#!/usr/bin/env ruby
-
-# == Synopsis
-#
-# arv-run-pipeline-instance --template pipeline-template-uuid [options] [--] [parameters]
-# arv-run-pipeline-instance --instance pipeline-instance-uuid [options]
-#
-# Satisfy a pipeline template by finding or submitting a mapreduce job
-# for each pipeline component.
-#
-# == Options
-#
-# [--template uuid] Use the specified pipeline template.
-#
-# [--template path] Load the pipeline template from the specified
-# local file.
-#
-# [--instance uuid] Use the specified pipeline instance.
-#
-# [-n, --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
-#
-# [--submit] Do not try to satisfy any components. Just
-# create an instance, print its UUID to
-# stdout, and exit.
-#
-# [--no-wait] Make only as much progress as possible without entering
-# a sleep/poll loop.
-#
-# [--no-reuse] Do not reuse existing jobs to satisfy pipeline
-# components. Submit a new job for every component.
-#
-# [--debug] Print extra debugging information on stderr.
-#
-# [--debug-level N] Increase amount of debugging information. Default
-# 1, possible range 0..3.
-#
-# [--status-text path] Print plain text status report to a file or
-# fifo. Default: /dev/stdout
-#
-# [--status-json path] Print JSON status report to a file or
-# fifo. Default: /dev/null
-#
-# == Parameters
-#
-# [param_name=param_value]
-#
-# [param_name param_value] Set (or override) the default value for
-# every 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
-# component.
+# Copyright (C) The Arvados Authors. All rights reserved.
#
+# SPDX-License-Identifier: Apache-2.0
+
class WhRunPipelineInstance
end
-$application_version = 1.0
-
if RUBY_VERSION < '1.9.3' then
abort <<-EOS
#{$0.gsub(/^\.\//,'')} requires Ruby version 1.9.3 or higher.
EOS
end
-$arvados_api_version = ENV['ARVADOS_API_VERSION'] || 'v1'
-$arvados_api_host = ENV['ARVADOS_API_HOST'] or
- abort "#{$0}: fatal: ARVADOS_API_HOST environment variable not set."
-$arvados_api_token = ENV['ARVADOS_API_TOKEN'] or
- abort "#{$0}: fatal: ARVADOS_API_TOKEN environment variable not set."
-
begin
require 'arvados'
require 'rubygems'
require 'trollop'
require 'google/api_client'
rescue LoadError => l
- puts $:
+ $stderr.puts $:
abort <<-EOS
#{$0}: fatal: #{l.message}
Some runtime dependencies may be missing.
$stderr.puts "#{File.split($0).last} #{$$}: #{message}" if $debuglevel >= verbosity
end
-module Kernel
- def suppress_warnings
- original_verbosity = $VERBOSE
- $VERBOSE = nil
- result = yield
- $VERBOSE = original_verbosity
- return result
- end
-end
-
-if $arvados_api_host.match /local/
- # You probably don't care about SSL certificate checks if you're
- # testing with a dev server.
- suppress_warnings { OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE }
-end
-
-class Google::APIClient
- def discovery_document(api, version)
- api = api.to_s
- return @discovery_documents["#{api}:#{version}"] ||=
- begin
- response = self.execute!(
- :http_method => :get,
- :uri => self.discovery_uri(api, version),
- :authenticated => false
- )
- response.body.class == String ? JSON.parse(response.body) : response.body
- end
- end
-end
-
-
# Parse command line options (the kind that control the behavior of
# this program, that is, not the pipeline component parameters).
p = Trollop::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 => :none,
:type => :string)
opt(:submit,
- "Do not try to satisfy any components. Just create a pipeline instance and output its UUID.",
+ "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,
- "Manage the pipeline in process.",
+ "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 = Trollop::with_standard_exception_handling p do
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]
- puts "error: you must supply a --template or --instance."
+ $stderr.puts "error: you must supply a --template or --instance."
p.educate
abort
end
-if $options[:run_here] == $options[:submit]
- abort "#{$0}: syntax error: you must supply either --run-here or --submit."
-end
-
-# Suppress SSL certificate checks if ARVADOS_API_HOST_INSECURE
-
-module Kernel
- def suppress_warnings
- original_verbosity = $VERBOSE
- $VERBOSE = nil
- result = yield
- $VERBOSE = original_verbosity
- return result
- end
-end
-
-if ENV['ARVADOS_API_HOST_INSECURE']
- suppress_warnings { OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE }
+if $options[:run_pipeline_here] == $options[:submit]
+ abort "#{$0}: error: you must supply --run-pipeline-here, --run-jobs-here, or --submit."
end
# Set up the API client.
-$client ||= Google::APIClient.
- new(:host => $arvados_api_host,
- :application_name => File.split($0).last,
- :application_version => $application_version.to_s)
-$arvados = $client.discovered_api('arvados', $arvados_api_version)
$arv = Arvados.new api_version: 'v1'
-
+$client = $arv.client
+$arvados = $arv.arvados_api
class PipelineInstance
def self.find(uuid)
},
:authenticated => false,
:headers => {
- authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
})
j = JSON.parse result.body, :symbolize_names => true
unless j.is_a? Hash and j[:uuid]
end
def self.create(attributes)
result = $client.execute(:api_method => $arvados.pipeline_instances.create,
- :body => {
- :pipeline_instance => attributes.to_json
+ :body_object => {
+ :pipeline_instance => attributes
},
:authenticated => false,
:headers => {
- authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
})
j = JSON.parse result.body, :symbolize_names => true
unless j.is_a? Hash and j[:uuid]
:parameters => {
:uuid => @pi[:uuid]
},
- :body => {
- :pipeline_instance => @attributes_to_update.to_json
+ :body_object => {
+ :pipeline_instance => @attributes_to_update
},
:authenticated => false,
:headers => {
- authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
})
j = JSON.parse result.body, :symbolize_names => true
unless j.is_a? Hash and j[:uuid]
def [](x)
@pi[x]
end
+
+ def log_stderr(msg)
+ $arv.log.create log: {
+ event_type: 'stderr',
+ object_uuid: self[:uuid],
+ owner_uuid: self[:owner_uuid],
+ properties: {"text" => msg},
+ }
+ end
+
protected
def initialize(j)
@attributes_to_update = {}
},
:authenticated => false,
:headers => {
- authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
})
@cache[uuid] = JSON.parse result.body, :symbolize_names => true
end
},
:authenticated => false,
:headers => {
- authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
})
list = JSON.parse result.body, :symbolize_names => true
if list and list[:items].is_a? Array
[]
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 = $client.execute(:api_method => $arvados.jobs.create,
- :body => body,
- :authenticated => false,
- :headers => {
- authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
- })
- j = JSON.parse result.body, :symbolize_names => true
- if j.is_a? Hash and j[:uuid]
+ 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
- debuglog "create job: #{j[:errors] rescue nil} with attributes #{body}", 0
+ errors = j[:errors] rescue []
+ debuglog "create job: [#{result.status}] #{errors.inspect} with attributes #{body}", 0
msg = ""
- j[:errors].each do |err|
+ errors.each do |err|
msg += "Error creating job for component #{component}: #{err}\n"
end
msg += "Job submission was: #{body.to_json}"
- $client.execute(:api_method => $arvados.logs.create,
- :body => {
- :log => {
- :object_uuid => pipeline[:uuid],
- :event_type => 'stderr',
- :owner_uuid => pipeline[:owner_uuid],
- :properties => {"text" => msg}
- }
- },
- :authenticated => false,
- :headers => {
- authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
- })
- nil
+ pipeline.log_stderr(msg)
+ return nil, nil
end
end
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
- if !@template[:components]
- abort ("#{$0}: Template loaded from #{template} " +
- "does not have a \"components\" key")
- end
else
result = $client.execute(:api_method => $arvados.pipeline_templates.get,
:parameters => {
},
:authenticated => false,
:headers => {
- authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN']
})
@template = JSON.parse result.body, :symbolize_names => true
if !@template[:uuid]
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
- value =
- (params["#{componentname}::#{parametername}"] ||
- parameter[:value] ||
- (parameter[:output_of].nil? &&
- (params[parametername.to_s] ||
- parameter[:default])) ||
- nil)
- if value.nil? and
- ![false,'false',0,'0'].index parameter[:required]
- if parameter[:output_of]
- next
+ 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] = value
+
+ component[:script_parameters][parametername] =
+ parameter.dup.merge(value: value)
end
end
if !errors.empty?
- abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nErrors:\n#{errors.collect { |c,p,e| "#{c}::#{p} - #{e}\n" }.join ""}"
+ 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
end
else
- @instance = PipelineInstance.
- create(components: @components,
- properties: {
- run_options: {
- enable_job_reuse: !@options[:no_reuse]
- }
- },
- pipeline_template_uuid: @template[:uuid],
- state: ($options[:submit] ? 'RunningOnServer' : 'RunningOnClient'))
+ 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
moretodo = true
interrupted = false
+ if @instance[:started_at].nil?
+ @instance[:started_at] = Time.now
+ end
+
job_creation_failed = 0
while moretodo
moretodo = false
# the job's current state")
c_already_finished = (c[:job] &&
c[:job][:uuid] &&
- !c[:job][:success].nil?)
+ ["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)
- job = JobCache.create(@instance, cname, {
+ my_submit_id = "instance #{@instance[:uuid]} rand #{rand(2**64).to_s(36)}"
+ job, err = JobCache.create(@instance, cname, {
:script => c[:script],
- :script_parameters => c[:script_parameters],
+ :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],
- :output_is_persistent => c[:output_is_persistent] || false,
: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.
if job
debuglog "component #{cname} new job #{job[:uuid]}"
c[:job] = job
- else
+ 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 (c[:job][:running] or
- not (c[:job][:finished_at] or c[:job][:cancelled_at]))
- # Job is running so update copy of job record
+ 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][:success]
+ 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] = c[:job][:output]
+ c2[:script_parameters][pname] = {value: c[:job][:output]}
moretodo = true
end
end
# 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 c[:output_is_persistent]
- # I need to make sure a resources/wants link is in
- # place to protect the output from garbage
- # collection. (Normally Crunch does this for me, but
- # here I might be reusing the output of someone else's
- # job and I need to make sure it's understood that the
- # output is valuable to me, too.)
- wanted = c[:job][:output]
- debuglog "checking for existing persistence link for #{wanted}"
- @my_user_uuid ||= $arv.user.current[:uuid]
- links = $arv.link.list(limit: 1,
- filters:
- [%w(link_class = resources),
- %w(name = wants),
- %w(tail_uuid =) + [@my_user_uuid],
- %w(head_uuid =) + [wanted]
- ])[:items]
- if links.any?
- debuglog "link already exists, uuid #{links.first[:uuid]}"
+
+ 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
- newlink = $arv.link.create link: \
- {
- link_class: 'resources',
- name: 'wants',
- tail_kind: 'arvados#user',
- tail_uuid: @my_user_uuid,
- head_kind: 'arvados#collection',
- head_uuid: wanted,
- owner_uuid: owner_uuid
- }
- debuglog "added link, uuid #{newlink[:uuid]}"
+ debuglog "Could not find a collection with portable data hash #{portable_data_hash}", 0
end
end
end
- elsif c[:job][:running] ||
- (!c[:job][:started_at] && !c[:job][:cancelled_at])
- # Job is still running
+ 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][:cancelled_at]
+ 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
end
end
- ended = 0
- succeeded = 0
- failed = 0
- @components.each do |cname, c|
- if c[:job]
- if c[:job][:finished_at] or c[:job][:cancelled_at] or (c[:job][:running] == false and c[:job][:success] == false)
- ended += 1
- if c[:job][:success] == true
- succeeded += 1
- elsif c[:job][:success] == false or c[:job][:cancelled_at]
- failed += 1
- end
- 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)
@instance[:state] = 'Complete'
else
@instance[:state] = 'Paused'
- end
+ 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.each do |cname, c|
jstatus = if !c[:job]
"-"
- elsif c[:job][:running]
- "#{c[:job][:tasks_summary].inspect}"
- elsif c[:job][:success]
- c[:job][:output]
- elsif c[:job][:cancelled_at]
- "cancelled #{c[:job][:cancelled_at]}"
- elsif c[:job][:finished_at]
- "failed #{c[:job][:finished_at]}"
- elsif c[:job][:started_at]
- "started #{c[:job][:started_at]}"
- else
- "queued #{c[:job][:created_at]}"
+ 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)
projects / arvados.git / blobdiff