ood_core 0.20.2 → 0.22.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 1e2b4ca05369c8072afe8d1069679a8f2744cdcb3ed766924a778e78af65afa2
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+  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 +7,24 @@ 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
+
+- Added the `fujitsu_tcs` adapter in [766](https://github.com/OSC/ood_core/pull/766).
+
 ## [0.20.2] - 07-28-2022
 
 - Fixed an issue with Slurm's `cluster_info` in [762](https://github.com/OSC/ood_core/pull/762).
@@ -437,7 +455,9 @@ Functionally the same as [0.17.3] but with some CI updates.
 ### Added
 - Initial release!
 
-[Unreleased]: https://github.com/OSC/ood_core/compare/v0.20.2...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
 [0.20.0]: https://github.com/OSC/ood_core/compare/v0.19.0...v0.20.0

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/fujitsu_tcs.rb

@@ -0,0 +1,403 @@
+require "time"
+require "ood_core/refinements/hash_extensions"
+require "ood_core/refinements/array_extensions"
+require "ood_core/job/adapters/helper"
+
+module OodCore
+  module Job
+    class Factory
+      using Refinements::HashExtensions
+      
+      # Build the Fujitsu TCS (Technical Computing Suite) adapter from a configuration
+      # @param config [#to_h] the configuration for job adapter
+      # @option config [Object] :bin (nil) Path to Fujitsu TCS resource manager binaries
+      # @option config [#to_h]  :bin_overrides ({}) Optional overrides to Fujitsu TCS resource manager executables
+      def self.build_fujitsu_tcs(config)
+        c = config.to_h.symbolize_keys
+        bin           = c.fetch(:bin, nil)
+        bin_overrides = c.fetch(:bin_overrides, {})
+        fujitsu_tcs   = Adapters::Fujitsu_TCS::Batch.new(bin: bin, bin_overrides: bin_overrides)
+        Adapters::Fujitsu_TCS.new(fujitsu_tcs: fujitsu_tcs)
+      end
+    end
+    
+    module Adapters
+      # An adapter object that describes the communication with a Fujitsu TCS
+      # resource manager for job management.
+      class Fujitsu_TCS < Adapter
+        using Refinements::HashExtensions
+        using Refinements::ArrayExtensions
+        
+        # Object used for simplified communication with a Fujitsu TCS batch server
+        # @api private
+        class Batch
+          # The path to the Fujitsu TCS binaries
+          # @example 
+          #   my_batch.bin.to_s #=> "/usr/local/fujitsu_tcs/10.0.0/bin"
+          # @return [Pathname] path to Fujitsu TCS binaries
+          attr_reader :bin
+
+          # Optional overrides for Fujitsu TCS executables
+          # @example
+          #  {'pjsub' => '/usr/local/bin/pjsub'}
+          # @return Hash<String, String>
+          attr_reader :bin_overrides
+
+          # The root exception class that all Fujitsu TCS specific exceptions inherit
+          # from
+          class Error < StandardError; end
+
+          # An error indicating the Fujitsu TCS command timed out
+          class Fujitsu_TCS_TimeoutError < Error; end
+
+          # @param bin [#to_s] path to Fujitsu TCS installation binaries
+          # @param bin_overrides [#to_h] a hash of bin ovverides to be used in job
+          def initialize(bin: nil, bin_overrides: {})
+            @bin           = Pathname.new(bin.to_s)
+            @bin_overrides = bin_overrides
+          end
+
+          # Get a list of hashes detailing each of the jobs on the batch server
+          # @example Status info for all jobs
+          #   my_batch.get_jobs
+          #   #=>
+          #   #[
+          #   #  {
+          #   #    :JOB_ID => "123",
+          #   #    :JOB_NAME => "my_job",
+          #   #    ...
+          #   #  },
+          #   #  {
+          #   #    :JOB_ID => "125",
+          #   #    :JOB_NAME => "my_other_job",
+          #   #    ...
+          #   #  },
+          #   #  ...
+          #   #]
+          # @param id [#to_s] the id of the job
+          # @param owner [String] the owner(s) of the job
+          # @raise [Error] if `pjstat` command exited unsuccessfully
+          # @return [Array<Hash>] list of details for jobs
+          def get_jobs(id: "", owner: nil)
+            args = ["-s", "--data", "--choose=jid,jnam,rscg,st,std,stde,adt,sdt,nnumr,usr,elpl,elp"]
+            args.concat ["--filter jid=" + id.to_s] unless id.to_s.empty?
+            args.concat ["--filter usr=" + owner.to_s] unless owner.to_s.empty?
+            
+            StringIO.open(call("pjstat", *args)) do |output|
+              output.gets() # Skip header
+              jobs = []
+              output.each_line do |line|
+                l = line.split(",")
+                jobs << {:JOB_ID => l[1],  :JOB_NAME   => l[2],  :RSC_GRP    => l[3].split(" ")[0],
+                         :ST     => l[4],  :STD        => l[5],  :STDE       => l[6],
+                         :ACCEPT => l[7],  :START_DATE => l[8],  :NODES      => l[9].split(":")[0],
+                         :USER   => l[10], :ELAPSE_LIM => l[11], :ELAPSE_TIM => l[12].split(" ")[0] }
+              end
+              jobs
+            end
+          rescue Fujitsu_TCS_TimeoutError
+            return [{ JOB_ID: id, ST: 'undetermined' }]
+          end
+
+          # Put a specified job on hold
+          # @example Put job "1234" on hold
+          #   my_batch.hold_job("1234")
+          # @param id [#to_s] the id of the job
+          # @raise [Error] if `pjhold` command exited unsuccessfully
+          # @return [void]
+          def hold_job(id)
+            call("pjhold", id.to_s)
+          end
+
+          # Release a specified job that is on hold
+          # @example Release job "1234" from on hold
+          #   my_batch.release_job("1234")
+          # @param id [#to_s] the id of the job
+          # @raise [Error] if `pjrls` command exited unsuccessfully
+          # @return [void]
+          def release_job(id)
+            call("pjrls", id.to_s)
+          end
+
+          # Delete a specified job from batch server
+          # @example Delete job "1234"
+          #   my_batch.delete_job("1234")
+          # @param id [#to_s] the id of the job
+          # @raise [Error] if `pjdel` command exited unsuccessfully
+          # @return [void]
+          def delete_job(id)
+            call("pjdel", id.to_s)
+          end
+
+          # Submit a script expanded as a string to the batch server
+          # @param str [#to_s] script as a string
+          # @param args [Array<#to_s>] arguments passed to `pjsub` command
+          # @raise [Error] if `pjsub` command exited unsuccessfully
+          # @return [String] the id of the job that was created
+          def submit_string(str, args: [])
+            args = args.map(&:to_s)
+            call("pjsub", *args, stdin: str.to_s).split(" ")[5]
+          end
+          
+          private
+            # Call a forked Fujitsu TCS command
+            def call(cmd, *args, stdin: "")
+              cmd = OodCore::Job::Adapters::Helper.bin_path(cmd, bin, bin_overrides)
+              args  = args.map(&:to_s)
+              o, e, s = Open3.capture3(cmd, *(args.map(&:to_s)), stdin_data: stdin.to_s)
+              s.success? ? o : raise(Error, e)
+            end
+        end
+
+        # Mapping of state codes for Fujitsu TCS resource manager
+        STATE_MAP = {
+          'ACC' => :queued,    # Accepted job submission
+          'RJT' => :completed, # Rejected job submission
+          'QUE' => :queued,    # Waiting for job execution
+          'RNA' => :queued,    # Acquiring resources required for job execution
+          'RNP' => :running,   # Executing prologue
+          'RUN' => :running,   # Executing job
+          'RNE' => :running,   # Executing epilogue
+          'RNO' => :running,   # Waiting for completion of job termination processing
+          'SPP' => :suspended, # Suspend in progress
+          'SPD' => :suspended, # Suspended
+          'RSM' => :running,   # Resume in progress
+          'EXT' => :completed, # Exited job end execution
+          'CCL' => :completed, # Exited job execution by interruption
+          'HLD' => :suspended, # In fixed state due to users
+          'ERR' => :completed, # In fixed state due to an error
+        }
+
+        # @api private
+        # @param opts [#to_h] the options defining this adapter
+        # @option opts [Batch] :the Fujitsu TCS batch object
+        # @see Factory.build_fujitsu_tcs
+        def initialize(opts = {})
+          o = opts.to_h.symbolize_keys
+
+          @fujitsu_tcs = o.fetch(:fujitsu_tcs) { raise ArgumentError, "No Fujitsu TCS object specified. Missing argument: fujitsu_tcs" }
+        end
+
+        # Submit a job with the attributes defined in the job template instance
+        # @param script [Script] script object that describes the script and
+        #   attributes for the submitted job
+        # @param after [#to_s, Array<#to_s>] this job may be scheduled for
+        #   execution at any point after dependent jobs have started execution
+        # @param afterok [#to_s, Array<#to_s>] this job may be scheduled for
+        #   execution only after dependent jobs have terminated with no errors
+        # @param afternotok [#to_s, Array<#to_s>] this job may be scheduled for
+        #   execution only after dependent jobs have terminated with errors
+        # @param afterany [#to_s, Array<#to_s>] this job may be scheduled for
+        #   execution after dependent jobs have terminated
+        # @raise [JobAdapterError] if something goes wrong submitting a job
+        # @return [String] the job id returned after successfully submitting a
+        #   job
+        # @see Adapter#submit
+        def submit(script, after: [], afterok: [], afternotok: [], afterany: [])
+          #after      = Array(after).map(&:to_s)
+          #afterok    = Array(afterok).map(&:to_s)
+          #afternotok = Array(afternotok).map(&:to_s)
+          #afterany   = Array(afterany).map(&:to_s)
+          if !after.empty? || !afterok.empty? || !afternotok.empty? || !afterany.empty?
+            raise JobAdapterError, "Dependency between jobs has not implemented yet."
+          end
+          
+          # Set pjsub options
+          args = []
+          args.concat (script.rerunnable ? ["--restart"] : ["--norestart"]) unless script.rerunnable.nil?
+          args.concat ["--mail-list", script.email.join(",")] unless script.email.nil?
+          if script.email_on_started && script.email_on_terminated
+            args.concat ["-m", "b,e"]
+          elsif script.email_on_started
+            args.concat ["-m", "b"]
+          elsif script.email_on_terminated
+            args.concat ["-m", "e"]
+          end
+
+          args.concat ["-N", script.job_name] unless script.job_name.nil?
+          args.concat ["-o", script.output_path] unless script.output_path.nil?
+          if script.error_path.nil?
+            args.concat ["-j"]
+          else
+            args.concat ["-e", script.error_path]
+          end
+          args.concat ["--rscgrp", script.queue_name] unless script.queue_name.nil?
+          args.concat ["-p", script.priority] unless script.priority.nil?
+          args.concat ["--at", script.start_time.localtime.strftime("%C%y-%m-%dT%H:%M:%S")] unless script.start_time.nil?
+          args.concat ["-L \"elapse=" + seconds_to_duration(script.wall_time) + "\""] unless script.wall_time.nil?
+          args.concat ["--bulk", "--sparam", script.job_array_request] unless script.job_array_request.nil?
+
+          # Set environment variables
+          envvars = script.job_environment.to_h
+          args.concat ["-x", envvars.map{|k,v| "#{k}=#{v}"}.join(",")] unless envvars.empty?
+          args.concat ["-X"] if script.copy_environment?
+
+          # Set native options
+          args.concat script.native if script.native
+          
+          # Set content
+          content = if script.shell_path.nil?
+                      script.content
+                    else
+                      "#!#{script.shell_path}\n#{script.content}"
+                    end
+          
+          # Submit job
+          @fujitsu_tcs.submit_string(content, args: args)
+        rescue Batch::Error => e
+          raise JobAdapterError, e.message
+        end
+
+        # Retrieve info for all jobs from the resource manager
+        # @raise [JobAdapterError] if something goes wrong getting job info
+        # @return [Array<Info>] information describing submitted jobs
+        # @see Adapter#info_all
+        def info_all(attrs: nil)
+          @fujitsu_tcs.get_jobs().map do |v|
+            parse_job_info(v)
+          end
+        rescue Batch::Error => e
+          raise JobAdapterError, e.message
+        end
+
+        # Retrieve job info from the resource manager
+        # @param id [#to_s] the id of the job
+        # @raise [JobAdapterError] if something goes wrong getting job info
+        # @return [Info] information describing submitted job
+        # @see Adapter#info
+        def info(id)
+          id = id.to_s
+          info_ary = @fujitsu_tcs.get_jobs(id: id).map do |v|
+            parse_job_info(v)
+          end
+
+          # If no job was found we assume that it has completed
+          info_ary.empty? ? Info.new(id: id, status: :completed) : info_ary.first # @fujitsu_tcs.get_jobs() must return only one element.
+        rescue Batch::Error => e
+          # set completed status if can't find job id
+          if /\[ERR\.\] PJM .+ Job .+ does not exist/ =~ e.message
+            Info.new(
+              id: id,
+              status: :completed
+            )
+          else
+            raise JobAdapterError, e.message
+          end
+        end
+
+        # 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
+        # @raise [JobAdapterError] if something goes wrong getting job info
+        # @return [Array<Info>] information describing submitted jobs
+        def info_where_owner(owner, attrs: nil)
+          owner = Array.wrap(owner).map(&:to_s).join('+')
+          @fujitsu_tcs.get_jobs(owner: owner).map do |v|
+            parse_job_info(v)
+          end
+        rescue Batch::Error => e
+          raise JobAdapterError, e.message
+        end
+
+        # Retrieve job status from resource manager
+        # @param id [#to_s] the id of the job
+        # @raise [JobAdapterError] if something goes wrong getting job status
+        # @return [Status] status of job
+        # @see Adapter#status
+        def status(id)
+          id = id.to_s
+          jobs = @fujitsu_tcs.get_jobs(id: id)
+
+          if job = jobs.detect { |j| j[:JOB_ID] == id }
+            Status.new(state: get_state(job[:ST]))
+          else
+            # set completed status if can't find job id
+            Status.new(state: :completed)
+          end
+        rescue Batch::Error => e
+          # set completed status if can't find job id
+          if /\[ERR\.\] PJM .+ Job .+ does not exist/ =~ e.message
+            Status.new(state: :completed)
+          else
+            raise JobAdapterError, e.message
+          end
+        end
+
+        # Put the submitted job on hold
+        # @param id [#to_s] the id of the job
+        # @raise [JobAdapterError] if something goes wrong holding a job
+        # @return [void]
+        # @see Adapter#hold
+        def hold(id)
+          @fujitsu_tcs.hold_job(id.to_s)
+        rescue Batch::Error => e
+          # assume successful job hold if can't find job id
+          raise JobAdapterError, e.message unless /\[ERR\.\] PJM .+ Job .+ does not exist/ =~ e.message
+        end
+
+        # Release the job that is on hold
+        # @param id [#to_s] the id of the job
+        # @raise [JobAdapterError] if something goes wrong releasing a job
+        # @return [void]
+        # @see Adapter#release
+        def release(id)
+          @fujitsu_tcs.release_job(id.to_s)
+        rescue Batch::Error => e
+          # assume successful job release if can't find job id
+          raise JobAdapterError, e.message unless /\[ERR\.\] PJM .+ Job .+ does not exist/ =~ e.message
+        end
+
+        # Delete the submitted job
+        # @param id [#to_s] the id of the job
+        # @raise [JobAdapterError] if something goes wrong deleting a job
+        # @return [void]
+        # @see Adapter#delete
+        def delete(id)
+          @fujitsu_tcs.delete_job(id.to_s)
+        rescue Batch::Error => e
+          # assume successful job deletion if can't find job id
+          raise JobAdapterError, e.message unless /\[ERR\.\] PJM .+ Job .+ does not exist/ =~ e.message
+        end
+
+        def directive_prefix
+          '#PJM'
+        end
+
+        private
+          # Convert duration to seconds
+          def duration_in_seconds(time)
+            return 0 if time.nil?
+            time, days = time.split("-").reverse
+            days.to_i * 24 * 3600 +
+              time.split(':').map { |v| v.to_i }.inject(0) { |total, v| total * 60 + v }
+          end
+
+          # Convert seconds to duration
+          def seconds_to_duration(time)
+            "%02d:%02d:%02d" % [time/3600, time/60%60, time%60]
+          end
+
+          # Determine state from Fujitsu TCS state code
+          def get_state(st)
+            STATE_MAP.fetch(st, :undetermined)
+          end
+
+          # Parse hash describing Fujitsu TCS job status
+          def parse_job_info(v)
+            Info.new(
+              id: v[:JOB_ID],
+              job_name: v[:JOB_NAME],
+              status: get_state(v[:ST]),
+              job_owner: v[:USER],
+              dispatch_time: v[:START_DATE],
+              wallclock_time: duration_in_seconds(v[:ELAPSE_TIM]),
+              wallclock_limit: duration_in_seconds(v[:ELAPSE_LIM]),
+              submission_time: v[:ACCEPT],
+              queue_name: v[:RSC_GRP],
+              native: v
+            )
+          end
+      end
+    end
+  end
+end

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 = "0.20.2"
+  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: 0.20.2
+  version: 0.22.0
 platform: ruby
 authors:
 - Eric Franz
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2022-07-28 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
@@ -179,6 +181,7 @@ files:
 - lib/ood_core/job/adapter.rb
 - lib/ood_core/job/adapters/ccq.rb
 - lib/ood_core/job/adapters/drmaa.rb
+- lib/ood_core/job/adapters/fujitsu_tcs.rb
 - lib/ood_core/job/adapters/helper.rb
 - lib/ood_core/job/adapters/kubernetes.rb
 - lib/ood_core/job/adapters/kubernetes/batch.rb