miga-base 1.3.17.1 → 1.3.18.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: ddf4e24b843afa0a046c4673710c4de785f850335764972604e89e3b4c0874ce
+  metadata.gz: bf9ebc2ca06846d9b76c981c2a89896080690bc44d979ba28b4a9173f7386c7a
+  data.tar.gz: a156a4f0894f1988862b8daf296b916c80cf197eb36fb7c13c4698975403c35e
 SHA512:
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-  data.tar.gz: 2e4da0abbe25f7c7f845c2fd64ba2ee2adbf0912ba05a616205f5ef655f7bae72a50f0a6d2bc3831e6d3046437fe04a9147567f6d80290d3867eba69e4470f88
+  metadata.gz: b6e1318553d24d93af467670754e86e5281c7418d4242ad11b56125889188fb7cde48a1858f20e1b07bab04a372c4aac718e04c005bdfadccf641c15cd7cf2ed
+  data.tar.gz: e584f1b4442a099fb16c4b0c07515b9332867c5b72438bae9e33467f9d0911c7bd4811a6861121482cada1b88f44aaec2efd6d2f668fa6a05c722c9fe56995bc

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

@@ -0,0 +1,57 @@
+# @package MiGA
+# @license Artistic-2.0
+
+require 'miga/cli/action'
+
+class MiGA::Cli::Action::Cmd < MiGA::Cli::Action
+  def parse_cli
+    cli.expect_files = true
+    cli.files_label  = 'CMD'
+    cli.defaults = {
+      raise: false, return: :status, source: :miga_env,
+      stdout: nil, stderr: nil, dry: false, show_cmd: false,
+      err2out: false
+    }
+    cli.parse do |opt|
+      opt.separator 'To separate command flags from MiGA flags, use --:'
+      opt.separator 'miga cmd --verbose -- rbm.rb --version'
+      opt.separator ''
+      opt.separator 'To run the command as is (no escaping), use single-quotes:'
+      opt.separator 'miga cmd \'echo $MIGA\''
+      opt.separator ''
+      opt.on(
+        '-o', '--stdout FILE',
+        'Save STDOUT to this file instead of displaying it'
+      ) { |v| cli[:stdout] = v }
+      opt.on(
+        '-e', '--stderr FILE',
+        'Save STDERR to this file instead of displaying it'
+      ) { |v| cli[:stderr] = v }
+      opt.on(
+        '--err2out',
+        'Combine STDERR and STDOUT into one single channel (STDOUT)'
+      ) { |v| cli[:err2out] = v }
+      opt.on(
+        '--show-cmd',
+        'Show exact command being launched before running it'
+      ) { |v| cli[:show_cmd] = v }
+      opt.on(
+        '--dry',
+        'Prepare the command but stop short of executing it',
+        'Useful in combination with --show-cmd; it always exits with code 1'
+      ) { |v| cli[:dry] = v }
+    end
+  end
+
+  def perform
+    cli.files
+    cli.say 'Running command:'
+    cmd = cli.files.size == 1 ? cli.files[0] : cli.files
+    cli.say cmd
+    status = MiGA::MiGA.run_cmd(cmd, cli.to_h)
+    cli.say 'Exit status: %s' % status
+    unless status&.success?
+      exit(status.nil? ? 1 : status.exitstatus)
+    end
+  end
+end

data/lib/miga/cli/base.rb

@@ -44,6 +44,7 @@ module MiGA::Cli::Base
     date:        'Return the current date in standard MiGA format',
     console:     'Open an IRB console with MiGA',
     env:         'Shell code to load MiGA environment',
+    cmd:         'Run a shell command within the MiGA environment',
     # Taxonomy
     tax_set:     'Register taxonomic information for datasets',
     tax_test:    'Return test of taxonomic distributions for query datasets',

data/lib/miga/cli/opt_helper.rb

@@ -9,7 +9,7 @@ module MiGA::Cli::OptHelper
     usage = "Usage: miga #{action.name}"
     usage += ' {operation}' if expect_operation
     usage += ' [options]'
-    usage += ' {FILES...}' if expect_files
+    usage += " {#{files_label || 'FILES'}...}" if expect_files
     opt.banner = "\n#{task_description}\n\n#{usage}\n"
     opt.separator ''
   end

data/lib/miga/cli.rb

@@ -34,6 +34,10 @@ class MiGA::Cli < MiGA::MiGA
   # If files are expected after the parameters, a boolean
   attr_accessor :expect_files
 
+  ##
+  # Label used in the usage instead of FILES if +#expect_files = true+
+  attr_accessor :files_label
+
   ##
   # Files passed after all other options, if +#expect_files = true+
   attr_accessor :files
@@ -145,7 +149,7 @@ class MiGA::Cli < MiGA::MiGA
   ##
   # Set default values in the Hash +hsh+
   def defaults=(hsh)
-    hsh.each { |k, v| @defaults[k] = v }
+    hsh.each { |k, v| @defaults[k.to_sym] = v }
   end
 
   ##
@@ -161,6 +165,12 @@ class MiGA::Cli < MiGA::MiGA
     @data[k.to_sym] = v
   end
 
+  ##
+  # Return parsed and default values as a hash
+  def to_h
+    @defaults.merge(@data)
+  end
+
   ##
   # Redefine #action based on #task
   def reset_action

data/lib/miga/common/system_call.rb

@@ -18,7 +18,9 @@ module MiGA::Common::SystemCall
     out_io, spawn_opts[:out] = IO.pipe if opts[:return] == :output
     spawn_opts[:err] = [:child, :out] if opts[:err2out] && spawn_opts[:out]
     opts[:source] = MiGA::MiGA.rc_path if opts[:source] == :miga
-    if opts[:source] && File.exist?(opts[:source])
+    if opts[:source] == :miga_env
+      cmd = "eval \"$(#{File.join(root_path, 'bin', 'miga').shellescape} env)\" && #{cmd}"
+    elsif opts[:source] && File.exist?(opts[:source])
       cmd = ". #{opts[:source].shellescape} && #{cmd}"
     end
 
@@ -76,7 +78,8 @@ module MiGA::Common::SystemCall
   # - err2out: Redirect STDERR to STDOUT
   # - env: Environmental variables as a Hash, keys and values must be strings
   # - source: A file to be sourced before running, or the Symbol +:miga+ to
-  #   source the MiGA configuration file
+  #   source the MiGA configuration file, or the Symbol +:miga_env+ to run
+  #   `eval $(miga env)` beforehand instead
   def run_cmd_opts(opts = {})
     {
       stdout: nil,

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 17, 1].freeze
+  VERSION = [1.3, 18, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 7, 11)
+  VERSION_DATE = Date.new(2024, 7, 12)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.17.1
+  version: 1.3.18.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-07-11 00:00:00.000000000 Z
+date: 2024-07-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -177,6 +177,7 @@ files:
 - lib/miga/cli/action/browse/style.css
 - lib/miga/cli/action/browse/summary.html
 - lib/miga/cli/action/classify_wf.rb
+- lib/miga/cli/action/cmd.rb
 - lib/miga/cli/action/console.rb
 - lib/miga/cli/action/daemon.rb
 - lib/miga/cli/action/date.rb