miniflow 0.0.1
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- checksums.yaml +7 -0
- data/LICENSE.txt +21 -0
- data/README.md +3 -0
- data/lib/miniflow.rb +11 -0
- data/lib/miniflow/filecheck.rb +43 -0
- data/lib/miniflow/flow.rb +127 -0
- data/lib/miniflow/tool.rb +54 -0
- data/lib/miniflow/tty_command.rb +57 -0
- data/lib/miniflow/version.rb +5 -0
- metadata +191 -0
checksums.yaml
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---
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SHA256:
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metadata.gz: a891bee3c3d611ddca2990643196bae2bd0c9b545e3234e3b67acb68e9661cf6
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data.tar.gz: 1ce90004f51af85a58dce4e72fb59812d0714302967216b227b61d12901e934c
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SHA512:
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metadata.gz: ded8fa695a81f5021eb916943a718fdc0ea31efbe2ad8457fb50be66d43975e0254258a1b92243a7c0ec245f1314072d2e1403aa5fe10f5d9183731229708bb4
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data.tar.gz: fbdf6fbf13522d926b80c441ba912a0e8cabf47f4f878108435fd605df4c010c2a8c5d11583ba32d4af3c83b9a637eb69fd95dc3c8e61c3ace22bb6ccb12a036
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data/LICENSE.txt
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The MIT License (MIT)
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Copyright (c) 2020 kojix2
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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data/README.md
ADDED
data/lib/miniflow.rb
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# frozen_string_literal: true
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require_relative 'miniflow/version'
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require_relative 'miniflow/tty_command'
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require_relative 'miniflow/filecheck'
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require_relative 'miniflow/flow'
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require_relative 'miniflow/tool'
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module Miniflow
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TTYCMD = TTYCommand.new
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end
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# frozen_string_literal: true
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require 'fileutils'
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module Miniflow
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module FileCheck
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module_function
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# Checks that the file exists and that the extension is correct.
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# @params path [String] The path to the file to check if it exists
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# @params extnames [Array, String] File extensions to check.
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# Multiple extensions can be specified in an array.
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def check_file(path, extnames)
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check_file_extname(path, extnames)
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check_file_exist(path)
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end
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# Checks if the file exists in the specified path.
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# @params path [String] The path to the file to check if it exists.
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def check_file_exist(path)
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raise "Cannot find: #{path}" unless File.exist?(path)
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end
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# Make sure that the file has the specified extension.
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# @params path [String] The path to the file.
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# @params extnames [Array, String] File extensions to check.
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def check_file_extname(path, extnames)
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case extnames
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when Array
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raise "Extension is not #{extnames}: #{path}" unless extnames.include?(File.extname(path))
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when File.extname(path)
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true
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else
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raise "Extension is not #{extnames}: #{path}"
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end
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end
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# Creates a directory and all its parent directories.
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def mkdir_p(*arg)
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FileUtils.mkdir_p(*arg)
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end
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end
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end
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# frozen_string_literal: true
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require 'tty-tree'
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require 'tty-screen'
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module Miniflow
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# Base class for all flows in Miniflow
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# The input file must be specified as an absolute path.
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# Each flow has one output directory
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class Flow
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include FileCheck
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# Define the initialize method according to the following rules
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# * Take file paths as arguments. The file paths can be either absolute or
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# relative.
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# * Other arguments are keyword arguments.
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def initialize
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raise NotImplementedError
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end
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def cmd
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TTYCMD
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end
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# This section is mainly for file validation.
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def before_run; end
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# This section is mainly used to validate the generated files, display
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# runtime information, etc.
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def after_run
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check_output_files
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show_results
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end
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# The main process. It must be implemented.
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def main_run
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raise NotImplementedError
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end
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# If you have a reason, you can overwrite it.
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# Normally, you should not change it.
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def run
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show_start
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before_run
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main_run
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after_run
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rescue TTY::Command::ExitError => e
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show_exit_error
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raise e
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rescue Errno::ENOENT => e # Maybe we should expand the scope of the error.
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show_exit_error
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raise e
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end
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# Show the banner when the workflow starts.
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def show_start
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@start_time = Time.now
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puts TTY::Box.frame(self.class.name,
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"Start : #{@start_time}",
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width: TTY::Screen.width, padding: 1,
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border: { left: false, right: false })
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end
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# Show the banner when the workflow is finished.
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def show_results(generated_files: true)
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@end_time = Time.now
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tree = if generated_files
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[' ',
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"Generated files: #{@out_dir}",
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' ',
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TTY::Tree.new(@out_dir).render]
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else
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''
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end
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puts
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puts TTY::Box.frame("Start : #{@start_time}",
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"End : #{@end_time}",
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"Time : #{@end_time - @start_time} sec",
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*tree,
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title: { top_left: " #{self.class.name} " },
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width: TTY::Screen.width, padding: 1)
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end
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# Show the banner when an error occurs and the workflow is abnormally interrupted.
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def show_exit_error
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@end_time = Time.now
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puts TTY::Box.error(
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"Flow : #{self.class.name}\n" \
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"Start : #{@start_time}\n" \
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"End : #{@end_time}\n" \
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"Time : #{@end_time - @start_time} sec",
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width: TTY::Screen.width, padding: 1
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)
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end
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# Returns the path in the output directory.
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# The file path is recorded. When the workflow is finished, the output
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# files are checked for existence in the `check_output_files` method.
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def odir(file_name)
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@output_files ||= []
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file_path = File.join(@out_dir, file_name)
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@output_files << file_path
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file_path
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end
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# Returns the path in the output directory.
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def dir(file_name)
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File.join(@out_dir, file_name)
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end
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# When the workflow is finished, make sure that all the registered output
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# files are present.Currently, the error does not occur even if the output
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# file does not exist. A warning will be shown.
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def check_output_files
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return if @output_files.nil?
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flag = true
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@output_files.uniq.each do |file_path|
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unless File.exist?(file_path)
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warn "Output file not found: #{file_path}"
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flag = false
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end
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end
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puts 'All output file exist.' if flag
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end
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end
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end
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@@ -0,0 +1,54 @@
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# frozen_string_literal: true
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require 'tty-box'
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require 'tty-screen'
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module Miniflow
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# Burrow-Wheeler Aligner for short-read alignment.
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class Tool
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include FileCheck
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# Use the version options to check if the command is available
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def available?(command)
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# puts Pastel.new.magenta("Check #{self.class.name}")
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pastel = Pastel.new
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class_name = self.class.name.split('::').last
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begin
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result = cmd.run!(command)
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rescue Errno::ENOENT => e
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pastel = Pastel.new
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msg = "\n" \
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"Please make sure that the #{class_name} is available.\n\n"
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e.message << msg
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raise e
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end
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if result.failure?
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msg = "The exit status of #{command} is not zero.\n" \
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"Please make sure that the #{command} is available.\n\n"
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raise Errno::ENOENT, msg # FIXME
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else
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puts pastel.green.bold("✔ #{class_name}")
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end
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end
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# Get tool options
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def [](key)
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@options[key]
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end
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|
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def cmd
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TTYCMD
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end
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|
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# Calling the Ruby method executes a subcommand with the same name.
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# Since the Ruby methods are called first, care must be taken to avoid
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# name collisions. For example, subcommands such as `call` need to be
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# redefined.
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def method_missing(name, *args)
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cmd.run2(@command, name, *args)
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end
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# respond_to_missing?(sym, include_private)g
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# end
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end
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end
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@@ -0,0 +1,57 @@
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# frozen_string_literal: true
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|
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require 'tty-command'
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|
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module Miniflow
|
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# Miniflow uses tty-command to execute the command.
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# Please see the following website for more information.
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# https://ttytoolkit.org/
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class TTYCommand < TTY::Command
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# TTY::Command custom printer
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# * change default colors.
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# https://github.com/piotrmurach/tty-command#34-custom-printer
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class CustomPretty < Printers::Pretty
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def print_command_start(cmd, *args)
|
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message = ["Running #{decorate(cmd.to_command, :cyan)}"]
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message << args.map(&:chomp).join(' ') unless args.empty?
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write(cmd, message.join)
|
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+
end
|
19
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+
|
20
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def print_command_err_data(cmd, *args)
|
21
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+
message = args.map(&:chomp).join(' ')
|
22
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write(cmd, "\t#{decorate(message, :white)}", err_data)
|
23
|
+
end
|
24
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+
|
25
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def write(cmd, message, data = nil)
|
26
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cmd_set_uuid = cmd.options.fetch(:uuid, true)
|
27
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uuid_needed = cmd.options[:uuid].nil? ? @uuid : cmd_set_uuid
|
28
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out = []
|
29
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out << "[#{decorate(cmd.uuid, :green)}] " if uuid_needed && !cmd.uuid.nil?
|
30
|
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out << "#{message}\n"
|
31
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target = cmd.only_output_on_error && !data.nil? ? data : output
|
32
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target << out.join
|
33
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+
end
|
34
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+
end
|
35
|
+
|
36
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def initialize(*args)
|
37
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# Do not output uuid
|
38
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super(*args, printer: CustomPretty, uuid: true)
|
39
|
+
end
|
40
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+
|
41
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# run2 can execute the command in which the UNIX pipeline is used.
|
42
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+
def run2(*args)
|
43
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+
args.map!(&:to_s)
|
44
|
+
command = args.join(' ')
|
45
|
+
if include_meta_character?(command)
|
46
|
+
run(command)
|
47
|
+
else
|
48
|
+
run(*args)
|
49
|
+
end
|
50
|
+
end
|
51
|
+
|
52
|
+
def include_meta_character?(str)
|
53
|
+
['*', '?', '{', '}', '[', ']', '<', '>', '(', ')', '~', '&', '|', '\\',
|
54
|
+
'$', ';', "'", '`', '"', "\n"].any? { |i| str.include?(i) }
|
55
|
+
end
|
56
|
+
end
|
57
|
+
end
|
metadata
ADDED
@@ -0,0 +1,191 @@
|
|
1
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--- !ruby/object:Gem::Specification
|
2
|
+
name: miniflow
|
3
|
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version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.1
|
5
|
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platform: ruby
|
6
|
+
authors:
|
7
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+
- kojix2
|
8
|
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autorequire:
|
9
|
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bindir: bin
|
10
|
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cert_chain: []
|
11
|
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date: 2020-12-11 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: tty-box
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - ">="
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '0'
|
20
|
+
type: :runtime
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - ">="
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: '0'
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: tty-command
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - ">="
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: '0'
|
34
|
+
type: :runtime
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - ">="
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: '0'
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: tty-screen
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - ">="
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '0'
|
48
|
+
type: :runtime
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - ">="
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '0'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: tty-tree
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - ">="
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '0'
|
62
|
+
type: :runtime
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - ">="
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '0'
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: bundler
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - ">="
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: '0'
|
76
|
+
type: :development
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - ">="
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: '0'
|
83
|
+
- !ruby/object:Gem::Dependency
|
84
|
+
name: minitest
|
85
|
+
requirement: !ruby/object:Gem::Requirement
|
86
|
+
requirements:
|
87
|
+
- - ">="
|
88
|
+
- !ruby/object:Gem::Version
|
89
|
+
version: '0'
|
90
|
+
type: :development
|
91
|
+
prerelease: false
|
92
|
+
version_requirements: !ruby/object:Gem::Requirement
|
93
|
+
requirements:
|
94
|
+
- - ">="
|
95
|
+
- !ruby/object:Gem::Version
|
96
|
+
version: '0'
|
97
|
+
- !ruby/object:Gem::Dependency
|
98
|
+
name: rake
|
99
|
+
requirement: !ruby/object:Gem::Requirement
|
100
|
+
requirements:
|
101
|
+
- - ">="
|
102
|
+
- !ruby/object:Gem::Version
|
103
|
+
version: '0'
|
104
|
+
type: :development
|
105
|
+
prerelease: false
|
106
|
+
version_requirements: !ruby/object:Gem::Requirement
|
107
|
+
requirements:
|
108
|
+
- - ">="
|
109
|
+
- !ruby/object:Gem::Version
|
110
|
+
version: '0'
|
111
|
+
- !ruby/object:Gem::Dependency
|
112
|
+
name: rubocop
|
113
|
+
requirement: !ruby/object:Gem::Requirement
|
114
|
+
requirements:
|
115
|
+
- - ">="
|
116
|
+
- !ruby/object:Gem::Version
|
117
|
+
version: '0'
|
118
|
+
type: :development
|
119
|
+
prerelease: false
|
120
|
+
version_requirements: !ruby/object:Gem::Requirement
|
121
|
+
requirements:
|
122
|
+
- - ">="
|
123
|
+
- !ruby/object:Gem::Version
|
124
|
+
version: '0'
|
125
|
+
- !ruby/object:Gem::Dependency
|
126
|
+
name: simplecov
|
127
|
+
requirement: !ruby/object:Gem::Requirement
|
128
|
+
requirements:
|
129
|
+
- - ">="
|
130
|
+
- !ruby/object:Gem::Version
|
131
|
+
version: '0'
|
132
|
+
type: :development
|
133
|
+
prerelease: false
|
134
|
+
version_requirements: !ruby/object:Gem::Requirement
|
135
|
+
requirements:
|
136
|
+
- - ">="
|
137
|
+
- !ruby/object:Gem::Version
|
138
|
+
version: '0'
|
139
|
+
- !ruby/object:Gem::Dependency
|
140
|
+
name: yard
|
141
|
+
requirement: !ruby/object:Gem::Requirement
|
142
|
+
requirements:
|
143
|
+
- - ">="
|
144
|
+
- !ruby/object:Gem::Version
|
145
|
+
version: '0'
|
146
|
+
type: :development
|
147
|
+
prerelease: false
|
148
|
+
version_requirements: !ruby/object:Gem::Requirement
|
149
|
+
requirements:
|
150
|
+
- - ">="
|
151
|
+
- !ruby/object:Gem::Version
|
152
|
+
version: '0'
|
153
|
+
description: A very small tool to help you execute workflows
|
154
|
+
email:
|
155
|
+
- 2xijok@gmail.com
|
156
|
+
executables: []
|
157
|
+
extensions: []
|
158
|
+
extra_rdoc_files: []
|
159
|
+
files:
|
160
|
+
- LICENSE.txt
|
161
|
+
- README.md
|
162
|
+
- lib/miniflow.rb
|
163
|
+
- lib/miniflow/filecheck.rb
|
164
|
+
- lib/miniflow/flow.rb
|
165
|
+
- lib/miniflow/tool.rb
|
166
|
+
- lib/miniflow/tty_command.rb
|
167
|
+
- lib/miniflow/version.rb
|
168
|
+
homepage: https://github.com/kojix2/miniflow
|
169
|
+
licenses:
|
170
|
+
- MIT
|
171
|
+
metadata: {}
|
172
|
+
post_install_message:
|
173
|
+
rdoc_options: []
|
174
|
+
require_paths:
|
175
|
+
- lib
|
176
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
177
|
+
requirements:
|
178
|
+
- - ">="
|
179
|
+
- !ruby/object:Gem::Version
|
180
|
+
version: 2.4.0
|
181
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
182
|
+
requirements:
|
183
|
+
- - ">="
|
184
|
+
- !ruby/object:Gem::Version
|
185
|
+
version: '0'
|
186
|
+
requirements: []
|
187
|
+
rubygems_version: 3.1.4
|
188
|
+
signing_key:
|
189
|
+
specification_version: 4
|
190
|
+
summary: A very small tool to help you execute workflows
|
191
|
+
test_files: []
|