miga-base 0.6.3.2 → 0.6.4.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: d1285c61c990a597f9ed65ba298467c7ea4aac49441af91e2711a5590fa8f05b
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+  data.tar.gz: 62898b0497e07db953534a24b40f9df1b76ba2304676a2c4763599be0ae8d03c7fa36e1a7d580745f04074c27d53f808dd1e8842f9bccda9641b01c76fda383b

data/lib/miga/cli.rb

@@ -106,9 +106,7 @@ class MiGA::Cli < MiGA::MiGA
   # otherwise it's sent to +$stderr+
   def say(*par)
     return unless self[:verbose]
-    par.map! { |i| "[#{Time.now}] #{i}" }
-    io = par.first.is_a?(IO) ? par.shift : $stderr
-    io.puts(*par)
+    super(*par)
   end
 
   ##

data/lib/miga/cli/action/lair.rb

@@ -0,0 +1,81 @@
+# @package MiGA
+# @license Artistic-2.0
+
+require 'miga/cli/action'
+require 'miga/lair'
+
+class MiGA::Cli::Action::Lair < MiGA::Cli::Action
+
+  def parse_cli
+    cli.defaults = { daemon_opts: [] }
+    cli.expect_operation = true
+    cli.parse do |opt|
+      opt.separator 'Available operations:'
+      { start:   'Start an instance of the application.',
+        stop:    'Start an instance of the application.',
+        restart: 'Stop all instances and restart them afterwards.',
+        reload:  'Send a SIGHUP to all instances of the application.',
+        run:     'Start the application and stay on top.',
+        zap:     'Set the application to a stopped state.',
+        status:  'Show status (PID) of application instances.'
+      }.each { |k,v| opt.separator sprintf '    %*s%s', -33, k, v }
+      opt.separator ''
+
+      opt.separator 'MiGA options:'
+      opt.on(
+        '-p', '--path PATH',
+        '(Mandatory) Path to the directory where the MiGA projects are located'
+      ) { |v| cli[:path] = v }
+      opt.on(
+        '--latency INT', Integer,
+        'Time to wait between iterations in seconds, by default: 120'
+      ) { |v| cli[:latency] = v }
+      opt.on(
+        '--wait-for INT', Integer,
+        'Time to wait for a daemon to report being alive in seconds',
+        'by default: 900'
+      ) { |v| cli[:wait_for] = v }
+      opt.on(
+        '--keep-inactive',
+        'If set, daemons are kept alive even when inactive;',
+        'i.e., when all tasks are complete'
+      ) { |v| cli[:keep_inactive] = v }
+      opt.on(
+        '--name STRING',
+        'A name for the chief daemon process'
+      ) { |v| cli[:name] = v }
+      opt.on(
+        '--json PATH',
+        'Path to a custom daemon definition in json format'
+      ) { |v| cli[:json] = v }
+      cli.opt_common(opt)
+
+      opt.separator 'Daemon options:'
+      opt.on(
+        '-t', '--ontop',
+        'Stay on top (does not daemonize)'
+      ) { cli[:daemon_opts] << '-t' }
+      opt.on(
+        '-f', '--force',
+        'Force operation'
+      ) { cli[:daemon_opts] << '-f' }
+      opt.on(
+        '-n', '--no_wait',
+        'Do not wait for processes to stop'
+      ) { cli[:daemon_opts] << '-n' }
+      opt.on(
+        '--shush',
+        'Silence the daemon'
+      ) { cli[:daemon_opts] << '--shush' }
+      opt.separator ''
+    end
+  end
+
+  def perform
+    cli.ensure_par(path: '-p')
+    k_opts = %i[latency wait_for keep_inactive name json]
+    opts = Hash[k_opts.map { |k| [k, cli[k]] }]
+    lair = MiGA::Lair.new(cli[:path], opts)
+    lair.daemon(cli.operation, cli[:daemon_opts])
+  end
+end

data/lib/miga/cli/base.rb

@@ -37,6 +37,7 @@ module MiGA::Cli::Base
     # System
     init:     'Initialize MiGA to process new projects',
     daemon:   'Controls the daemon of a MiGA project',
+    lair:     'Controls groups of daemons for several MiGA projects',
     date:     'Returns the current date in standard MiGA format',
     console:  'Opens an IRB console with MiGA',
     # Taxonomy

data/lib/miga/common.rb

@@ -36,5 +36,15 @@ class MiGA::MiGA
     end
   end
 
+  ##
+  # Print +par+ ensuring new line at the end.
+  # Date/time-stamp each line.
+  # If the first parameter is +IO+, the output is sent there,
+  # otherwise it's sent to +$stderr+
+  def say(*par)
+    io = par.first.is_a?(IO) ? par.shift : $stderr
+    io.puts(*par.map { |i| "[#{Time.now}] #{i}" })
+  end
+
 end
 

data/lib/miga/lair.rb

@@ -0,0 +1,153 @@
+# @package MiGA
+# @license Artistic-2.0
+
+require 'daemons'
+require 'miga/daemon'
+
+##
+# Lair of MiGA Daemons handling job submissions
+class MiGA::Lair < MiGA::MiGA
+  ##
+  # When was the last time the chief daemon in this lair was seen active?
+  # Returns Time
+  def self.last_alive(path)
+    f = File.expand_path('.lair-alive', path)
+    return nil unless File.exist? f
+    Time.parse(File.read(f))
+  end
+
+  # Absolute path to the directory where the projects are located
+  attr_reader :path
+
+  # Options used to setup the chief daemon
+  attr_accessor :options
+
+  # Integer indicating the current iteration
+  attr_reader :loop_i
+
+  ##
+  # Initialize an inactive daemon for the directory at +path+. See #daemon
+  # to wake the chief daemon. Supported options include:
+  # - json: json definition for all children daemons, by default: nil
+  # - latency: time to wait between iterations in seconds, by default: 120
+  # - wait_for: time to wait for a daemon to report being alive in seconds,
+  #   by default: 900
+  # - keep_inactive: boolean indicating if daemons should stay alive even when
+  #   inactive (when all tasks are complete), by default: false
+  # - name: A name for the chief daemon process, by default: basename of +path+
+  def initialize(path, opts = {})
+    @path = File.expand_path(path)
+    @options = opts
+    @loop_i = -1
+    {
+      json: nil,
+      latency: 120,
+      wait_for: 900,
+      keep_inactive: false,
+      name: File.basename(@path)
+    }.each { |k, v| @options[k] = v if @options[k].nil? }
+  end
+
+  ##
+  # When was the last time the chief daemon for was seen active here?
+  # Returns Time.
+  def last_alive
+    MiGA::Lair.last_alive path
+  end
+
+  ##
+  # Returns Hash containing the default options for the daemon.
+  def default_options
+    { dir_mode: :normal, dir: path, multiple: false, log_output: true }
+  end
+
+  ##
+  # Launches the +task+ with options +opts+ (as command-line arguments) and
+  # returns the process ID as an Integer. If +wait+ it waits for the process to
+  # complete, immediately returns otherwise.
+  # Supported tasks: start, stop, restart, status.
+  def daemon(task, opts = [], wait = true)
+    MiGA.DEBUG "Lair.daemon #{task} #{opts}"
+    config = default_options
+    opts.unshift(task.to_s)
+    config[:ARGV] = opts
+    # This additional degree of separation below was introduced so the Daemons
+    # package doesn't kill the parent process in workflows.
+    pid = fork do
+      Daemons.run_proc("MiGA:#{options[:name]}", config) { while in_loop; end }
+    end
+    Process.wait(pid) if wait
+    pid
+  end
+
+  ##
+  # Tell the world that you're alive.
+  def declare_alive
+    File.open(File.join(path, '.lair-alive'), 'w') do |fh|
+      fh.print Time.now.to_s
+    end
+  end
+
+  ##
+  # Perform block for each project in the +dir+ directory,
+  # passing the absolute path of the project to the block.
+  # Searches for MiGA projects recursively in all
+  # subdirectories that are not MiGA projects.
+  def each_project(dir = path)
+    Dir.entries(dir) do |f|
+      f = File.join(dir, f)
+      if MiGA::Project.exists? f
+        yield(f)
+      elsif Dir.exists? f
+        each_project(f) { |p| yield(p) }
+      end
+    end
+  end
+
+  ##
+  # Traverse directories checking MiGA projects
+  def check_directories
+    each_project do |dir|
+      alive = MiGA::Daemon.last_alive(dir)
+      next if !alive.nil? && alive > Time.now - options[:wait_for]
+      launch_daemon(dir)
+    end
+  end
+
+  ##
+  # Launch daemon for the project stored in +dir+
+  def launch_daemon(dir)
+    project = MiGA::Project.load(dir)
+    raise "Cannot load project: #{dir}" if project.nil?
+    d = MiGA::Daemon.new(project, options[:json])
+    d.runopts(:shutdown_when_done, true) unless options[:keep_inactive]
+    say "Launching daemon: #{dir}"
+    d.daemon(:start, [], false)
+  end
+
+  ##
+  # Run one loop step. Returns a Boolean indicating if the loop should continue.
+  def in_loop
+    declare_alive
+    if loop_i == -1
+      say '-----------------------------------'
+      say 'MiGA:%s launched' % options[:name]
+      say '-----------------------------------'
+      say 'Configuration options:'
+      say options.to_s
+      @loop_i = 0
+    end
+    @loop_i += 1
+    check_directories
+    sleep(options[:latency])
+    true
+  end
+
+  ##
+  # Terminates a chief daemon
+  def terminate
+    say 'Terminating chief daemon...'
+    f = File.expand_path('.lair-alive', project.path)
+    File.unlink(f) if File.exist? f
+  end
+end

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.6, 3, 2]
+  VERSION = [0.6, 4, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 4, 13)
+  VERSION_DATE = Date.new(2020, 4, 15)
 
   ##
   # Reference of MiGA.

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.6.3.2
+  version: 0.6.4.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-04-13 00:00:00.000000000 Z
+date: 2020-04-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -133,6 +133,7 @@ files:
 - lib/miga/cli/action/index_wf.rb
 - lib/miga/cli/action/init.rb
 - lib/miga/cli/action/init/daemon_helper.rb
+- lib/miga/cli/action/lair.rb
 - lib/miga/cli/action/ln.rb
 - lib/miga/cli/action/ls.rb
 - lib/miga/cli/action/ncbi_get.rb
@@ -165,6 +166,7 @@ files:
 - lib/miga/dataset/hooks.rb
 - lib/miga/dataset/result.rb
 - lib/miga/json.rb
+- lib/miga/lair.rb
 - lib/miga/metadata.rb
 - lib/miga/project.rb
 - lib/miga/project/base.rb