diff --git a/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm b/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm index e03796abe561828bb43762dcdb0c0e1854faf17c..9cc4c6b9c8f1570ac6ff1dfab4106514ae4e1915 100644 --- a/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm +++ b/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm @@ -516,7 +516,10 @@ sub upload_xref { $sth->execute(@fields); } $fh->close(); -} + + log_progress("Uploading for 'xref' done\n"); + +} ## end sub upload_xref #----------------------------------------------------------------------- @@ -574,7 +577,10 @@ sub upload_object_xref { $sth->execute(@fields); } $fh->close(); -} + + log_progress("Uploading for 'object_xref' done\n"); + +} ## end sub upload_object_xref #----------------------------------------------------------------------- @@ -626,6 +632,34 @@ sub dump_unmapped_reason { #----------------------------------------------------------------------- +sub upload_unmapped_reason { + my ( $filename, $dbh ) = @_; + + ###################################################################### + # Upload for 'unmapped_reason'. # + ###################################################################### + + my $fh = IO::File->new( '<' . $filename ) + or croak( sprintf( "Can not open '%s' for reading", $filename ) ); + + log_progress( "Uploading for 'unmapped_reason' from '%s'\n", + $filename ); + + my $sql = 'INSERT INTO unmapped_reason VALUES(?, ?, ?)'; + my $sth = $dbh->prepare($sql); + + while ( my $line = $fh->getline() ) { + chomp($line); + my @fields = split( /\t/, $line ); + $sth->execute(@fields); + } + $fh->close(); + + log_progress("Uploading for 'unmapped_reason' done\n"); +} ## end sub upload_unmapped_reason + +#----------------------------------------------------------------------- + sub dump_unmapped_object { my ( $filename, $unmapped_object_id, $analysis_id, $unmapped ) = @_; @@ -663,10 +697,44 @@ sub dump_unmapped_object { $fh->close(); log_progress("Dumping for 'unmapped_object' done\n"); + } ## end sub dump_unmapped_object #----------------------------------------------------------------------- +sub upload_unmapped_reason { + my ( $filename, $dbh ) = @_; + + ###################################################################### + # Upload for 'unmapped_object'. # + ###################################################################### + + my $fh = IO::File->new( '<' . $filename ) + or croak( sprintf( "Can not open '%s' for reading", $filename ) ); + + log_progress( "Uploading for 'unmapped_object' from '%s'\n", + $filename ); + + my $sql = 'INSERT INTO unmapped_object ' + . 'VALUES(?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)'; + my $sth = $dbh->prepare($sql); + + while ( my $line = $fh->getline() ) { + chomp($line); + my @fields = split( /\t/, $line ); + + # FIXME (when 'analysis_id' is -1) + + $sth->execute(@fields); + } + $fh->close(); + + log_progress("Uploading for 'unmapped_object' done\n"); + +} ## end sub upload_unmapped_reason + +#----------------------------------------------------------------------- + sub log_progress { my ( $fmt, @params ) = @_; printf( STDERR "COORD==> %s", sprintf( $fmt, @params ) );