         "", "", "Login ID not found: $sp_person_id" );
  29 }
  30 unless ( $sp->get_username() ) {
  31     $page->error_page( "Username not found.",
  32         "", "", "Username not found for sp_person_id '$sp_person_id'" );
  33 }
  34 my $username = $sp->get_first_name() . " " . $sp->get_last_name();
  35
  36 #my $research_update=$sp->get_research_update();
  37 #my $contact_update=$sp->get_contact_update();
  38
  39 $page->add_style( text => <<EOS);
  40 div#queryTable
  41 {
  42 margin: 0px 0px 0px 0px;
  43 display: none;
  44 }
  45 EOS
  46 $page->header();
  47
  48 print <<END_HTML;
  49
  50 <script type = "text/javascript">
  51 <!--
  52     function toggleLayer(whichLayer) {
  53         if (document.getElementById) {
  54             var style2 = document.getElementById(whichLayer).style;
  55             style2.display = style2.display? "":"block";
  56         }
  57         else if (document.all) {
  58             var style2 = document.all[whichLayer].style;
  59             style2.display = style2.display? "":"block";
  60         }
  61         else if (document.layers) {
  62             var style2 = document.layers[whichLayer].style;
  63             style2.display = style2.display? "":"block";
  64         }
  65     }
  66     function showSequence(sequence) {
  67         document.getElementById("Heading").innerHTML="<strong>Full sequence: </strong>";
  68         document.getElementById("fullSequence").innerHTML=sequence;
  69     }
  70     function hideSequence() {
  71         document.getElementById("Heading").innerHTML="";
  72         document.getElementById("fullSequence").innerHTML="";
  73     }
  74 //-->
  75 </script>
  76 END_HTML
  77
  78 print page_title_html("My $site_name");
  79 print qq|<div align="center">Welcome <b>$username</b></div>\n|;
  80 print
  81 qq|<div align="right" style="margin-bottom: 0.5em">Not $username? <a href="login.pl?logout=yes">[log out]</a></div>\n|;
  82 print info_section_html( title => 'General Tools', contents => <<EOHTML);
  83     <a href="personal-info.pl?action=edit&sp_person_id=$sp_person_id">View or update personal (contact and research) information</a><br />
  84     <a href="change-account.pl?action=edit&sp_person_id=$sp_person_id">Update account information</a><br />
  85     <a href="/forum/topics.pl">Post to SGN forum</a><br />
  86 EOHTML
  87 my $queries =
  88     qq|<div id="queryTable">|
  89   . CXGN::BlastWatch::get_queries( $dbh, $sp_person_id )
  90   . '</div>';
  91 print info_section_html( title => 'BLAST Watch', contents => <<EOHTML);
  92     <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>
  93     <a href="/tools/blast/watch/index.pl">Submit a query to SGN BLAST Watch</a><br />
  94     <a href="javascript:toggleLayer('queryTable');" title="View your BLAST Watch queries">View your BLAST Watch queries</a>
  95     $queries
  96 EOHTML
  97
  98 #return 1 if the first term is eq to one of the other terms given
  99 sub in(@) {
 100     my $t = shift;
 101     ( grep { $t eq $_ } @_ ) ? 1 : 0;
 102 }
 103
 104 #now assemble the sequencing tools stuff
 105 if ( in( $sp->get_user_type, qw/curator sequencer/ ) ) {
 106
 107     #make a form for uploading TPF and AGP files
 108     my $tpf_agp_upload = do {
 109         if ( $sp->get_user_type eq 'curator' ) {
 110             tpf_agp_upload_forms(<<EOHTML);
 111       <!-- the string 'TYPE' will be replaced in each instance by tpf_agp_upload_forms() -->
 112 <label for="chrnuminputTYPE">For Chromosome #: </label><input id="chrnuminputTYPE" name="chr" type="text" size="2" maxlength="2" />
 113 EOHTML
 114         }
 115         elsif ( $sp->get_user_type eq 'sequencer'
 116             and my @projects =
 117             grep { $_ >= 1 && $_ <= 12 }
 118             $sp->get_projects_associated_with_person )
 119         {
 120             my $chrinput =
 121               @projects > 1
 122               ? simple_selectbox_html(
 123                 name    => 'chr',
 124                 choices => \@projects,
 125                 label   => 'For Chromosome #:',
 126               )
 127               : qq|For Chromosome #: <b>$projects[0]</b> <input type="hidden" value="$projects[0]" name="chr" />|;
 128             tpf_agp_upload_forms($chrinput);
 129         }
 130     };
 131
 132     print info_section_html( title => 'Sequencer Tools', contents => <<EOHTML);
 133 <a href="attribute_bacs.pl">Attribute a BAC to your chromosome sequencing project</a><br />
 134 <a href="/maps/physical/clone_il_view.pl">View/update BAC IL mapping information (list view)</a><br />
 135 <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>
 136 <a href="/sequencing/tpf.pl">View TPF Files</a><br />
 137 <a href="/sequencing/agp.pl">View AGP Files</a><br />
 138 $tpf_agp_upload
 139 EOHTML
 140 }
 141
 142 # if( in( $sp->get_user_type(), qw/submitter curator/ ) )
 143 # {
 144 #   print info_section_html(title => 'EST Submission Pages', contents => <<EOHTML);
 145 # <a href="/data-submit/top-level.pl">Data submission start page</a>
 146 # EOHTML
 147 # }
 148
 149 if ( in( $sp->get_user_type(), qw/submitter curator/ ) ) {
 150     print info_section_html( title => 'QTL data submission',
 151         contents => <<EOHTML);
 152 <a href="/phenome/qtl_form.pl">Upload and analyse your QTL data</a>
 153 EOHTML
 154 }
 155
 156 my @pops = CXGN::Phenome::Population->my_populations($sp_person_id);
 157
 158 if (@pops) {
 159     my $pop_list = my_populations(@pops);
 160     print info_section_html( title => 'Populations', contents => $pop_list );
 161 }
 162
 163 if ( $sp->get_user_type() eq 'curator' ) {
 164     print info_section_html( title => 'Curator Tools', contents => <<EOHTML);
 165 <a href="/solpeople/admin/crash_test.pl">Test website error handling</a><br />
 166 <a href="/solpeople/admin/stats.pl">View user stats</a><br />
 167 <a href="/solpeople/admin/quick_create_account.pl">Create new user account</a><br />
 168 <a href="/solpeople/admin/create_organization.pl">Create new organization</a>
 169 EOHTML
 170 }
 171
 172 if ( $sp->get_user_type() =~ /curator/i ) {
 173     my $publications =
 174 qq| <a href= "/search/pub_search.pl">Search the SGN publication database </a><br />|;
 175     $publications .=
 176 qq| <a href= "/search/pub_search.pl?w9b3_assigned_to=$sp_person_id">See your assigned publications</a><br />|;
 177     $publications .=
 178 qq| <a href= "/search/pub_search.pl?w9b3_status=pending">See publications pending curation</a><br />|;
 179     $publications .=
 180 qq| <a href= "/chado/fetch_pubmed.pl">Load new publications from PubMed</a><br />|;
 181
 182     print info_section_html(
 183         title    => 'Literature mining',
 184         contents => $publications
 185     );
 186 }
 187
 188 if ( $sp->get_user_type() =~ /submitter|curator|sequencer/i ) {
 189
 190     my @loci =
 191       CXGN::Phenome::Locus::get_locus_ids_by_editor( $dbh, $sp_person_id );
 192     my $top  = 50;
 193     my $more = 0;
 194     my $max  = @loci;
 195     if ( @loci > 24 ) {
 196         $more = @loci - 24;
 197         $max  = 24;
 198     }
 199
 200     my $locus_editor_info = qq { None.<br /> };
 201     if ( @loci > 0 ) {
 202         $locus_editor_info = "";
 203     }
 204
 205     for ( my $i = 0 ; $i < ($max) ; $i++ ) {
 206         my $locus    = CXGN::Phenome::Locus->new( $dbh, $loci[$i] );
 207         my $symbol   = $locus->get_locus_symbol();
 208         my $locus_id = $locus->get_locus_id();
 209
 210         $locus_editor_info .=
 211 qq { <a href="/phenome/locus_display.pl?locus_id=$locus_id&amp;action=view">$symbol</a> };
 212     }
 213     if ($more) {
 214         $locus_editor_info .=
 215 qq|<br><b>and <a href="/search/locus_search.pl?w8e4_editor=$sp_person_id">$more more</a></b><br />|;
 216     }
 217
 218     print info_section_html(
 219         title    => 'Loci with Editor Privileges',
 220         contents => $locus_editor_info
 221     );
 222
 223     my @annotated_loci =
 224       CXGN::Phenome::Locus::get_locus_ids_by_annotator( $dbh, $sp_person_id );
 225
 226     my $more = 0;
 227     my $max  = @annotated_loci;
 228     if ( @annotated_loci > 24 ) {
 229         $more = @annotated_loci - 24;
 230         $max  = 24;
 231     }
 232
 233     my ( $locus_annotations, $more_annotations );
 234
 235     for ( my $i = 0 ; $i < $top ; $i++ ) {
 236         my $locus    = CXGN::Phenome::Locus->new( $dbh, $annotated_loci[$i] );
 237         my $symbol   = $locus->get_locus_symbol();
 238         my $locus_id = $locus->get_locus_id();
 239
 240         if ( $i < $max ) {
 241             $locus_annotations .=
 242 qq | <a href="/phenome/locus_display.pl?locus_id=$locus_id&amp;action=view">$symbol</a> |;
 243         }
 244         else {
 245             $more_annotations .=
 246 qq { <a href="/phenome/locus_display.pl?locus_id=$locus_id&amp;action=view">$symbol</a> };
 247         }
 248     }
 249
 250     if ($more) {
 251         $locus_annotations .= " and $more more, not shown.<br />";
 252
 253         $locus_annotations .=
 254           html_optional_show( 'locus_annotations', 'Show more',
 255             qq|<div class="minorbox">$more_annotations</div> |,
 256           );
 257     }
 258
 259     $locus_annotations .=
 260 qq| <a href="../phenome/recent_annotated_loci.pl">[View annotated loci by date]</a> |;
 261     print info_section_html(
 262         title    => 'Annotated Loci',
 263         contents => $locus_annotations
 264     );
 265
 266     my $map_factory = CXGN::Cview::MapFactory->new($dbh);
 267     my @user_maps   = $map_factory->get_user_maps();
 268     my $html        = "";
 269
 270     if ( @user_maps > 0 ) {
 271         $html .=
 272 "<table alt=\"\" ><tr><td><i>Name</i></td><td></td><td></td><td><i>status</i></td></tr>";
 273         foreach my $um (@user_maps) {
 274             my $public = " (not public) ";
 275             if ( $um->get_map()->get_is_public() ) { $public = "(public)"; }
 276             $html .=
 277                 "<tr><td><b>"
 278               . $um->get_short_name()
 279               . "</b></td><td> <a href=\"/cview/umap.pl?action=view&amp;user_map_id="
 280               . $um->get_id()
 281               . "\" >[view]</a></td><td><a href=\"/cview/umap.pl?action=edit&amp;user_map_id="
 282               . $um->get_id()
 283               . "\">[configure]</a></td><td>$public</td></tr>";
 284
 285         }
 286         $html .= "</table>";
 287     }
 288
 289     # BROKEN!
 290     #    print info_section_html(title => 'User Maps', contents=> <<EOHTML);
 291     #    <a href="/cview/upload_usermap.pl">Upload new user map</a><br />
 292     #   <br />
 293     #   $html
 294     #EOHTML
 295
 296 }
 297
 298 my $user_type = $sp->get_user_type();
 299 my $user_info = {
 300     user => qq{ Your current user status is <b>$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. },
 301
 302     submitter => qq{ Your current user status is <b>$user_type</b>. You have the maximum user privileges on SGN. Please contact <a href="mailto:sgn-feedback\@sgn.cornell.edu">SGN</a> if you would like to change your user status.},
 303
 304     curator => qq{ Your current user status is <b>$user_type</b>. },
 305
 306     sequencer => qq{ Your current user status is <b>$user_type</b>. You have maximum user privileges on SGN. },
 307
 308     genefamily_editor => qq{ Your current user status is <b>$user_type</b>. },
 309 };
 310
 311 print info_section_html( title => 'User Status',
 312     contents => $user_info->{$user_type} );
 313
 314 $page->footer();
 315
 316 #returns a string containing a TPF and an AGP upload form,
 317 #with the single argument interpolated in
 318 sub tpf_agp_upload_forms {
 319     my $chrinput = shift;
 320     my ( $chrinput_agp, $chrinput_tpf ) = ( $chrinput, $chrinput );
 321     $chrinput_agp =~ s/TYPE/_agp/g;
 322     $chrinput_tpf =~ s/TYPE/_tpf/g;
 323     return <<EOHTML;
 324 <div style="margin-top: 1em">
 325   <b>Upload Accessioned Golden Path (AGP) File</b><br />
 326   <form action="/sequencing/agp.pl" method="post" enctype="multipart/form-data">
 327     $chrinput_agp
 328     <input type="hidden" name="filetype" value="agp" />
 329     <label for="agpinput">File: </label>
 330     <input id="agpinput" type="file" name="agp_file" value="Upload AGP file" /><input type="submit" value="Submit" />
 331   </form>
 332 </div>
 333 <div style="margin-top: 1em">
 334   <b>Upload Tiling Path Format (TPF) File</b><br />
 335   <form action="/sequencing/tpf.pl" method="post" enctype="multipart/form-data">
 336     $chrinput_tpf
 337     <input type="hidden" name="filetype" value="tpf" />
 338     <label for="tpfinput">File: </label>
 339     <input id="tpfinput" type="file" name="tpf_file" value="Upload TPF file" /><input type="submit" value="Submit" />
 340   </form>
 341 </div>
 342 EOHTML
 343 }
 344
 345 sub my_populations {
 346     my @pops = @_;
 347     my $pop_list;
 348
 349     foreach my $pops (@pops) {
 350         my $pop_name  = $pops->get_name();
 351         my $pop_id    = $pops->get_population_id();
 352         my $is_public = $pops->get_privacy_status();
 353         if ($is_public)    { $is_public = 'is publicly available'; }
 354         if ( !$is_public ) { $is_public = 'is not publicly available yet'; }
 355         $pop_list .=
 356 qq |<a href="/phenome/population.pl?population_id=$pop_id">$pop_name</a> <i>($is_public)</i><br/>|;
 357     }
 358     return $pop_list;
 359 }