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revision 1.4, Thu Dec 13 21:17:21 2007 UTC revision 1.14, Mon Apr 7 21:02:18 2008 UTC
# Line 19  Line 19 
19    my ( $self ) = @_;    my ( $self ) = @_;
20    
21    $self->application->register_component( 'Table', 'sstable'  );    $self->application->register_component( 'Table', 'sstable'  );
22      $self->application->register_component(  'Table', 'VarDescTable'  );
23  }  }
24    
25  #################################  #################################
# Line 36  Line 37 
37  sub output {  sub output {
38    my ( $self ) = @_;    my ( $self ) = @_;
39    
   use Data::Dumper;  
   
40    my $fig = new FIG;    my $fig = new FIG;
41    my $cgi = $self->application->cgi;    my $cgi = $self->application->cgi;
42    
# Line 64  Line 63 
63      }      }
64    }    }
65    
66    if ( $user && $user->has_right( $self->application, 'edit', 'subsystem', $name ) ) {    if ( $user ) {
67        if ( $user->has_right( $self->application, 'edit', 'subsystem', $name ) ) {
68      $can_alter = 1;      $can_alter = 1;
69      $fig->set_user( $seeduser );      $fig->set_user( $seeduser );
70    }    }
71        else {
72          # we might have the problem that the user has not yet got the right for editing the
73          # subsystem due to that it was created in the old seed or what do I know where.
74          my $curatorOfSS = $fig->subsystem_curator( $name );
75          my $su = lc( $seeduser );
76          my $cu = lc( $curatorOfSS );
77          if ( $su eq $cu ) {
78            # now set the rights...
79            my $right = $dbmaster->Rights->create( { name => 'edit',
80                                                     scope => $user->get_user_scope,
81                                                     data_type => 'subsystem',
82                                                     data_id => $name,
83                                                     granted => 1,
84                                                     delegated => 0 } );
85            if ( $right ) {
86              $can_alter = 1;
87              $fig->set_user( $seeduser );
88            }
89          }
90        }
91      }
92    
93    ######################    ######################
94    # Construct the menu #    # Construct the menu #
95    ######################    ######################
# Line 77  Line 99 
99    # Build nice tab menu here    # Build nice tab menu here
100    $menu->add_category( 'Subsystem Info', "SubsysEditor.cgi?page=ShowSubsystem&subsystem=$name" );    $menu->add_category( 'Subsystem Info', "SubsysEditor.cgi?page=ShowSubsystem&subsystem=$name" );
101    $menu->add_category( 'Functional Roles', "SubsysEditor.cgi?page=ShowFunctionalRoles&subsystem=$name" );    $menu->add_category( 'Functional Roles', "SubsysEditor.cgi?page=ShowFunctionalRoles&subsystem=$name" );
102    $menu->add_category( 'Subsystem Diagram', "SubsysEditor.cgi?page=ShowDiagram&subsystem=$name" );    $menu->add_category( 'Diagram', "SubsysEditor.cgi?page=ShowDiagram&subsystem=$name" );
103    $menu->add_category( 'Subsystem Spreadsheet', "SubsysEditor.cgi?page=ShowSpreadsheet&subsystem=$name" );    $menu->add_category( 'Illustrations', "SubsysEditor.cgi?page=ShowIllustrations&subsystem=$name" );
104    $menu->add_category( 'Subsystem Check', "SubsysEditor.cgi?page=ShowCheck&subsystem=$name" );    $menu->add_category( 'Spreadsheet', "SubsysEditor.cgi?page=ShowSpreadsheet&subsystem=$name" );
105    $menu->add_category( 'Subsystem Tree', "SubsysEditor.cgi?page=ShowTree&subsystem=$name" );    $menu->add_category( 'Show Check', "SubsysEditor.cgi?page=ShowCheck&subsystem=$name" );
106      $menu->add_category( 'Show Connections', "SubsysEditor.cgi?page=ShowTree&subsystem=$name" );
107    
108    
109    ##############################    ##############################
# Line 143  Line 166 
166      }      }
167      $subsystem->set_classification( [ $class1, $class2 ] );      $subsystem->set_classification( [ $class1, $class2 ] );
168    
169        my $litstoset = $cgi->param( 'SUBSYSLIT' );
170        my @lits = split( ', ', $litstoset );
171        setLiteratures( $fig, $name, \@lits );
172    
173        my $wlstoset = $cgi->param( 'SUBSYSWL' );
174        if ( defined( $wlstoset ) && $wlstoset =~ /.+\s+.+/ ) {
175          my @wls = split( '\n', $wlstoset );
176          setWeblinks( $fig, $name, \@wls );
177        }
178    
179      # here we really edit the files in the subsystem directory #      # here we really edit the files in the subsystem directory #
180      $subsystem->incr_version();      $subsystem->incr_version();
181      $subsystem->db_sync();      $subsystem->db_sync();
# Line 156  Line 189 
189    my ( $ssversion, $sscurator, $pedigree, $ssroles ) = $fig->subsystem_info( $name );    my ( $ssversion, $sscurator, $pedigree, $ssroles ) = $fig->subsystem_info( $name );
190    
191    my $versionlink = '';    my $versionlink = '';
192  print STDERR $can_alter." CANALTER\n";  
193    if ( $can_alter ) {    if ( $can_alter ) {
194      $versionlink = " -- <A HREF='".$self->application->url()."?page=ResetSubsystem&subsystem=$name'>Reset to Previous Timestamp</A>";      $versionlink = " -- <A HREF='".$self->application->url()."?page=ResetSubsystem&subsystem=$name'>Reset to Previous Timestamp</A>";
     print STDERR $versionlink . " VL\n";  
195    }    }
196    
197    my $mod_time = get_mod_time( $name );    my $mod_time = get_mod_time( $name );
# Line 184  Line 216 
216      $classification_stuff .= "<TR><TH></TH><TD>$class->[1]</TD></TR>";      $classification_stuff .= "<TR><TH></TH><TD>$class->[1]</TD></TR>";
217    }    }
218    
219      print STDERR $versionlink . " VL\n";    my $infotable = "<TABLE><TR><TH>Name:</TH><TD>$ssname</TD></TR>";
   my $infotable = "<TABLE><TR><TH>Name:</TH><TD>$ssname</TD><TR>";  
220    $infotable .= "<TR><TH>Author:</TH><TD>$sscurator</TD></TR>";    $infotable .= "<TR><TH>Author:</TH><TD>$sscurator</TD></TR>";
221    $infotable .= "<TR><TH>Version:</TH><TD>$ssversion $versionlink</TD></TR>";    $infotable .= "<TR><TH>Version:</TH><TD>$ssversion $versionlink</TD></TR>";
222    $infotable .= "<TR><TH>Last Modified:</TH><TD>$mod_time</TD></TR>";    $infotable .= "<TR><TH>Last Modified:</TH><TD>$mod_time</TD></TR>";
223    
224      # Literature #
225      my $lit = getLiteratures( $fig, $name );
226      my $litstring = '';
227      my $litvoid = '';
228      if ( defined( $lit ) && scalar( @$lit ) > 0 ) {
229        my @litlinks;
230        foreach my $l ( @$lit ) {
231          my $thislink = "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=" . $l ."')\">$l</a>";
232          push @litlinks, $thislink;
233        }
234        $litstring = join( ', ', @litlinks );
235        $litvoid = join( ', ', @$lit );
236      }
237    
238      # Weblinks #
239      my ( $wl, $wlvoid ) = getLinks( $fig, $name );
240    
241      my $variants = $subsystem->get_variants();
242    
243    if ( $can_alter ) {    if ( $can_alter ) {
244    
245        my $editLitButton = "<INPUT TYPE=BUTTON ID='EditLitButton' VALUE='Edit Literature' ONCLICK='MakeEditableLit( \"0\" );'><INPUT TYPE=BUTTON ID='ShowLitButton' VALUE='Show Links' STYLE='display: none;' ONCLICK='MakeEditableLit( \"1\" );'>";
246        my $editWLButton = "<INPUT TYPE=BUTTON ID='EditWLButton' VALUE='Edit Weblinks' ONCLICK='MakeEditableWL( \"0\" );'><INPUT TYPE=BUTTON ID='ShowWLButton' VALUE='Show Weblinks' STYLE='display: none;' ONCLICK='MakeEditableWL( \"1\" );'>";
247    
248        $infotable .= "<TR><TH>Literature</TH><TD><TABLE><TR><TD><SPAN ID='LitSpan'>$litstring</SPAN></TD><TD>$editLitButton</TD><TD><INPUT TYPE=TEXT STYLE='width: 200px; display: none;' NAME='SUBSYSLIT' ID='SUBSYSLIT' VALUE='$litvoid'></TD><TD><SPAN ID='TEXTSPAN' STYLE='display: none;'>Multiple PMIDs should be separated by \', \'</SPAN></TD></TR></TABLE></TD></TR>";
249        $infotable .= "<TR><TH>Websites</TH><TD><TABLE><TR><TD><SPAN ID='WLSpan'>$wl</SPAN></TD><TD>$editWLButton</TD><TD><TEXTAREA ROWS=3 STYLE='width: 400px; display: none;' NAME='SUBSYSWL' ID='SUBSYSWL'>$wlvoid</TEXTAREA></TD><TD><SPAN ID='AREASPAN' STYLE='display: none;'>Please use the following format:<BR>Description1 http://www.xyz.org/...<BR>Description2 http://www.xzy.de/...</SPAN></TD></TR></TABLE></TD></TR>";
250      $infotable .= "<TR><TH>Description</TH><TD><TEXTAREA NAME='SSDESC' ROWS=6 STYLE='width: 772px;'>$ssdesc</TEXTAREA></TD></TR>";      $infotable .= "<TR><TH>Description</TH><TD><TEXTAREA NAME='SSDESC' ROWS=6 STYLE='width: 772px;'>$ssdesc</TEXTAREA></TD></TR>";
251      $infotable .= "<TR><TH>Notes</TH><TD><TEXTAREA NAME='SSNOTES' ROWS=6 STYLE='width: 772px;'>$ssnotes</TEXTAREA></TD></TR>";      $infotable .= "<TR><TH>Notes</TH><TD><TEXTAREA NAME='SSNOTES' ROWS=6 STYLE='width: 772px;'>$ssnotes</TEXTAREA></TD></TR>";
252    }    }
# Line 201  Line 258 
258      my $ssnotes_brs = $ssnotes;      my $ssnotes_brs = $ssnotes;
259      $ssnotes_brs =~ s/(\n\s)+/\n/g;      $ssnotes_brs =~ s/(\n\s)+/\n/g;
260      $ssnotes_brs =~ s/\n/<BR>/g;      $ssnotes_brs =~ s/\n/<BR>/g;
261        $infotable .= "<TR><TH>Literature</TH><TD>$litstring</TD></TR>";
262        $infotable .= "<TR><TH>Websites</TH><TD>$wl</TD></TR>";
263      $infotable .= "<TR><TH>Description</TH><TD>$ssdesc_brs</TD></TR>";      $infotable .= "<TR><TH>Description</TH><TD>$ssdesc_brs</TD></TR>";
264      $infotable .= "<TR><TH>Notes</TH><TD>$ssnotes_brs</TD></TR>";      $infotable .= "<TR><TH>Notes</TH><TD>$ssnotes_brs</TD></TR>";
265    }    }
266      # variants
267      my $vartable = $self->application->component( 'VarDescTable' );
268      $vartable->columns( [ { name => "Variant" }, { name => "Description" } ] );
269    
270      my $vardata;
271      my $has_variants = 0;
272      foreach my $kv ( sort keys %$variants ) {
273        $has_variants = 1;
274        push @$vardata, [ $kv, $variants->{ $kv } ];
275      }
276      $vartable->data( $vardata );
277      $infotable .= "<TR><TH>Variants</TH><TD>";
278      if ( $has_variants ) {
279        $infotable .= $vartable->output();
280      }
281    
282      if ( $can_alter ) {
283        my $variant_outside = "<INPUT TYPE=BUTTON VALUE='Edit Variants in Variant Overview' NAME='EditVariantsOverview' ID='EditVariantsOverview' ONCLICK='window.open( \"".$self->application->url()."?page=ShowVariants&subsystem=$name\" )'>";
284      $infotable .= $variant_outside;
285      }
286    
287      $infotable .= "</TD</TR>";
288    
289    $infotable .= $classification_stuff;    $infotable .= $classification_stuff;
290    $infotable .= "</TABLE>";    $infotable .= "</TABLE>";
291    
# Line 293  Line 375 
375      my $opt = "<SELECT SIZE=5 ID='$firstc' NAME='SUBSYSH2' STYLE='width: 386px;' class='hideme'>";      my $opt = "<SELECT SIZE=5 ID='$firstc' NAME='SUBSYSH2' STYLE='width: 386px;' class='hideme'>";
376      my $optstring = '';      my $optstring = '';
377      foreach my $secc ( sort @{ $ssclass->{ $firstc } } ) {      foreach my $secc ( sort @{ $ssclass->{ $firstc } } ) {
378        if ( defined( $SUBSYSH2 ) && $SUBSYSH2 eq $secc ) {        if ( defined( $SUBSYSH2 ) && $SUBSYSH2 eq $secc && $SUBSYSH1 eq $firstc ) {
379          $optstring .= "<OPTION SELECTED VALUE='$secc'>$secc</OPTION>";          $optstring .= "<OPTION SELECTED VALUE='$secc'>$secc</OPTION>";
380          # we have to show the selectbox if there is a selected value          # we have to show the selectbox if there is a selected value
381          $opt = "<SELECT SIZE=5 ID='$firstc' NAME='SUBSYSH2' STYLE='width: 386px;' class='showme'>";          $opt = "<SELECT SIZE=5 ID='$firstc' NAME='SUBSYSH2' STYLE='width: 386px;' class='showme'>";
# Line 341  Line 423 
423    return $sdContent;    return $sdContent;
424  }  }
425    
426    ########################################
427    # get Literature-string for subsystems #
428    ########################################
429    sub getLiteratures {
430      my ( $fig, $name ) = @_;
431    
432      my $frpubs;
433      my @rel_lit_num = $fig->get_attributes( 'Subsystem:'.$name, "SUBSYSTEM_PUBMED_RELEVANT" );
434    
435      foreach my $k ( @rel_lit_num ) {
436        my ( $ss, $key, $value ) = @$k;
437        push @$frpubs, $value;
438      }
439    
440      return $frpubs;
441    }
442    
443    ######################################
444    # get Weblinks-string for subsystems #
445    ######################################
446    sub getLinks {
447      my ( $fig, $name ) = @_;
448    
449      my $links;
450      my $linksstring = '';
451      my $linksvoid = '';
452      my @rel_link_num = $fig->get_attributes( 'Subsystem:'.$name, "SUBSYSTEM_WEBLINKS" );
453    
454      foreach my $k ( @rel_link_num ) {
455        my ( $ss, $key, @value ) = @$k;
456        $linksstring .= $value[0].": <a href=\"javascript:void(0)\"onclick=\"window.open('".$value[1]."','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes')\">". $value[1]."</a><BR>";
457        $linksvoid .= $value[0]." ".$value[1]."\n";
458      }
459    
460      return ( $linksstring, $linksvoid );
461    }
462    
463    ########################################
464    # set Literature-string for subsystems #
465    ########################################
466    sub setLiteratures {
467      my ( $fig, $name, $newpubs ) = @_;
468    
469      my @values;
470      my @rel_lit_num = $fig->get_attributes( 'Subsystem:'.$name, "SUBSYSTEM_PUBMED_RELEVANT" );
471    
472      foreach my $k ( @rel_lit_num ) {
473        my ( $ss, $key, $value ) = @$k;
474        $fig->delete_matching_attributes( "Subsystem:$name", "SUBSYSTEM_PUBMED_RELEVANT", $value );
475      }
476    
477      foreach my $np ( @$newpubs ) {
478        $fig->add_attribute( "Subsystem:$name", "SUBSYSTEM_PUBMED_RELEVANT", $np );
479      }
480    }
481    
482    ########################################
483    # set Literature-string for subsystems #
484    ########################################
485    sub setWeblinks {
486      my ( $fig, $name, $newpubs ) = @_;
487    
488      my @values;
489      my @rel_lit_num = $fig->get_attributes( 'Subsystem:'.$name, "SUBSYSTEM_WEBLINKS" );
490    
491      foreach my $k ( @rel_lit_num ) {
492        my ( $ss, $key, $value ) = @$k;
493        $fig->delete_matching_attributes( "Subsystem:$name", "SUBSYSTEM_WEBLINKS", $value );
494      }
495    
496      foreach my $np ( @$newpubs ) {
497        my @h = split( /\s+/, $np );
498        $fig->add_attribute( "Subsystem:$name", "SUBSYSTEM_WEBLINKS", @h );
499      }
500    }
501    
502  sub supported_rights {  sub supported_rights {
503    
504    return [ [ 'edit', 'subsystem', '*' ] ];    return [ [ 'edit', 'subsystem', '*' ] ];

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