added static link to BGB

git-svn-id: http://biopieces.googlecode.com/svn/trunk@897 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/www/index.cgi b/www/index.cgi
index aa9842db94266b4b8a367158f1ba69a28ebcfd2b..ec03bf65bfd2322c54aad064ac8393c46b08ef34 100755 (executable)
--- a/www/index.cgi
+++ b/www/index.cgi
@@ -61,7 +61,7 @@ push @html, Maasha::XHTML::form_end;
 push @html, Maasha::XHTML::body_end;
 push @html, Maasha::XHTML::html_end;
 
-# push @html, Maasha::XHTML::hdump( [ $cgi->Vars ] );  # DEBUG
+# push @html, Maasha::XHTML::hdump( { $cgi->Vars } );  # DEBUG
 # push @html, Maasha::XHTML::hdump( \%ENV );           # DEBUG
 # push @html, Maasha::XHTML::hdump( $cookie );         # DEBUG
 
@@ -117,6 +117,16 @@ sub cookie_default
     cookie_login( $cookie );
 
     $cookie->{ 'PAGE' }          ||= $cgi->param( 'page' )     || 'login';
+
+    if ( $cookie->{ 'LOGIN' } eq 'OK' )
+    {
+        if ( $cgi->param( 'genome' ) ) {
+            $cookie->{ 'PAGE' } = 'browse';
+        } else {
+            $cookie->{ 'PAGE' } = 'clade';
+        }
+    }
+
     $cookie->{ 'CLADE' }           = $cgi->param( 'clade' )    || '';
     $cookie->{ 'GENOME' }          = $cgi->param( 'genome' )   || '';
     $cookie->{ 'ASSEMBLY' }        = $cgi->param( 'assembly' ) || '';
@@ -155,18 +165,22 @@ sub cookie_default
     $cookie->{ 'FEAT_MAX' }        = 5000;   # TODO: Reduntant?
 
     $cookie->{ 'LIST_USER' }       = Maasha::BGB::Track::list_users();
-    $cookie->{ 'LIST_CLADE' }      = Maasha::BGB::Track::list_clades(     $cookie->{ 'USER' } );
-    $cookie->{ 'LIST_GENOME' }     = Maasha::BGB::Track::list_genomes(    $cookie->{ 'USER' }, $cookie->{ 'CLADE' } );
-    $cookie->{ 'LIST_ASSEMBLY' }   = Maasha::BGB::Track::list_assemblies( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' } );
-    $cookie->{ 'LIST_CONTIG' }     = Maasha::BGB::Track::list_contigs(    $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' } );
 
-    if ( $cookie->{ 'CONTIG' } )
+    if ( $cookie->{ 'USER' } )
     {
-        cookie_start( $cookie );
-        cookie_end( $cookie );
-        cookie_zoom( $cookie );
-        cookie_move( $cookie );
-        cookie_center( $cookie );
+        $cookie->{ 'LIST_CLADE' }      = Maasha::BGB::Track::list_clades(     $cookie->{ 'USER' } );
+        $cookie->{ 'LIST_GENOME' }     = Maasha::BGB::Track::list_genomes(    $cookie->{ 'USER' }, $cookie->{ 'CLADE' } );
+        $cookie->{ 'LIST_ASSEMBLY' }   = Maasha::BGB::Track::list_assemblies( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' } );
+        $cookie->{ 'LIST_CONTIG' }     = Maasha::BGB::Track::list_contigs(    $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' } );
+
+        if ( $cookie->{ 'CONTIG' } )
+        {
+            cookie_start( $cookie );
+            cookie_end( $cookie );
+            cookie_zoom( $cookie );
+            cookie_move( $cookie );
+            cookie_center( $cookie );
+        }
     }
 
     $cookie->{ 'STRAND' } = '+' if defined $cookie->{ 'STRAND' } and $cookie->{ 'STRAND' } eq ' ';   # FIXME ugly HTML fix
@@ -194,29 +208,29 @@ sub cookie_session
     # {
     #     if ( $cookie->{ 'SESSION_ID' } ne $ENV{ 'SSL_SESSION_ID' } ) {
     #         $cookie->{ 'PAGE' } = 'login';
-    #         print STDERR "HER1"; # DEBUG
+    #         print STDERR "HER1\n"; # DEBUG
     #     }
     # }
     # else
     # {
     #     $cookie->{ 'PAGE' } = 'login';
     # 
-    #     print STDERR "HER2"; # DEBUG
+    #     print STDERR "HER2\n"; # DEBUG
     # }
 
     if ( exists $session->{ $cookie->{ 'USER' } } and $cookie->{ 'SESSION_ID' } )
     {
         if ( $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } ne $cookie->{ 'SESSION_ID' } ) {
             $cookie->{ 'PAGE' } = 'login';
-            print STDERR "HER3"; # DEBUG
+            print STDERR "HER3\n"; # DEBUG
         }
     }
     else
     {
         $cookie->{ 'PAGE' } = 'login';
-        print STDERR "HER4"; # DEBUG
-        print STDERR "NO COOKIE SESSION ID\n" if not $cookie->{ 'SESSION_ID' }; # DEBUG
-        print STDERR "NO COOKIE USER\n" if not $cookie->{ 'USER' }; # DEBUG
+        print STDERR "HER4\n";                                                                 # DEBUG
+        print STDERR "NO COOKIE SESSION ID\n" if not $cookie->{ 'SESSION_ID' };                # DEBUG
+        print STDERR "NO COOKIE USER\n"       if not $cookie->{ 'USER' };                      # DEBUG
         print STDERR "NO SESSION USER\n"      if not exists $session->{ $cookie->{ 'USER' } }; # DEBUG
     }
 }
@@ -249,7 +263,6 @@ sub cookie_login
 
             $cookie->{ 'SESSION_ID' } = $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' };
             $cookie->{ 'LOGIN' }      = "OK";
-            $cookie->{ 'PAGE' }       = 'clade'; 
 
             Maasha::BGB::Session::session_store( "$cookie->{ 'SESSION_DIR' }/sessions.txt", $session );
         }
@@ -548,6 +561,7 @@ sub page_browse
     push @html, section_taxonomy_table( $cookie );
     push @html, section_navigate( $cookie );
     push @html, section_browse( $cookie );
+    push @html, section_linkout( $cookie );
 
     return wantarray ? @html : \@html;
 }
@@ -641,6 +655,22 @@ sub section_login
     push @html, Maasha::XHTML::table_row_simple( tr => [ "", $login ] );
     push @html, Maasha::XHTML::table_end;
 
+    if ( defined $cookie->{ 'CLADE' }     and
+         defined $cookie->{ 'GENOME' }    and
+         defined $cookie->{ 'ASSEMBLY' }  and
+         defined $cookie->{ 'CONTIG' }    and
+         defined $cookie->{ 'NAV_START' } and
+         defined $cookie->{ 'NAV_END' }
+    )
+    {
+        push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "clade",     value => $cookie->{ 'CLADE' } ) );
+        push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "genome",    value => $cookie->{ 'GENOME' } ) );
+        push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "assembly",  value => $cookie->{ 'ASSEMBLY' } ) );
+        push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "contig",    value => $cookie->{ 'CONTIG' } ) );
+        push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "nav_start", value => $cookie->{ 'NAV_START' } ) );
+        push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "nav_end",   value => $cookie->{ 'NAV_END' } ) );
+    }
+
     if ( $cookie->{ 'LOGIN' } and $cookie->{ 'LOGIN' } eq 'ERROR' ) {
         push @html, Maasha::XHTML::h3( txt => "Bad user or password - please retry", class => 'error' );
     }
@@ -785,6 +815,38 @@ sub section_navigate
 }
 
 
+sub section_linkout
+{
+    # Martin A. Hansen, March 2010.
+
+    # Returns a HTML section for a static link based on information in the cookie.
+
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns a list.
+
+    my ( $link, @html );
+
+    $link = Maasha::XHTML::ln(
+        txt  => 'link',
+        href => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
+                           "clade=$cookie->{ 'CLADE' }",
+                           "genome=$cookie->{ 'GENOME' }",
+                           "assembly=$cookie->{ 'ASSEMBLY' }",
+                           "contig=$cookie->{ 'CONTIG' }",
+                           "nav_start=$cookie->{ 'NAV_START' }",
+                           "nav_end=$cookie->{ 'NAV_END' }",
+              ),
+        title  => "Static link to this view",
+    );
+
+    push @html, Maasha::XHTML::p( txt => $link, class => 'center' );
+
+    return wantarray ? @html : \@html;
+}
+
+
 sub section_browse
 {
     my ( $cookie,
@@ -847,8 +909,8 @@ sub section_browse
                                    "user=$cookie->{ 'USER' }",
                                    "clade=$cookie->{ 'CLADE' }",
                                    "genome=$cookie->{ 'GENOME' }",
-                                   "contig=$cookie->{ 'CONTIG' }",
                                    "assembly=$cookie->{ 'ASSEMBLY' }",
+                                   "contig=$cookie->{ 'CONTIG' }",
                                    "nav_start=$cookie->{ 'NAV_START' }",
                                    "nav_end=$cookie->{ 'NAV_END' }",
                                    "nav_center=$center",
@@ -879,8 +941,8 @@ sub section_browse
                                        "user=$cookie->{ 'USER' }",
                                        "clade=$cookie->{ 'CLADE' }",
                                        "genome=$cookie->{ 'GENOME' }",
-                                       "contig=$cookie->{ 'CONTIG' }",
                                        "assembly=$cookie->{ 'ASSEMBLY' }",
+                                       "contig=$cookie->{ 'CONTIG' }",
                                        "s_beg=$cookie->{ 'S_BEG' }",
                                        "s_end=$cookie->{ 'S_END' }",
                                        "strand=$cookie->{ 'STRAND' }",
@@ -984,8 +1046,8 @@ sub section_search
                                    "user=$cookie->{ 'USER' }",
                                    "clade=$cookie->{ 'CLADE' }",
                                    "genome=$cookie->{ 'GENOME' }",
-                                   "contig=$cookie->{ 'CONTIG' }",
                                    "assembly=$cookie->{ 'ASSEMBLY' }",
+                                   "contig=$cookie->{ 'CONTIG' }",
                                    "nav_start=$cookie->{ 'NAV_START' }",
                                    "nav_end=$cookie->{ 'NAV_END' }",
                 ),
@@ -999,8 +1061,8 @@ sub section_search
                                    "user=$cookie->{ 'USER' }",
                                    "clade=$cookie->{ 'CLADE' }",
                                    "genome=$cookie->{ 'GENOME' }",
-                                   "contig=$cookie->{ 'CONTIG' }",
                                    "assembly=$cookie->{ 'ASSEMBLY' }",
+                                   "contig=$cookie->{ 'CONTIG' }",
                                    "s_beg=$cookie->{ 'S_BEG' }",
                                    "s_end=$cookie->{ 'S_END' }",
                                    "strand=$cookie->{ 'STRAND' }",