-class BioPieces
- RECORD_DELIMITER = "\n---\n"
-
- class Record
- attr_reader :__hash__
-
- def initialize( data )
- @__hash__ = data
- end
-
- def method_missing( name, *args, &block )
- if args.empty? && @__hash__.has_key?( name ) then
- @__hash__[ name ]
- else
- super # get the original exception
- end
- end
-
- def to_s
- @__hash__.map { | key, value | "#{ key }: #{ value }" }.join( "\n" ) + RECORD_DELIMITER
- end
-
- def to_hash
- @__hash__.dup
- end
- end
-
- def self.file( path )
- bp = new( File.open( path ) )
- yield bp if block_given?
- bp
- ensure
- # if no block was given, the user wants the BioPieces instance
- # with a still open File so he can read it, so only close if a block
- # had been given.
- bp.close if block_given?
- end
-
- def initialize( stream )
- @stream = stream
- end
-
- def close
- @stream.close if @stream.respond_to? :close
- end
-
- def record_get
- return unless block = @stream.gets( RECORD_DELIMITER )
-
- block.chomp!( RECORD_DELIMITER )
- data = Hash[ *block.split( /: |\n/, 2 ) ]
- Record.new( data )
- end
-
- def each
- yield record_get until @stream.eof?
- self # not to have a messy return value
- end
+require 'fileutils'
+require 'date'
+require 'optparse'
+require 'open3'
+require 'pp'
+
+# Biopieces are command line scripts and uses OptionParser to parse command line
+# options according to a list of casts. Each cast prescribes the long and short
+# name of the option, the type, if it is mandatory, the default value, and allowed
+# and disallowed values. An optional list of extra casts can be supplied, and the
+# integrity of the casts are checked. Following the command line parsing, the
+# options are checked according to the casts. Methods are also included for handling
+# the parsing and emitting of Biopiece records, which are ASCII text records consisting
+# of lines with a key/value pair seperated by a colon and a white space ': '.
+# Each record is separated by a line with three dashes '---'.
+class Biopieces
+ # Initialize a Biopiece and write the status to file.
+ # Options are for testing purposes only.
+ def initialize(test=nil, input=STDIN, output=STDOUT)
+ @test = test
+ @input = input
+ @output = output
+ @status = Status.new
+ @status.set unless @test
+ end
+
+ # Check the integrity of a list of casts, followed by parsion options from argv
+ # and finally checking the options according to the casts. Returns nil if argv
+ # is empty, otherwise an options hash.
+ def parse(argv, cast_list=[], script_path=$0)
+ casts = Casts.new(cast_list)
+ option_handler = OptionHandler.new(argv, casts, script_path, @test)
+ @options = option_handler.options_parse
+ end
+
+ # Open Biopiece input stream if not open and iterate over all Biopiece
+ # records in the stream.
+ def each_record
+ @in = Stream::open(@options, mode="r", @input) unless @in.is_a? IO
+
+ record = {}
+
+ @in.each_line do |line|
+ case line
+ when /^([^:]+): (.*)$/
+ record[$1] = $2
+ when /^---$/
+ yield record unless record.empty?
+ record = {}
+ else
+ raise "Bad record format: #{line}"
+ end
+ end
+
+ yield record unless record.empty?
+
+ self # conventionally
+ end
+
+ alias :each :each_record
+
+ # Open Biopiece output stream if not open and puts record to the stream.
+ def puts(record)
+ @out = Stream::open(@options, mode="w", @output) unless @out.is_a? IO
+
+ record.each do |key,value|
+ @out.print "#{key}: #{value}\n"
+ end
+
+ @out.print "---\n"
+ end
+
+ # Create a temporary directory inside the ENV["BP_TMP"] dir.
+ def mktmpdir
+ time = Time.now.to_i
+ user = ENV["USER"]
+ pid = $$
+ path = ENV["BP_TMP"] + "/" + [user, time + pid, pid, "bp_tmp"].join("_")
+ Dir.mkdir(path)
+ @status.set_tmpdir(path)
+ path
+ end
+end
+
+
+# Error class for all exceptions to do with option casts.
+class CastError < StandardError; end
+
+
+# Class to handle casts of command line options. Each cast prescribes the long and
+# short name of the option, the type, if it is mandatory, the default value, and
+# allowed and disallowed values. An optional list of extra casts can be supplied,
+# and the integrity of the casts are checked.
+class Casts < Array
+ TYPES = %w[flag string list int uint float file file! files files! dir dir! genome]
+ MANDATORY = %w[long short type mandatory default allowed disallowed]
+
+ # Initialize cast object with an optional options cast list to which
+ # ubiquitous casts are added after which all casts are checked.
+ def initialize(cast_list=[])
+ @cast_list = cast_list
+ ubiquitous
+ check
+ self.push *@cast_list
+ end
+
+ private
+
+ # Add ubiquitous options casts.
+ def ubiquitous
+ @cast_list << {:long => 'help', :short => '?', :type => 'flag', :mandatory => false, :default => nil, :allowed => nil, :disallowed => nil}
+ @cast_list << {:long => 'stream_in', :short => 'I', :type => 'files!', :mandatory => false, :default => nil, :allowed => nil, :disallowed => nil}
+ @cast_list << {:long => 'stream_out', :short => 'O', :type => 'file', :mandatory => false, :default => nil, :allowed => nil, :disallowed => nil}
+ @cast_list << {:long => 'verbose', :short => 'v', :type => 'flag', :mandatory => false, :default => nil, :allowed => nil, :disallowed => nil}
+ end
+
+ # Check integrity of the casts.
+ def check
+ check_keys
+ check_values
+ check_duplicates
+ end
+
+ # Check if all mandatory keys are present in casts and raise if not.
+ def check_keys
+ @cast_list.each do |cast|
+ MANDATORY.each do |mandatory|
+ raise CastError, "Missing symbol in cast: '#{mandatory.to_sym}'" unless cast.has_key? mandatory.to_sym
+ end
+ end
+ end
+
+ # Check if all values in casts are valid.
+ def check_values
+ @cast_list.each do |cast|
+ check_val_long(cast)
+ check_val_short(cast)
+ check_val_type(cast)
+ check_val_mandatory(cast)
+ check_val_default(cast)
+ check_val_allowed(cast)
+ check_val_disallowed(cast)
+ end
+ end
+
+ # Check if the values to long are legal and raise if not.
+ def check_val_long(cast)
+ unless cast[:long].is_a? String and cast[:long].length > 1
+ raise CastError, "Illegal cast of long: '#{cast[:long]}'"
+ end
+ end
+
+ # Check if the values to short are legal and raise if not.
+ def check_val_short(cast)
+ unless cast[:short].is_a? String and cast[:short].length == 1
+ raise CastError, "Illegal cast of short: '#{cast[:short]}'"
+ end
+ end
+
+ # Check if values to type are legal and raise if not.
+ def check_val_type(cast)
+ type_hash = {}
+ TYPES.each do |type|
+ type_hash[type] = true
+ end
+
+ unless type_hash.has_key? cast[:type]
+ raise CastError, "Illegal cast of type: '#{cast[:type]}'"
+ end
+ end
+
+ # Check if values to mandatory are legal and raise if not.
+ def check_val_mandatory(cast)
+ unless cast[:mandatory] == true or cast[:mandatory] == false
+ raise CastError, "Illegal cast of mandatory: '#{cast[:mandatory]}'"
+ end
+ end
+
+ # Check if values to default are legal and raise if not.
+ def check_val_default(cast)
+ unless cast[:default].nil? or
+ cast[:default].is_a? String or
+ cast[:default].is_a? Integer or
+ cast[:default].is_a? Float
+ raise CastError, "Illegal cast of default: '#{cast[:default]}'"
+ end
+ end
+
+ # Check if values to allowed are legal and raise if not.
+ def check_val_allowed(cast)
+ unless cast[:allowed].is_a? String or cast[:allowed].nil?
+ raise CastError, "Illegal cast of allowed: '#{cast[:allowed]}'"
+ end
+ end
+
+ # Check if values to disallowed are legal and raise if not.
+ def check_val_disallowed(cast)
+ unless cast[:disallowed].is_a? String or cast[:disallowed].nil?
+ raise CastError, "Illegal cast of disallowed: '#{cast[:disallowed]}'"
+ end
+ end
+
+ # Check cast for duplicate long or short options names.
+ def check_duplicates
+ check_hash = {}
+ @cast_list.each do |cast|
+ raise CastError, "Duplicate argument: '--#{cast[:long]}'" if check_hash.has_key? cast[:long]
+ raise CastError, "Duplicate argument: '-#{cast[:short]}'" if check_hash.has_key? cast[:short]
+ check_hash[cast[:long]] = true
+ check_hash[cast[:short]] = true
+ end
+ end
end
+# Class for parsing argv using OptionParser according to given casts.
+# Default options are set, file glob expressions expanded, and options are
+# checked according to the casts. Usage information is printed and exit called
+# if required.
+class OptionHandler
+ REGEX_LIST = /^(list|files|files!)$/
+ REGEX_INT = /^(int|uint)$/
+ REGEX_STRING = /^(string|file|file!|dir|dir!|genome)$/
+
+ def initialize(argv, casts, script_path, test=nil)
+ @argv = argv
+ @casts = casts
+ @script_path = script_path
+ @test = test
+ end
+
+ # Parse options from argv using OptionParser and casts denoting long and
+ # short option names. Usage information is printed and exit called.
+ # A hash with options is returned.
+ def options_parse
+ @options = {}
+
+ option_parser = OptionParser.new do |option|
+ @casts.each do |cast|
+ if cast[:type] == 'flag'
+ option.on("-#{cast[:short]}", "--#{cast[:long]}") do |o|
+ @options[cast[:long]] = o
+ end
+ elsif cast[:type] =~ REGEX_LIST
+ option.on( "-#{cast[:short]}", "--#{cast[:long]} A", Array) do |a|
+ @options[cast[:long]] = a
+ end
+ elsif cast[:type] =~ REGEX_INT
+ option.on("-#{cast[:short]}", "--#{cast[:long]} I", Integer) do |i|
+ @options[cast[:long]] = i
+ end
+ elsif cast[:type] =~ REGEX_STRING
+ option.on("-#{cast[:short]}", "--#{cast[:long]} S", String) do |s|
+ @options[cast[:long]] = s
+ end
+ elsif cast[:type] == 'float'
+ option.on("-#{cast[:short]}", "--#{cast[:long]} F", Float) do |f|
+ @options[cast[:long]] = f
+ end
+ else
+ raise ArgumentError, "Unknown option type: '#{cast[:type]}'"
+ end
+ end
+ end
+
+ option_parser.parse!(@argv)
+
+ if print_usage_full?
+ print_usage_and_exit(true)
+ elsif print_usage_short?
+ print_usage_and_exit
+ end
+
+ options_default
+ options_glob
+ options_check
+
+ @options
+ end
+
+ # Given the script name determine the path of the wiki file with the usage info.
+ def wiki_path
+ path = ENV["BP_DIR"] + "/bp_usage/" + File.basename(@script_path) + ".wiki"
+ raise "No such wiki file: #{path}" unless File.file? path
+ path
+ end
+
+ # Check if full "usage info" should be printed.
+ def print_usage_full?
+ @options["help"]
+ end
+
+ # Check if short "usage info" should be printed.
+ def print_usage_short?
+ if not $stdin.tty?
+ return false
+ elsif @options["stream_in"]
+ return false
+ elsif @options["data_in"]
+ return false
+ elsif wiki_path =~ /^(list_biopieces|list_genomes|list_mysql_databases|biostat)$/ # TODO get rid of this!
+ return false
+ else
+ return true
+ end
+ end
+
+ # Print usage info by Calling an external script 'print_wiki'
+ # using a system() call and exit. An optional 'full' flag
+ # outputs the full usage info.
+ def print_usage_and_exit(full=nil)
+ if @test
+ return
+ else
+ if full
+ system("print_wiki --data_in #{wiki_path} --help")
+ else
+ system("print_wiki --data_in #{wiki_path}")
+ end
+
+ raise "Failed printing wiki: #{wiki_path}" unless $?.success?
+
+ exit
+ end
+ end
+
+ # Set default options value from cast unless a value is set.
+ def options_default
+ @casts.each do |cast|
+ if cast[:default]
+ @options[cast[:long]] = cast[:default] unless @options.has_key? cast[:long]
+ end
+ end
+ end
+
+ # Expands glob expressions to a full list of paths.
+ # Examples: "*.fna" or "foo.fna,*.fna" or "foo.fna,/bar/*.fna"
+ def options_glob
+ @casts.each do |cast|
+ if cast[:type] == 'files' or cast[:type] == 'files!'
+ if @options.has_key? cast[:long]
+ files = []
+
+ @options[cast[:long]].each do |path|
+ if path.include? "*"
+ Dir.glob(path).each do |file|
+ files << file if File.file? file
+ end
+ else
+ files << path
+ end
+ end
+
+ @options[cast[:long]] = files
+ end
+ end
+ end
+ end
+
+ # Check all options according to casts.
+ def options_check
+ @casts.each do |cast|
+ options_check_mandatory(cast)
+ options_check_int(cast)
+ options_check_uint(cast)
+ options_check_file(cast)
+ options_check_files(cast)
+ options_check_dir(cast)
+ options_check_allowed(cast)
+ options_check_disallowed(cast)
+ end
+ end
+
+ # Check if a mandatory option is set and raise if it isn't.
+ def options_check_mandatory(cast)
+ if cast[:mandatory]
+ raise ArgumentError, "Mandatory argument: --#{cast[:long]}" unless @options.has_key? cast[:long]
+ end
+ end
+
+ # Check int type option and raise if not an integer.
+ def options_check_int(cast)
+ if cast[:type] == 'int' and @options.has_key? cast[:long]
+ unless @options[cast[:long]].is_a? Integer
+ raise ArgumentError, "Argument to --#{cast[:long]} must be an integer, not '#{@options[cast[:long]]}'"
+ end
+ end
+ end
+
+ # Check uint type option and raise if not an unsinged integer.
+ def options_check_uint(cast)
+ if cast[:type] == 'uint' and @options.has_key? cast[:long]
+ unless @options[cast[:long]].is_a? Integer and @options[cast[:long]] >= 0
+ raise ArgumentError, "Argument to --#{cast[:long]} must be an unsigned integer, not '#{@options[cast[:long]]}'"
+ end
+ end
+ end
+
+ # Check file! type argument and raise if file don't exists.
+ def options_check_file(cast)
+ if cast[:type] == 'file!' and @options.has_key? cast[:long]
+ raise ArgumentError, "No such file: '#{@options[cast[:long]]}'" unless File.file? @options[cast[:long]]
+ end
+ end
+
+ # Check files! type argument and raise if files don't exists.
+ def options_check_files(cast)
+ if cast[:type] == 'files!' and @options.has_key? cast[:long]
+ @options[cast[:long]].each do |path|
+ raise ArgumentError, "No such file: '#{path}'" unless File.file? path
+ end
+ end
+ end
+
+ # Check dir! type argument and raise if directory don't exist.
+ def options_check_dir(cast)
+ if cast[:type] == 'dir!' and @options.has_key? cast[:long]
+ raise ArgumentError, "No such directory: '#{@options[cast[:long]]}'" unless File.directory? @options[cast[:long]]
+ end
+ end
+
+ # Check options and raise unless allowed.
+ def options_check_allowed(cast)
+ if cast[:allowed] and @options.has_key? cast[:long]
+ allowed_hash = {}
+ cast[:allowed].split(',').each { |a| allowed_hash[a] = 1 }
+
+ raise ArgumentError, "Argument '#{@options[cast[:long]]}' to --#{cast[:long]} not allowed" unless allowed_hash.has_key? @options[cast[:long]]
+ end
+ end
+
+ # Check disallowed argument values and raise if disallowed.
+ def options_check_disallowed(cast)
+ if cast[:disallowed] and @options.has_key? cast[:long]
+ cast[:disallowed].split(',').each do |val|
+ raise ArgumentError, "Argument '#{@options[cast[:long]]}' to --#{cast[:long]} is disallowed" if val == @options[cast[:long]]
+ end
+ end
+ end
+end
+
+# Class for manipulating the execution status of Biopieces by setting a
+# status file with a time stamp, process id, and command arguments. The
+# status file is used for creating log entries and for displaying the
+# runtime status of Biopieces.
+class Status
+ # Write the status to a status file.
+ def set
+ time0 = Time.new.strftime("%Y-%m-%d %X")
+
+ File.open(path, mode="w") { |file| file.puts [time0, ARGV.join(" ")].join(";") }
+ end
+
+ # Append the a temporary directory path to the status file.
+ def set_tmpdir(tmp_path)
+ status = File.open(path, mode="r").read.chomp
+
+ File.open(path, mode="w") do |fh|
+ fh << [status, tmp_path].join(";") + "\n"
+ end
+ end
+
+ # Extract the temporary directory path from the status file,
+ # and return this or nil if not found.
+ def get_tmpdir
+ tmp_path = File.open(path, mode="r").read.chomp.split(";").last
+
+ File.directory?(tmp_path) ? tmp_path : nil
+ end
+
+ # Write the Biopiece status to the log file.
+ def log(exit_status)
+ time1 = Time.new.strftime("%Y-%m-%d %X")
+ user = ENV["USER"]
+ script = File.basename($0)
+
+ stream = File.open(path)
+ time0, args, tmp_dir = stream.first.split(";")
+ stream.close
+
+ elap = time_diff(time0, time1)
+ command = [script, args].join(" ")
+ log_file = ENV["BP_LOG"] + "/biopieces.log"
+
+ File.open(log_file, mode="a") { |file| file.puts [time0, time1, elap, user, exit_status, command].join("\t") }
+ end
+
+ # Delete status file.
+ def delete
+ File.delete(path)
+ end
+
+ private
+
+ # Path to status file
+ def path
+ user = ENV["USER"]
+ script = File.basename($0)
+ pid = $$
+ path = ENV["BP_TMP"] + "/" + [user, script, pid, "status"].join(".")
+ end
+
+ # Get the elapsed time from the difference between two time stamps.
+ def time_diff(t0, t1)
+ Time.at((DateTime.parse(t1).to_time - DateTime.parse(t0).to_time).to_i).gmtime.strftime('%X')
+ end
+end
+
+
+class Stream < IO
+ # Open Biopieces output data stream for reading from stdin or a file
+ # specified in options["stream_in"] OR writing to stdout or a file
+ # specified in options["stream_out"].
+ def self.open(options, mode, stdio)
+ if mode == "r"
+ $stdin.tty? ? read(options["stream_in"]) : stdio
+ elsif mode == "w"
+ options["stream_out"] ? self.write(options["stream_out"], options["compress"]) : stdio
+ else
+ raise "Bad mode #{mode}"
+ end
+ end
+
+ private
+
+ # Opens a reads stream to a list of files.
+ def self.read(files)
+ self.zipped?(files) ? self.zread(files) : self.nread(files)
+ end
+
+ # Opens a write stream to a file and returns a _io_ object.
+ def self.write(file, zip=nil)
+ zip ? self.zwrite(file) : self.nwrite(file)
+ end
+
+ # Opens a list of gzipped files for reading and return an _io_ object.
+ def self.zread(files)
+ stdin, stdout, stderr = Open3.popen3("zcat " + files.join(' '));
+ stdin.close
+ stderr.close
+ stdout
+ end
+
+ # Opens a file for gzipped writing and return an _io_ object.
+ def self.zwrite(file)
+ stdin, stdout, stderr = Open3.popen3("gzip -f > #{file}")
+ stderr.close
+ stdout.close
+ stdin
+ end
+
+ # Opens a list of files for reading and return an _io_ object.
+ def self.nread(files)
+ stdin, stdout, stderr = Open3.popen3("cat " + files.join(' '));
+ stdin.close
+ stderr.close
+ stdout
+ end
+
+ # Opens a file for writing and return an _io_ object.
+ def self.nwrite(file)
+ File.open(file, mode="w")
+ end
+
+ # Test if a list of files are gzipped or not.
+ # Raises if files are mixed zipped and unzipped.
+ def self.zipped?(files)
+ type_hash = {}
+
+ files.each do |file|
+ type = `file #{file}`
+
+ if type =~ /gzip compressed/
+ type_hash[:gzip] = true
+ else
+ type_hash[:ascii] = true
+ end
+ end
+
+ raise "Mixture of zipped and unzipped files" if type_hash.size == 2
+
+ type_hash[:gzip]
+ 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
+
+# Make sure that file streams are closed, tmpdir removed, and
+# exit status is written to log file.
+def do_at_exit(exit_status="OK-martin")
+ 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
+ end
+ end
+end
+
+exit_status = do_at_begin
+
+END {
+ do_at_exit(exit_status)
+}
+
__END__
projects / biopieces.git / blobdiff