+require 'fileutils'
+require 'date'
require 'optparse'
require 'open3'
require 'pp'
@test = test
@input = input
@output = output
- status_set unless @test
+ @status = Status.new
+ @status.set unless @test
end
# Check the integrity of a list of casts, followed by parsion options from argv
# Open Biopiece input stream if not open and iterate over all Biopiece
# records in the stream.
def each_record
- @in = stream_in_open unless @in.is_a? IO
+ @in = Stream::open(@options, mode="r", @input) unless @in.is_a? IO
record = {}
# Open Biopiece output stream if not open and puts record to the stream.
def puts(record)
- @out = stream_out_open unless @out.is_a? IO
+ @out = Stream::open(@options, mode="w", @output) unless @out.is_a? IO
record.each do |key,value|
@out.print "#{key}: #{value}\n"
@out.print "---\n"
end
- # Close Biopiece streams, remove tmp_dir, end log status.
+ # 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
+
+ # Close Biopiece streams, remove tmp_dir, log status, and delete status file.
def clean
@in.close if @in.respond_to? :close
@out.close if @out.respond_to? :close
- # remove tmpdir if found
- status_log
- # remove status file
+ rmtmpdir
+ @status.log
+ @status.delete
end
private
- # Open Biopieces input data stream for reading from either
- # stdin or from a list of files specified in options["stream_in"].
- def stream_in_open
- $stdin.tty? ? read(@options["stream_in"]) : @input
- end
-
- # Open Biopieces output data stream for writing to stdout
- # or a file specified in options["stream_out"].
- def stream_out_open
- @options["stream_out"] ? write(@options["stream_out"], @options["compress"]) : @output
- end
-
- # Opens a reads stream to a list of files.
- def read(files)
- zipped?(files) ? zread(files) : nread(files)
- end
+ # Remove temporary directory, if existing, and it's content.
+ def rmtmpdir
+ tmp_path = @status.get_tmpdir
- # Opens a write stream to a file and returns a _io_ object.
- def write(file, zip=nil)
- zip ? zwrite(file) : nwrite(file)
- end
-
- # Test if a list of files are gzipped or not.
- # Raises if files are mixed zipped and unzipped.
- def 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
-
- # Opens a list of gzipped files for reading and return an _io_ object.
- def 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 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 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 nwrite(file)
- File.open(file, mode="w")
- end
-
- # Write the status to a status file.
- def status_set
- now = Time.new
- time = now.strftime("%Y-%m-%d %X")
- user = ENV["USER"]
- script = File.basename($0, ".rb")
- pid = $$
- path = ENV["BP_TMP"] + "/" + [user, script, pid, "status"].join(".")
-
- File.open(path, mode="w") { |file| file.puts [time, ARGV.join(" ")].join(";") }
- end
-
- # Write the Biopiece status to the log file.
- def status_log(status="OK")
- now = Time.new
- time1 = now.strftime("%Y-%m-%d %X")
- user = ENV["USER"]
- script = File.basename($0, ".rb")
- pid = $$
- path = ENV["BP_TMP"] + "/" + [user, script, pid, "status"].join(".")
-
- stream = File.open(path)
- time0, args, tmp_dir = stream.first.split(";")
-
- # Dir.rmdir(tmp_dir) unless tmp_dir.nil? and File.directory? tmp_dir #TODO fix this!
-
- 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, status, command].join("\t") }
- end
-
- # Get the elapsed time from the difference between two time stamps.
- def time_diff(t0, t1)
- t0 =~ /(\d+)-(\d+)-(\d+) (\d+):(\d+):(\d+)/
- year0 = $1.to_i
- mon0 = $2.to_i
- day0 = $3.to_i
- hour0 = $4.to_i
- min0 = $5.to_i
- sec0 = $6.to_i
-
- sec0 += day0 * 24 * 60 * 60
- sec0 += hour0 * 60 * 60
- sec0 += min0 * 60
-
- t1 =~ /(\d+)-(\d+)-(\d+) (\d+):(\d+):(\d+)/
- year1 = $1.to_i
- mon1 = $2.to_i
- day1 = $3.to_i
- hour1 = $4.to_i
- min1 = $5.to_i
- sec1 = $6.to_i
-
- sec1 += day1 * 24 * 60 * 60
- sec1 += hour1 * 60 * 60
- sec1 += min1 * 60
-
- year = year1 - year0
- mon = mon1 - mon0
- day = day1 - day0
-
- sec = sec1 - sec0
-
- hour = ( sec / ( 60 * 60 ) ).to_i
- sec -= hour * 60 * 60
-
- min = ( sec / 60 ).to_i
- sec -= min * 60
-
- [sprintf("%02d", hour), sprintf("%02d", min), sprintf("%02d", sec)].join(":")
+ FileUtils.remove_entry_secure(tmp_path)
end
end
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
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(status="OK")
+ time1 = Time.new.strftime("%Y-%m-%d %X")
+ user = ENV["USER"]
+ script = File.basename($0, ".rb")
+
+ 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, 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, ".rb")
+ 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
__END__
projects / biopieces.git / commitdiff