arvados-cli 1.4.3.pre20200103204428 → 2.0.3.1

checksums.yaml

@@ -1,7 +1,7 @@
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+SHA256:
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data/bin/arv

@@ -131,16 +131,6 @@ def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
       puts "Available methods: ls, get, put, docker"
     end
     abort
-  when 'pipeline'
-    sub = remaining_opts.shift
-    if sub == 'run'
-      exec_bin "arv-run-pipeline-instance", remaining_opts
-    else
-      puts "Usage: arv pipeline [method] [--parameters]\n"
-      puts "Use 'arv pipeline [method] --help' to get more information about specific methods.\n\n"
-      puts "Available methods: run"
-    end
-    abort
   end
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: arvados-cli
 version: !ruby/object:Gem::Version
-  version: 1.4.3.pre20200103204428
+  version: 2.0.3.1
 platform: ruby
 authors:
 - Arvados Authors
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-12-04 00:00:00.000000000 Z
+date: 2020-04-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: arvados
@@ -152,6 +152,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: launchy
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '2.5'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '2.5'
 - !ruby/object:Gem::Dependency
   name: faraday
   requirement: !ruby/object:Gem::Requirement
@@ -166,22 +180,17 @@ dependencies:
     - - "<"
       - !ruby/object:Gem::Version
         version: '0.16'
-description: Arvados command line tools, git commit b702e93a96fededd1cfb46e862f9209596063156
+description: Arvados command line tools, git commit b51b3fc069dfbf88de0ca064c2018628d9b9737f
 email: gem-dev@curoverse.com
 executables:
 - arv
-- arv-run-pipeline-instance
-- arv-crunch-job
 - arv-tag
 extensions: []
 extra_rdoc_files: []
 files:
 - LICENSE-2.0.txt
 - bin/arv
-- bin/arv-crunch-job
-- bin/arv-run-pipeline-instance
 - bin/arv-tag
-- bin/crunch-job
 homepage: https://arvados.org
 licenses:
 - Apache-2.0
@@ -197,12 +206,12 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: 2.1.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.5.2
+rubygems_version: 2.7.10
 signing_key: 
 specification_version: 4
 summary: Arvados CLI tools

data/bin/arv-crunch-job

@@ -1,6 +0,0 @@
-#!/usr/bin/env ruby
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
-exec File.join(File.dirname(File.realpath(__FILE__)), 'crunch-job'), *ARGV

data/bin/arv-run-pipeline-instance

@@ -1,781 +0,0 @@
-#!/usr/bin/env ruby
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
-class WhRunPipelineInstance
-end
-
-if RUBY_VERSION < '1.9.3' then
-  abort <<-EOS
-#{$0.gsub(/^\.\//,'')} requires Ruby version 1.9.3 or higher.
-  EOS
-end
-
-begin
-  require 'arvados'
-  require 'rubygems'
-  require 'json'
-  require 'pp'
-  require 'optimist'
-  require 'google/api_client'
-rescue LoadError => l
-  $stderr.puts $:
-  abort <<-EOS
-#{$0}: fatal: #{l.message}
-Some runtime dependencies may be missing.
-Try: gem install arvados pp google-api-client json optimist
-  EOS
-end
-
-def debuglog(message, verbosity=1)
-  $stderr.puts "#{File.split($0).last} #{$$}: #{message}" if $debuglevel >= verbosity
-end
-
-# Parse command line options (the kind that control the behavior of
-# this program, that is, not the pipeline component parameters).
-
-p = Optimist::Parser.new do
-  version __FILE__
-  banner(<<EOF)
-
-Usage:
-  arv-run-pipeline-instance --template TEMPLATE_UUID [options] [--] [parameters]
-  arv-run-pipeline-instance --instance INSTANCE_UUID [options] [--] [parameters]
-
-Parameters:
-  param_name=param_value
-  param_name param_value
-                         Set (or override) the default value for every
-                         pipeline component parameter with the given
-                         name.
-
-  component_name::param_name=param_value
-  component_name::param_name param_value
-  --component_name::param_name=param_value
-  --component_name::param_name param_value
-                         Set the value of a parameter for a single
-                         pipeline component.
-
-Options:
-EOF
-  opt(:dry_run,
-      "Do not start any new jobs or wait for existing jobs to finish. Just find out whether jobs are finished, queued, or running for each component.",
-      :type => :boolean,
-      :short => :n)
-  opt(:status_text,
-      "Store plain text status in given file.",
-      :short => :none,
-      :type => :string,
-      :default => '/dev/stdout')
-  opt(:status_json,
-      "Store json-formatted pipeline in given file.",
-      :short => :none,
-      :type => :string,
-      :default => '/dev/null')
-  opt(:no_wait,
-      "Do not wait for jobs to finish. Just look up status, submit new jobs if needed, and exit.",
-      :short => :none,
-      :type => :boolean)
-  opt(:no_reuse,
-      "Do not reuse existing jobs to satisfy pipeline components. Submit a new job for every component.",
-      :short => :none,
-      :type => :boolean)
-  opt(:debug,
-      "Print extra debugging information on stderr.",
-      :type => :boolean)
-  opt(:debug_level,
-      "Set debug verbosity level.",
-      :short => :none,
-      :type => :integer)
-  opt(:template,
-      "UUID of pipeline template, or path to local pipeline template file.",
-      :short => :none,
-      :type => :string)
-  opt(:instance,
-      "UUID of pipeline instance.",
-      :short => :none,
-      :type => :string)
-  opt(:submit,
-      "Submit the pipeline instance to the server, and exit. Let the Crunch dispatch service satisfy the components by finding/running jobs.",
-      :short => :none,
-      :type => :boolean)
-  opt(:run_pipeline_here,
-      "Manage the pipeline instance in-process. Submit jobs to Crunch as needed. Do not exit until the pipeline finishes (or fails).",
-      :short => :none,
-      :type => :boolean)
-  opt(:run_jobs_here,
-      "Run jobs in the local terminal session instead of submitting them to Crunch. Implies --run-pipeline-here. Note: this results in a significantly different job execution environment, and some Crunch features are not supported. It can be necessary to modify a pipeline in order to make it run this way.",
-      :short => :none,
-      :type => :boolean)
-  opt(:run_here,
-      "Synonym for --run-jobs-here.",
-      :short => :none,
-      :type => :boolean)
-  opt(:description,
-      "Description for the pipeline instance.",
-      :short => :none,
-      :type => :string)
-  opt(:project_uuid,
-      "UUID of the project for the pipeline instance.",
-      short: :none,
-      type: :string)
-  stop_on [:'--']
-end
-$options = Optimist::with_standard_exception_handling p do
-  p.parse ARGV
-end
-$debuglevel = $options[:debug_level] || ($options[:debug] && 1) || 0
-
-$options[:run_jobs_here] ||= $options[:run_here] # old flag name
-$options[:run_pipeline_here] ||= $options[:run_jobs_here] # B requires A
-
-if $options[:instance]
-  if $options[:template] or $options[:submit]
-    abort "#{$0}: syntax error: --instance cannot be combined with --template or --submit."
-  end
-elsif not $options[:template]
-  $stderr.puts "error: you must supply a --template or --instance."
-  p.educate
-  abort
-end
-
-if $options[:run_pipeline_here] == $options[:submit]
-  abort "#{$0}: error: you must supply --run-pipeline-here, --run-jobs-here, or --submit."
-end
-
-# Set up the API client.
-
-$arv = Arvados.new api_version: 'v1'
-$client = $arv.client
-$arvados = $arv.arvados_api
-
-class PipelineInstance
-  def self.find(uuid)
-    result = $client.execute(:api_method => $arvados.pipeline_instances.get,
-                             :parameters => {
-                               :uuid => uuid
-                             },
-                             :authenticated => false,
-                             :headers => {
-                               authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
-                             })
-    j = JSON.parse result.body, :symbolize_names => true
-    unless j.is_a? Hash and j[:uuid]
-      debuglog "Failed to get pipeline_instance: #{j[:errors] rescue nil}", 0
-      nil
-    else
-      debuglog "Retrieved pipeline_instance #{j[:uuid]}"
-      self.new(j)
-    end
-  end
-  def self.create(attributes)
-    result = $client.execute(:api_method => $arvados.pipeline_instances.create,
-                             :body_object => {
-                               :pipeline_instance => attributes
-                             },
-                             :authenticated => false,
-                             :headers => {
-                               authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
-                             })
-    j = JSON.parse result.body, :symbolize_names => true
-    unless j.is_a? Hash and j[:uuid]
-      abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nFailed to create pipeline_instance: #{j[:errors] rescue nil} #{j.inspect}"
-    end
-    debuglog "Created pipeline instance: #{j[:uuid]}"
-    self.new(j)
-  end
-  def save
-    result = $client.execute(:api_method => $arvados.pipeline_instances.update,
-                             :parameters => {
-                               :uuid => @pi[:uuid]
-                             },
-                             :body_object => {
-                               :pipeline_instance => @attributes_to_update
-                             },
-                             :authenticated => false,
-                             :headers => {
-                               authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
-                             })
-    j = JSON.parse result.body, :symbolize_names => true
-    unless j.is_a? Hash and j[:uuid]
-      debuglog "Failed to save pipeline_instance: #{j[:errors] rescue nil}", 0
-      nil
-    else
-      @attributes_to_update = {}
-      @pi = j
-    end
-  end
-  def []=(x,y)
-    @attributes_to_update[x] = y
-    @pi[x] = y
-  end
-  def [](x)
-    @pi[x]
-  end
-
-  def log_stderr(msg)
-    $arv.log.create log: {
-      event_type: 'stderr',
-      object_uuid: self[:uuid],
-      owner_uuid: self[:owner_uuid],
-      properties: {"text" => msg},
-    }
-  end
-
-  protected
-  def initialize(j)
-    @attributes_to_update = {}
-    @pi = j
-  end
-end
-
-class JobCache
-  def self.get(uuid)
-    @cache ||= {}
-    result = $client.execute(:api_method => $arvados.jobs.get,
-                             :parameters => {
-                               :uuid => uuid
-                             },
-                             :authenticated => false,
-                             :headers => {
-                               authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
-                             })
-    @cache[uuid] = JSON.parse result.body, :symbolize_names => true
-  end
-  def self.where(conditions)
-    result = $client.execute(:api_method => $arvados.jobs.list,
-                             :parameters => {
-                               :limit => 10000,
-                               :where => conditions.to_json
-                             },
-                             :authenticated => false,
-                             :headers => {
-                               authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
-                             })
-    list = JSON.parse result.body, :symbolize_names => true
-    if list and list[:items].is_a? Array
-      list[:items]
-    else
-      []
-    end
-  end
-
-  # create() returns [job, exception]. If both job and exception are
-  # nil, there was a non-retryable error and the call should not be
-  # attempted again.
-  def self.create(pipeline, component, job, create_params)
-    @cache ||= {}
-
-    body = {job: no_nil_values(job)}.merge(no_nil_values(create_params))
-
-    result = nil
-    begin
-      result = $client.execute(
-        :api_method => $arvados.jobs.create,
-        :body_object => body,
-        :authenticated => false,
-        :headers => {
-          authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
-        })
-      if result.status == 429 || result.status >= 500
-        raise Exception.new("HTTP status #{result.status}")
-      end
-    rescue Exception => e
-      return nil, e
-    end
-    j = JSON.parse(result.body, :symbolize_names => true) rescue nil
-    if result.status == 200 && j.is_a?(Hash) && j[:uuid]
-      @cache[j[:uuid]] = j
-      return j, nil
-    else
-      errors = j[:errors] rescue []
-      debuglog "create job: [#{result.status}] #{errors.inspect} with attributes #{body}", 0
-
-      msg = ""
-      errors.each do |err|
-        msg += "Error creating job for component #{component}: #{err}\n"
-      end
-      msg += "Job submission was: #{body.to_json}"
-
-      pipeline.log_stderr(msg)
-      return nil, nil
-    end
-  end
-
-  protected
-
-  def self.no_nil_values(hash)
-    hash.reject { |key, value| value.nil? }
-  end
-end
-
-class WhRunPipelineInstance
-  attr_reader :instance
-
-  def initialize(_options)
-    @options = _options
-  end
-
-  def fetch_template(template)
-    if template.match /[^-0-9a-z]/
-      # Doesn't look like a uuid -- use it as a filename.
-      @template = JSON.parse File.read(template), :symbolize_names => true
-    else
-      result = $client.execute(:api_method => $arvados.pipeline_templates.get,
-                               :parameters => {
-                                 :uuid => template
-                               },
-                               :authenticated => false,
-                               :headers => {
-                                 authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
-                               })
-      @template = JSON.parse result.body, :symbolize_names => true
-      if !@template[:uuid]
-        abort "#{$0}: fatal: failed to retrieve pipeline template #{template} #{@template[:errors].inspect rescue nil}"
-      end
-    end
-    self
-  end
-
-  def fetch_instance(instance_uuid)
-    @instance = PipelineInstance.find(instance_uuid)
-    @template = @instance
-    self
-  end
-
-  def apply_parameters(params_args)
-    params_args.shift if params_args[0] == '--'
-    params = {}
-    while !params_args.empty?
-      if (re = params_args[0].match /^(--)?([^-].*?)=(.+)/)
-        params[re[2]] = re[3]
-        params_args.shift
-      elsif params_args.size > 1
-        param = params_args.shift.sub /^--/, ''
-        params[param] = params_args.shift
-      else
-        abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: I do not know what to do with arg \"#{params_args[0]}\""
-      end
-    end
-
-    if not @template[:components].is_a?(Hash)
-      abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Template missing \"components\" hash"
-    end
-    @components = @template[:components].dup
-
-    bad_components = @components.each_pair.select do |cname, cspec|
-      not cspec.is_a?(Hash)
-    end
-    if bad_components.any?
-      abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Components not specified with hashes: #{bad_components.map(&:first).join(', ')}"
-    end
-
-    bad_components = @components.each_pair.select do |cname, cspec|
-      not cspec[:script_parameters].is_a?(Hash)
-    end
-    if bad_components.any?
-      abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Components missing \"script_parameters\" hashes: #{bad_components.map(&:first).join(', ')}"
-    end
-
-    errors = []
-    @components.each do |componentname, component|
-      component[:script_parameters].each do |parametername, parameter|
-        parameter = { :value => parameter } unless parameter.is_a? Hash
-        if params.has_key?("#{componentname}::#{parametername}")
-          value = params["#{componentname}::#{parametername}"]
-        elsif parameter.has_key?(:value)
-          value = parameter[:value]
-        elsif parameter.has_key?(:output_of)
-          if !@components[parameter[:output_of].intern]
-            errors << [componentname, parametername, "output_of refers to nonexistent component '#{parameter[:output_of]}'"]
-          else
-            # value will be filled in later when the upstream
-            # component's output becomes known
-          end
-          next
-        elsif params.has_key?(parametername.to_s)
-          value = params[parametername.to_s]
-        elsif parameter.has_key?(:default)
-          value = parameter[:default]
-        elsif [false, 'false', 0, '0'].index(parameter[:required])
-          value = nil
-        else
-          errors << [componentname, parametername, "required parameter is missing"]
-          next
-        end
-        debuglog "parameter #{componentname}::#{parametername} == #{value}"
-
-        component[:script_parameters][parametername] =
-          parameter.dup.merge(value: value)
-      end
-    end
-    if !errors.empty?
-      all_errors = errors.collect do |c,p,e|
-        "#{c}::#{p} - #{e}\n"
-      end.join("")
-      abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nErrors:\n#{all_errors}"
-    end
-    debuglog "options=" + @options.pretty_inspect
-    self
-  end
-
-  def setup_instance
-    if @instance
-      @instance[:properties][:run_options] ||= {}
-      if @options[:no_reuse]
-        # override properties of existing instance
-        @instance[:properties][:run_options][:enable_job_reuse] = false
-      else
-        # Default to "enable reuse" if not specified. (This code path
-        # can go away when old clients go away.)
-        if @instance[:properties][:run_options][:enable_job_reuse].nil?
-          @instance[:properties][:run_options][:enable_job_reuse] = true
-        end
-      end
-    else
-      description = $options[:description] ||
-                    ("Created at #{Time.now.localtime}" + (@template[:name].andand.size.andand>0 ? " using the pipeline template *#{@template[:name]}*" : ""))
-      instance_body = {
-        components: @components,
-        properties: {
-          run_options: {
-            enable_job_reuse: !@options[:no_reuse]
-          }
-        },
-        pipeline_template_uuid: @template[:uuid],
-        description: description,
-        state: ($options[:submit] ? 'RunningOnServer' : 'RunningOnClient')
-      }
-      if @options[:project_uuid]
-        instance_body[:owner_uuid] = @options[:project_uuid]
-      end
-      @instance = PipelineInstance.create(instance_body)
-    end
-    self
-  end
-
-  def run
-    moretodo = true
-    interrupted = false
-
-    if @instance[:started_at].nil?
-      @instance[:started_at] = Time.now
-    end
-
-    job_creation_failed = 0
-    while moretodo
-      moretodo = false
-      @components.each do |cname, c|
-        job = nil
-        owner_uuid = @instance[:owner_uuid]
-        # Is the job satisfying this component already known to be
-        # finished? (Already meaning "before we query API server about
-        # the job's current state")
-        c_already_finished = (c[:job] &&
-                              c[:job][:uuid] &&
-                              ["Complete", "Failed", "Cancelled"].include?(c[:job][:state]))
-        if !c[:job] and
-            c[:script_parameters].select { |pname, p| p.is_a? Hash and p[:output_of]}.empty?
-          # No job yet associated with this component and is component inputs
-          # are fully specified (any output_of script_parameters are resolved
-          # to real value)
-          my_submit_id = "instance #{@instance[:uuid]} rand #{rand(2**64).to_s(36)}"
-          job, err = JobCache.create(@instance, cname, {
-            :script => c[:script],
-            :script_parameters => Hash[c[:script_parameters].map do |key, spec|
-                                         [key, spec[:value]]
-                                       end],
-            :script_version => c[:script_version],
-            :repository => c[:repository],
-            :nondeterministic => c[:nondeterministic],
-            :runtime_constraints => c[:runtime_constraints],
-            :owner_uuid => owner_uuid,
-            :is_locked_by_uuid => (@options[:run_jobs_here] ? owner_uuid : nil),
-            :submit_id => my_submit_id,
-            :state => (if @options[:run_jobs_here] then "Running" else "Queued" end)
-          }, {
-            # This is the right place to put these attributes when
-            # dealing with new API servers.
-            :minimum_script_version => c[:minimum_script_version],
-            :exclude_script_versions => c[:exclude_minimum_script_versions],
-            :find_or_create => (@instance[:properties][:run_options].andand[:enable_job_reuse] &&
-                                !c[:nondeterministic]),
-            :filters => c[:filters]
-          })
-          if job
-            debuglog "component #{cname} new job #{job[:uuid]}"
-            c[:job] = job
-            c[:run_in_process] = (@options[:run_jobs_here] and
-                                  job[:submit_id] == my_submit_id)
-          elsif err.nil?
-            debuglog "component #{cname} new job failed", 0
-            job_creation_failed += 1
-          else
-            debuglog "component #{cname} new job failed, err=#{err}", 0
-          end
-        end
-
-        if c[:job] and c[:run_in_process] and not ["Complete", "Failed", "Cancelled"].include? c[:job][:state]
-          report_status
-          begin
-            require 'open3'
-            Open3.popen3("arv-crunch-job", "--force-unlock",
-                         "--job", c[:job][:uuid]) do |stdin, stdout, stderr, wait_thr|
-              debuglog "arv-crunch-job pid #{wait_thr.pid} started", 0
-              stdin.close
-              while true
-                rready, wready, = IO.select([stdout, stderr], [])
-                break if !rready[0]
-                begin
-                  buf = rready[0].read_nonblock(2**20)
-                rescue EOFError
-                  break
-                end
-                (rready[0] == stdout ? $stdout : $stderr).write(buf)
-              end
-              stdout.close
-              stderr.close
-              debuglog "arv-crunch-job pid #{wait_thr.pid} exit #{wait_thr.value.to_i}", 0
-            end
-            if not $arv.job.get(uuid: c[:job][:uuid])[:finished_at]
-              raise Exception.new("arv-crunch-job did not set finished_at.")
-            end
-          rescue Exception => e
-            debuglog "Interrupted (#{e}). Failing job.", 0
-            $arv.job.update(uuid: c[:job][:uuid],
-                            job: {
-                              state: "Failed"
-                            })
-          end
-        end
-
-        if c[:job] and c[:job][:uuid]
-          if ["Running", "Queued"].include?(c[:job][:state])
-            # Job is running (or may be soon) so update copy of job record
-            c[:job] = JobCache.get(c[:job][:uuid])
-          end
-
-          if c[:job][:state] == "Complete"
-            # Populate script_parameters of other components waiting for
-            # this job
-            @components.each do |c2name, c2|
-              c2[:script_parameters].each do |pname, p|
-                if p.is_a? Hash and p[:output_of] == cname.to_s
-                  debuglog "parameter #{c2name}::#{pname} == #{c[:job][:output]}"
-                  c2[:script_parameters][pname] = {value: c[:job][:output]}
-                  moretodo = true
-                end
-              end
-            end
-            unless c_already_finished
-              # This is my first time discovering that the job
-              # succeeded. (At the top of this loop, I was still
-              # waiting for it to finish.)
-
-              if @instance[:name].andand.length.andand > 0
-                pipeline_name = @instance[:name]
-              elsif @template.andand[:name].andand.length.andand > 0
-                pipeline_name = @template[:name]
-              else
-                pipeline_name = @instance[:uuid]
-              end
-              if c[:output_name] != false
-                # Create a collection located in the same project as the pipeline with the contents of the output.
-                portable_data_hash = c[:job][:output]
-                collections = $arv.collection.list(limit: 1,
-                                                   filters: [['portable_data_hash', '=', portable_data_hash]],
-                                                   select: ["portable_data_hash", "manifest_text"]
-                                                   )[:items]
-                if collections.any?
-                  name = c[:output_name] || "Output #{portable_data_hash[0..7]} of #{cname} of #{pipeline_name}"
-
-                  # check if there is a name collision.
-                  name_collisions = $arv.collection.list(filters: [["owner_uuid", "=", owner_uuid],
-                                                                   ["name", "=", name]])[:items]
-
-                  newcollection_actual = nil
-                  if name_collisions.any? and name_collisions.first[:portable_data_hash] == portable_data_hash
-                    # There is already a collection with the same name and the
-                    # same contents, so just point to that.
-                    newcollection_actual = name_collisions.first
-                  end
-
-                  if newcollection_actual.nil?
-                    # Did not find a collection with the same name (or the
-                    # collection has a different portable data hash) so create
-                    # a new collection with ensure_unique_name: true.
-                    newcollection = {
-                      owner_uuid: owner_uuid,
-                      name: name,
-                      portable_data_hash: collections.first[:portable_data_hash],
-                      manifest_text: collections.first[:manifest_text]
-                    }
-                    debuglog "Creating collection #{newcollection}", 0
-                    newcollection_actual = $arv.collection.create collection: newcollection, ensure_unique_name: true
-                  end
-
-                  c[:output_uuid] = newcollection_actual[:uuid]
-                else
-                  debuglog "Could not find a collection with portable data hash #{portable_data_hash}", 0
-                end
-              end
-            end
-          elsif ["Queued", "Running"].include? c[:job][:state]
-            # Job is running or queued to run, so indicate that pipeline
-            # should continue to run
-            moretodo = true
-          elsif c[:job][:state] == "Cancelled"
-            debuglog "component #{cname} job #{c[:job][:uuid]} cancelled."
-            moretodo = false
-          elsif c[:job][:state] == "Failed"
-            moretodo = false
-          end
-        end
-      end
-      @instance[:components] = @components
-      report_status
-
-      if @options[:no_wait]
-        moretodo = false
-      end
-
-      # If job creation fails, just give up on this pipeline instance.
-      if job_creation_failed > 0
-        moretodo = false
-      end
-
-      if moretodo
-        begin
-          sleep 10
-        rescue Interrupt
-          debuglog "interrupt", 0
-          interrupted = true
-          break
-        end
-      end
-    end
-
-    c_in_state = @components.values.group_by { |c|
-      c[:job] and c[:job][:state]
-    }
-    succeeded = c_in_state["Complete"].andand.count || 0
-    failed = (c_in_state["Failed"].andand.count || 0) + (c_in_state["Cancelled"].andand.count || 0)
-    ended = succeeded + failed
-
-    success = (succeeded == @components.length)
-
-    # A job create call failed. Just give up.
-    if job_creation_failed > 0
-      debuglog "job creation failed - giving up on this pipeline instance", 0
-      success = false
-      failed += 1
-    end
-
-    if interrupted
-     if success
-        @instance[:state] = 'Complete'
-     else
-        @instance[:state] = 'Paused'
-     end
-    else
-      if ended == @components.length or failed > 0
-        @instance[:state] = success ? 'Complete' : 'Failed'
-      end
-    end
-
-    if @instance[:finished_at].nil? and ['Complete', 'Failed'].include? @instance[:state]
-      @instance[:finished_at] = Time.now
-    end
-
-    debuglog "pipeline instance state is #{@instance[:state]}"
-
-    # set components_summary
-    components_summary = {"todo" => @components.length - ended, "done" => succeeded, "failed" => failed}
-    @instance[:components_summary] = components_summary
-
-    @instance.save
-  end
-
-  def cleanup
-    if @instance and @instance[:state] == 'RunningOnClient'
-      @instance[:state] = 'Paused'
-      @instance.save
-    end
-  end
-
-  def uuid
-    @instance[:uuid]
-  end
-
-  protected
-
-  def report_status
-    @instance.save
-
-    if @options[:status_json] != '/dev/null'
-      File.open(@options[:status_json], 'w') do |f|
-        f.puts @components.pretty_inspect
-      end
-    end
-
-    if @options[:status_text] != '/dev/null'
-      File.open(@options[:status_text], 'w') do |f|
-        f.puts ""
-        f.puts "#{Time.now} -- pipeline_instance #{@instance[:uuid]}"
-        namewidth = @components.collect { |cname, c| cname.size }.max
-        @components.each do |cname, c|
-          jstatus = if !c[:job]
-                      "-"
-                    else case c[:job][:state]
-                         when "Running"
-                           "#{c[:job][:tasks_summary].inspect}"
-                         when "Complete"
-                           c[:job][:output]
-                         when "Cancelled"
-                           "cancelled #{c[:job][:cancelled_at]}"
-                         when "Failed"
-                           "failed #{c[:job][:finished_at]}"
-                         when "Queued"
-                           "queued #{c[:job][:created_at]}"
-                         end
-                    end
-          f.puts "#{cname.to_s.ljust namewidth} #{c[:job] ? c[:job][:uuid] : '-'.ljust(27)} #{jstatus}"
-        end
-      end
-    end
-  end
-
-  def abort(msg)
-    if @instance
-      if ["New", "Ready", "RunningOnClient",
-          "RunningOnServer"].include?(@instance[:state])
-        @instance[:state] = "Failed"
-        @instance[:finished_at] = Time.now
-        @instance.save
-      end
-      @instance.log_stderr(msg)
-    end
-    Kernel::abort(msg)
-  end
-end
-
-runner = WhRunPipelineInstance.new($options)
-begin
-  if $options[:template]
-    runner.fetch_template($options[:template])
-  else
-    runner.fetch_instance($options[:instance])
-  end
-  runner.apply_parameters(p.leftovers)
-  runner.setup_instance
-  if $options[:submit]
-    runner.instance.save
-    puts runner.instance[:uuid]
-  else
-    runner.run
-  end
-rescue Exception => e
-  runner.cleanup
-  raise e
-end