scout-gear 10.7.8 → 10.7.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 68a4a6cd64e357c099695cee41af47fd35b2c3b78475ca90baf8e55078b224da
-  data.tar.gz: 289ed4ac91ec47e7c108c395df28cc3d0050668f5e59e9dc6cfa1ebc3e795c0f
+  metadata.gz: 6399697b155a59acc6b18d1767bfc8c062a9d354c650478f8a57a82946f3593d
+  data.tar.gz: 9fa7e065c8d9f56484e2a8e63bb215aafc28b032c6bcc95691d0a725855154a5
 SHA512:
-  metadata.gz: 70626145e7e3d51790384c594f8d6896b2a033007e76a9547aba74857fce9d0916f0a25d8b08424e90605af93800168b4ec339c1c73b47c7f6094aa545016667
-  data.tar.gz: d731d71fc54d2c95314fbb2f07cceda081e312b5bf270fa9b42ac4b842c51b32f7302070bc98f271ac5603a57d46158fd7cbd646e5c7eed6c233a016e0cad820
+  metadata.gz: ae10dd542865799ab9abfc453caf2833687bfd4b74df51c4a52144a3a59bda31c41ab48078c6e5eb6f22df4053974867a0e8b163dfb7b9e843008d21279534b5
+  data.tar.gz: 48054781097bf5be8f59f1331cb830db7dffa543d3034c96e3d64288bdd14cea91af104f73a70aecdd60ac4d8cf02760ef6b5e5b7fe18aa5609e52948322c0fa

data/.vimproject

@@ -131,7 +131,6 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
   }
   scout-gear.rb
   workflow-scout.rb
-  rbbt-scout.rb
   scout.rb
  }
  scout_commands=scout_commands filter="*"{

data/Rakefile

@@ -55,5 +55,4 @@ Rake::RDocTask.new do |rdoc|
   rdoc.title = "scout-gear #{version}"
   rdoc.rdoc_files.include('README*')
   rdoc.rdoc_files.include('lib/**/*.rb')
-  rdoc.rdoc_files.include('../modules/rbbt-util/lib/**/*.rb')
 end

data/VERSION

@@ -1 +1 @@
-10.7.8
+10.7.9

data/bin/scout

@@ -62,9 +62,8 @@ if _i = ARGV.index("--require")
   end
 end
 
-require 'scout-gear'
-
 require 'scout/simple_opt'
+require 'scout/log'
 
 options = SOPT.setup <<EOF
 Ruby bioinformatics toolkit
@@ -90,7 +89,10 @@ end
 
 if options[:log]
   Log.severity = options.delete(:log).to_i
+  require 'scout-gear'
 else
+  require 'scout-gear'
+
   global_severity = Log.get_level(Scout.etc.log_severity.read.strip) if Scout.etc.log_severity.exists?
   if ENV["SCOUT_LOG"]
     Log.severity = ENV["SCOUT_LOG"].to_i 

data/lib/scout/workflow/deployment/queue.rb

@@ -9,6 +9,7 @@ module Workflow
 
     if Open.directory?(file)
       clean_name = name2clean_name name
+      clean_name = nil if clean_name == Task::DEFAULT_NAME
       inputs = workflow.tasks[task].load_inputs(file)
       workflow.job(task, clean_name, inputs)
     else

data/lib/scout/workflow/step/inputs.rb

@@ -1,15 +1,13 @@
 class Step
   def save_inputs(inputs_dir)
     if clean_name != name
-      hash = name[clean_name.length..-1]
-      inputs_dir += hash
+      #hash = name[clean_name.length..-1]
+      #inputs_dir += hash
       Log.medium "Saving job inputs to: #{Log.fingerprint inputs_dir}"
       self.task.save_inputs(inputs_dir, provided_inputs)
-      inputs_dir
     else
       Log.medium "Saving no input job: #{Log.fingerprint inputs_dir}"
       Open.touch(inputs_dir)
-      inputs_dir
     end
   end
 end

data/lib/scout/workflow/task/inputs.rb

@@ -133,16 +133,19 @@ module Task
   end
 
   def save_inputs(directory, provided_inputs = {})
+    saved = []
     self.recursive_inputs.each_with_index do |p,i|
       name, type, desc, value, options = p
       next unless provided_inputs.include?(name)
-      value = provided_inputs[name]
 
+      saved << name
+
+      value = provided_inputs[name]
       Task.save_input(directory, name, type, value)
     end
+    saved
   end
 
-
   def self.load_input_from_file(filename, type, options = nil)
     if Open.exists?(filename) || filename = Dir.glob(File.join(filename + ".*")).first
       if filename.end_with?('.as_file')

data/scout-gear.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: scout-gear 10.7.8 ruby lib
+# stub: scout-gear 10.7.9 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "scout-gear".freeze
-  s.version = "10.7.8".freeze
+  s.version = "10.7.9".freeze
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Miguel Vazquez".freeze]
-  s.date = "2025-04-11"
+  s.date = "2025-04-16"
   s.description = "Scout gear: workflow, TSVs, persistence, entities, associations, and knowledge_bases.".freeze
   s.email = "mikisvaz@gmail.com".freeze
   s.executables = ["scout".freeze]
@@ -30,7 +30,6 @@ Gem::Specification.new do |s|
     "bin/scout",
     "doc/lib/scout/path.md",
     "doc/lib/scout/workflow/task.md",
-    "lib/rbbt-scout.rb",
     "lib/scout-gear.rb",
     "lib/scout.rb",
     "lib/scout/association.rb",
@@ -251,7 +250,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/mikisvaz/scout-gear".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "3.6.5".freeze
+  s.rubygems_version = "3.6.6".freeze
   s.summary = "basic gear for scouts".freeze
 
   s.specification_version = 4

data/scout_commands/resource/sync

@@ -15,6 +15,7 @@ Path map defaults to :user
 -h--help Print this help
 -s--source* Host of source path
 -t--target* Host of target path
+-d--delete Delete source files
 EOF
 if options[:help]
   if defined? scout_usage

data/scout_commands/workflow/process

@@ -1,6 +1,7 @@
 #!/usr/bin/env ruby
 
 require 'scout'
+require 'scout/aws/s3'
 require 'scout/workflow/deployment/queue'
 require 'scout/workflow/deployment/orchestrator'
 
@@ -17,6 +18,7 @@ $ #{$0} [<options>] ([<workflow>] [<task>] [<name>] | <filename>)
 --continuous Process continuously
 --produce_timer* Produce timer for sleeping
 --produce_cpus* Cpus to use concurrently producing jobs
+-r--requires* Require files
 EOF
 if options[:help]
   if defined? scout_usage
@@ -26,7 +28,13 @@ if options[:help]
   end
   exit 0
 end
-list, continuous = IndiferentHash.process_options options, :list, :continuous
+list, continuous, requires = IndiferentHash.process_options options, :list, :continuous, :requires
+
+if requires
+  requires.split(",").each do |file|
+    require file
+  end
+end
 
 queue_dir = Scout.var.queue
 
@@ -34,7 +42,7 @@ class TrayAgain < Exception; end
 
 begin
   if ARGV.empty?
-    files = queue_dir.glob("*/*/*")
+    files = queue_dir.glob_all("*/*/*")
     if list
       puts files * "\n"
       exit
@@ -49,12 +57,12 @@ begin
         exit
 
       else
-        files = queue_dir.glob("#{workflow}/*/*")
+        files = queue_dir.glob_all("#{workflow}/*/*")
       end
     elsif name.nil?
-      files = queue_dir.glob("#{workflow}/#{task}/*")
+      files = queue_dir.glob_all("#{workflow}/#{task}/*")
     else
-      files = queue_dir.glob("#{workflow}/#{task}/#{name}*")
+      files = queue_dir.glob_all("#{workflow}/#{task}/#{name}*")
     end
   end
 
@@ -71,7 +79,11 @@ begin
 
   Workflow.job_cache.clear
 
-  if continuous
+  if files.any?
+    Log.debug "Re-checking for new jobs"
+    sleep 1
+    raise Workflow::Orchestrator::NoWork
+  elsif continuous
     Log.debug "Continuous processing"
     sleep 1
     raise Workflow::Orchestrator::NoWork

data/scout_commands/workflow/task

@@ -107,8 +107,9 @@ else
   case deploy
   when "queue"
     if ! job.done?
-      save_inputs = Scout.var.queue[workflow.to_s][task_name][job.clean_name].find
-      puts job.save_inputs(save_inputs)
+      save_inputs = Scout.var.queue[workflow.to_s][task_name][job.name].find
+      job.save_inputs(save_inputs)
+      puts save_inputs
       exit
     end
   when "serial"

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: scout-gear
 version: !ruby/object:Gem::Version
-  version: 10.7.8
+  version: 10.7.9
 platform: ruby
 authors:
 - Miguel Vazquez
 bindir: bin
 cert_chain: []
-date: 2025-04-11 00:00:00.000000000 Z
+date: 2025-04-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: scout-essentials
@@ -99,7 +99,6 @@ files:
 - bin/scout
 - doc/lib/scout/path.md
 - doc/lib/scout/workflow/task.md
-- lib/rbbt-scout.rb
 - lib/scout-gear.rb
 - lib/scout.rb
 - lib/scout/association.rb
@@ -335,7 +334,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.6.5
+rubygems_version: 3.6.6
 specification_version: 4
 summary: basic gear for scouts
 test_files: []

data/lib/rbbt-scout.rb

@@ -1,8 +0,0 @@
-$LOAD_PATH.unshift File.join(__dir__, '../modules/rbbt-util/lib')
-module Scout
-  extend Resource
-  self.path_maps = Path.path_maps.merge(:rbbt_lib => File.expand_path(File.join(__dir__, '../modules/rbbt-util/', '{TOPLEVEL}','{SUBPATH}')))
-end
-Rbbt = Scout
-
-Resource.set_software_env Rbbt.software