miga-base 0.7.16.5 → 0.7.16.11

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 4d2acaa97a065024d8031dcfcaaba3ac067a0f8fd76ad48230c8f2614310bcf5
+  metadata.gz: 7a5ac8da23d463724b4c9d056fee6d8a2ec19fbb7c5734d68c834ccd1e654bb8
+  data.tar.gz: 46c0a01f19e30edf4af734fedb5e8c0decf848cf2cfd3a40a8a19772d7040618
 SHA512:
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-  data.tar.gz: 9c0dbc607c231304b414e0442630f8cfb9ad2ab14e93b8a12d30f9aead5f1abe8c98dd2fe242a635efb1edd2d0f5ac194e6a954724c6651c04c851948a981fe2
+  metadata.gz: 4c36c082efdc4aabe6e6af023517029b718e9658c3fa34b2f9734793b79c6a6676d761e1efd03aa9e1ee91393c1f34747a49add8608fcd0d67268a83acd3d50a
+  data.tar.gz: 9137f435f69e0cad7485eca2aa595b1063f8cc31752bd3497e041c7e891c5f0606c1c5bc29bc654d276f6c4a25227ac81a566a46a240c3a011b3de74b260ea34

data/bin/miga

@@ -4,7 +4,10 @@
 # @license Artistic-2.0
 
 $LOAD_PATH.push File.expand_path('../../lib', __FILE__)
+$LOAD_PATH.push File.expand_path('../../lib', File.realpath(__FILE__))
+
 require 'miga'
 require 'miga/cli'
 
-MiGA::Cli.new(ARGV).launch
+MiGA::Cli.new(ARGV).launch(true)
+

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

@@ -73,6 +73,7 @@ class MiGA::Cli::Action::Daemon < MiGA::Cli::Action
   end
 
   def perform
+    cli.operation or raise 'Please specify a daemon operation'
     p = cli.load_project
     d = MiGA::Daemon.new(p, cli[:json])
     dopts = %i[latency maxjobs nodelist ppn shutdown_when_done]

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

@@ -8,7 +8,7 @@ class MiGA::Cli::Action::Run < MiGA::Cli::Action
   def parse_cli
     cli.defaults = { try_load: false, thr: 1, env: false }
     cli.parse do |opt|
-      cli.opt_object(opt, [:project, :dataset_opt, :result])
+      cli.opt_object(opt, [:project, :dataset_opt, :result_opt])
       opt.on(
         '-t', '--threads INT', Integer,
         "Threads to use in the local run (by default: #{cli[:thr]})"
@@ -37,12 +37,18 @@ class MiGA::Cli::Action::Run < MiGA::Cli::Action
       cli[:thr] ||= ENV['CORES'].to_i unless ENV['CORES'].nil?
       cli[:result] = File.basename(cli[:result].to_s, '.bash').to_sym
     end
+    %i[project dataset result].each do |i|
+      cli[i] = nil if cli[i].nil? || cli[i].empty?
+    end
 
     # Unset dataset if the requested result is for projects
     if (MiGA::Project.RESULT_DIRS.keys + [:p]).include? cli[:result]
       cli[:dataset] = nil
     end
 
+    # Use virtual result if not explicitly passed
+    cli[:result] ||= cli[:dataset] ? :d : :p
+
     # Load project
     p = cli.load_project
 

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

@@ -184,7 +184,7 @@ module MiGA::Cli::Action::Wf
   def call_cli(cmd)
     cmd << '-v' if cli[:verbose]
     MiGA::MiGA.DEBUG "Cli::Action::Wf.call_cli #{cmd}"
-    MiGA::Cli.new(cmd.map(&:to_s)).launch
+    MiGA::Cli.new(cmd.map(&:to_s)).launch(true)
   end
 
   def run_daemon

data/lib/miga/cli/opt_helper.rb

@@ -56,10 +56,11 @@ module MiGA::Cli::OptHelper
   # - :project_type To allow (optionally) a type of project
   # - :project_type_req To require a type of project
   # - :result To require a type of project or dataset result
+  # - :result_opt To allow (optionally) a type of result
   # - :result_dataset To require a type of dataset result
   # - :result_project To require a type of project result
-  # The options :result, :result_dataset, and :result_project are mutually
-  # exclusive
+  # The options :result, :result_opt, :result_dataset, and :result_project
+  # are mutually exclusive
   def opt_object(opt, what = [:project, :dataset])
     what.each do |w|
       case w
@@ -82,10 +83,10 @@ module MiGA::Cli::OptHelper
           "#{req}Type of #{obj}. Recognized types include:",
           *klass.KNOWN_TYPES.map { |k, v| "~ #{k}: #{v[:description]}" }
         ) { |v| self[:type] = v.downcase.to_sym }
-      when :result
+      when :result, :result_opt
         opt.on(
           '-r', '--result STRING',
-          '(Mandatory) Name of the result',
+          "#{"(Mandatory) " if w == :result}Name of the result",
           'Recognized names for dataset-specific results include:',
           *MiGA::Dataset.RESULT_DIRS.keys.map { |n| " ~ #{n}" },
           'Recognized names for project-wide results include:',

data/lib/miga/daemon.rb

@@ -309,11 +309,13 @@ class MiGA::Daemon < MiGA::MiGA
       job[:hostk] = hostk
       job[:cmd] = job[:cmd].miga_variables(host: nodelist[hostk])
       job[:pid] = spawn job[:cmd]
-      Process.detach job[:pid] unless [nil, '', 0].include?(job[:pid])
+      MiGA::MiGA.DEBUG "Detaching PID: #{job[:pid]}"
+      Process.detach(job[:pid]) unless [nil, '', 0].include?(job[:pid])
     when 'bash'
       # Local job
       job[:pid] = spawn job[:cmd]
-      Process.detach job[:pid] unless [nil, '', 0].include?(job[:pid])
+      MiGA::MiGA.DEBUG "Detaching PID: #{job[:pid]}"
+      Process.detach(job[:pid]) unless [nil, '', 0].include?(job[:pid])
     else
       # Schedule cluster job (qsub, msub, slurm)
       job[:pid] = `#{job[:cmd]}`.chomp

data/lib/miga/remote_dataset.rb

@@ -156,10 +156,12 @@ class MiGA::RemoteDataset < MiGA::MiGA
     return nil unless metadata[:ncbi_asm]
 
     ncbi_asm_id = self.class.ncbi_asm_acc2id metadata[:ncbi_asm]
-    doc = MiGA::Json.parse(
-      self.class.download(:ncbi_summary, :assembly, ncbi_asm_id, :json),
-      symbolize: false, contents: true
-    )
+    txt = nil
+    3.times do
+      txt = self.class.download(:ncbi_summary, :assembly, ncbi_asm_id, :json)
+      txt.empty? ? sleep(1) : break
+    end
+    doc = MiGA::Json.parse(txt, symbolize: false, contents: true)
     @_ncbi_asm_json_doc = doc['result'][ doc['result']['uids'].first ]
   end
 

data/lib/miga/version.rb

@@ -8,7 +8,7 @@ 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 = [0.7, 16, 5]
+  VERSION = [0.7, 16, 11]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 11, 2)
+  VERSION_DATE = Date.new(2020, 12, 10)
 
   ##
   # Reference of MiGA.

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.16.5
+  version: 0.7.16.11
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-11-02 00:00:00.000000000 Z
+date: 2020-12-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons