miga-base 0.7.16.6 → 0.7.16.12

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: fcd30efdaa8cf3a8ae87b5cc658363c2d37c0beb3c13491595beb983b1629b32
-  data.tar.gz: '0441764548f4199a8f3df253c151dc856aa414f5a91d02126bcb893ee2fe6835'
+  metadata.gz: 1e89d0bc90eef4ca458fbc415cbeff6eaa6c2b07ee4df77268826ecfbe0720df
+  data.tar.gz: b082d83022262e82d309e8ff70f077fe28cebddacf5b85844547ed24a8a877f7
 SHA512:
-  metadata.gz: 18e829f1cb4141df9515565bd19af32e67b9920689a75dd4b5f2f5a79d0a5b7d86ea425f64e7702766e09a14c5b70af4d07ccb16df94aeef3ba4ade54e9506ab
-  data.tar.gz: 72ad22fd3386214825c463edc9232f2deeae24d06257a523f73592fd2d9496e452d192d10f37cf493b52a936578c3111a1a8801a78494688d51fc75b01e489f2
+  metadata.gz: fa0746c6173b1b7a504b6d40ed0a158ef647694970f9222aeeaa5465dcad73f4647894164d0edc823b54dce837410393ac61186a6b217ff5edacbfc81a01591d
+  data.tar.gz: b8411e7c9fb0f62de20e5a909dbf7b4c998bcb18aa4fa79fbe48dc128292f8983ce1dfae54d9e3082807449b6c5cf9d4a3bb913bc9dde77c1c2d4bab6aa8fe27

data/bin/miga

@@ -4,6 +4,8 @@
 # @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'
 

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

@@ -37,6 +37,9 @@ 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]

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/daemon.rb

@@ -92,8 +92,7 @@ class MiGA::Daemon < MiGA::MiGA
     flush!
     if (loop_i % 12).zero?
       purge!
-      # TEMPORARILY DISABLED:
-      # recalculate_status!
+      recalculate_status!
     end
     save_status
     sleep(latency)
@@ -102,8 +101,10 @@ class MiGA::Daemon < MiGA::MiGA
   end
 
   def recalculate_status!
-    say 'Recalculating status for all datasets'
-    project.each_dataset(&:recalculate_status)
+    say 'Recalculating status for all complete datasets'
+    project.each_dataset do |ds|
+      ds.recalculate_status if ds.status == :complete
+    end
   end
 
   ##
@@ -309,11 +310,13 @@ 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, 6]
+  VERSION = [0.7, 16, 12]
 
   ##
   # 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, 22)
+  VERSION_DATE = Date.new(2020, 12, 24)
 
   ##
   # Reference of MiGA.

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.16.6
+  version: 0.7.16.12
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-11-22 00:00:00.000000000 Z
+date: 2020-12-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons