fixed upload pipe

[biopieces.git] / bp_bin / BGB_upload

diff --git a/bp_bin/BGB_upload b/bp_bin/BGB_upload
index 916ffa803bd540c2847e2506292b89a68c19aadc..611f60425bc5122326ca8876944fcf94960bd68d 100755 (executable)
--- a/bp_bin/BGB_upload
+++ b/bp_bin/BGB_upload
@@ -33,6 +33,7 @@ use Maasha::Common;
 use Maasha::KISS;
 use Maasha::Biopieces;
 use Maasha::Fasta;
+use Maasha::BGB::Common;
 use Maasha::Filesys;
 
 use constant {
@@ -44,10 +45,10 @@ use constant {
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $data_dir, $user, $options, $path, $in, $out, $tmp_dir, %fh_hash, $fh_out, $record, $entry, $key, @dirs, $dir, $dst_dir, @nums, $num, $contig_dir );
+my ( $data_dir, $user, $options, $path, $in, $out, $tmp_dir, %fh_hash, $fh_out, $record, $entry, $key, $dst_dir, @nums, $num, $contig_dir );
 
-$data_dir = Maasha::Biopieces::biopiecesrc( "KISS_DATA_DIR" );
-$user     = Maasha::Biopieces::biopiecesrc( "KISS_USER" );
+$data_dir = Maasha::Biopieces::biopiecesrc( "BGB_DATA_DIR" );
+$user     = Maasha::Biopieces::biopiecesrc( "BGB_USER" );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -68,7 +69,7 @@ if ( $options->{ 'track_name' } )
 {
     $options->{ 'track_name' } =~ tr/ /_/;
 
-    $path = join "/", $data_dir, "Users/", $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' };
+    $path = join "/", $data_dir, "Users", $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' };
 
     Maasha::Common::error( qq(Path not found: "$path") ) if not -d $path;
 
@@ -92,6 +93,9 @@ if ( $options->{ 'track_name' } )
         Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
     }
 
+    $num = Maasha::BGB::Common::max_track( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
+    $num = sprintf( "%04d", $num + 10 );
+
     foreach $key ( keys %fh_hash )
     {
         close $fh_hash{ $key };
@@ -99,23 +103,6 @@ if ( $options->{ 'track_name' } )
         $dst_dir = Maasha::Filesys::dir_create_if_not_exists( "$path/$key" );
         $dst_dir = Maasha::Filesys::dir_create_if_not_exists( "$dst_dir/Tracks" );
 
-        @dirs = Maasha::Filesys::ls_dirs( $dst_dir );
-
-        foreach $dir ( @dirs )
-        {
-            $dir = ( split "/", $dir )[ -1 ];
-
-            if ( $dir =~ /^(\d+)/ ) {
-                push @nums, $1;
-            }
-        }
-
-        @nums = sort { $a <=> $b } @nums;
-
-        $num = $nums[ -1 ] || 0;
-
-        $num += 10;
-
         $dst_dir = "$dst_dir/$num" . "_$options->{ 'track_name' }";
 
         Maasha::Filesys::dir_create( $dst_dir );