miniflow 0.0.1

checksums.yaml

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+  data.tar.gz: 1ce90004f51af85a58dce4e72fb59812d0714302967216b227b61d12901e934c
+SHA512:
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data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2020 kojix2
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# Miniflow
+
+A very small tool to help you execute workflows

data/lib/miniflow.rb

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+# frozen_string_literal: true
+
+require_relative 'miniflow/version'
+require_relative 'miniflow/tty_command'
+require_relative 'miniflow/filecheck'
+require_relative 'miniflow/flow'
+require_relative 'miniflow/tool'
+
+module Miniflow
+  TTYCMD = TTYCommand.new
+end

data/lib/miniflow/filecheck.rb

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+# frozen_string_literal: true
+
+require 'fileutils'
+
+module Miniflow
+  module FileCheck
+    module_function
+
+    # Checks that the file exists and that the extension is correct.
+    # @params path [String] The path to the file to check if it exists
+    # @params extnames [Array, String] File extensions to check.
+    # Multiple extensions can be specified in an array.
+    def check_file(path, extnames)
+      check_file_extname(path, extnames)
+      check_file_exist(path)
+    end
+
+    # Checks if the file exists in the specified path.
+    # @params path [String] The path to the file to check if it exists.
+    def check_file_exist(path)
+      raise "Cannot find: #{path}" unless File.exist?(path)
+    end
+
+    # Make sure that the file has the specified extension.
+    # @params path [String] The path to the file.
+    # @params extnames [Array, String] File extensions to check.
+    def check_file_extname(path, extnames)
+      case extnames
+      when Array
+        raise "Extension is not #{extnames}: #{path}" unless extnames.include?(File.extname(path))
+      when File.extname(path)
+        true
+      else
+        raise "Extension is not #{extnames}: #{path}"
+      end
+    end
+
+    # Creates a directory and all its parent directories.
+    def mkdir_p(*arg)
+      FileUtils.mkdir_p(*arg)
+    end
+  end
+end

data/lib/miniflow/flow.rb

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+# frozen_string_literal: true
+
+require 'tty-tree'
+require 'tty-screen'
+
+module Miniflow
+  # Base class for all flows in Miniflow
+  # The input file must be specified as an absolute path.
+  # Each flow has one output directory
+  class Flow
+    include FileCheck
+
+    # Define the initialize method according to the following rules
+    # * Take file paths as arguments. The file paths can be either absolute or
+    # relative.
+    # * Other arguments are keyword arguments.
+    def initialize
+      raise NotImplementedError
+    end
+
+    def cmd
+      TTYCMD
+    end
+
+    # This section is mainly for file validation.
+    def before_run; end
+
+    # This section is mainly used to validate the generated files, display
+    # runtime information, etc.
+    def after_run
+      check_output_files
+      show_results
+    end
+
+    # The main process. It must be implemented.
+    def main_run
+      raise NotImplementedError
+    end
+
+    # If you have a reason, you can overwrite it.
+    # Normally, you should not change it.
+    def run
+      show_start
+      before_run
+      main_run
+      after_run
+    rescue TTY::Command::ExitError => e
+      show_exit_error
+      raise e
+    rescue Errno::ENOENT => e # Maybe we should expand the scope of the error.
+      show_exit_error
+      raise e
+    end
+
+    # Show the banner when the workflow starts.
+    def show_start
+      @start_time = Time.now
+      puts TTY::Box.frame(self.class.name,
+                          "Start  : #{@start_time}",
+                          width: TTY::Screen.width, padding: 1,
+                          border: { left: false, right: false })
+    end
+
+    # Show the banner when the workflow is finished.
+    def show_results(generated_files: true)
+      @end_time = Time.now
+      tree = if generated_files
+               [' ',
+                "Generated files: #{@out_dir}",
+                ' ',
+                TTY::Tree.new(@out_dir).render]
+             else
+               ''
+             end
+      puts
+      puts TTY::Box.frame("Start  : #{@start_time}",
+                          "End    : #{@end_time}",
+                          "Time   : #{@end_time - @start_time} sec",
+                          *tree,
+                          title: { top_left: " #{self.class.name} " },
+                          width: TTY::Screen.width, padding: 1)
+    end
+
+    # Show the banner when an error occurs and the workflow is abnormally interrupted.
+    def show_exit_error
+      @end_time = Time.now
+      puts TTY::Box.error(
+        "Flow   : #{self.class.name}\n" \
+        "Start  : #{@start_time}\n" \
+        "End    : #{@end_time}\n" \
+        "Time   : #{@end_time - @start_time} sec",
+        width: TTY::Screen.width, padding: 1
+      )
+    end
+
+    # Returns the path in the output directory.
+    # The file path is recorded. When the workflow is finished, the output
+    # files are checked for existence in the `check_output_files` method.
+    def odir(file_name)
+      @output_files ||= []
+      file_path = File.join(@out_dir, file_name)
+      @output_files << file_path
+      file_path
+    end
+
+    # Returns the path in the output directory.
+    def dir(file_name)
+      File.join(@out_dir, file_name)
+    end
+
+    # When the workflow is finished, make sure that all the registered output
+    # files are present.Currently, the error does not occur even if the output
+    # file does not exist. A warning will be shown.
+    def check_output_files
+      return if @output_files.nil?
+
+      flag = true
+      @output_files.uniq.each do |file_path|
+        unless File.exist?(file_path)
+          warn "Output file not found: #{file_path}"
+          flag = false
+        end
+      end
+      puts 'All output file exist.' if flag
+    end
+  end
+end

data/lib/miniflow/tool.rb

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+# frozen_string_literal: true
+
+require 'tty-box'
+require 'tty-screen'
+
+module Miniflow
+  # Burrow-Wheeler Aligner for short-read alignment.
+  class Tool
+    include FileCheck
+
+    # Use the version options to check if the command is available
+    def available?(command)
+      # puts Pastel.new.magenta("Check #{self.class.name}")
+      pastel = Pastel.new
+      class_name = self.class.name.split('::').last
+      begin
+        result = cmd.run!(command)
+      rescue Errno::ENOENT => e
+        pastel = Pastel.new
+        msg = "\n" \
+              "Please make sure that the #{class_name} is available.\n\n"
+        e.message << msg
+        raise e
+      end
+      if result.failure?
+        msg = "The exit status of #{command} is not zero.\n" \
+              "Please make sure that the #{command} is available.\n\n"
+        raise Errno::ENOENT, msg # FIXME
+      else
+        puts pastel.green.bold("✔ #{class_name}")
+      end
+    end
+
+    # Get tool options
+    def [](key)
+      @options[key]
+    end
+
+    def cmd
+      TTYCMD
+    end
+
+    # Calling the Ruby method executes a subcommand with the same name.
+    # Since the Ruby methods are called first, care must be taken to avoid
+    # name collisions. For example, subcommands such as `call` need to be
+    # redefined.
+    def method_missing(name, *args)
+      cmd.run2(@command, name, *args)
+    end
+
+    # respond_to_missing?(sym, include_private)g
+    # end
+  end
+end

data/lib/miniflow/tty_command.rb

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+# frozen_string_literal: true
+
+require 'tty-command'
+
+module Miniflow
+  # Miniflow  uses tty-command to execute the command.
+  # Please see the following website for more information.
+  # https://ttytoolkit.org/
+  class TTYCommand < TTY::Command
+    # TTY::Command custom printer
+    # * change default colors.
+    # https://github.com/piotrmurach/tty-command#34-custom-printer
+    class CustomPretty < Printers::Pretty
+      def print_command_start(cmd, *args)
+        message = ["Running #{decorate(cmd.to_command, :cyan)}"]
+        message << args.map(&:chomp).join(' ') unless args.empty?
+        write(cmd, message.join)
+      end
+
+      def print_command_err_data(cmd, *args)
+        message = args.map(&:chomp).join(' ')
+        write(cmd, "\t#{decorate(message, :white)}", err_data)
+      end
+
+      def write(cmd, message, data = nil)
+        cmd_set_uuid = cmd.options.fetch(:uuid, true)
+        uuid_needed = cmd.options[:uuid].nil? ? @uuid : cmd_set_uuid
+        out = []
+        out << "[#{decorate(cmd.uuid, :green)}] " if uuid_needed && !cmd.uuid.nil?
+        out << "#{message}\n"
+        target = cmd.only_output_on_error && !data.nil? ? data : output
+        target << out.join
+      end
+    end
+
+    def initialize(*args)
+      # Do not output uuid
+      super(*args, printer: CustomPretty, uuid: true)
+    end
+
+    # run2 can execute the command in which the UNIX pipeline is used.
+    def run2(*args)
+      args.map!(&:to_s)
+      command = args.join(' ')
+      if include_meta_character?(command)
+        run(command)
+      else
+        run(*args)
+      end
+    end
+
+    def include_meta_character?(str)
+      ['*', '?', '{', '}', '[', ']', '<', '>', '(', ')', '~', '&', '|', '\\',
+       '$', ';', "'", '`', '"', "\n"].any? { |i| str.include?(i) }
+    end
+  end
+end

data/lib/miniflow/version.rb

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+# frozen_string_literal: true
+
+module Miniflow
+  VERSION = '0.0.1'
+end

metadata

@@ -0,0 +1,191 @@
+--- !ruby/object:Gem::Specification
+name: miniflow
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- kojix2
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2020-12-11 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: tty-box
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: tty-command
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: tty-screen
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: tty-tree
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: A very small tool to help you execute workflows
+email:
+- 2xijok@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- LICENSE.txt
+- README.md
+- lib/miniflow.rb
+- lib/miniflow/filecheck.rb
+- lib/miniflow/flow.rb
+- lib/miniflow/tool.rb
+- lib/miniflow/tty_command.rb
+- lib/miniflow/version.rb
+homepage: https://github.com/kojix2/miniflow
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.4.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.1.4
+signing_key: 
+specification_version: 4
+summary: A very small tool to help you execute workflows
+test_files: []