scout-essentials 1.0.0

checksums.yaml

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+---
+SHA256:
+  metadata.gz: a6c2774d7bf55f2336b53d962d7f471a18d415bf4c8734c32abe669d0214d6c8
+  data.tar.gz: ded38f35d4277f86af691c301113c464587093db4925294bdb46c76c9ff16b3b
+SHA512:
+  metadata.gz: '0128a95c09d025382f373b3aef9ceaba29845eccac7270bfcf9ac9513b90a2d22b5fc3a096a3e0f516748c03e201d91f6969a79c6fd2fcecb2000ab2eae9f6bc'
+  data.tar.gz: a76999c366fc0e18c95d2874c19067472eeb6801199afb276a07887f94ab2cbe4b0ad20a457d475264cd4bca01ad8efa5bac167ebfa5b3ac20e6f074c0a6304d

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.vimproject

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+scout-essentials=/$PWD filter="*.rb *.txt *.md *.conf *.yaml" {
+ LICENSE.txt
+ Rakefile
+ lib=lib {
+  scout-essentials.rb
+  scout=scout{
+   exceptions.rb
+   meta_extension.rb
+   misc.rb
+   misc=misc{
+    digest.rb
+    filesystem.rb
+    format.rb
+    helper.rb
+    insist.rb
+    monitor.rb
+    system.rb
+   }
+   named_array.rb
+   indiferent_hash.rb
+   indiferent_hash=indiferent_hash{
+    case_insensitive.rb
+    options.rb
+   }
+   log.rb
+   log=log{
+    color.rb
+    color_class.rb
+    fingerprint.rb
+    progress.rb
+    trap.rb
+   }
+   tmpfile.rb
+   simple_opt.rb
+   simple_opt=simple_opt{
+    accessor.rb
+    doc.rb
+    get.rb
+    parse.rb
+    setup.rb
+   }
+   path.rb
+   path=path{
+    find.rb
+    tmpfile.rb
+    util.rb
+   }
+   concurrent_stream.rb
+   cmd.rb
+   open.rb
+   open=open{
+    lock.rb
+    remote.rb
+    stream.rb
+    util.rb
+   }
+   resource.rb
+   resource=resource{
+    open.rb
+    path.rb
+    produce.rb
+    scout.rb
+    software.rb
+    util.rb
+   }
+   config.rb
+   persist.rb
+   persist=persist{
+    open.rb
+    path.rb
+    serialize.rb
+   }
+  }
+ }
+ test=test{
+  test_helper.rb
+ }
+}

data/Gemfile

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+source "https://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "~> 1.0"
+  gem "juwelier", "~> 2.1.0"
+  gem "simplecov", ">= 0"
+end

data/LICENSE.txt

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+Copyright (c) 2023 Miguel Vazquez
+
+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.rdoc

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+= scout-essentials
+
+Description goes here.
+
+== Contributing to scout-essentials
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2023 Miguel Vazquez. See LICENSE.txt for
+further details.

data/Rakefile

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+# encoding: utf-8
+
+ENV["BRANCH"] = 'main'
+
+require 'rubygems'
+require 'rake'
+require 'juwelier'
+Juwelier::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "scout-essentials"
+  gem.homepage = "http://github.com/mikisvaz/scout-essentials"
+  gem.license = "MIT"
+  gem.summary = %Q{Scout essential tools}
+  gem.description = %Q{Things a scout can use anywhere}
+  gem.email = "mikisvaz@gmail.com"
+  gem.authors = ["Miguel Vazquez"]
+
+  # dependencies defined in Gemfile
+  
+  gem.add_runtime_dependency 'term-ansicolor'
+  gem.add_runtime_dependency 'yaml'
+end
+Juwelier::RubygemsDotOrgTasks.new
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['test'].execute
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "scout-essentials #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+1.0.0

data/lib/scout/cmd.rb

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+require_relative 'indiferent_hash'
+require_relative 'concurrent_stream'
+require_relative 'log'
+require_relative 'open/stream'
+require 'stringio'
+require 'open3'
+
+module CMD
+
+  TOOLS = IndiferentHash.setup({})
+  def self.tool(tool, claim = nil, test = nil, cmd = nil, &block)
+    TOOLS[tool] = [claim, test, block, cmd]
+  end
+
+  def self.conda(tool, env = nil, channel = 'bioconda')
+    if env
+      CMD.cmd("bash -l -c '(conda activate #{env} && conda install #{tool} -c #{channel})'")
+    else
+      CMD.cmd("bash -l -c 'conda install #{tool} -c #{channel}'")
+    end
+  end
+
+
+  def self.get_tool(tool)
+    return tool.to_s unless TOOLS[tool]
+
+    @@init_cmd_tool ||= IndiferentHash.setup({})
+
+    claim, test, block, cmd = TOOLS[tool]
+    cmd = tool.to_s if cmd.nil?
+
+    if !@@init_cmd_tool[tool]
+
+      begin
+        if test
+          CMD.cmd(test + " ")
+        else
+          CMD.cmd("#{cmd} --help")
+        end
+      rescue
+        if claim
+          claim.produce
+        else
+          block.call
+        end
+      end
+      version_txt = ""
+      version = nil
+      ["--version", "-version", "--help", ""].each do |f|
+        begin
+          version_txt += CMD.cmd("#{cmd} #{f} 2>&1", :nofail => true).read
+          version = CMD.scan_version_text(version_txt, tool)
+          break if version
+        rescue
+          Log.exception $!
+        end
+      end
+
+      @@init_cmd_tool[tool] = version || true
+
+      return cmd if cmd
+    end
+
+    cmd
+  end
+
+  def self.scan_version_text(text, cmd = nil)
+    cmd = "NOCMDGIVE" if cmd.nil? || cmd.empty?
+    text = Misc.fixutf8 text
+    text.split("\n").each do |line|
+      next unless line =~ /\W#{cmd}\W/i
+      m = line.match(/(v(?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
+      return m[1] if m
+      m = line.match(/((?:\d+\.)*\d+(?:-[a-z_]+)?v)/i)
+      return m[1] if m
+      next unless line =~ /\Wversion\W/i
+      m = line.match(/((?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
+      return m[1] if m
+    end
+    m = text.match(/(?:version.*?|#{cmd}.*?|#{cmd.to_s.split(/[-_.]/).first}.*?|v)((?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
+    return m[1] if m
+    m = text.match(/(?:#{cmd}.*(v.*|.*v))/i)
+    return m[1] if m
+    nil
+  end
+  def self.versions
+    return {} unless defined? @@init_cmd_tool
+    @@init_cmd_tool.select{|k,v| v =~ /\d+\./ }
+  end
+
+  def self.bash(cmd)
+    cmd = %Q(bash <<EOF\n#{cmd}\nEOF\n)
+    CMD.cmd(cmd, :autojoin => true)
+  end
+
+  def self.process_cmd_options(options = {})
+    add_dashes = IndiferentHash.process_options options, :add_option_dashes
+
+    string = ""
+    options.each do |option, value|
+      raise "Invalid option key: #{option.inspect}" if option.to_s !~ /^[a-z_0-9\-=.]+$/i
+      #raise "Invalid option value: #{value.inspect}" if value.to_s.include? "'"
+      value = value.gsub("'","\\'") if value.to_s.include? "'"
+
+      option = "--" << option.to_s if add_dashes and option.to_s[0] != '-'
+
+      case
+      when value.nil? || FalseClass === value
+        next
+      when TrueClass === value
+        string << "#{option} "
+      else
+        if option.to_s.chars.to_a.last == "="
+          string << "#{option}'#{value}' "
+        else
+          string << "#{option} '#{value}' "
+        end
+      end
+    end
+
+    string.strip
+  end
+
+  def self.cmd(tool, cmd = nil, options = {}, &block)
+    options, cmd = cmd, nil if Hash === cmd
+
+    options    = IndiferentHash.add_defaults options, :stderr => Log::DEBUG
+    in_content = options.delete(:in)
+    stderr     = options.delete(:stderr)
+    post       = options.delete(:post)
+    pipe       = options.delete(:pipe)
+    log        = options.delete(:log)
+    no_fail    = options.delete(:no_fail)
+    no_fail    = options.delete(:nofail) if no_fail.nil?
+    no_wait    = options.delete(:no_wait)
+    xvfb       = options.delete(:xvfb)
+    bar        = options.delete(:progress_bar)
+    save_stderr = options.delete(:save_stderr)
+    autojoin   = options.delete(:autojoin)
+    autojoin   = no_wait if autojoin.nil?
+
+    dont_close_in  = options.delete(:dont_close_in)
+
+    log = true if log.nil?
+
+    if cmd.nil? && ! Symbol === tool
+      cmd = tool
+    else
+      tool = get_tool(tool)
+      if cmd.nil?
+        cmd = tool
+      else
+        cmd = tool + ' ' + cmd
+      end
+
+    end
+
+    case xvfb
+    when TrueClass
+      cmd = "xvfb-run --server-args='-screen 0 1024x768x24' --auto-servernum #{cmd}"
+    when String
+      cmd = "xvfb-run --server-args='#{xvfb}' --auto-servernum --server-num=1 #{cmd}"
+    when String
+    end
+
+    if stderr == true
+      stderr = Log::HIGH
+    end
+
+    cmd_options = process_cmd_options options
+    if cmd =~ /'\{opt\}'/
+      cmd.sub!('\'{opt}\'', cmd_options)
+    else
+      cmd << " " << cmd_options
+    end
+
+    in_content = StringIO.new in_content if String === in_content
+
+    sin, sout, serr, wait_thr = begin
+                                  Open3.popen3(ENV, cmd)
+                                rescue
+                                  Log.warn $!.message
+                                  raise ProcessFailed, nil, cmd unless no_fail
+                                  return
+                                end
+    pid = wait_thr.pid
+
+    Log.debug{"CMD: [#{pid}] #{cmd}".strip if log}
+
+    if in_content.respond_to?(:read)
+      in_thread = Thread.new(Thread.current) do |parent|
+        begin
+          Thread.current.report_on_exception = false if no_fail
+          Thread.current["name"] = "CMD in"
+          while c = in_content.read(Open::BLOCK_SIZE)
+            sin << c
+          end
+          sin.close  unless sin.closed?
+
+          unless dont_close_in
+            in_content.close unless in_content.closed?
+            in_content.join if in_content.respond_to? :join
+          end
+        rescue
+          Log.error "Error in CMD  [#{pid}] #{cmd}: #{$!.message}" unless no_fail
+          raise $!
+        end
+      end
+      Thread.pass until in_thread["name"]
+    else
+      in_thread = nil
+      sin.close
+    end
+
+    pids = [pid]
+
+    if pipe
+
+      ConcurrentStream.setup sout, :pids => pids, :autojoin => autojoin, :no_fail => no_fail
+
+      sout.callback = post if post
+
+      if (Integer === stderr and log) || bar
+        err_thread = Thread.new do
+          Thread.current["name"] = "Error log: [#{pid}] #{ cmd }"
+          begin
+          while line = serr.gets
+            bar.process(line) if bar
+            sout.log = line
+            sout.std_err << line if save_stderr
+            Log.log "STDERR [#{pid}]: " +  line, stderr if log
+          end
+          serr.close
+          rescue
+            Log.exception $!
+            raise $!
+          end
+        end
+      else
+        err_thread = Open.consume_stream(serr, true)
+      end
+
+      sout.threads = [in_thread, err_thread, wait_thr].compact
+
+      sout
+    else
+
+      if bar
+        err = ""
+        err_thread = Thread.new do
+          while not serr.eof?
+            line = serr.gets
+            bar.process(line)
+            err << line if Integer === stderr and log
+          end
+          serr.close
+        end
+      elsif log and Integer === stderr
+        err = ""
+        err_thread = Thread.new do
+          while not serr.eof?
+            err << serr.gets
+          end
+          serr.close
+        end
+      else
+        Open.consume_stream(serr, true)
+        err_thread = nil
+        err = ""
+      end
+
+      ConcurrentStream.setup sout, :pids => pids, :threads => [in_thread, err_thread].compact, :autojoin => autojoin, :no_fail => no_fail
+
+      begin
+        out = StringIO.new sout.read
+        sout.close unless sout.closed?
+
+        status = wait_thr.value
+        if status && ! status.success? && ! no_fail
+          if !err.empty?
+            raise ProcessFailed.new pid, "#{cmd} failed with error status #{status.exitstatus}.\n#{err}"
+          else
+            raise ProcessFailed.new pid, "#{cmd} failed with error status #{status.exitstatus}"
+          end
+        else
+          Log.log err, stderr if Integer === stderr and log
+        end
+        out
+      ensure
+        post.call if post
+      end
+    end
+  end
+
+  def self.cmd_pid(*args)
+    all_args = *args
+
+    bar = all_args.last[:progress_bar] if Hash === all_args.last
+
+    all_args << {} unless Hash === all_args.last
+
+    level = all_args.last[:log] || 0
+    level = 0 if TrueClass === level
+    level = 10 if FalseClass === level
+    level = level.to_i
+
+    all_args.last[:log] = true
+    all_args.last[:pipe] = true
+
+    io = cmd(*all_args)
+    pid = io.pids.first
+
+    line = "" if bar
+    starting = true
+    while c = io.getc
+      if starting
+        if pid
+          Log.logn "STDOUT [#{pid}]: ", level
+        else
+          Log.logn "STDOUT: ", level
+        end
+        starting = false
+      end
+      STDERR << c if Log.severity <= level
+      line << c if bar
+      if c == "\n"
+        bar.process(line) if bar
+        starting = true
+        line = "" if bar
+      end
+    end
+    begin
+      io.join
+      bar.remove if bar
+    rescue
+      bar.remove(true) if bar
+      raise $!
+    end
+
+    nil
+  end
+
+  def self.cmd_log(*args)
+    cmd_pid(*args)
+    nil
+  end
+
+end