ood_core 0.10.0 → 0.11.1

checksums.yaml

@@ -1,7 +1,7 @@
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+SHA256:
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data/.travis.yml

@@ -1,8 +1,8 @@
 sudo: false
 language: ruby
 rvm:
-  - 2.4.1
-before_install: gem install bundler -v 1.7.8
+  - 2.5.5
+before_install: gem install bundler -v '~> 1.17'
 notifications:
   email:
     on_success: never

data/CHANGELOG.md

@@ -6,6 +6,29 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+
+## [0.11.1] - 2012-03-18
+### Changed
+- Only the version changed. Had to republish to rubygems.org
+
+## [0.11.0] - 2012-03-18
+### Added
+- Added directive prefixes to each adapter (e.g. `#QSUB`) ([#161](https://github.com/OSC/ood_core/issues/161))
+- LHA supports `submit_host` field in native ([#164](https://github.com/OSC/ood_core/issues/164))
+- Cluster files can be yaml or yml extensions ([#171](https://github.com/OSC/ood_core/issues/171))
+- Users can add a flag `OOD_JOB_NAME_ILLEGAL_CHARS` to sanitize job names ([#183](https://github.com/OSC/ood_core/issues/183)
+
+### Changed
+- Simplified job array parsing ([#144](https://github.com/OSC/ood_core/issues/144))
+
+### Fixed
+- Issue where environment variables were not properly exported to the job ([#158](https://github.com/OSC/ood_core/issues/158))
+- Parsing bad cluster files ([#150](https://github.com/OSC/ood_core/issues/150) and [#178](https://github.com/OSC/ood_core/issues/178))
+- netcat is no longer a hard dependency. Now lsof, python and bash can be used ([153](https://github.com/OSC/ood_core/issues/153))
+- GE crash when nil config file was given ([#175](https://github.com/OSC/ood_core/issues/175))
+- GE sometimes reported incorrect core count ([#168](https://github.com/OSC/ood_core/issues/168))
+
+
 ## [0.10.0] - 2019-11-05
 ### Added
 - Added an adapter for submitting work on Linux hosted systems without using a scheduler
@@ -196,7 +219,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### Added
 - Initial release!
 
-[Unreleased]: https://github.com/OSC/ood_core/compare/v0.10.0...HEAD
+[Unreleased]: https://github.com/OSC/ood_core/compare/v0.11.1...HEAD
+[0.11.1]: https://github.com/OSC/ood_core/compare/v0.11.0...v0.11.1
+[0.11.0]: https://github.com/OSC/ood_core/compare/v0.10.0...v0.11.0
 [0.10.0]: https://github.com/OSC/ood_core/compare/v0.9.3...v0.10.0
 [0.9.3]: https://github.com/OSC/ood_core/compare/v0.9.2...v0.9.3
 [0.9.2]: https://github.com/OSC/ood_core/compare/v0.9.1...v0.9.2

data/lib/ood_core.rb

@@ -2,6 +2,7 @@ require "ood_core/version"
 require "ood_core/errors"
 require "ood_core/cluster"
 require "ood_core/clusters"
+require "ood_core/invalid_cluster"
 
 # The main namespace for ood_core
 module OodCore

data/lib/ood_core/batch_connect/template.rb

@@ -117,11 +117,47 @@ module OodCore
                 }
                 export -f random_number
 
+                port_used_python() {
+                  python -c "import socket; socket.socket().connect(('$1',$2))" >/dev/null 2>&1
+                }
+
+                port_used_python3() {
+                  python3 -c "import socket; socket.socket().connect(('$1',$2))" >/dev/null 2>&1
+                }
+
+                port_used_nc(){
+                  nc -w 2 "$1" "$2" < /dev/null > /dev/null 2>&1
+                }
+
+                port_used_lsof(){
+                  lsof -i :"$2" >/dev/null 2>&1
+                }
+
+                port_used_bash(){
+                  local bash_supported=$(strings /bin/bash 2>/dev/null | grep tcp)
+                  if [ "$bash_supported" == "/dev/tcp/*/*" ]; then
+                    (: < /dev/tcp/$1/$2) >/dev/null 2>&1
+                  else
+                    return 127
+                  fi
+                }
+
                 # Check if port $1 is in use
                 port_used () {
                   local port="${1#*:}"
                   local host=$((expr "${1}" : '\\(.*\\):' || echo "localhost") | awk 'END{print $NF}')
-                  nc -w 2 "${host}" "${port}" < /dev/null &> /dev/null
+                  local port_strategies=(port_used_nc port_used_lsof port_used_bash port_used_python port_used_python3)
+
+                  for strategy in ${port_strategies[@]};
+                  do
+                    $strategy $host $port
+                    status=$?
+                    if [[ "$status" == "0" ]] || [[ "$status" == "1" ]]; then
+                      return $status
+                    fi
+                  done
+
+                  return 127
                 }
                 export -f port_used
 
@@ -143,8 +179,14 @@ module OodCore
                   local port="${1}"
                   local time="${2:-30}"
                   for ((i=1; i<=time*2; i++)); do
-                    if port_used "${port}"; then
+                    port_used "${port}"
+                    port_status=$?
+                    if [ "$port_status" == "0" ]; then
                       return 0
+                    elif [ "$port_status" == "127" ]; then
+                       echo "commands to find port were either not found or inaccessible."
+                       echo "command options are lsof, nc, bash's /dev/tcp, or python (or python3) with socket lib."
+                       return 127
                     fi
                     sleep 0.5
                   done

data/lib/ood_core/cluster.rb

@@ -28,6 +28,10 @@ module OodCore
     # @return [Hash] the acls configuration
     attr_reader :acls_config
 
+    # The errors encountered with configuring this cluster
+    # @return Array<String> the errors
+    attr_reader :errors
+
     # @param cluster [#to_h] the cluster object
     # @option cluster [#to_sym] :id The cluster id
     # @option cluster [#to_h] :metadata ({}) The cluster's metadata
@@ -39,6 +43,8 @@ module OodCore
     #   against
     # @option cluster [#to_h] :batch_connect ({}) Configuration for batch
     #   connect templates
+    # @option cluster [#to_a] :errors ([]) List of configuration errors
+    #
     def initialize(cluster)
       c = cluster.to_h.symbolize_keys
 
@@ -52,6 +58,9 @@ module OodCore
       @custom_config   = c.fetch(:custom, {})  .to_h.symbolize_keys
       @acls_config     = c.fetch(:acls, [])    .map(&:to_h)
       @batch_connect_config = c.fetch(:batch_connect, {}).to_h.symbolize_keys
+
+      # side affects from object creation and validation
+      @errors          = c.fetch(:errors, [])  .to_a
     end
 
     # Metadata that provides extra information about this cluster
@@ -159,6 +168,12 @@ module OodCore
       }
     end
 
+    # This cluster is always valid
+    # @return true
+    def valid?
+      return true
+    end
+
     private
       # Build acl adapter objects from array
       def build_acls(ary)

data/lib/ood_core/clusters.rb

@@ -21,16 +21,30 @@ module OodCore
         if config.file?
           if config.readable?
             CONFIG_VERSION.any? do |version|
-              YAML.safe_load(config.read).fetch(version, {}).each do |k, v|
-                clusters << Cluster.new(send("parse_#{version}", id: k, cluster: v))
+              begin
+                YAML.safe_load(config.read)&.fetch(version, {}).each do |k, v|
+                  clusters << Cluster.new(send("parse_#{version}", id: k, cluster: v))
+                end
+              rescue Psych::SyntaxError => e
+                clusters << InvalidCluster.new(
+                  id: config.basename(config.extname).to_s,
+                  errors: [ e.message.to_s ]
+                )
               end
             end
           end
         elsif config.directory?
-          Pathname.glob(config.join("*.yml")).select(&:file?).select(&:readable?).each do |p|
+          Pathname.glob([config.join("*.yml"), config.join("*.yaml")]).select(&:file?).select(&:readable?).each do |p|
             CONFIG_VERSION.any? do |version|
-              if cluster = YAML.safe_load(p.read).fetch(version, nil)
-                clusters << Cluster.new(send("parse_#{version}", id: p.basename(".yml").to_s, cluster: cluster))
+              begin
+                if cluster = YAML.safe_load(p.read)&.fetch(version, nil)
+                  clusters << Cluster.new(send("parse_#{version}", id: p.basename(p.extname()).to_s, cluster: cluster))
+                end
+              rescue Psych::SyntaxError => e
+                clusters << InvalidCluster.new(
+                  id: p.basename(p.extname).to_s,
+                  errors: [ e.message.to_s ]
+                )
               end
             end
           end

data/lib/ood_core/invalid_cluster.rb

@@ -0,0 +1,37 @@
+module OodCore
+  # A special case of an OodCore::Cluster where something went awry in the
+  # creation and it's invalid for some reason.  Users should only be able
+  # to rely on id and metadata.error_msg. All *allow? related functions
+  # false, meaning nothing is allowed.
+  class InvalidCluster < Cluster
+    # Jobs are not allowed
+    # @return false
+    def login_allow?
+      false
+    end
+
+    # Jobs are not allowed
+    # @return false
+    def job_allow?
+      false
+    end
+
+    # Custom features are not allowed
+    # @return false
+    def custom_allow?(_)
+      false
+    end
+
+    # This cluster is not allowed to be used
+    # @return false
+    def allow?
+      false
+    end
+
+    # This cluster is never valid
+    # @return false
+    def valid?
+      return false
+    end
+  end
+end

data/lib/ood_core/job/adapter.rb

@@ -36,7 +36,7 @@ module OodCore
       # Retrieve info for all jobs from the resource manager
       # @abstract Subclass is expected to implement {#info_all}
       # @raise [NotImplementedError] if subclass did not define {#info_all}
-      # @param attrs [Array<symbol>] defaults to nil (and all attrs are provided) 
+      # @param attrs [Array<symbol>] defaults to nil (and all attrs are provided)
       #   This array specifies only attrs you want, in addition to id and status.
       #   If an array, the Info object that is returned to you is not guarenteed
       #   to have a value for any attr besides the ones specified and id and status.
@@ -51,7 +51,7 @@ module OodCore
       # Retrieve info for all jobs for a given owner or owners from the
       # resource manager
       # @param owner [#to_s, Array<#to_s>] the owner(s) of the jobs
-      # @param attrs [Array<symbol>] defaults to nil (and all attrs are provided) 
+      # @param attrs [Array<symbol>] defaults to nil (and all attrs are provided)
       #   This array specifies only attrs you want, in addition to id and status.
       #   If an array, the Info object that is returned to you is not guarenteed
       #   to have a value for any attr besides the ones specified and id and status.
@@ -69,7 +69,7 @@ module OodCore
       end
 
       # Iterate over each job Info object
-      # @param attrs [Array<symbol>] defaults to nil (and all attrs are provided) 
+      # @param attrs [Array<symbol>] defaults to nil (and all attrs are provided)
       #   This array specifies only attrs you want, in addition to id and status.
       #   If an array, the Info object that is returned to you is not guarenteed
       #   to have a value for any attr besides the ones specified and id and status.
@@ -88,7 +88,7 @@ module OodCore
 
       # Iterate over each job Info object
       # @param owner [#to_s, Array<#to_s>] the owner(s) of the jobs
-      # @param attrs [Array<symbol>] defaults to nil (and all attrs are provided) 
+      # @param attrs [Array<symbol>] defaults to nil (and all attrs are provided)
       #   This array specifies only attrs you want, in addition to id and status.
       #   If an array, the Info object that is returned to you is not guarenteed
       #   to have a value for any attr besides the ones specified and id and status.
@@ -157,6 +157,37 @@ module OodCore
       def delete(id)
         raise NotImplementedError, "subclass did not define #delete"
       end
+
+      # Return the scheduler-specific directive prefix
+      #
+      # Examples of directive prefixes include #QSUB, #BSUB and allow placing what would
+      # otherwise be command line options inside the job launch script.
+      #
+      # The method should return nil if the adapter does not support prefixes
+      #
+      # @abstract Subclass is expected to implement {#directive_prefix}
+      # @raise [NotImplementedError] if subclass did not defined {#directive_prefix}
+      # @return [String]
+      def directive_prefix
+        raise NotImplementedError, "subclass did not define #directive_prefix"
+      end
+
+      # Replace illegal chars in job name with a dash
+      #
+      # @return [String] job name with dashes replacing illegal chars
+      def sanitize_job_name(job_name)
+        # escape ^ and omit -
+        chars = job_name_illegal_chars.to_s.gsub("^", "\\^").gsub("-", "")
+        job_name.tr(chars, "-")
+      end
+
+      # Illegal chars that should not be used in a job name
+      # A dash is assumed to be legal in job names in all batch schedulers
+      #
+      # @return [String] string of chars
+      def job_name_illegal_chars
+        ENV["OOD_JOB_NAME_ILLEGAL_CHARS"].to_s
+      end
     end
   end
 end

data/lib/ood_core/job/adapters/drmaa.rb

@@ -13,7 +13,7 @@
 #  The contents of this file are subject to the Sun Industry Standards
 #  Source License Version 1.2 (the "License"); You may not use this file
 #  except in compliance with the License. You may obtain a copy of the
-#  License at http://gridengine.sunsource.net/Gridengine_SISSL_license.html
+#  License at http://gridscheduler.sourceforge.net/Gridengine_SISSL_license.html
 #
 #  Software provided under this License is provided on an "AS IS" basis,
 #  WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,

data/lib/ood_core/job/adapters/linux_host.rb

@@ -201,6 +201,10 @@ module OodCore
           raise JobAdapterError, e.message
         end
 
+        def directive_prefix
+          nil
+        end
+
         private
 
         def host_permitted?(destination_host)

data/lib/ood_core/job/adapters/linux_host/launcher.rb

@@ -11,7 +11,7 @@ require 'time'
 class OodCore::Job::Adapters::LinuxHost::Launcher
   attr_reader :contain, :debug, :site_timeout, :session_name_label, :singularity_bin,
     :site_singularity_bindpath, :default_singularity_image, :ssh_hosts,
-    :strict_host_checking, :submit_host, :tmux_bin, :username
+    :strict_host_checking, :tmux_bin, :username
   # The root exception class that all LinuxHost adapter-specific exceptions inherit
   # from
   class Error < StandardError; end
@@ -57,7 +57,7 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
   # @param hostname [#to_s] The hostname to submit the work to
   # @param script [OodCore::Job::Script] The script object defining the work
   def start_remote_session(script)
-    cmd = ssh_cmd(submit_host)
+    cmd = ssh_cmd(submit_host(script))
 
     session_name = unique_session_name
     output = call(*cmd, stdin: wrapped_script(script, session_name))
@@ -98,6 +98,14 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
     }
   end
 
+  def submit_host(script = nil)
+    if script && script.native && script.native['submit_host_override']
+      script.native['submit_host_override']
+    else
+      @submit_host
+    end
+  end
+
   private
 
   # Call a forked Slurm command for a given cluster

data/lib/ood_core/job/adapters/lsf.rb

@@ -167,6 +167,10 @@ module OodCore
           raise JobAdapterError, e.message
         end
 
+        def directive_prefix
+          '#BSUB'
+        end
+
         private
           # Determine state from LSF state code
           def get_state(st)

data/lib/ood_core/job/adapters/lsf/helper.rb

@@ -92,6 +92,15 @@ class OodCore::Job::Adapters::Lsf::Helper
     args += ["-W", (script.wall_time / 60).to_i] unless script.wall_time.nil?
     args += ["-L", script.shell_path.to_s] unless script.shell_path.nil?
 
+    # environment
+    env = script.job_environment || {}
+    # To preserve pre-existing behavior we only act when true or false, when nil we do nothing
+    if script.copy_environment?
+      args += ["-env", (["all"] + env.keys).join(",")]
+    elsif script.copy_environment? == false
+      args += ["-env", (["none"] + env.keys).join(",")]
+    end
+
     # input and output files
     args += ["-i", script.input_path] unless script.input_path.nil?
     args += ["-o", script.output_path] unless script.output_path.nil?
@@ -104,9 +113,6 @@ class OodCore::Job::Adapters::Lsf::Helper
 
     args += script.native unless script.native.nil?
 
-    # environment
-    env = script.job_environment || {}
-
     {args: args, env: env}
   end
 end

data/lib/ood_core/job/adapters/pbspro.rb

@@ -261,6 +261,7 @@ module OodCore
           # Set environment variables
           envvars = script.job_environment.to_h
           args += ["-v", envvars.map{|k,v| "#{k}=#{v}"}.join(",")] unless envvars.empty?
+          args += ["-V"] if script.copy_environment?
 
           # If error_path is not specified we join stdout & stderr (as this
           # mimics what the other resource managers do)
@@ -397,6 +398,10 @@ module OodCore
           raise JobAdapterError, e.message unless /Unknown Job Id/ =~ e.message || /Job has finished/ =~ e.message
         end
 
+        def directive_prefix
+          '#PBS'
+        end
+
         private
           # Convert duration to seconds
           def duration_in_seconds(time)

data/lib/ood_core/job/adapters/sge.rb

@@ -157,6 +157,10 @@ module OodCore
         rescue Batch::Error => e
           raise JobAdapterError, e.message
         end
+
+        def directive_prefix
+          '#$'
+        end
       end
     end
   end

data/lib/ood_core/job/adapters/sge/batch.rb

@@ -33,8 +33,7 @@ class OodCore::Job::Adapters::Sge::Batch
   # @see Factory.build_sge
   def initialize(config)
     @cluster          = config.fetch(:cluster, nil)
-    @conf             = Pathname.new(config.fetch(:conf, nil))
-    @bin              = Pathname.new(config.fetch(:bin, nil))
+    @bin              = Pathname.new(config.fetch(:bin, nil).to_s)
     @sge_root         = Pathname.new(config[:sge_root] || ENV['SGE_ROOT'] || "/var/lib/gridengine")
     @bin_overrides    = config.fetch(:bin_overrides, {})
 

data/lib/ood_core/job/adapters/sge/helper.rb

@@ -20,6 +20,7 @@ class OodCore::Job::Adapters::Sge::Helper
     args += ['-h'] if script.submit_as_hold
     args += ['-r', 'yes'] if script.rerunnable
     script.job_environment.each_pair {|k, v| args += ['-v', "#{k.to_s}=#{v.to_s}"]} unless script.job_environment.nil?
+    args += ["-V"] if script.copy_environment?
 
     if script.workdir
       args += ['-wd', script.workdir]

data/lib/ood_core/job/adapters/sge/qstat_xml_j_r_listener.rb

@@ -27,13 +27,15 @@ class QstatXmlJRListener
     @parsed_job = {
       :tasks => [],
       :status => :queued,
-      :procs => 1,  # un-knowable from SGE qstat output
+      :procs => 1,
       :native => {}  # TODO: improve native attribute reporting
     }
     @current_text = nil
     @current_request = nil
 
     @processing_job_array_spec = false
+    @adding_slots = false
+
     @job_array_spec = {
       start: nil,
       stop: nil,
@@ -46,6 +48,8 @@ class QstatXmlJRListener
     case name
     when 'task_id_range'
       toggle_processing_array_spec
+    when 'JB_pe_range'
+      toggle_adding_slots
     end
   end
 
@@ -78,13 +82,16 @@ class QstatXmlJRListener
     when 'djob_info'
       finalize_parsed_job
     when 'RN_min'
-      set_job_array_piece(:start)
+      set_job_array_piece(:start) if @processing_job_array_spec
+      set_slots if @adding_slots
     when 'RN_max'
-      set_job_array_piece(:stop)
+      set_job_array_piece(:stop) if @processing_job_array_spec
     when 'RN_step'
-      set_job_array_piece(:step)
+      set_job_array_piece(:step) if @processing_job_array_spec
     when 'task_id_range'
       toggle_processing_array_spec
+    when 'JB_pe_range'
+      toggle_adding_slots
     end
   end
 
@@ -186,5 +193,13 @@ class QstatXmlJRListener
   def toggle_processing_array_spec
     @processing_job_array_spec = ! @processing_job_array_spec
   end
+
+  def toggle_adding_slots
+    @adding_slots = ! @adding_slots
+  end
+
+  def set_slots
+    @parsed_job[:procs] = @current_text.to_i
+  end
 end
 

data/lib/ood_core/job/adapters/slurm.rb

@@ -192,7 +192,7 @@ module OodCore
           # @return [String] the id of the job that was created
           def submit_string(str, args: [], env: {})
             args = args.map(&:to_s) + ["--parsable"]
-            env = {"SBATCH_EXPORT" => "NONE"}.merge env.each_with_object({}) { |(k, v), h| h[k.to_s] = v.to_s }
+            env = env.to_h.each_with_object({}) { |(k, v), h| h[k.to_s] = v.to_s }
             call("sbatch", *args, env: env, stdin: str.to_s).strip.split(";").first
           end
 
@@ -394,7 +394,10 @@ module OodCore
 
           # Set environment variables
           env = script.job_environment || {}
-          args += ["--export", script.job_environment.keys.join(",")] unless script.job_environment.nil? || script.job_environment.empty?
+          unless (script.job_environment.nil? || script.job_environment.empty?)
+            prefix = script.copy_environment? ? "ALL," : "NONE,"  # NONE if false or nil
+            args += ["--export", prefix + script.job_environment.keys.join(",")]
+          end
 
           # Set native options
           args += script.native if script.native
@@ -530,6 +533,10 @@ module OodCore
           raise JobAdapterError, e.message unless /Invalid job id specified/ =~ e.message
         end
 
+        def directive_prefix
+          '#SBATCH'
+        end
+
         private
           # Convert duration to seconds
           def duration_in_seconds(time)

data/lib/ood_core/job/adapters/torque.rb

@@ -155,6 +155,7 @@ module OodCore
             # Set environment variables
             env = script.job_environment.to_h
             args += ["-v", env.keys.join(",")] unless env.empty?
+            args += ["-V"] if script.copy_environment?
 
             # If error_path is not specified we join stdout & stderr (as this
             # mimics what the other resource managers do)
@@ -288,6 +289,10 @@ module OodCore
           raise JobAdapterError, e.message
         end
 
+        def directive_prefix
+          '#QSUB'
+        end
+
         private
           # Convert duration to seconds
           def duration_in_seconds(time)

data/lib/ood_core/job/array_ids.rb

@@ -10,68 +10,33 @@
 module OodCore
   module Job
     class ArrayIds
-      class Error < StandardError ; end
+      attr_reader :spec_string
 
-      attr_reader :ids
       def initialize(spec_string)
-        @ids = []
-        begin
-          parse_spec_string(spec_string) if spec_string
-        rescue Error
-        end
-      end
-
-      protected
-      def parse_spec_string(spec_string)
-        @ids = get_components(spec_string).map{
-          |component| process_component(component)
-        }.reduce(:+).sort
+        @spec_string = spec_string
       end
 
-      def get_components(spec_string)
-        base = discard_percent_modifier(spec_string)
-        raise Error unless base
-        base.split(',')
+      def ids
+        @ids ||= parse_spec_string(spec_string)
       end
 
-      # A few adapters use percent to define an arrays maximum number of
-      # simultaneous tasks. The percent is expected to come at the end.
-      def discard_percent_modifier(spec_string)
-        spec_string.split('%').first
-      end
+      protected
 
-      def process_component(component)
-        if is_range?(component)
-          get_range(component)
-        elsif numbers_valid?([component])
-          [ component.to_i ]
-        else
-          raise Error
+      def parse_spec_string(spec_string)
+        return [] unless spec_string
+
+        rx = /^(\d+)-?(\d+)?:?(\d+)?%?\d*$/
+        spec_string.split(',').reduce([]) do |ids, spec|
+          if rx =~ spec
+            start = ($1 || 1).to_i
+            finish = ($2 || start).to_i
+            step = ($3 || 1).to_i
+            ids.concat (start..finish).step(step).to_a
+          end
+
+          ids
         end
       end
-
-      def get_range(component)
-        raw_range, raw_step = component.split(':')
-        start, stop = raw_range.split('-')
-        raise Error unless numbers_valid?(
-          # Only include Step if it is not nil
-          [start, stop].tap { |a| a << raw_step if raw_step }
-        )
-        range = Range.new(start.to_i, stop.to_i)
-        step = raw_step.to_i
-        step = 1 if step == 0
-
-        range.step(step).to_a
-      end
-
-      def is_range?(component)
-        component.include?('-')
-      end
-
-      # Protect against Ruby's String#to_i returning 0 for arbitrary strings
-      def numbers_valid?(numbers)
-        numbers.all? { |str| /^[0-9]+$/ =~ str }
-      end
     end
   end
 end

data/lib/ood_core/job/script.rb

@@ -104,6 +104,11 @@ module OodCore
       # @return [Object, nil] native specifications
       attr_reader :native
 
+      # Flag whether the job should contain a copy of its calling environment
+      # @return [Boolean] copy environment
+      attr_reader :copy_environment
+      alias_method :copy_environment?, :copy_environment
+
       # @param content [#to_s] the script content
       # @param args [Array<#to_s>, nil] arguments supplied to script
       # @param submit_as_hold [Boolean, nil] whether job is held after submit
@@ -132,7 +137,8 @@ module OodCore
                      job_name: nil, shell_path: nil, input_path: nil,
                      output_path: nil, error_path: nil, reservation_id: nil,
                      queue_name: nil, priority: nil, start_time: nil,
-                     wall_time: nil, accounting_id: nil, job_array_request: nil, native: nil, **_)
+                     wall_time: nil, accounting_id: nil, job_array_request: nil,
+                     native: nil, copy_environment: nil, **_)
         @content = content.to_s
 
         @submit_as_hold      = submit_as_hold
@@ -157,6 +163,7 @@ module OodCore
         @accounting_id      = accounting_id     && accounting_id.to_s
         @job_array_request  = job_array_request && job_array_request.to_s
         @native             = native
+        @copy_environment   = (copy_environment.nil?) ? nil : !! copy_environment
       end
 
       # Convert object to hash
@@ -184,7 +191,8 @@ module OodCore
           wall_time:           wall_time,
           accounting_id:       accounting_id,
           job_array_request:   job_array_request,
-          native:              native
+          native:              native,
+          copy_environment:    copy_environment
         }
       end
 

data/lib/ood_core/version.rb

@@ -1,4 +1,4 @@
 module OodCore
   # The current version of {OodCore}
-  VERSION = "0.10.0"
+  VERSION = "0.11.1"
 end

data/ood_core.gemspec

@@ -25,8 +25,9 @@ Gem::Specification.new do |spec|
   spec.add_runtime_dependency "ood_support", "~> 0.0.2"
   spec.add_runtime_dependency "ffi", "~> 1.9", ">= 1.9.6"
   spec.add_development_dependency "bundler", "~> 1.7"
-  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rake", "~> 13.0.1"
   spec.add_development_dependency "rspec", "~> 3.0"
   spec.add_development_dependency "pry", "~> 0.10"
   spec.add_development_dependency "timecop", "~> 0.8"
+  spec.add_development_dependency "climate_control", "~> 0.2.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ood_core
 version: !ruby/object:Gem::Version
-  version: 0.10.0
+  version: 0.11.1
 platform: ruby
 authors:
 - Eric Franz
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-11-05 00:00:00.000000000 Z
+date: 2020-03-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ood_support
@@ -66,14 +66,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: 13.0.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: 13.0.1
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -116,6 +116,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: climate_control
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
 description: Open OnDemand core library that provides support for an HPC Center to
   globally define HPC services that web applications can then take advantage of.
 email:
@@ -147,6 +161,7 @@ files:
 - lib/ood_core/cluster.rb
 - lib/ood_core/clusters.rb
 - lib/ood_core/errors.rb
+- lib/ood_core/invalid_cluster.rb
 - lib/ood_core/job/adapter.rb
 - lib/ood_core/job/adapters/drmaa.rb
 - lib/ood_core/job/adapters/helper.rb
@@ -201,7 +216,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.11
+rubygems_version: 2.7.6.2
 signing_key: 
 specification_version: 4
 summary: Open OnDemand core library