ood_core 0.21.0 → 0.22.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 3d438089095a42b66f4edee0d3a6afe683e1d87ebb865d908120b977733c6169
+  metadata.gz: b8700bb802df78b66c3bb58ec5464a7f5e54a4dc3ebdc978f9816b8b5e5f7373
+  data.tar.gz: 1e2b4ca05369c8072afe8d1069679a8f2744cdcb3ed766924a778e78af65afa2
 SHA512:
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-  data.tar.gz: a3caaaf21cc6ee4bd68fea96817f58b61592c93993813f69333e8acdce95df8b0d8b49b169000a50ddcb7bcd6031d151272882e5dc3cd02e09a0595ef1d31116
+  metadata.gz: a40fc234d2be728b697b9b68884b2286ac68e63ed36eeaa4a48487af99c262fdc1f9b3010554f9e369555734c6d2c0693ca54bc2308c5817f424ec4032759563
+  data.tar.gz: 5215f5c924002bfdc40576560898cae49b9a9750ff8d11c87d1e43cd43d0e86327a511ee97eea765a20f8ce6d6903acfaece7b26ad8e7733fd1d3f985b8a97e2

data/.gitignore

@@ -50,4 +50,8 @@ Gemfile.lock
 .rvmrc
 
 # SSHFS temp files
-._*
+._*
+
+# docs are only held in the gh-pages branch
+/docs/*
+!/docs/.keep

data/CHANGELOG.md

@@ -7,6 +7,18 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
+## [0.22.0] - 10-31-2022
+
+### Added
+
+- Added the `vnc_container` batch connect template in [774](https://github.com/OSC/ood_core/pull/774).
+- https://osc.github.io/ood_core is now updated on every commit to master in [765](https://github.com/OSC/ood_core/pull/765).
+
+### Fixed
+
+- Kubernetes can now read mulitple secrets in [778](https://github.com/OSC/ood_core/pull/778).
+- PBSPro correctly reads usernames with periods in them in [780](https://github.com/OSC/ood_core/pull/780).
+
 ## [0.21.0] - 08-01-2022
 
 ### Added
@@ -443,7 +455,8 @@ Functionally the same as [0.17.3] but with some CI updates.
 ### Added
 - Initial release!
 
-[Unreleased]: https://github.com/OSC/ood_core/compare/v0.21.0...HEAD
+[Unreleased]: https://github.com/OSC/ood_core/compare/v0.22.0...HEAD
+[0.22.0]: https://github.com/OSC/ood_core/compare/v0.21.0...v0.22.0
 [0.21.0]: https://github.com/OSC/ood_core/compare/v0.20.2...v0.21.0
 [0.20.2]: https://github.com/OSC/ood_core/compare/v0.20.1...v0.20.2
 [0.20.1]: https://github.com/OSC/ood_core/compare/v0.20.0...v0.20.1

data/lib/ood_core/batch_connect/templates/vnc_container.rb

@@ -0,0 +1,252 @@
+require "ood_core/refinements/hash_extensions"
+require "securerandom"
+
+module OodCore
+  module BatchConnect
+    class Factory
+      using Refinements::HashExtensions
+
+      # Build the VNC template from a configuration
+      # @param config [#to_h] the configuration for the batch connect template
+      def self.build_vnc_container(config)
+        context = config.to_h.symbolize_keys.reject { |k, _| k == :template }
+        
+        unless context.key?(:container_path)
+          raise JobAdapterError, "You are missing the configuration 'container_path' for a vnc_container template."
+        end
+
+        Templates::VNC_Container.new(context)
+      end
+    end
+
+    module Templates
+      # A batch connect template that starts up a VNC server within a batch job
+      class VNC_Container < Template
+        # @param context [#to_h] the context used to render the template
+        # @option context [#to_sym, Array<#to_sym>] :conn_params ([]) A list of
+        #   connection parameters added to the connection file (`:host`,
+        #   `:port`, `:password`, `:spassword`, `:display` and `:websocket`
+        #   will always exist)
+        # @option context [#to_s] :websockify_cmd
+        #   ("${WEBSOCKIFY_CMD:-/opt/websockify/run}") the path to the
+        #   websockify script (assumes you don't modify `:after_script`)
+        # @option context [#to_s] :vnc_log ("vnc.log") path to vnc server log
+        #   file (assumes you don't modify `:before_script` or `:after_script`)
+        # @option context [#to_s] :vnc_passwd ("vnc.passwd") path to the file
+        #   generated that contains the encrypted vnc password (assumes you
+        #   don't modify `:before_script`)
+        # @option context [#to_s] :vnc_args arguments used when starting up the
+        #   vnc server (overrides any specific vnc argument) (assumes you don't
+        #   modify `:before_script`)
+        # @option context [#to_s] :name ("") name of the vnc server session
+        #   (not set if blank or `:vnc_args` is set) (assumes you don't modify
+        #   `:before_script`)
+        # @option context [#to_s] :geometry ("") resolution of vnc display (not
+        #   set if blank or `:vnc_args` is set) (assumes you don't modify
+        #   `:before_script`)
+        # @option context [#to_s] :dpi ("") dpi of vnc display (not set if
+        #   blank or `:vnc_args` is set) (assumes you don't modify
+        #   `:before_script`)
+        # @option context [#to_s] :fonts ("") command delimited list of fonts
+        #   available in vnc display (not set if blank or `:vnc_args` is set)
+        #   (assumes you don't modify `:before_script`)
+        # @option context [#to_s] :idle ("") timeout vnc server if no
+        #   connection in this amount of time in seconds (not set if blank or
+        #   `:vnc_args` is set) (assumes you don't modify `:before_script`)
+        # @option context [#to_s] :extra_args ("") any extra arguments used
+        #   when initializing the vnc server process (not set if blank or
+        #   `:vnc_args` is set) (assumes you don't modify `:before_script`)
+        # @option context [#to_s] :vnc_clean ("...") script used to clean up
+        #   any active vnc sessions (assumes you don't modify `:before_script`
+        #   or `:clean_script`)
+        # @option context [#to_s] :container_path ("vnc_container.sif") the path
+        #   to the container with VNC
+        # @option context [#to_s] :container_bindpath ("") paths to bind into
+        #   the container with VNC
+        # @option context [#to_s] :container_module ("singularity") the module
+        #   that loads Singularity or Apptainer with Lmod. Supports versions (i.e.
+        #   apptainer/1.10). If Singularity or Apptainer are installed at a 
+        #   system level (i.e., no module loaded to activate), set this to an
+        #   empty string.
+        # @option context [#to_s] :container_command ("singularity") the 
+        #   singularity or apptainer execution command
+        # @param instance_name (uuid) a name for the instance
+        # @see Template
+
+        def initialize(context = {})
+          @instance_name = SecureRandom.uuid
+          super
+        end
+
+        private
+          # We need to know the VNC and websockify connection information
+          def conn_params
+            (super + [:display, :websocket, :spassword, :instance_name]).uniq
+          end
+
+          # Before running the main script, start up a VNC server and record
+          # the connection information
+          def before_script
+            container_path = context.fetch(:container_path, "vnc_container.sif").to_s
+            container_bindpath = context.fetch(:container_bindpath, "").to_s
+
+            <<-EOT.gsub(/^ {14}/, "")
+
+              # Load #{container_module}
+              echo "Loading #{container_module}..."
+              module load #{container_module}
+              export #{container_command.upcase}_BINDPATH="#{container_bindpath}"
+              export INSTANCE_NAME="#{@instance_name}"
+              export instance_name="#{@instance_name}"
+              echo "Starting instance..."
+              #{container_command} instance start #{container_path} #{@instance_name}
+              
+              # Setup one-time use passwords and initialize the VNC password
+              function change_passwd () {
+                echo "Setting VNC password..."
+                password=$(create_passwd "#{password_size}")
+                spassword=${spassword:-$(create_passwd "#{password_size}")}
+                (
+                  umask 077
+                  echo -ne "${password}\\n${spassword}" | #{container_command} exec instance://#{@instance_name} vncpasswd -f > "#{vnc_passwd}"
+                )
+              }
+              change_passwd
+
+              
+              # Start up vnc server (if at first you don't succeed, try, try again)
+              echo "Starting VNC server..."
+              for i in $(seq 1 10); do
+                # Clean up any old VNC sessions that weren't cleaned before
+                #{vnc_clean}
+
+                # for turbovnc 3.0 compatability.
+                if timeout 2 #{container_command} exec instance://#{@instance_name} vncserver --help 2>&1 | grep 'nohttpd' >/dev/null 2>&1; then
+                  HTTPD_OPT='-nohttpd'
+                fi
+
+                # Attempt to start VNC server
+                VNC_OUT=$(#{container_command} exec instance://#{@instance_name} vncserver -log "#{vnc_log}" -rfbauth "#{vnc_passwd}" $HTTPD_OPT -noxstartup #{vnc_args} 2>&1)
+                VNC_PID=$(pgrep -s 0 Xvnc) # the script above will daemonize the Xvnc process
+                echo "${VNC_PID}"
+                echo "${VNC_OUT}"
+
+                # Sometimes Xvnc hangs if it fails to find working disaply, we
+                # should kill it and try again
+                kill -0 ${VNC_PID} 2>/dev/null && [[ "${VNC_OUT}" =~ "Fatal server error" ]] && kill -TERM ${VNC_PID}
+
+                # Check that Xvnc process is running, if not assume it died and
+                # wait some random period of time before restarting
+                kill -0 ${VNC_PID} 2>/dev/null || sleep 0.$(random_number 1 9)s
+
+                # If running, then all is well and break out of loop
+                kill -0 ${VNC_PID} 2>/dev/null && break
+              done
+
+              # If we fail to start it after so many tries, then just give up
+              kill -0 ${VNC_PID} 2>/dev/null || clean_up 1
+
+              # Parse output for ports used
+              display=$(echo "${VNC_OUT}" | awk -F':' '/^Desktop/{print $NF}')
+              port=$((5900+display))
+
+              echo "Successfully started VNC server on ${host}:${port}..."
+
+              #{super}
+            EOT
+          end
+
+          # Run the script under the VNC server's display
+          def run_script
+            %(DISPLAY=:${display} #{super})
+          end
+
+          # After startup the main script, scan the VNC server log file for
+          # successful connections so that the password can be reset
+          def after_script
+            websockify_cmd = context.fetch(:websockify_cmd, "${WEBSOCKIFY_CMD:-/opt/websockify/run}").to_s
+
+            <<-EOT.gsub(/^ {14}/, "")
+              #{super}
+
+              # Launch websockify websocket server
+              module load #{container_module}
+              echo "Starting websocket server..."
+              websocket=$(find_port)
+              #{container_command} exec instance://#{@instance_name} #{websockify_cmd} -D ${websocket} localhost:${port}
+
+              # Set up background process that scans the log file for successful
+              # connections by users, and change the password after every
+              # connection
+              echo "Scanning VNC log file for user authentications..."
+              while read -r line; do
+                if [[ ${line} =~ "Full-control authentication enabled for" ]]; then
+                  change_passwd
+                  create_yml
+                fi
+              done < <(tail -f --pid=${SCRIPT_PID} "#{vnc_log}") &
+            EOT
+          end
+
+          # Clean up the running VNC server and any other stale VNC servers
+          def clean_script
+            <<-EOT.gsub(/^ {14}/, "")
+              #{super}
+              module load #{container_module}
+
+              #{vnc_clean}
+              [[ -n ${display} ]] && vncserver -kill :${display}
+              #{container_command} instance stop #{@instance_name}
+            EOT
+          end
+
+          # Log file for VNC server
+          def vnc_log
+            context.fetch(:vnc_log, "vnc.log").to_s
+          end
+
+          # Password file for VNC server
+          def vnc_passwd
+            context.fetch(:vnc_passwd, "vnc.passwd").to_s
+          end
+
+          def container_module 
+            context.fetch(:container_module, "singularity").to_s
+          end
+
+          def container_command 
+            context.fetch(:container_command, "singularity").to_s
+          end
+
+          # Arguments sent to `vncserver` command
+          def vnc_args
+            context.fetch(:vnc_args) do
+              name       = context.fetch(:name, "").to_s
+              geometry   = context.fetch(:geometry, "").to_s
+              dpi        = context.fetch(:dpi, "").to_s
+              fonts      = context.fetch(:fonts, "").to_s
+              idle       = context.fetch(:idle, "").to_s
+              extra_args = context.fetch(:extra_args, "").to_s
+
+              args = []
+              args << "-name #{name}" unless name.empty?
+              args << "-geometry #{geometry}" unless geometry.empty?
+              args << "-dpi #{dpi}" unless dpi.empty?
+              args << "-fp #{fonts}" unless fonts.empty?
+              args << "-idletimeout #{idle}" unless idle.empty?
+              args << extra_args
+
+              args.join(" ")
+            end.to_s
+          end
+
+          # Clean up any stale VNC sessions
+          def vnc_clean
+            context.fetch(:vnc_clean) do
+              %(#{container_command} exec instance://#{@instance_name} vncserver -list | awk '/^:/{system("kill -0 "$2" 2>/dev/null || #{container_command} exec instance://#{@instance_name} vncserver -kill "$1)}')
+            end.to_s
+          end
+      end
+    end
+  end
+end

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

@@ -23,6 +23,7 @@ module OodCore
 
       class PromptError < StandardError; end
 
+      # The adapter class for the Cloudy Cluster product CCQ.
       class CCQ < Adapter
         using Refinements::ArrayExtensions
 

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

@@ -1,6 +1,8 @@
 require "ood_core/refinements/hash_extensions"
 require "json"
 
+# Utility class for the Kubernetes adapter to interact
+# with the Kuberenetes APIs.
 class OodCore::Job::Adapters::Kubernetes::Batch
 
   require_relative "helper"

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

@@ -1,3 +1,5 @@
+# Utility class for the Kubernetes adapter to parse
+# json data into Ruby objects.
 class OodCore::Job::Adapters::Kubernetes::Helper
 
   require_relative 'resources'
@@ -193,10 +195,14 @@ class OodCore::Job::Adapters::Kubernetes::Helper
   end
 
   def secret_info_from_json(json_data)
-    raw = json_data.dig(:data, :password)
-    { ood_connection_info: { password: Base64.decode64(raw) } }
-  rescue
-    {}
+    data = json_data.to_h[:data] || {}
+
+    info = data.symbolize_keys.each_with_object({}) do |data_kv, hash|
+      hash[data_kv[0]] = Base64.decode64(data_kv[1])
+    rescue
+      next
+    end
+    { ood_connection_info: info }
   end
 
   def dispatch_time(json_data)

data/lib/ood_core/job/adapters/kubernetes/k8s_job_info.rb

@@ -1,4 +1,4 @@
-# An object that describes a submitted kubernetes job with extended information
+# An object that describes a submitted kubernetes job with extended information.
 class OodCore::Job::Adapters::Kubernetes::K8sJobInfo < OodCore::Job::Info
   attr_reader :ood_connection_info
 

data/lib/ood_core/job/adapters/kubernetes/resources.rb

@@ -1,5 +1,5 @@
 module OodCore::Job::Adapters::Kubernetes::Resources
-
+  # Utility class for kubernetes configmap objects.
   class ConfigMap
     attr_accessor :name, :files
 
@@ -20,6 +20,7 @@ module OodCore::Job::Adapters::Kubernetes::Resources
     end
   end
 
+  # Utility class for mounting files in kubernetes configmap objects.
   class ConfigMapFile
     attr_accessor :filename, :data, :mount_path, :sub_path, :init_mount_path, :init_sub_path
 
@@ -33,6 +34,7 @@ module OodCore::Job::Adapters::Kubernetes::Resources
     end
   end
 
+  # Utility class for kuberenetes probe settings.
   class TCPProbe
     attr_accessor :port, :initial_delay_seconds, :failure_threshold, :period_seconds
 
@@ -54,6 +56,7 @@ module OodCore::Job::Adapters::Kubernetes::Resources
     end
   end
 
+  # Utility class for kuberenetes container object.
   class Container
     attr_accessor :name, :image, :command, :port, :env, :working_dir,
                   :memory_limit, :memory_request, :cpu_limit, :cpu_request, 
@@ -106,6 +109,7 @@ module OodCore::Job::Adapters::Kubernetes::Resources
     end
   end
 
+  # Utility class for kuberenetes podspec object.
   class PodSpec
     attr_accessor :container, :init_containers
     def initialize(container, init_containers: nil)

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

@@ -13,6 +13,8 @@ module OodCore
     end
 
     module Adapters
+
+      # The adapter class for Kubernetes.
       class Kubernetes < Adapter
 
         using Refinements::ArrayExtensions

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

@@ -22,6 +22,8 @@ module OodCore
     end
 
     module Adapters
+
+      # The adapter class for the LSF scheduler.
       class Lsf < Adapter
         using Refinements::ArrayExtensions
 

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

@@ -453,7 +453,7 @@ module OodCore
 
           # Parse hash describing PBS Pro job status
           def parse_job_info(v)
-            /^(?<job_owner>[\w-]+)@(?<submit_host>.+)$/ =~ v[:Job_Owner]
+            /^(?<job_owner>[\w\-.]+)@(?<submit_host>.+)$/ =~ v[:Job_Owner]
             allocated_nodes = parse_nodes(v[:exec_host] || "")
             procs = allocated_nodes.inject(0) { |sum, x| sum + x[:procs] }
             if allocated_nodes.empty? # fill in with requested resources

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

@@ -1,3 +1,5 @@
+# Utility helper class for the SGE adapter to parse
+# input and generate submission arguements.
 class OodCore::Job::Adapters::Sge::Helper
   require 'ood_core/job/adapters/sge'
 

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

@@ -16,7 +16,6 @@ require 'ood_core/job/array_ids'
 # :status
 # :wallclock_limit
 # :wallclock_time
-
 class QstatXmlJRListener
   # [Hash]
   attr_reader :parsed_job

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

@@ -13,7 +13,6 @@ require 'date'
 # :queue_name
 # :status
 # :wallclock_limit
-
 class QstatXmlRListener
   # [Array<Hash>]
   attr_reader :parsed_jobs

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

@@ -22,6 +22,8 @@ module OodCore
     end
 
     module Adapters
+
+      # The adpater class for Grid Engine (GE) flavors like Sun Grid Engine.
       class Sge < Adapter
         using Refinements::HashExtensions
         using Refinements::ArrayExtensions

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

@@ -37,8 +37,7 @@ module OodCore
     end
 
     module Adapters
-      # An adapter object that describes the communication with a remote host
-      # for job management.
+      # The adapter for using systemd timers as the scheduler.
       class LinuxSystemd < Adapter
         using Refinements::ArrayExtensions
 

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

@@ -1,3 +1,4 @@
+# Utility class to maintain all the Torque attributes available.
 class OodCore::Job::Adapters::Torque
   # Maintains a constant Hash of defined PBS attribute types
   # Includes:

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

@@ -1,5 +1,7 @@
 require 'open3'
 
+# Utility class for the Torque adapter to communicate with the
+# Torque scheduler.
 class OodCore::Job::Adapters::Torque
   # Object used for simplified communication with a batch server
   class Batch

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

@@ -1,3 +1,4 @@
+# FFI errors for the Torque adapter.
 class OodCore::Job::Adapters::Torque::FFI
   # The root exception class that all PBS-specific exceptions inherit from
   class Error < StandardError; end

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

@@ -1,6 +1,6 @@
 require 'ffi'
 
-# An interface to the C-library of Torque
+# An interface to the C-library of Torque.
 class OodCore::Job::Adapters::Torque::FFI
 
   extend ::FFI::Library

data/lib/ood_core/job/array_ids.rb

@@ -1,14 +1,14 @@
-# Builds a sorted array of job ids given a job array spec string
-#
-# Job array spec strings:
-#   1         Single id
-#   1-10      Range
-#   1-10:2    Range with step
-#   1-10,13   Compound (range with single id)
-#
-# Note that Ranges are expected to be inclusive
 module OodCore
   module Job
+    # Builds a sorted array of job ids given a job array spec string
+    #
+    # Job array spec strings:
+    #   1         Single id
+    #   1-10      Range
+    #   1-10:2    Range with step
+    #   1-10,13   Compound (range with single id)
+    #
+    # Note that Ranges are expected to be inclusive
     class ArrayIds
       attr_reader :spec_string
 

data/lib/ood_core/job/cluster_info.rb

@@ -1,6 +1,6 @@
 module OodCore
   module Job
-    # An object that contains details about the cluster's active and total nodes, processors, and gpus
+    # An object that contains details about the cluster's active and total nodes, processors and gpus.
     class ClusterInfo
       using Refinements::HashExtensions
 

data/lib/ood_core/job/info.rb

@@ -2,7 +2,7 @@ require 'time'
 
 module OodCore
   module Job
-    # An object that describes a submitted job
+    # An object that describes a submitted job.
     class Info
       # The identifier of the job
       # @return [String] job id

data/lib/ood_core/job/node_info.rb

@@ -1,6 +1,6 @@
 module OodCore
   module Job
-    # An object that describes the resources used on a specific node
+    # An object that describes the resources used on a specific node.
     class NodeInfo
       # The name of the host machine
       # @return [String] node name

data/lib/ood_core/job/status.rb

@@ -1,6 +1,6 @@
 module OodCore
   module Job
-    # An object that describes the current state of a submitted job
+    # An object that describes the current state of a submitted job.
     class Status
       class << self
         # Possible states a submitted job can be in:

data/lib/ood_core/version.rb

@@ -1,4 +1,4 @@
 module OodCore
   # The current version of {OodCore}
-  VERSION = "0.21.0"
+  VERSION = "0.22.0"
 end

data/ood_core.gemspec

@@ -30,5 +30,5 @@ Gem::Specification.new do |spec|
   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", "~> 1.1.1"
+  spec.add_development_dependency "climate_control", "~> 1.2.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ood_core
 version: !ruby/object:Gem::Version
-  version: 0.21.0
+  version: 0.22.0
 platform: ruby
 authors:
 - Eric Franz
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2022-08-01 00:00:00.000000000 Z
+date: 2022-10-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ood_support
@@ -136,14 +136,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.1.1
+        version: 1.2.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.1.1
+        version: 1.2.0
 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:
@@ -164,6 +164,7 @@ files:
 - Rakefile
 - bin/console
 - bin/setup
+- docs/.keep
 - lib/ood_core.rb
 - lib/ood_core/acl/adapter.rb
 - lib/ood_core/acl/adapters/group.rb
@@ -172,6 +173,7 @@ files:
 - lib/ood_core/batch_connect/template.rb
 - lib/ood_core/batch_connect/templates/basic.rb
 - lib/ood_core/batch_connect/templates/vnc.rb
+- lib/ood_core/batch_connect/templates/vnc_container.rb
 - lib/ood_core/cluster.rb
 - lib/ood_core/clusters.rb
 - lib/ood_core/errors.rb