--- /dev/null
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Test mock-up of a Biopiece written in Ruby.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'biopieces'
+
+casts = []
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV,casts)
+
+bp.each_record do |record|
+ record["SEQ"].swapcase! if record.has_key? "SEQ"
+ bp.puts record
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
end
-# Stuff to be done at begin such as setting the exit status
-# and signal handlers
-def do_at_begin
- status = Status.new
- status.set
- exit_status = "OK"
-
- # Install signal handlers
- %w( INT TERM QUIT ).each do |signal|
- Signal.trap(signal) do
- exit_status = signal
- exit
- end
- end
-
- exit_status
-end
-
-exit_status = do_at_begin
+Status.new.set
-# Make sure that file streams are closed, tmpdir removed, and
-# exit status is written to log file.
at_exit do
- begin
- @in.close if @in.respond_to? :close # FIXME: This can never work
- @out.close if @out.respond_to? :close # FIXME: Same
- rescue Exception => exception
- $stderr.puts "Exception caught!" # DEBUG
- case exit_status
- when 'INT' then exit_status = 'INTERRUPTED'
- when 'TERM' then exit_status = 'TERMINATED'
- end
- exit_status = "DIED" unless exit_status =~ /INT|TERM|QUIT/
- $stderr.puts exit_status
- $stderr.puts exception.backtrace
- ensure
- status = Status.new
- FileUtils.remove_entry_secure(status.get_tmpdir)
- status.log(exit_status)
- status.delete
- puts "DEBUG EXIT STATUS: #{exit_status}" # DEBUG
+ exit_status = $! ? $!.inspect : "OK"
+
+ case exit_status
+ when /error/i
+ exit_status = "ERROR"
+ when "Interrupt"
+ exit_status = "INTERRUPTED"
+ when /SIGTERM/
+ exit_status = "TERMINATED"
+ when /SIGQUIT/
+ exit_status = "QUIT"
end
+
+ status = Status.new
+ tmpdir = status.get_tmpdir
+ FileUtils.remove_entry_secure(tmpdir) unless tmpdir.nil?
+ status.log(exit_status)
+ status.delete
end