fixed BGB issues terrible

git-svn-id: http://biopieces.googlecode.com/svn/trunk@901 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/www/index.cgi b/www/index.cgi
index c0235f0549bf96d3d107629ae151d5e0de80d7a1..62e62491e854722de741a9fa56118c3c34491edc 100755 (executable)
--- a/www/index.cgi
+++ b/www/index.cgi
@@ -236,22 +236,52 @@ sub session_store
 
     # Returns nothing.
 
+    my ( $new_session );
+
     if ( defined $cookie->{ 'USER' } and $cookie->{ 'USER' } ne '' and -d "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }" )
     {
-        $session->{ 'TIME' }      = Maasha::Common::time_stamp();
-        $session->{ 'PAGE' }      = $cookie->{ 'PAGE' };
-        $session->{ 'CLADE' }     = $cookie->{ 'CLADE' };
-        $session->{ 'GENOME' }    = $cookie->{ 'GENOME' };
-        $session->{ 'ASSEMBLY' }  = $cookie->{ 'ASSEMBLY' };
-        $session->{ 'CONTIG' }    = $cookie->{ 'CONTIG' };
-        $session->{ 'Q_ID' }      = $cookie->{ 'Q_ID' };
-        $session->{ 'S_BEG' }     = $cookie->{ 'S_BEG' };
-        $session->{ 'S_END' }     = $cookie->{ 'S_END' };
-        $session->{ 'STRAND' }    = $cookie->{ 'STRAND' };
-        $session->{ 'NAV_START' } = $cookie->{ 'PAGE' } eq 'browse' ? $cookie->{ 'NAV_START' } : undef;
-        $session->{ 'NAV_END' }   = $cookie->{ 'PAGE' } eq 'browse' ? $cookie->{ 'NAV_END' }   : undef;
-
-        Maasha::BGB::Session::session_store( "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }/session.json", $session );
+        $new_session->{ 'PASSWORD' }   = $session->{ 'PASSWORD' };
+        $new_session->{ 'SESSION_ID' } = $session->{ 'SESSION_ID' };
+        $new_session->{ 'TIME' }       = Maasha::Common::time_stamp();
+        $new_session->{ 'PAGE' }       = $cookie->{ 'PAGE' };
+
+        if ( $cookie->{ 'PAGE' } eq 'browse' )
+        {
+            $new_session->{ 'CLADE' }     = $cookie->{ 'CLADE' };
+            $new_session->{ 'GENOME' }    = $cookie->{ 'GENOME' };
+            $new_session->{ 'ASSEMBLY' }  = $cookie->{ 'ASSEMBLY' };
+            $new_session->{ 'CONTIG' }    = $cookie->{ 'CONTIG' };
+            $new_session->{ 'NAV_START' } = $cookie->{ 'NAV_START' };
+            $new_session->{ 'NAV_END' }   = $cookie->{ 'NAV_END' };
+        }
+        elsif ( $cookie->{ 'PAGE' } eq 'contig' )
+        {
+            $new_session->{ 'CLADE' }     = $cookie->{ 'CLADE' };
+            $new_session->{ 'GENOME' }    = $cookie->{ 'GENOME' };
+            $new_session->{ 'ASSEMBLY' }  = $cookie->{ 'ASSEMBLY' };
+        }
+        elsif ( $cookie->{ 'PAGE' } eq 'assembly' )
+        {
+            $new_session->{ 'CLADE' }     = $cookie->{ 'CLADE' };
+            $new_session->{ 'GENOME' }    = $cookie->{ 'GENOME' };
+        }
+        elsif ( $cookie->{ 'PAGE' } eq 'genome' )
+        {
+            $new_session->{ 'CLADE' }     = $cookie->{ 'CLADE' };
+        }
+        elsif ( $cookie->{ 'PAGE' } eq 'export' )
+        {
+            $new_session->{ 'CLADE' }     = $cookie->{ 'CLADE' };
+            $new_session->{ 'GENOME' }    = $cookie->{ 'GENOME' };
+            $new_session->{ 'ASSEMBLY' }  = $cookie->{ 'ASSEMBLY' };
+            $new_session->{ 'CONTIG' }    = $cookie->{ 'CONTIG' };
+            $new_session->{ 'Q_ID' }      = $cookie->{ 'Q_ID' };
+            $new_session->{ 'S_BEG' }     = $cookie->{ 'S_BEG' };
+            $new_session->{ 'S_END' }     = $cookie->{ 'S_END' };
+            $new_session->{ 'STRAND' }    = $cookie->{ 'STRAND' };
+        }
+
+        Maasha::BGB::Session::session_store( "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }/session.json", $new_session );
     }
 }
 
@@ -492,27 +522,6 @@ sub cookie_center
 }
 
 
-sub cookie_page_next
-{
-    # Martin A. Hansen, November 2009.
-    
-    # Returns the next page in the taxonomy path.
-
-    my ( $cookie,   # cookie hash
-       ) = @_;
-
-    # Returns a string.
-
-    my ( $i );
-
-    for ( $i = 0; $i < @{ $cookie->{ 'LIST_PAGES' } }; $i++ ) {
-        last if $cookie->{ 'PAGE' } eq $cookie->{ 'LIST_PAGES' }->[ $i ];
-    }
-
-    return $cookie->{ 'LIST_PAGES' }->[ $i + 1 ];
-}
-
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PAGES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
@@ -544,8 +553,14 @@ sub page
         push @html, page_dna( $cookie );
     } elsif ( $cookie->{ 'PAGE' } eq 'export' ) {
         push @html, page_export( $cookie );
-    } else {
-        push @html, page_taxonomy( $cookie );
+    } elsif ( $cookie->{ 'PAGE' } eq 'clade' ) {
+        push @html, page_clade( $cookie );
+    } elsif ( $cookie->{ 'PAGE' } eq 'genome' ) {
+        push @html, page_genome( $cookie );
+    } elsif ( $cookie->{ 'PAGE' } eq 'assembly' ) {
+        push @html, page_assembly( $cookie );
+    } elsif ( $cookie->{ 'PAGE' } eq 'contig' ) {
+        push @html, page_contig( $cookie );
     }
 
     return wantarray ? @html : \@html;
@@ -653,7 +668,67 @@ sub page_export
 }
 
 
-sub page_taxonomy
+sub page_clade
+{
+    # Martin A. Hansen, March 2010.
+    
+    # Renders the clade selection page.
+
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @html );
+
+    push @html, section_taxonomy_table( $cookie );
+    push @html, section_clade( $cookie );
+
+    return wantarray ? @html : \@html;
+}
+
+
+sub page_genome
+{
+    # Martin A. Hansen, March 2010.
+    
+    # Renders the genome selection page.
+
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @html );
+
+    push @html, section_taxonomy_table( $cookie );
+    push @html, section_genome( $cookie );
+
+    return wantarray ? @html : \@html;
+}
+
+
+sub page_assembly
+{
+    # Martin A. Hansen, March 2010.
+    
+    # Renders the clade selection page.
+
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @html );
+
+    push @html, section_taxonomy_table( $cookie );
+    push @html, section_assembly( $cookie );
+
+    return wantarray ? @html : \@html;
+}
+
+
+sub page_contig
 {
     # Martin A. Hansen, November 2009.
     
@@ -667,7 +742,7 @@ sub page_taxonomy
     my ( @html );
 
     push @html, section_taxonomy_table( $cookie );
-    push @html, section_taxonomy_select( $cookie );
+    push @html, section_contig( $cookie );
 
     return wantarray ? @html : \@html;
 }
@@ -766,11 +841,11 @@ sub section_taxonomy_table
 }
 
 
-sub section_taxonomy_select
+sub section_clade
 {
-    # Martin A. Hansen, November 2009.
+    # Martin A. Hansen, March 2010.
     
-    # Returns a HTML section with selection choices
+    # Returns a HTML section with clade selection choices
     # for navigating the taxonomy tree.
 
     my ( $cookie,   # cookie hash
@@ -778,27 +853,128 @@ sub section_taxonomy_select
 
     # Returns a list.
 
-    my ( $list, @html, $item, $href );
+    my ( @html, $clade, $href );
+
+    push @html, Maasha::XHTML::h2( txt => "Select clade", class => 'center' );
+
+    push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
+
+    foreach $clade ( @{ $cookie->{ 'LIST_CLADE' } } )
+    {
+        $href  = "$cookie->{ 'SCRIPT' }?page=genome";
+        $href .= "&session_id=$cookie->{ 'SESSION_ID' }";
+        $href .= "&user=$cookie->{ 'USER' }";
+        $href .= "&clade=$clade";
+
+        push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $clade, href => $href ) ] );
+    }
+
+    push @html, Maasha::XHTML::table_end;
+
+    return wantarray ? @html : \@html;
+}
+
+
+sub section_genome
+{
+    # Martin A. Hansen, March 2010.
+    
+    # Returns a HTML section with genome selection choices
+    # for navigating the taxonomy tree.
+
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns a list.
 
-    $list = "LIST_" . uc $cookie->{ 'PAGE' };
+    my ( @html, $genome, $href );
 
-    push @html, Maasha::XHTML::h2( txt => "Select $cookie->{ 'PAGE' }", class => 'center' );
+    push @html, Maasha::XHTML::h2( txt => "Select genome", class => 'center' );
 
     push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
 
-    foreach $item ( @{ $cookie->{ $list } } )
+    foreach $genome ( @{ $cookie->{ 'LIST_GENOME' } } )
     {
-        $cookie->{ uc $cookie->{ 'PAGE' } } = $item;
+        $href  = "$cookie->{ 'SCRIPT' }?page=assembly";
+        $href .= "&session_id=$cookie->{ 'SESSION_ID' }";
+        $href .= "&user=$cookie->{ 'USER' }";
+        $href .= "&clade=$cookie->{ 'CLADE' }";
+        $href .= "&genome=$genome";
+
+        push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $genome, href => $href ) ] );
+    }
+
+    push @html, Maasha::XHTML::table_end;
+
+    return wantarray ? @html : \@html;
+}
+
 
-        $href  = "$cookie->{ 'SCRIPT' }?page=" . cookie_page_next( $cookie );
+sub section_assembly
+{
+    # Martin A. Hansen, March 2010.
+    
+    # Returns a HTML section with assembly selection choices
+    # for navigating the taxonomy tree.
+
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @html, $assembly, $href );
+
+    push @html, Maasha::XHTML::h2( txt => "Select assembly", class => 'center' );
+
+    push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
+
+    foreach $assembly ( @{ $cookie->{ 'LIST_ASSEMBLY' } } )
+    {
+        $href  = "$cookie->{ 'SCRIPT' }?page=contig";
+        $href .= "&session_id=$cookie->{ 'SESSION_ID' }";
+        $href .= "&user=$cookie->{ 'USER' }";
+        $href .= "&clade=$cookie->{ 'CLADE' }";
+        $href .= "&genome=$cookie->{ 'GENOME' }";
+        $href .= "&assembly=$assembly";
+
+        push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $assembly, href => $href ) ] );
+    }
+
+    push @html, Maasha::XHTML::table_end;
+
+    return wantarray ? @html : \@html;
+}
+
+
+sub section_contig
+{
+    # Martin A. Hansen, March 2010.
+    
+    # Returns a HTML section with contig selection choices
+    # for navigating the taxonomy tree.
+
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @html, $contig, $href );
+
+    push @html, Maasha::XHTML::h2( txt => "Select contig", class => 'center' );
+
+    push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
+
+    foreach $contig ( @{ $cookie->{ 'LIST_CONTIG' } } )
+    {
+        $href  = "$cookie->{ 'SCRIPT' }?page=browse";
         $href .= "&session_id=$cookie->{ 'SESSION_ID' }";
         $href .= "&user=$cookie->{ 'USER' }";
         $href .= "&clade=$cookie->{ 'CLADE' }";
-        $href .= "&genome=$cookie->{ 'GENOME' }"     if $cookie->{ 'GENOME' };
-        $href .= "&assembly=$cookie->{ 'ASSEMBLY' }" if $cookie->{ 'ASSEMBLY' };
-        $href .= "&contig=$cookie->{ 'CONTIG' }"     if $cookie->{ 'CONTIG' };
+        $href .= "&genome=$cookie->{ 'GENOME' }";
+        $href .= "&assembly=$cookie->{ 'ASSEMBLY' }";
+        $href .= "&contig=$contig";
 
-        push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $item, href => $href ) ] );
+        push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $contig, href => $href ) ] );
     }
 
     push @html, Maasha::XHTML::table_end;