BioDSL 1.0.0

data/lib/BioDSL/helpers/options_helper.rb

@@ -0,0 +1,405 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# 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 software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+module BioDSL
+  # Module containing methods to check options in various ways.
+  module OptionsHelper
+    require 'csv'
+
+    BioDSL::OptionError = Class.new(StandardError)
+
+    private
+
+    # Method that fails if options include any non-allowed options.
+    #
+    # @param options [Hash] The Hash with options to be checked.
+    # @param allowed [Symbol, Array] One or more allowed options.
+    #
+    # @example That raises:
+    #   options_allowed({foo: 'bar'}, :foobar)
+    #
+    # @example That passes:
+    #   options_allowed({foo: 'bar'}, :foo, :one)
+    #
+    # @raise [BioDSL::OptionError] If non-allowed options located.
+    def options_allowed(options, *allowed)
+      options.each_key do |option|
+        unless allowed.include? option
+          fail BioDSL::OptionError, "Disallowed option: #{option}. " \
+            "Allowed options: #{allowed.join(', ')}"
+        end
+      end
+    end
+
+    # Method that raises if options include any non-allowed values.
+    #
+    # @param options [Hash] The Hash with options to be checked.
+    # @param allowed [Symbol, Array] One or more allowed options.
+    #
+    # @example That raises:
+    #   options_allowed_values({foo: 'bar'}, foo: 1)
+    #
+    # @example That passes:
+    #   options_allowed_values({foo: 'bar'}, foo: ['bar', 'rab'])
+    #
+    # @raise [BioDSL::OptionError] If non-allowed options located.
+    def options_allowed_values(options, allowed)
+      allowed.each do |key, values|
+        next unless options[key]
+
+        unless values.include? options[key]
+          fail BioDSL::OptionError, 'Disallowed option value: ' \
+            "#{options[key]}. Allowed options: #{values.join(', ')}"
+        end
+      end
+    end
+
+    # Method that raises if options don't include all required options.
+    #
+    # @param options [Hash] The Hash with options to be checked.
+    # @param required [Symbol, Array] One or more required options.
+    #
+    # @example That raises:
+    #   options_required({foo: 'bar'}, foo: 1)
+    #
+    # @example That passes:
+    #   options_required({foo: 'bar', one: 'two'}, :foo, :one)
+    #
+    # @raise [BioDSL::OptionError] Unless all required options are given.
+    def options_required(options, *required)
+      required.each do |option|
+        unless options[option]
+          fail BioDSL::OptionError, "Required option missing: #{option}. " \
+            "Required options: #{required.join(', ')}"
+        end
+      end
+    end
+
+    # Method that raises if options include multiple required options.
+    #
+    # @param options [Hash] The Hash with options to be checked.
+    # @param unique [Symbol, Array] Options that must be unique.
+    #
+    # @example That raises:
+    #   options_required_unique({foo: 'bar', one: 'two'}, :foo, :one)
+    #
+    # @example That passes:
+    #   options_required_unique({foo: 'bar', one: 'two'}, :foo)
+    #
+    # @raise [BioDSL::OptionError] If multiple required options are found.
+    def options_required_unique(options, *unique)
+      return unless unique.select { |option| options[option] }.size > 1
+
+      fail BioDSL::OptionError, 'Multiple required uniques options ' \
+        "used: #{unique.join(', ')}"
+    end
+
+    # Method that raises if options include non-unique options.
+    #
+    # @param options [Hash] Hash with options to check.
+    # @param unique [Symbol, Array] List of options that must be unique.
+    #
+    # @example That raises:
+    #   options_unique({foo: 'bar', one: 1}, :foo, :one)
+    #
+    # @example That passes:
+    #   options_unique({foo: 'bar', one: 'two'}, :foo)
+    #
+    # @example That passes:
+    #   options_unique({}, :foo)
+    #
+    # @raise [BioDSL::OptionError] If non-unique options are found.
+    def options_unique(options, *unique)
+      return unless unique.select { |option| options[option] }.size > 1
+
+      fail BioDSL::OptionError, 'Multiple uniques options used: ' \
+        "#{unique.join(', ')}"
+    end
+
+    # Method that raises if options include lists with duplicate elements.
+    #
+    # @param options [Hash] Hash with options to check.
+    # @param lists [Symbol, Array] Lists whos element to check for duplicates.
+    #
+    # @example That raises:
+    #   options_unique_list({foo: [0, 0]}, :foo)
+    #
+    # @example That passes:
+    #   options_unique_list({foo: [0, 1]}, :foo)
+    #
+    # @raise [BioDSL::OptionError] If duplicate elements are found.
+    def options_list_unique(options, *lists)
+      lists.each do |list|
+        if options[list] && options[list].uniq.size != options[list].size
+          fail BioDSL::OptionError, 'Duplicate elements found in list ' \
+            "#{list}: #{options[list]}"
+        end
+      end
+    end
+
+    # Method that raises if one option is given without some other.
+    # Example: options_tie gzip: :output, bzip2: :output
+    #
+    # @param options [Hash] Hash with options to check.
+    # @param others [Hash] Hash with key/value pairs denoting ties.
+    #
+    # @example That raises:
+    #   options_tie({gzip: true}, gzip: :output)
+    #
+    # @example That passes:
+    #   options_tie({output: "foo", gzip: true}, gzip: :output)
+    #
+    # @raise [BioDSL::OptionError] If option found without it's tie.
+    def options_tie(options, others)
+      others.each do |option, other|
+        if options[option] && !options[other]
+          fail BioDSL::OptionError, "Tie option: #{other} not in options: " \
+            "#{options.keys.join(', ')}"
+        end
+      end
+    end
+
+    # Method that raises if conflicting options are used.
+    # Example: select: :evaluate, reject: :evaluate
+    #
+    # @param options [Hash] Hash with options to check.
+    # @param conflicts [Hash] Hash with conflicting key/value pairs.
+    #
+    # @example That raises:
+    #   options_tie({reject: true, select: true}, reject: :select)
+    #
+    # @example That passes:
+    #   options_tie({reject: true}, reject: :select)
+    #
+    # @raise [BioDSL::OptionError] If conflicting options are found.
+    def options_conflict(options, conflicts)
+      conflicts.each do |option, conflict|
+        if options[option] && options[conflict]
+          fail BioDSL::OptionError, "Conflicting options: #{option}, " \
+            "#{conflict}"
+        end
+      end
+    end
+
+    # Method that fails if given files don't exist.
+    #
+    # @param options [Hash]
+    #   Hash with options to check.
+    #
+    # @param args [Symbol, Array]
+    #   Symbol or Array of Symbols which are keys in the option Hash and whos
+    #   values to check.
+    #
+    # @example With a given Symbol.
+    #   options_files_exist(options, :input)
+    #
+    # @example With a given Array.
+    #   options_files_exist(options, [:input1, :input2])
+    #
+    # @raise [BioDSL::OptionError] on non-existing files.
+    def options_files_exist(options, *args)
+      args.each do |arg|
+        next unless options[arg]
+        files = (options[arg].is_a? Array) ? options[arg] : [options[arg]]
+
+        files.each do |file|
+          file = glob_check(file, arg) if file.include? '*'
+
+          unless File.file? File.expand_path(file)
+            fail BioDSL::OptionError, "For option #{arg} - no such file: " \
+              "#{file}"
+          end
+        end
+      end
+    end
+
+    # Method that fails if files exist unless the force option flag is set.
+    #
+    # @param options [Hash]
+    #   Hash with options to check.
+    #
+    # @param args [Symbol, Array]
+    #   Symbol or Array of Symbols which are keys in the option Hash and whos
+    #   values to check.
+    #
+    # @example That raises
+    #   options_files_exist_force({file: __FILE__}}, :file)
+    #
+    # @example That passes
+    #   options_files_exist_force({file: __FILE__, force: true}, :file)
+    #
+    # @raise [BioDSL::OptionError]
+    #   If files exist and the force option flag is not set
+    def options_files_exist_force(options, *args)
+      args.each do |arg|
+        next unless options[arg]
+
+        files = (options[arg].is_a? Array) ? options[arg] : [options[arg]]
+
+        files.each do |file|
+          if File.file?(file) && !options[:force]
+            fail BioDSL::OptionError, "File exist: #{file} - use " \
+              "'force: true' to override"
+          end
+        end
+      end
+    end
+
+    # Method that fails if given directories don't exist.
+    #
+    # @param options [Hash]
+    #   Hash with options to check.
+    #
+    # @param args [Symbol, Array]
+    #   Symbol or Array of Symbols which are keys in the option Hash and whos
+    #   values to check.
+    #
+    # @example With a given Symbol.
+    #   options_dirs_exist(options, :input)
+    #
+    # @example With a given Array.
+    #   options_dirs_exist(options, [:input1, :input2])
+    #
+    # @raise [BioDSL::OptionError] on non-existing directories.
+    def options_dirs_exist(options, *args)
+      args.each do |arg|
+        next unless options[arg]
+
+        dirs = (options[arg].is_a? Array) ? options[arg] : [options[arg]]
+
+        dirs.each do |dir|
+          unless File.directory? File.expand_path(dir)
+            fail BioDSL::OptionError, "For option #{arg} - no such " \
+              "directory: #{dir}"
+          end
+        end
+      end
+    end
+
+    # Assert a given expression.
+    #
+    # @param options [Hash] Hash with options to check.
+    #
+    # @param expression [String] Expersion to assert.
+    #
+    # @example That raises:
+    #   options_assert({min: 0}, ':min > 0')
+    #
+    # @example That passes:
+    #   options_assert({{min: 0}, ':min == 0')
+    #
+    # @raise [BioDSL::OptionError] If assertion fails.
+    def options_assert(options, expression)
+      options.each do |key, value|
+        expression.gsub!(/:#{key}/, value.to_s)
+      end
+
+      return if expression[0] == ':'
+      return if eval expression
+
+      fail BioDSL::OptionError, "Assertion failed: #{expression}"
+    end
+
+    # Expand a given glob expression into lists of paths.
+    #
+    # @param expr [String] Comma sperated glob expressions.
+    #
+    # @example
+    #   options_glob('foo*')
+    #     # => ['foo.rb', 'foo.txt']
+    #
+    # @return [Array] List of expanded paths.
+    def options_glob(expr)
+      paths = []
+      list  = expr.is_a?(Array) ? expr.join(',') : expr
+
+      list.split(/, */).each do |glob|
+        if glob.include? '*'
+          paths += Dir.glob(glob).sort.select { |file| File.file? file }
+        else
+          paths << glob
+        end
+      end
+
+      paths
+    end
+
+    # Load options from rc file and use these unless given or default options
+    # are specified. Option precedence: specified > default > rc.
+    #
+    # @param options [Hash] Hash with options to check.
+    # @param command [Symbol] Command for which to load options.
+    # @param file    [String] Path to file with defaults.
+    #
+    # @example
+    #   options = {}
+    #   options_load_rc(options, :some_option)
+    #   options == {option1: 'value1', option2: 'value2'}
+    def options_load_rc(options, command, file = BioDSL::Config::RC_FILE)
+      return unless File.exist? file
+
+      rc_options = Hash.new { |h, k| h[k] = [] }
+      rc_table   = ::CSV.read(file, col_sep: "\s").
+                   select { |row| row.first && row.first.to_sym == command }
+
+      add_to_rc_options(rc_table, rc_options, options)
+      add_to_options(rc_options, options)
+    end
+
+    # Check if a glob expressoin, a string with a *, matches any files and fail
+    # if that is not the case.
+    #
+    # @param glob [String] Glob expression (containing *) to check.
+    #
+    # @param key [Symbol] Option Hash key whos value is the glob expression.
+    #
+    # @raise [BioDSL::OptionError] If the glob expression fail to match.
+    #
+    # @return [String] The first mathing file.
+    def glob_check(glob, key)
+      first = Dir.glob(glob).select { |f| File.file? f }.first
+      fail BioDSL::OptionError, "For option #{key} - glob expression: " \
+        "#{glob} didn't match any files" if first.nil?
+      first
+    end
+
+    def add_to_options(rc_options, options)
+      rc_options.each do |key, value|
+        if value.size == 1
+          options[key] = value.first
+        else
+          options[key] = value
+        end
+      end
+    end
+
+    def add_to_rc_options(rc_table, rc_options, options)
+      rc_table.each do |row|
+        options.key?(row[1].to_sym) || rc_options[row[1].to_sym] << row[2]
+      end
+    end
+  end
+end

data/lib/BioDSL/helpers/status_helper.rb

@@ -0,0 +1,132 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# 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 software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+module BioDSL
+  # Namespace with methods to record and manipulate cammand status.
+  module StatusHelper
+    require 'tempfile'
+    require 'terminal-table'
+
+    # Given a list of symbols initialize all as status hash keys with the value
+    # 0.
+    #
+    # @param status [Hash]  Status hash.
+    # @param args   [Array] List of symbols.
+    def status_init(status, args)
+      args.each { |arg| status[arg] = 0 }
+      @status = status
+    end
+
+    # Track the status progress of a running command in a seperate thread and
+    # output the status at speficied intervals.
+    #
+    # @param commands [Array] List of commands whos status should be output.
+    # @param block    [Proc]  Track the command in the given block.
+    #
+    # @raise [RunTimeError] If no block is given.
+    def status_progress(commands, &block)
+      fail 'No block given' unless block
+
+      thread = Thread.new do
+        print "\e[H\e[2J"   # Console code to clear screen
+
+        loop do
+          progress_print(commands)
+
+          sleep BioDSL::Config::STATUS_PROGRESS_INTERVAL
+        end
+      end
+
+      block.call
+
+      thread.terminate
+
+      progress_print(commands)
+    end
+
+    private
+
+    # Print the progress table to terminal.
+    #
+    # @param commands [Array] List of commands whos status should be output.
+    def progress_print(commands)
+      print "\e[1;1H"    # Console code to move cursor to 1,1 coordinate.
+      puts "Started: #{commands.first.status[:time_start]}"
+      puts status_tabulate(commands)
+    end
+
+    # Create status table.
+    #
+    # @param commands [Array] List of commands whos status should be output.
+    #
+    # @return [String] Status table.
+    def status_tabulate(commands)
+      return unless commands.first.status[:records_in]
+
+      table = Terminal::Table.new
+      table.style = {border_x: '', border_y: '', border_i: ''}
+      table.rows = status_rows(commands)
+
+      table.align_column(1, :right)
+      table.align_column(2, :right)
+
+      table.to_s
+    end
+
+    # Compile rows with table data.
+    #
+    # @param commands [Array] List of commands whos status should be output.
+    #
+    # @return [Array] List of rows.
+    def status_rows(commands)
+      rows = [%w(name records_in records_out time_elapsed status)]
+
+      commands.each do |command|
+        update_time(command)
+
+        row = []
+        row << command.name
+        row << command.status[:records_in].commify
+        row << command.status[:records_out].commify
+        row << command.status[:time_elapsed]
+        row << command.run_status
+        rows << row
+      end
+
+      rows
+    end
+
+    # Update the time_stop and time_elapsed for a given command.
+    #
+    # @param command [BioDSL::Command] Command object.
+    def update_time(command)
+      command.status[:time_stop] = Time.now unless command.run_status == 'done'
+
+      command.calc_time_elapsed
+    end
+  end
+end

data/lib/BioDSL/helpers.rb

@@ -0,0 +1,35 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# 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 software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Namespace for BioDSL.
+module BioDSL
+  require 'BioDSL/helpers/history_helper'
+  require 'BioDSL/helpers/log_helper'
+  require 'BioDSL/helpers/options_helper'
+  require 'BioDSL/helpers/status_helper'
+  require 'BioDSL/helpers/aux_helper'
+end